add new type to xvg converter

some edit of python files

combine-qti/combine-qti.py

@@ -0,0 +1,104 @@
+#!/usr/bin/python2
+# combine-qti
+# Copyright (C) 2014 Evgeniy Alekseev <esalexeev@gmail.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+
+import argparse, os
+
+
+def readData(file):
+    """function to read data"""
+    windows = 0
+    data = []
+    # preread
+    with open (file, "r") as input:
+        for line in input:
+            if (line.split('\t')[0] == "<windows>"):
+                windows = int(line.split('\t')[1].strip())
+    with open (file, "r") as input:
+        for window in range(windows):
+            for line in input:
+                if (line.strip() == "<table>"):
+                    data.append("<table>\n")
+                    break
+                elif (line.strip() == "<multiLayer>"):
+                    data.append("<multiLayer>\n")
+                    break
+            for line in input:
+                if (line.strip() == '</table>'):
+                    data.append("</table>\n")
+                    break
+                elif (line.strip() == '</multiLayer>'):
+                    data.append("</multiLayer>\n")
+                    break
+                data.append(line)
+    return windows, data
+
+
+def printHeader(file, windowsNum=1):
+    """function to print header"""
+    iter = 0
+    suffix = ""
+    while (os.path.exists(file + suffix)):
+        suffix = ".%i" % (iter)
+        iter = iter + 1
+    if (suffix != ""):
+        os.rename(file, file + suffix)
+    with open(file, "w") as output:
+        output.write("QtiPlot 0.9.8 project file\n")
+        output.write("<scripting-lang>\tPython\n")
+        output.write("<windows>\t%i\n" % (windowsNum))
+
+
+def printData(file, data):
+    """function to print data"""
+    with open(file, "a") as output:
+        for line in data:
+            output.write(line)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description = 'Combine several *.qti files into one')
+    parser.add_argument('-d', '--directory', dest = 'dir',
+        help = 'Directory with input files or use --input', action = 'store', default = False)
+    parser.add_argument('-i', '--input', dest = 'input',
+        help = 'Input files, comma separated', action = 'store', default = False)
+    parser.add_argument('-o', '--output', dest = 'output',
+        help = 'Output file', action = 'store', default = False)
+    args = parser.parse_args()
+
+    input = []
+    if (args.dir):
+        if (os.path.isdir(args.dir)):
+            input = [os.path.join(args.dir, file) for file in os.listdir(args.dir) if (os.path.splitext(file)[1] == ".qti")]
+    else:
+        if (args.input):
+            for file in args.input.split(','):
+                if (os.path.isfile(file)): input.append(file)
+    output = args.output
+    if (not input) or (not output):
+        print ("Files are not set")
+        exit()
+
+    totalWindows = 0
+    totalData = []
+    for file in input:
+        windows, data = readData(file)
+        totalWindows = totalWindows + windows
+        totalData.append(data)
+    printHeader(output, totalWindows)
+    for data in totalData:
+        printData(output, data)

dynamic-hb/dynamic-hb.py

@@ -0,0 +1,109 @@
+#!/usr/bin/python
+
+import argparse
+import os
+
+
+def calculate(splited, system):
+    """function to calculate results"""
+    matrix = []
+    for i in range(system['mols']):
+        matrix.append(0)
+    for file in splited:
+        for aggl in file:
+            matrix[len(aggl)-1] += 1
+    results = {}
+    while matrix[-1] == 0:
+        matrix.pop(-1)
+    for i, item in enumerate(matrix, start = 1):
+        results[i] = item
+    summ = 0
+    for i in results:
+        if i == 1: continue
+        results[i] = i * results[i] / (system['steps'] * system['mols'])
+        summ += results[i]
+    results[1] = 1.0 - summ
+    return results
+
+
+def parse_file(splited):
+    """function to parse input file"""
+    for file in splited:
+        for agl in file:
+            for i, molecule in enumerate(agl):
+                agl[i] = [int(molecule.split('=')[0]), [int(conn) for conn in molecule.split('=')[1].split(',') if conn]]
+    return splited
+
+
+def print_result(output, matrix):
+    """function to print result to file"""
+    with open(output, 'w') as out:
+        out.write("|   n   |   p   |\n-----------------\n")
+        for i in matrix:
+            out.write(" %7i %7.5f \n" % (i, matrix[i]))
+        out.write("-----------------\n")
+
+
+def read_file(input_file):
+    """function to read file from statgen"""
+    file = open(input_file).read()
+    if not file.startswith("statgen"):
+        print("It is not a statgen file")
+        exit(2)
+    prepare = file.split("\n")
+    system = {'steps': 0, 'mols': 0}
+    while not prepare[-1].startswith("SUMMARY STATISTIC"):
+        statistic = prepare.pop(-1)
+        if not statistic.startswith("       1"): continue
+        values = [float(item) for item in statistic.split()]
+        system['steps'] = int(round(values[1] / values[2], 0))
+        system['mols'] = int(round(values[2] / values[3], 0))
+    prepare.pop(-1)
+    splited = '\n'.join(prepare).split("FILE")[1:]
+    for i, item in enumerate(splited):
+        text = item.split("AGL")[1:]
+        for j, agl in enumerate(text):
+            text[j] = [single for single in agl.split("\n")[1:] if single]
+        text[-1].pop(-1)
+        splited[i] = text
+    return splited, system
+
+
+def select_aggl(splited, step):
+    """function to select agglomerates"""
+    for i, file in enumerate(splited):
+        first = (i - step) if (i - step) > 0 else 0
+        last = (i + step) if (i + step) < (len(splited) - 1) else (len(splited) - 1)
+        for j, aggl in enumerate(file):
+            for k, mol in enumerate(aggl):
+                table = []
+                for other_file in splited[first:last]:
+                    for aggl_other in other_file:
+                        if not mol[0] in [other_single[0] for other_single in aggl_other]: continue
+                        table.extend(mols for other_single in aggl_other for mols in other_single[1] if other_single[0] == mol[0])
+                for l, conn in enumerate(mol[1]):
+                    if table.count(conn) == last - first: continue
+                    splited[i][j][k][1].pop(l)
+                if len(mol[1]) == 0:
+                    splited[i][j].pop(k)
+            if len(aggl) == 0:
+                splited[i].pop(j)
+    return splited
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description = "Sort agglomerates using dynamic criteria")
+    parser.add_argument('input', help = "file from statgen")
+    parser.add_argument('-s', '--step', type = int, help = "step to check agglomerates",
+                        default = 1)
+    parser.add_argument('-o', '--output', help = "output file", default = "dhb-output.dat")
+    args = parser.parse_args()
+
+
+    if not os.path.isfile(args.input):
+        print("Could not find file %s" % args.input)
+        exit(1)
+    splited, system = read_file(args.input)
+    splited = parse_file(splited)
+    matrix = calculate(select_aggl(splited, args.step), system)
+    print_result(args.output, matrix)

get_dipole/get-dipole.py

@@ -0,0 +1,70 @@
+#!/usr/bin/python2
+
+import argparse, math
+
+
+def get_aver_dipole(dipole):
+    """function to get average dipole moment"""
+    aver_dipole = math.sqrt((dipole[0] * dipole[0] +
+        dipole[1] * dipole[1] +
+        dipole[2] * dipole[2]))
+    aver_dipole = round(aver_dipole, 4)
+    return aver_dipole
+
+
+def get_charges(file_name):
+    """function to get charges from GROMACS files"""
+    charges = {}
+    with open(file_name, 'r') as input_file:
+        for line in input_file:
+            try:
+                charges[line.split()[0]] = float(line.split()[2])
+            except:
+                pass
+    return charges
+
+
+def get_coordinates(file_name):
+    """function to get coordinates from PDB"""
+    coords = []
+    with open(file_name, 'r') as input_file:
+        for line in input_file:
+            if ((line[0:4] == "ATOM") or (line[0:6] == "HETATM")):
+                coords.append({"type":line.split()[2], "coords":[float(line[30:38]), float(line[38:46]), float(line[46:54])]})
+    return coords
+
+
+def get_dipole(charges, coords):
+    """function to get dipole moment"""
+    dipole = [0.0, 0.0, 0.0]
+    for atom in coords:
+        dipole[0] = dipole[0] + charges[atom["type"]] * atom["coords"][0]
+        dipole[1] = dipole[1] + charges[atom["type"]] * atom["coords"][1]
+        dipole[2] = dipole[2] + charges[atom["type"]] * atom["coords"][2]
+    dipole[0] = math.fabs(round(16.0218 * dipole[0] / 3.3356, 4))
+    dipole[1] = math.fabs(round(16.0218 * dipole[1] / 3.3356, 4))
+    dipole[2] = math.fabs(round(16.0218 * dipole[2] / 3.3356, 4))
+    return dipole
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description = 'Calculate dipole moment from PDB')
+    parser.add_argument('-i', '--input', dest = 'input',
+        help = 'File with charges', action = 'store')
+    parser.add_argument('-c', '--coord', dest = 'coord',
+        help = 'File with coordinates', action = 'store')
+    parser.add_argument('-v', '--vector', dest = 'vector',
+        help = 'Return vector', action = 'store_true', default = False)
+    args = parser.parse_args()
+
+    if ((not args.input) or (not args.coord)):
+        print "Input files are not set"
+        exit()
+
+    charges = get_charges(args.input)
+    coords = get_coordinates(args.coord)
+    if (args.vector):
+        print get_dipole(charges, coords)
+    else:
+        print get_aver_dipole(get_dipole(charges, coords))
+

hb-select/hb-select.py

@@ -0,0 +1,70 @@
+#!/usr/bin/python2
+
+import argparse
+
+def readAtoms(file):
+    """function to read *gro file"""
+    atoms = {}
+    with open(file, 'r') as coordFile:
+        coordFile.readline()
+        num = int(coordFile.readline())
+        for i in range(num):
+            line = coordFile.readline()
+            resNum = int(line[0:5])
+            atomNum = int(line[15:20])
+            atoms[atomNum] = resNum
+    return atoms
+
+
+def readHb(files):
+    """function to read *.ndx file"""
+    hbs = []
+    start = False
+    for file in files:
+        with open(file, 'r') as ndxFile:
+            for line in ndxFile:
+                if (line[0:9] == "[ hbonds_"):
+                    start = True
+                    continue
+                elif (line.count('[') > 0):
+                    start = False
+                    continue
+                elif (start):
+                    donor = int(line[0:7])
+                    hydrogen = int(line[7:14])
+                    acceptor = int(line[14:21])
+                    if (hbs.count([donor, hydrogen, acceptor]) == 0):
+                        hbs.append([donor, hydrogen, acceptor])
+    return hbs
+
+
+def selectHb(atoms, hbs):
+    """funtion to select hydrogen bond"""
+    selectedHbs = []
+    for hb in hbs:
+        if ((atoms[hb[0]] - atoms[hb[2]]) > 5):
+            selectedHbs.append(hb)
+    return selectedHbs
+
+
+def printToFile(selectedHbs, file):
+    """function to print results"""
+    with open(file, 'w') as ndxFile:
+        ndxFile.write("[ sel_hbs ]\n")
+        for hb in selectedHbs:
+            ndxFile.write("%7i%7i%7i\n" % (hb[0], hb[1], hb[2]))
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description = 'Select hidrogen bond from GROMACS index file')
+    parser.add_argument('-i', '--input', dest = 'input',
+        help = '*.gro file', action = 'store')
+    parser.add_argument('-n', '--ndx', dest = 'ndx',
+        help = '*.ndx files, comma separated', action = 'store')
+    parser.add_argument('-o', '--output', dest = 'output',
+        help = 'output *.ndx file', action = 'store')
+    args = parser.parse_args()
+
+    atoms = readAtoms(args.input)
+    hbs = readHb(args.ndx.split(','))
+    selectedHbs = selectHb(atoms, hbs)
+    printToFile(selectedHbs, args.output)

mathmech/CHANGELOG

@@ -0,0 +1,18 @@
+V.1.2.0 ()
+ * change license from GPL to Beerware
+ * changes in the architecture
+ + added library
+
+V.1.1.1 (2013-09-03)
+ * optimization
+
+V.1.1.0 (2013-09-02)
+ + added help window
+ + added help docs
+ - small bug fixes
+
+V.1.0.3 (2013-08-30)
+ * bug fixes
+
+V.1.0.1 (2013-07-27)
+ + initial release

mathmech/CMakeLists.txt

@@ -1,31 +1,70 @@
-set ("PROJECT_VERSION_MAJOR" 1)
-set ("PROJECT_VERSION_MINOR" 0)
-set ("PROJECT_VERSION_PATCH" 3)
-set ("PROJECT_VERSION" ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH})
+cmake_minimum_required (VERSION 2.8)
+
+cmake_policy (SET CMP0003 OLD)
+cmake_policy (SET CMP0002 OLD)
+cmake_policy (SET CMP0011 NEW)
+cmake_policy (SET CMP0015 NEW)
+
+project (mathmech)
+set (PROJECT_VERSION_MAJOR 1)
+set (PROJECT_VERSION_MINOR 2)
+set (PROJECT_VERSION_PATCH 0)
+set (PROJECT_VERSION ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH})
+configure_file (${CMAKE_SOURCE_DIR}/version.h.in ${CMAKE_CURRENT_BINARY_DIR}/version.h)
 
 message (STATUS "Version ${PROJECT_VERSION}")
 
 set (COMPS mathmech
-           mm_agl
-           mm_envir
-           mm_radf
-           mm_statgen
-           mm_trj
-           mm_trj2pdb)
+           agl
+           envir
+           radf
+           statgen
+           trj
+           trj2pdb)
 
 # install options
 set (MM_PREFIX "mm_" CACHE STRING "Prefix for mathmech tools")
-OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
-OPTION (ADD_INCLUDE "Add include files" OFF)
-OPTION (ADD_DOCS "Add documentation" OFF)
+option (WITH_DEBUG_MODE "Build with debug mode" OFF)
+option (ADD_DOCS "Add documentation" OFF)
+option (ADD_INCLUDE "Add include files" OFF)
 if (CMAKE_SYSTEM_NAME MATCHES Linux)
   set (QWT_INCLUDE_PATH "/usr/include" CACHE STRING "Path to qwt include")
   set (QWT_LIBRARY_PATH "/usr/lib" CACHE STRING "Path to qwt library")
 elseif (CMAKE_SYSTEM_NAME MATCHES Windows)
   set (QWT_INCLUDE_PATH "C:/Qwt-6.1.0/include" CACHE STRING "Path to qwt include")
   set (QWT_LIBRARY_PATH "C:/Qwt-6.1.0/lib" CACHE STRING "Path to qwt library")
-endif()
+endif ()
+
+# verbose
+set (CMAKE_VERBOSE_MAKEFILE ON)
+
+# flags
+if ( WITH_DEBUG_MODE )
+  add_definitions ( -DDEBUG_MODE=1 )
+endif ()
+if ( CMAKE_COMPILER_IS_GNUCXX )
+  set (ADD_CXX_FLAGS  "-Wall")
+  set (CMAKE_CXX_FLAGS "-O0 ${ADD_CXX_FLAGS}")
+  set (CMAKE_CXX_FLAGS_DEBUG "-g -O0")
+  set (CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG")
+elseif ( MSVC )
+  set (ADD_CXX_FLAGS  "/W4")
+  set (CMAKE_CXX_FLAGS "${ADD_CXX_FLAGS}")
+else ()
+  message ("Unknown compiler")
+endif ()
+
+# set libraries
+set (LIBRARIES mm)
+foreach (LIBRARY ${LIBRARIES})
+  add_subdirectory (${LIBRARY})
+endforeach ()
 
 foreach (COMP ${COMPS})
   add_subdirectory (${COMP})
-endforeach()
+endforeach ()
+
+# set docs file
+if (ADD_DOCS)
+  include (docs.cmake)
+endif ()

mathmech/COPYING

@@ -1,341 +1,4 @@
-                    GNU GENERAL PUBLIC LICENSE
-                       Version 2, June 1991
-
-     Copyright (C) 1989, 1991 Free Software Foundation, Inc.
-     59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
-
-   Everyone is permitted to copy and distribute verbatim copies
-    of this license document, but changing it is not allowed.
-
-                            Preamble
-
-  The licenses for most software are designed to take away your
-freedom to share and change it.  By contrast, the GNU General Public
-License is intended to guarantee your freedom to share and change free
-software--to make sure the software is free for all its users.  This
-General Public License applies to most of the Free Software
-Foundation's software and to any other program whose authors commit to
-using it.  (Some other Free Software Foundation software is covered by
-the GNU Library General Public License instead.)  You can apply it to
-your programs, too.
-
-  When we speak of free software, we are referring to freedom, not
-price.  Our General Public Licenses are designed to make sure that you
-have the freedom to distribute copies of free software (and charge for
-this service if you wish), that you receive source code or can get it
-if you want it, that you can change the software or use pieces of it
-in new free programs; and that you know you can do these things.
-
-  To protect your rights, we need to make restrictions that forbid
-anyone to deny you these rights or to ask you to surrender the rights.
-These restrictions translate to certain responsibilities for you if you
-distribute copies of the software, or if you modify it.
-
-  For example, if you distribute copies of such a program, whether
-gratis or for a fee, you must give the recipients all the rights that
-you have.  You must make sure that they, too, receive or can get the
-source code.  And you must show them these terms so they know their
-rights.
-
-  We protect your rights with two steps: (1) copyright the software, and
-(2) offer you this license which gives you legal permission to copy,
-distribute and/or modify the software.
-
-  Also, for each author's protection and ours, we want to make certain
-that everyone understands that there is no warranty for this free
-software.  If the software is modified by someone else and passed on, we
-want its recipients to know that what they have is not the original, so
-that any problems introduced by others will not reflect on the original
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-
-  Finally, any free program is threatened constantly by software
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-program proprietary.  To prevent this, we have made it clear that any
-patent must be licensed for everyone's free use or not licensed at all.
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-  The precise terms and conditions for copying, distribution and
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-
-                    GNU GENERAL PUBLIC LICENSE
-   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
-
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-a notice placed by the copyright holder saying it may be distributed
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-itself accompanies the executable.
-
-If distribution of executable or object code is made by offering
-access to copy from a designated place, then offering equivalent
-access to copy the source code from the same place counts as
-distribution of the source code, even though third parties are not
-compelled to copy the source along with the object code.
-
-  4. You may not copy, modify, sublicense, or distribute the Program
-except as expressly provided under this License.  Any attempt
-otherwise to copy, modify, sublicense or distribute the Program is
-void, and will automatically terminate your rights under this License.
-However, parties who have received copies, or rights, from you under
-this License will not have their licenses terminated so long as such
-parties remain in full compliance.
-
-  5. You are not required to accept this License, since you have not
-signed it.  However, nothing else grants you permission to modify or
-distribute the Program or its derivative works.  These actions are
-prohibited by law if you do not accept this License.  Therefore, by
-modifying or distributing the Program (or any work based on the
-Program), you indicate your acceptance of this License to do so, and
-all its terms and conditions for copying, distributing or modifying
-the Program or works based on it.
-
-  6. Each time you redistribute the Program (or any work based on the
-Program), the recipient automatically receives a license from the
-original licensor to copy, distribute or modify the Program subject to
-these terms and conditions.  You may not impose any further
-restrictions on the recipients' exercise of the rights granted herein.
-You are not responsible for enforcing compliance by third parties to
-this License.
-
-  7. If, as a consequence of a court judgment or allegation of patent
-infringement or for any other reason (not limited to patent issues),
-conditions are imposed on you (whether by court order, agreement or
-otherwise) that contradict the conditions of this License, they do not
-excuse you from the conditions of this License.  If you cannot
-distribute so as to satisfy simultaneously your obligations under this
-License and any other pertinent obligations, then as a consequence you
-may not distribute the Program at all.  For example, if a patent
-license would not permit royalty-free redistribution of the Program by
-all those who receive copies directly or indirectly through you, then
-the only way you could satisfy both it and this License would be to
-refrain entirely from distribution of the Program.
-
-If any portion of this section is held invalid or unenforceable under
-any particular circumstance, the balance of the section is intended to
-apply and the section as a whole is intended to apply in other
-circumstances.
-
-It is not the purpose of this section to induce you to infringe any
-patents or other property right claims or to contest validity of any
-such claims; this section has the sole purpose of protecting the
-integrity of the free software distribution system, which is
-implemented by public license practices.  Many people have made
-generous contributions to the wide range of software distributed
-through that system in reliance on consistent application of that
-system; it is up to the author/donor to decide if he or she is willing
-to distribute software through any other system and a licensee cannot
-impose that choice.
-
-This section is intended to make thoroughly clear what is believed to
-be a consequence of the rest of this License.
-
-  8. If the distribution and/or use of the Program is restricted in
-certain countries either by patents or by copyrighted interfaces, the
-original copyright holder who places the Program under this License
-may add an explicit geographical distribution limitation excluding
-those countries, so that distribution is permitted only in or among
-countries not thus excluded.  In such case, this License incorporates
-the limitation as if written in the body of this License.
-
-  9. The Free Software Foundation may publish revised and/or new versions
-of the General Public License from time to time.  Such new versions will
-be similar in spirit to the present version, but may differ in detail to
-address new problems or concerns.
-
-Each version is given a distinguishing version number.  If the Program
-specifies a version number of this License which applies to it and "any
-later version", you have the option of following the terms and conditions
-either of that version or of any later version published by the Free
-Software Foundation.  If the Program does not specify a version number of
-this License, you may choose any version ever published by the Free Software
-Foundation.
-
-  10. If you wish to incorporate parts of the Program into other free
-programs whose distribution conditions are different, write to the author
-to ask for permission.  For software which is copyrighted by the Free
-Software Foundation, write to the Free Software Foundation; we sometimes
-make exceptions for this.  Our decision will be guided by the two goals
-of preserving the free status of all derivatives of our free software and
-of promoting the sharing and reuse of software generally.
-
-                            NO WARRANTY
-
-  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
-FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
-OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
-PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
-OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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-TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU.  SHOULD THE
-PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
-REPAIR OR CORRECTION.
-
-  12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
-WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
-REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
-INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
-OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
-TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
-YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
-PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
-POSSIBILITY OF SUCH DAMAGES.
-
-                     END OF TERMS AND CONDITIONS
-
-            How to Apply These Terms to Your New Programs
-
-  If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
-
-  To do so, attach the following notices to the program.  It is safest
-to attach them to the start of each source file to most effectively
-convey the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
-    <one line to give the program's name and a brief idea of what it does.>
-    Copyright (C) 19yy  <name of author>
-
-    This program is free software; you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation; either version 2 of the License, or
-    (at your option) any later version.
-
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with this program; if not, write to the Free Software
-    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
-
-
-Also add information on how to contact you by electronic and paper mail.
-
-If the program is interactive, make it output a short notice like this
-when it starts in an interactive mode:
-
-    Gnomovision version 69, Copyright (C) 19yy name of author
-    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
-    This is free software, and you are welcome to redistribute it
-    under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License.  Of course, the commands you use may
-be called something other than `show w' and `show c'; they could even be
-mouse-clicks or menu items--whatever suits your program.
-
-You should also get your employer (if you work as a programmer) or your
-school, if any, to sign a "copyright disclaimer" for the program, if
-necessary.  Here is a sample; alter the names:
-
-  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
-  `Gnomovision' (which makes passes at compilers) written by James Hacker.
-
-  <signature of Ty Coon>, 1 April 1989
-  Ty Coon, President of Vice
-
-This General Public License does not permit incorporating your program into
-proprietary programs.  If your program is a subroutine library, you may
-consider it more useful to permit linking proprietary applications with the
-library.  If this is what you want to do, use the GNU Library General
-Public License instead of this License.
+"THE BEER-WARE LICENSE" (Revision 42):
+Evgeniy Alekseev wrote this file. As long as you retain this notice you 
+can do whatever you want with this stuff. If we meet some day, and you think 
+this stuff is worth it, you can buy me a beer in return.

mathmech/PKGBUILD

@@ -1,36 +1,39 @@
-# Author: Evgeniy "arcanis" Alexeev <esalexeev@gmail.com>
-# Maintainer: Evgeniy "arcanis" Alexeev <esalexeev@gmail.com>
+# Author: Evgeniy "arcanis" Alexeev <arcanis.arch at gmail dot com>
+# Maintainer: Evgeniy "arcanis" Alexeev <arcanis.arch at gmail dot com>
 
 pkgname=mathmech
-pkgver=1.0.3
-pkgrel=1
+pkgver=1.2.0
+pkgrel=2
 pkgdesc="Software package for analysis of molecular dynamics trajectories"
-arch=(any)
-url="https://github.com/arcan1s/moldyn/mathmech"
-license=('GPL')
-depends=('qt4' 'qwt')
-makedepends=('unzip' 'cmake' 'automoc4')
+arch=('i686' 'x86_64')
+url="http://arcan1s.github.io/projects/moldyn"
+license=('Beerware')
+depends=('qwt')
+makedepends=('cmake' 'automoc4')
 source=(https://github.com/arcan1s/moldyn/releases/download/mm-${pkgver}/${pkgname}-${pkgver}-src.zip)
-md5sums=('4eccb72efd4a8a531d7fda1aabc04f62')
+md5sums=('de893eee2230269b10099c5fd925502b')
 _cmakekeys="-DCMAKE_INSTALL_PREFIX=/usr
             -DQWT_INCLUDE_PATH=/usr/include/qwt
+            -DQWT_LIBRARY_PATH=/usr/lib
             -DMM_PREFIX=mm_
+            -DADD_DOCS:BOOL=0
+            -DADD_INCLUDE:BOOL=0
             -DCMAKE_BUILD_TYPE=Release"
 
-build ()
-{
-  unzip -o -q ${srcdir}/${pkgname}-${pkgver}-src.zip -d ${srcdir}/${pkgname}
-  if [ -d ${srcdir}/${pkgname}/build ]; then
-    rm -rf ${srcdir}/${pkgname}/build
-  fi
-  mkdir ${srcdir}/${pkgname}/build && cd ${srcdir}/${pkgname}/build
+prepare() {
+  [[ -d ${srcdir}/build ]] && rm -rf "${srcdir}/build"
+  mkdir "${srcdir}/build"
+}
+
+build() {
+  cd "${srcdir}/build"
   cmake ${_cmakekeys} ../
   make
 }
 
-package() 
-{
-  cd ${srcdir}/${pkgname}/build
-  make DESTDIR=${pkgdir} install
+package() {
+  cd "${srcdir}/build"
+  make DESTDIR="${pkgdir}" install
+  install -Dm644 "${srcdir}/COPYING" "${pkgdir}/usr/share/licenses/${pkgname}/COPYING"
 }
  

mathmech/PKGBUILD-mingw

@@ -0,0 +1,40 @@
+# Author: Evgeniy "arcanis" Alexeev <arcanis.arch at gmail dot com>
+# Maintainer: Evgeniy "arcanis" Alexeev <arcanis.arch at gmail dot com>
+
+pkgname=mathmech
+pkgver=1.2.0
+pkgrel=2
+pkgdesc="Software package for analysis of molecular dynamics trajectories"
+arch=('any')
+url="http://arcan1s.github.io/projects/moldyn"
+license=('Beerware')
+depends=('mingw-w64-qwt')
+makedepends=('mingw-w64-cmake' 'automoc4')
+source=(https://github.com/arcan1s/moldyn/releases/download/mm-${pkgver}/${pkgname}-${pkgver}-src.zip)
+md5sums=('46d8e1a3d6bc30d5b0b57ccf485986b1')
+_cmakekeys="-DCMAKE_INSTALL_PREFIX=/usr
+            -DQWT_INCLUDE_PATH=/usr/x86_64-w64-mingw32/qwt
+            -DQWT_LIBRARY_PATH=/usr/x86_64-w64-mingw32/lib
+            -DMM_PREFIX=mm_
+            -DADD_DOCS:BOOL=1
+            -DADD_INCLUDE:BOOL=1
+            -DCMAKE_BUILD_TYPE=Release"
+
+prepare() {
+  [[ -d ${srcdir}/build ]] && rm -rf "${srcdir}/build"
+  mkdir "${srcdir}/build"
+}
+
+build() {
+  unset LDFLAGS
+  cd "${srcdir}/build"
+  x86_64-w64-mingw32-cmake ${_cmakekeys} ../
+  make
+}
+
+package() {
+  cd "${srcdir}/build"
+  make DESTDIR="${pkgdir}" install
+  install -Dm644 "${srcdir}/COPYING" "${pkgdir}/usr/share/licenses/${pkgname}/COPYING"
+}
+ 

mathmech/agl/CMakeLists.txt

@@ -0,0 +1,21 @@
+# set project name
+set (SUBPROJECT agl)
+# set additional cmake file
+include (${SUBPROJECT}.cmake)
+
+# set libraries
+set (LIBRARIES mm)
+foreach (LIBRARY ${LIBRARIES})
+  include_directories (${CMAKE_CURRENT_SOURCE_DIR}/../${LIBRARY}/include/)
+  if (CMAKE_COMPILER_IS_GNUCXX)
+    link_directories (${LIBRARY}/src/lib)
+  elseif (CMAKE_COMPILER_IS_MSVC)
+    link_directories (${LIBRARY}/src/Release)
+  endif ()
+endforeach ()
+
+# additional targets
+set (TARGETS "")
+set (HEADERS "")
+
+add_subdirectory (${SUBPROJECT_SOURCE_DIR})

mathmech/agl/README

@@ -1,9 +1,7 @@
-mm_agl - program that creates PDB file with chosen agglomerate
-Version: 1.0.3
-License: GPL
+agl - program that creates PDB file with chosen agglomerate
 
 Usage:
-  mm_agl -a FILENAME -i FILENAME -c X,Y,Z -o FILEMANE [ -l LOGFILE ] [ -q ] [ -h ]
+  agl -a FILENAME -i FILENAME -c X,Y,Z -o FILEMANE [ -l LOGFILE ] [ -q ] [ -h ]
 
 Parametrs:
   -a          - input file with agglomerates (in format statgen)

mathmech/agl/agl.cmake

@@ -0,0 +1,10 @@
+# set directories
+set (SUBPROJECT_BINARY_DIR bin)
+set (SUBPROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
+
+# include_path
+include_directories (${SUBPROJECT_SOURCE_DIR}
+                     ${CMAKE_CURRENT_BINARY_DIR}/../)
+
+# executable path
+set (EXECUTABLE_OUTPUT_PATH ${SUBPROJECT_BINARY_DIR})

mathmech/agl/src/CMakeLists.txt

@@ -0,0 +1,23 @@
+# set files
+file (GLOB SOURCES *.c)
+file (GLOB HEADERS *.h)
+
+# set library
+if (CMAKE_COMPILER_IS_GNUCXX)
+  set (ADDITIONAL_LIB m)
+else ()
+  set (ADDITIONAL_LIB)
+endif ()
+
+# message
+message (STATUS "${SUBPROJECT} SOURCES: ${SOURCES}")
+message (STATUS "${SUBPROJECT} HEADERS: ${HEADERS}")
+
+# link libraries and compile
+add_executable (${SUBPROJECT} ${SOURCES} ${HEADERS})
+set_target_properties (${SUBPROJECT} PROPERTIES OUTPUT_NAME ${MM_PREFIX}${SUBPROJECT})
+add_dependencies (${SUBPROJECT} ${LIBRARIES})
+target_link_libraries (${SUBPROJECT} ${ADDITIONAL_LIB} ${LIBRARIES})
+
+# install properties
+install (TARGETS ${SUBPROJECT} DESTINATION bin)

mathmech/agl/src/add_main.c

@@ -0,0 +1,73 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file add_main.c
+ * Source code of agl
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
+#include <stdio.h>
+
+#include "add_main.h"
+#include <mathmech/messages.h>
+#include <mathmech/var_types.h>
+
+
+/**
+ * @fn error_checking
+ */
+int error_checking (const char *aglinp, const system_info _system_info, const char *input, 
+                    const char *output)
+{
+  if (input[0] == '#')
+    return 12;
+  if (output[0] == '#')
+    return 13;
+  if (aglinp[0] == '#')
+    return 14;
+  
+  return 0;
+}
+
+
+/**
+ * @fn print_message
+ */
+int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log, 
+                   const int mode, const char *str)
+{
+  if ((quiet != 1) && (std_output != stderr))
+    message (0, mode, str, std_output);
+  if (log == 1)
+    message (1, mode, str, f_log);
+  
+  return 0;
+}
+
+
+/**
+ * @fn set_defaults
+ */
+int set_defaults (char *aglinp, system_info *_system_info, char *input, int *log, 
+                  char *output, int *quiet)
+{
+  int i;
+  
+  aglinp[0] = '#';
+  for (i=0; i<3; i++)
+    (*_system_info).cell[i] = 0.0;
+  input[0] = '#';
+  *log = 0;
+  output[0] = '#';
+  *quiet = 0;
+  
+  return 0;
+}

mathmech/agl/src/add_main.h

@@ -1,25 +1,36 @@
-/**
- * @file
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
  */
+/**
+ * @file add_main.h
+ * Header of agl
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
+#ifndef ADD_MAIN_H
+#define ADD_MAIN_H
 
 #include <stdio.h>
 
-#include "messages.h"
+#include <mathmech/messages.h>
+#include <mathmech/var_types.h>
 
 
-/**
- * @fn error_checking
- */
-int error_checking (const char *aglinp, const float *cell, const char *input, 
-                    const char *output)
 /**
  * @brief function that checks errors in input variables
  * @code
- * error_checking (aglinp, cell, input, output);
+ * error_checking (aglinp, _system_info, input, output);
  * @endcode
  * 
  * @param aglinp          agglomerate file name
- * @param cell            massive of cell size
+ * @param _system_info    system information structure
  * @param input           input file name
  * @param output          output file name
  * 
@@ -29,25 +40,10 @@ int error_checking (const char *aglinp, const float *cell, const char *input,
  * @return 14             - error in 'aglinp'
  * @return 0              - exit without errors
  */
-{
-  if ((cell[0] == 0.0) || (cell[1] == 0.0) || (cell[2] == 0.0))
-    return 11;
-  if (input[0] == '#')
-    return 12;
-  if (output[0] == '#')
-    return 13;
-  if (aglinp[0] == '#')
-    return 14;
-  
-  return 0;
-}
+int error_checking (const char *aglinp, const system_info _system_info, 
+                    const char *input, const char *output);
 
 
-/**
- * @fn print_message
- */
-int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log, 
-                   const int mode, const char *str)
 /**
  * @brief function that prints message in log and stdout
  * @code
@@ -63,28 +59,18 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
  * 
  * @return 0              - exit without errors
  */
-{
-  if ((quiet != 1) && (std_output != stderr))
-    message (0, mode, str, std_output);
-  if (log == 1)
-    message (1, mode, str, f_log);
-  
-  return 0;
-}
+int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log, 
+                   const int mode, const char *str);
 
 
-/**
- * @fn set_defaults
- */
-int set_defaults (char *aglinp, float *cell, char *input, int *log, char *output, int *quiet)
 /**
  * @brief function that sets default values of variables
  * @code
- * set_defaults (aglinp, cell, input, &log, output, &quiet);
+ * set_defaults (aglinp, &_system_info, input, &log, output, &quiet);
  * @endcode
  * 
  * @param aglinp          agglomerate file name
- * @param cell            massive of cell size
+ * @param _system_info    system information structure
  * @param input           mask of trajectory files
  * @param log             status of log-mode
  * @param output          output file name
@@ -92,16 +78,8 @@ int set_defaults (char *aglinp, float *cell, char *input, int *log, char *output
  * 
  * @return 0              - exit without errors
  */
-{
-  int i;
-  
-  aglinp[0] = '#';
-  for (i=0; i<3; i++)
-    cell[i] = 0.0;
-  input[0] = '#';
-  *log = 0;
-  output[0] = '#';
-  *quiet = 0;
-  
-  return 0;
-}
+int set_defaults (char *aglinp, system_info *_system_info, char *input, int *log, char *output, 
+                  int *quiet);
+
+
+#endif /* ADD_MAIN_H */

mathmech/agl/src/main.c

@@ -1,75 +1,18 @@
-/**
- * @file
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
  */
 /**
- * @mainpage mm_agl
- * @image latex ./logo.png
- *
- * @section intro_sec Introduction
- *
- * <b>About this program</b>:
- * <ul>
- * <li>Program that creates PDB file with chosen agglomerate
- * </ul>
- *
- * <b>Developer</b>:
- * <ul>
- * <li>Evgeniy Alekseev aka arcanis <pre><esalexeev (at) gmail (dot) com></pre>
- *</ul>
- * <b>License</b>:
- * <ul>
- * <li>GPL
- * </ul>
- *
- * @section How-To-Use How to use
- * Usage:
- * <pre>
- * mm_agl -a AGL_INP -i INPUT -c X,Y,Z -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]
- *
- * Parametrs:
- *    -a          - input file with agglomerates (in format statgen)
- *    -i          - input file with coordinates
- *    -c          - cell size (float), A
- *    -o          - output file name
- *    -l          - log enable
- *    -q          - quiet enable
- *    -h          - show this help and exit
- * </pre>
- * 
- * @page Install
- * 
- * @section Requirements Requirements
- * The application mm_agl requires the following external stuff:
- * - cmake  >= 2.8
- * - gcc    >= 4.8
- *
- * @section How-To How to install
- *
- * @subsection Linux Linux
- * @code
- * mkdir build && cd build
- * cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../
- * make
- * make install
- * @endcode
- * 
- * @subsection Windows Windows
- * @code
- * create project file using 'cmake'
- * compile project
- * @endcode
- * You may also download compiled executable file for Win_x86.
- *
- * @page Changelog
- * V.1.0.3 (2013-08-30)
- * <ul>
- * <li> Bug fixes
- * </ul>
- * V.1.0.1 (2013-07-27)
- * <ul>
- * <li> initial release
- * </ul>
- */ 
+ * @file main.c
+ * Source code of agl
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
 
 #include <math.h>
 #include <stdio.h>
@@ -77,12 +20,14 @@
 #include <string.h>
 
 #include "add_main.h"
-#include "coords.h"
-#include "messages.h"
-#include "print_struct.h"
-#include "read_agl.h"
-#include "select_mol.h"
-#include "set_center.h"
+#include <version.h>
+#include <mathmech/coords.h>
+#include <mathmech/messages.h>
+#include <mathmech/print_struct.h>
+#include <mathmech/read_agl.h>
+#include <mathmech/select_mol.h>
+#include <mathmech/set_center.h>
+#include <mathmech/var_types.h>
 
 
 /**
@@ -98,35 +43,33 @@ int main(int argc, char *argv[])
  */
 {
   char tmp_str[2048];
-  int error, i, *tmp_int;
+  int error, i;
   FILE *f_inp, *f_log;
   
-  char aglinp[256], *ch_type_atoms, input[256], logfile[256], output[256];
-  float cell[3], *centr_coords, *coords;
-  int *label_mol, log, num_atoms, num_mol, num_needed_mol, *needed_mol, quiet, 
-      *true_label_mol;
+  char aglinp[256], input[256], logfile[256], output[256];
+  float *centr_coords;
+  int log, num_needed_mol, *needed_mol, quiet, *true_label_mol;
+  atom_info *_atom_info;
+  system_info _system_info;
   
 /* aglinp                 agglomerate file name
- * ch_type_atoms          massive of char atom types
  * input                  input file name
  * logfile                log file name
  * output                 output file name
  * 
- * cell                   massive of cell size
  * centr_coords           massive of centered coordinates
- * coords                 massive of coordinates
  * 
- * label_mol              massive of numbers of molecule for atoms
  * log                    status of log-mode
- * num_atoms              number of atoms
- * num_mol                number of molecules
  * num_needed_mol         number of needed molecules
  * needed_mol             massive of number of needed molecules
  * quiet                  status of quiet-mode
  * true_label_mol         massive of true numbers of molecule for atoms
+ * 
+ * _atom_info             atom information structure
+ * _system_info           system information structure
  */
   
-  set_defaults (aglinp, cell, input, &log, output, &quiet);
+  set_defaults (aglinp, &_system_info, input, &log, output, &quiet);
   
   for (i=1; i<argc; i++)
   {
@@ -134,15 +77,14 @@ int main(int argc, char *argv[])
     {
       sprintf (tmp_str, "                                     mm_agl\n");
       sprintf (tmp_str, "%sProgram for create PDB file with chosen agglomerate\n", tmp_str);
-      sprintf (tmp_str, "%sVersion : 1.0.3                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : %s                                               License : Beerware\n", tmp_str, PROJ_VERSION);
       sprintf (tmp_str, "%s                                                    Evgeniy Alekseev aka arcanis\n", tmp_str);
       sprintf (tmp_str, "%s                                                    E-mail : esalexeev@gmail.com\n\n", tmp_str);
       sprintf (tmp_str, "%sUsage:\n", tmp_str);
-      sprintf (tmp_str, "%smm_agl -a AGL_INP -i INPUT -c X,Y,Z -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
+      sprintf (tmp_str, "%smm_agl -a AGL_INP -i INPUT -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
       sprintf (tmp_str, "%sParametrs:\n", tmp_str);
       sprintf (tmp_str, "%s  -a          - input file with agglomerates (in format statgen)\n", tmp_str);
       sprintf (tmp_str, "%s  -i          - input file with coordinates\n", tmp_str);
-      sprintf (tmp_str, "%s  -c          - cell size (float), A\n", tmp_str);
       sprintf (tmp_str, "%s  -o          - output file name\n", tmp_str);
       sprintf (tmp_str, "%s  -l          - log enable\n", tmp_str);
       sprintf (tmp_str, "%s  -q          - quiet enable\n", tmp_str);
@@ -162,12 +104,6 @@ int main(int argc, char *argv[])
       strcpy (input, argv[i+1]);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'c') && (argv[i][2] == '\0'))
-// cell size
-    {
-      sscanf (argv[i+1], "%f,%f,%f", &cell[0], &cell[1], &cell[2]);
-      i++;
-    }
     else if ((argv[i][0] == '-') && (argv[i][1] == 'o') && (argv[i][2] == '\0'))
 // output file
     {
@@ -200,7 +136,7 @@ int main(int argc, char *argv[])
   print_message (quiet, stdout, log, f_log, 1, argv[0]);
   
 // error check
-  error = error_checking (aglinp, cell, input, output);
+  error = error_checking (aglinp, _system_info, input, output);
   if (error != 0)
   {
     print_message (quiet, stderr, log, f_log, 17, argv[0]);
@@ -218,20 +154,14 @@ int main(int argc, char *argv[])
     print_message (quiet, stderr, log, f_log, 18, input);
     return 2;
   }
-  fscanf (f_inp, "%i", &num_atoms);
+  fscanf (f_inp, "%i", &_system_info.num_atoms);
   fclose (f_inp);
-  ch_type_atoms = (char *) malloc (2 * num_atoms * sizeof (char));
-  coords = (float *) malloc (3 * 8 * num_atoms * sizeof (float));
-  label_mol = (int *) malloc (8 * num_atoms * sizeof (int));
-  needed_mol = (int *) malloc (num_atoms * sizeof (int));
-  tmp_int = (int *) malloc (8 * num_atoms * sizeof (int));
-  true_label_mol = (int *) malloc (num_atoms * sizeof (int));
+  _atom_info = (atom_info *) malloc (8 * _system_info.num_atoms * sizeof (atom_info));
+  needed_mol = (int *) malloc (_system_info.num_atoms * sizeof (int));
+  true_label_mol = (int *) malloc (_system_info.num_atoms * sizeof (int));
 // error checking
-  if ((ch_type_atoms == NULL) ||
-     (coords == NULL) || 
-     (label_mol == NULL) || 
+  if ((_atom_info == NULL) ||
      (needed_mol == NULL) || 
-     (tmp_int == NULL) || 
      (true_label_mol == NULL))
   {
     print_message (quiet, stderr, log, f_log, 19, argv[0]);
@@ -239,7 +169,8 @@ int main(int argc, char *argv[])
   }
   sprintf (tmp_str, "%6cAglomerate file: '%s';\n%6cInput file: '%s';\n\
 %6cOutput file: '%s';\n%6cLog: %i;\n%6cQuiet: %i;\n%6cCell size: %.4f, %.4f, %.4f\n", 
-' ', aglinp, ' ', input, ' ', output, ' ', log, ' ', quiet, ' ', cell[0], cell[1], cell[2]);
+' ', aglinp, ' ', input, ' ', output, ' ', log, ' ', quiet, ' ', _system_info.cell[0], 
+_system_info.cell[1], _system_info.cell[2]);
   print_message (quiet, stdout, log, f_log, 5, tmp_str);
   
   print_message (quiet, stdout, log, f_log, 6, argv[0]);
@@ -255,10 +186,9 @@ int main(int argc, char *argv[])
 // reading coordinates
     print_message (quiet, stdout, log, f_log, 7, input);
     error = 1;
-    error = reading_coords (2, input, num_needed_mol, needed_mol, cell, &num_mol, 
-                            &num_atoms, true_label_mol, label_mol, tmp_int, coords, 
-                            ch_type_atoms);
-    centr_coords = (float *) malloc (3 * 8 * num_mol * sizeof (float));
+    error = reading_coords (2, input, num_needed_mol, needed_mol, &_system_info, 
+                            true_label_mol, _atom_info);
+    centr_coords = (float *) malloc (3 * 8 * _system_info.num_mol * sizeof (float));
     if (centr_coords == NULL)
     {
       print_message (quiet, stderr, log, f_log, 19, argv[0]);
@@ -270,10 +200,10 @@ int main(int argc, char *argv[])
   if (error == 0)
   {
     sprintf (tmp_str, "%6cNumber of molecules: %i; %6cNumber of atoms: %i\n", 
-            ' ', num_mol, ' ', num_atoms);
+            ' ', _system_info.num_mol, ' ', _system_info.num_atoms);
     print_message (quiet, stdout, log, f_log, 8, tmp_str);
     error = 1;
-    error = set_center (num_atoms, num_mol, label_mol, coords, centr_coords);
+    error = set_center (_system_info, _atom_info, centr_coords);
   }
   if (error == 0)
   {
@@ -285,8 +215,8 @@ int main(int argc, char *argv[])
   {
     print_message (quiet, stderr, log, f_log, 4, argv[0]);
     error = 1;
-    error = print_structure (output, num_needed_mol, needed_mol, num_atoms, 
-                              label_mol, ch_type_atoms, coords);
+    error = print_structure (output, num_needed_mol, needed_mol, _system_info, 
+                             _atom_info);
   }
   if (error == 0)
     print_message (quiet, stderr, log, f_log, 12, output);
@@ -295,12 +225,9 @@ int main(int argc, char *argv[])
   
   print_message (quiet, stdout, log, f_log, 15, argv[0]);
 // free memory
-  free (ch_type_atoms);
+  free (_atom_info);
   free (centr_coords);
-  free (coords);
-  free (label_mol);
   free (needed_mol);
-  free (tmp_int);
   free (true_label_mol);
   
   print_message (quiet, stdout, log, f_log, 16, argv[0]);
@@ -308,4 +235,4 @@ int main(int argc, char *argv[])
   if (log == 1)
     fclose (f_log);
   return 0;
-}
+}

mathmech/create_archive.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+SUBS="docs mathmech mm agl envir radf statgen trj trj2pdb"
+ADDS="AUTHORS CHANGELOG CMakeLists.txt COPYING docs.cmake doxygen.conf.in INSTALL version.h.in"
+ARCHIVE="mathmech"
+VERSION=`grep -m1 PROJECT_VERSION_MAJOR CMakeLists.txt | awk '{print $3}' | cut -c 1`.\
+`grep -m1 PROJECT_VERSION_MINOR CMakeLists.txt | awk '{print $3}' | cut -c 1`.\
+`grep -m1 PROJECT_VERSION_PATCH CMakeLists.txt | awk '{print $3}' | cut -c 1`
+
+# create archive
+if [ -e ${ARCHIVE}-${VERSION}-src.zip ]; then
+  rm -f ${ARCHIVE}-${VERSION}-src.zip
+fi
+zip -9qry ${ARCHIVE}-${VERSION}-src.zip ${ADDS} ${SUBS}
+
+# update md5sum
+MD5SUMS=`md5sum ${ARCHIVE}-${VERSION}-src.zip | awk '{print $1}'`
+sed -i "/md5sums=('[0-9A-Fa-f]*/s/[^'][^)]*/md5sums=('${MD5SUMS}'/" PKGBUILD
+sed -i "s/pkgver=[0-9.]*/pkgver=${VERSION}/" PKGBUILD

mathmech/docs.cmake

@@ -0,0 +1,15 @@
+# standart documentation
+set (PROJECT_DOCS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/docs/)
+install (DIRECTORY ${PROJECT_DOCS_DIR} DESTINATION share/doc/${PROJECT_NAME})
+
+# doxygen documentation
+find_package (Doxygen)
+  if (DOXYGEN_FOUND)
+    set (DOXYGEN_INPUT ${CMAKE_SOURCE_DIR})
+    configure_file (${CMAKE_SOURCE_DIR}/doxygen.conf.in ${CMAKE_CURRENT_BINARY_DIR}/doxygen.conf)
+    add_custom_target (oxygen-docs ALL COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/doxygen.conf)
+    install (DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/docs/html DESTINATION share/doc/${PROJECT_NAME})
+    install (DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/docs/man DESTINATION share/)
+  else (DOXYGEN_FOUND)
+    message (STATUS "WARNING: Doxygen not found - Reference manual will not be created")
+endif ()

mathmech/docs/eng/help_agl.html

@@ -0,0 +1,31 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
+<html><head><meta name="qrichtext" content="1" /><style type="text/css">
+p, li { white-space: pre-wrap; }
+</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;">
+<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">agl</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that creates PDB file with chosen agglomerate.</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Usage</span><br />mm_agl -a FILE -i FILE -c X,Y,Z -o FILE [ -l FILE ] [ -q ] [ -h ]<br />	<span style=" text-decoration: underline;">Parametrs</span><br />-a FILE 		– input file with agglomerate<br />-i FILE 		– input trajectory file<br />-c X,Y,Z 		– cell size, A<br />-o FILE 		– output PDB file<br />-l FILE 		– print log to specified file<br />-q 		– do not print messages to STDOUT<br />-h 		– show this help and exit</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">File formats</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">	<span style=" font-style:italic;">Agglomerate file (*.agl)</span></p>
+<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified).</li>
+<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of molecules in the agglomerate (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).</li></ul>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">	<span style=" font-style:italic;">Trajectory file (*.pdb)</span></p>
+<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Operation of the application</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Search for the best configuration.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.</li></ol>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Working with GUI</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select Menu -&gt; File creator -&gt; Agglomerate file.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the file generated by statgen. Push &quot;Select&quot;.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select the trajectory file from the drop down list. Select the agglomerate.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file. Create file.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate PDB&quot;. Select &quot;From agglomerate&quot; from the drop down list.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the work directory.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the agglomerate file.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html>

mathmech/docs/eng/help_envir.html

@@ -0,0 +1,23 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
+<html><head><meta name="qrichtext" content="1" /><style type="text/css">
+p, li { white-space: pre-wrap; }
+</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;">
+<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">envir</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that searchs environment for chosen molecule by geometric criterion.</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Usage</span><br />mm_envir -i FILE -c X,Y,Z -o FILE [ -n NUMBER ] [ -r NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br />	<span style=" text-decoration: underline;">Parametrs</span><br />-i FILE 		– input trajectory file<br />-c X,Y,Z 		– cell size, A<br />-o FILE 		– output PDB file<br />-n NUMBER 		– number of molecule for search. Default is 1<br />-r NUMBER 		– radius of environment. Default is 6.0<br />-l FILE 		– print log to specified file<br />-q 		– do not print messages to STDOUT<br />-h 		– show this help and exit</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">File formats</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">	<span style=" font-style:italic;">Trajectory file (*.pdb)</span></p>
+<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Operation of the application</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Search for the environment.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the environment to the file.</li></ol>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Working with GUI</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Environment&quot;. Set the work directory.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the number of molecule for search and the radius of environment.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html>

mathmech/docs/eng/help_radf.html

@@ -0,0 +1,27 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
+<html><head><meta name="qrichtext" content="1" /><style type="text/css">
+p, li { white-space: pre-wrap; }
+</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;">
+<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">radf</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that calculates radial distribution function (RDF) or radial-angles distribution function (RADF).</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Usage</span><br />mm_radf -i MASK -s NUMBER,NUMBER -c X,Y,Z -at FORMAT -o FILE [ -r NUMBER,NUMBER ] [ -rs NUMBER ] [ -a NUMBER,NUMBER ] [ -as NUMBER ] [ -m ] [ -l FILE ] [ -q ] [ -h ]<br />	<span style=" text-decoration: underline;">Parametrs</span><br />-i MASK 		– mask of trajectory files<br />-s NUMBER,NUMBER 	– first and last trajectory steps<br />-c X,Y,Z 		– cell size, A<br />-at FORMAT 		– numerical atom types between which the function is calculated. Format is &quot;1-2&quot; or &quot;1,2,3-4,5,6&quot; (automatically enable calculation of radial distribution function between centers of mass)<br />-o FILE 		– output file<br />-r NUMBER,NUMBER 	– radial criteria, A. Default is 2.0 and 15.0<br />-rs NUMBER 		– radius change step, A. Default is 0.2<br />-a NUMBER,NUMBER 	– angular criteria, deg. Default is 0.0 and 90.0<br />-as NUMBER 		– angle change step, deg. This option will enable calculation of radial-angles distribution function<br />-as 		– enable matrix output<br />-l FILE 		– print log to specified file<br />-q 		– do not print messages to STDOUT<br />-h 		– show this help and exit</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">File formats</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">	<span style=" font-style:italic;">Output file (*.dat)</span></p>
+<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;radf ::: V.1.1.0&quot;. Blank line.</li>
+<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), matrix output (MATRIX=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), mode (MODE=0) (0 – radial distribution function, 1 – radial distribution function between centers of mass, 2 – radial-angles distribution function), radial criteria (R_MIN=0.100) (R_MAX=0.100) (R_STEP=0.100), angular criteria for radial-angles distribution function (ANG_MIN=0.10) (ANG_MAX=0.10) (ANG_STEP=0.10), atom types (ATOM=1-2) or (ATOM=1,2,3-4,5,6). Blank line.</li>
+<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.<br />The table format for radial distribution function (matrix output disables)<br /> 0001.0000 2.0000e-01 000000003 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, segment volume (10 characters, 4 decimal part), space, number of molecules in this radius (9 characters), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial distribution function (matrix output enables)<br /> 0001.0000 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output disables)<br /> 0001.0000 000005.00 2.0000e-01 000000003 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, segment angle (9 characters, 2 decimal part), segment volume (10 characters, 4 decimal part), space, number of molecules in this segment (9 characters), space, radial-angles distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title<br /> 0001.0000 04.000000 ...<br />Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.</li>
+<li style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">End of the table</li></ul>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Operation of the application</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, settings values of variables.<br />Calculating of the number of pairs of molecules in various relative configurations.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.<br />Radial distribution function calculated by:<br />RDF(r) = (1 / norm) * sum(d(r_n-r), n),<br />norm(r) = (4*PI*r^2*dr) * ro * N * N_step,<br />where d(r_n-r) is the delta function, r is a shpere radius, n is a number of molecule, dr is the radius change step, ro is the number of molecules per volume unit, N is the number of molecules, N_step is a number of trajectory step.<br />Radial-angles distribution function calculated by:<br />RADF(r, fi) = (1 / norm) * sum(sum(d(r_n-r)*d(fi_n-fi), n), n),<br />norm(r, fi) = (4*PI*r^2*sin(fi)*dr*dfi) * ro * N * N_step,<br />where d(r_n-r) and d(fi_n-fi) are the delta functions, r is a shpere radius, fi is a segment angle, n is a number of molecule, dr is the radius change step, dfi is the angle change step, ro is the number of molecules per volume unit, N is the number of molecules, N_step is a number of trajectory step.</li></ol>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Working with GUI</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;RADF&quot;. Set the work directory.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of trajectory files.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the first and the last trajectory steps.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set needed atoms.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set radial criteria. Set angular criteria if this needed.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the matrix output, the log file and the graph generate if this needed.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html>

mathmech/docs/eng/help_statgen.html

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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
+<html><head><meta name="qrichtext" content="1" /><style type="text/css">
+p, li { white-space: pre-wrap; }
+</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;">
+<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">statgen</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that analyzes molecular dynamics trajectories using topological analysis.</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Usage</span><br />mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br />	<span style=" text-decoration: underline;">Parametrs</span><br />-i MASK 		– mask of trajectory files<br />-s NUMBER,NUMBER 	– first and last trajectory steps<br />-c X,Y,Z 		– cell size, A<br />-a FORMAT 		– numerical atom types. Maximum number of different atom types is 4. Types are comma separated<br />-r FORMAT 		– criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &quot;0-0:2.4,0-1:3.0&quot; means set 0-0 interaction as &lt;2.4 А and 0-1 interaction as &lt;3.0 A<br />-o FILE 		– output file<br />-g NUMBER 		– chech graph isomorphism. NUMBER is a maximum depth for search cycles (&gt;= 3)<br />-l FILE 		– print log to specified file<br />-q 		– do not print messages to STDOUT<br />-h 		– show this help and exit</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">File formats</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">	<span style=" font-style:italic;">Output file (*.dat)</span></p>
+<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;statgen ::: V.1.1.0&quot;. Blank line.</li>
+<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), atom types (ATOMS=1,2,3,4), interactions (INTERACTION=format), maximum depth for check cycle number (DEPTH=0, 0 - do not check graph isomorphism). Blank line.</li>
+<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of statistics on individual files.<br />File name (FILE=mask.001), the statistic block for file &quot;STATISTIC ... -----------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000001 <br />Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).<br />The enumeration of agglomerates in the file. Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified). The enumeration of molecules in the agglomerate. (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).</li>
+<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The summary statistic block &quot;SUMMARY STATISTIC … ------------------------------------------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000002 000003.00 004.00000 0005.00000<br />Space, agglomerate size (7 characters), space, total number of agglomerates of this size (7 characters), space, average concentration of agglomerates of this size (9 characters, 2 decimal part), space, probability of finding molecules in agglomerates of this size (9 characters, 5 decimal part), space, probability of finding molecules in agglomerates of this size multiplied by the size (10 characters, 5 decimal part).</li>
+<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Summary statistic of agglomerates on classes (if verification of isomorphism is specified). The proportion of linear (LINEAR=0.10000) and cyclic (CYCLE=0.10000) agglomerates, blank line, the proportion of not branched (NOT BRANCHED=0.10000) and branched (BRANCHED=0.10000) agglomerates, blank line, the proportion of found cycles of the specified size (CYCLE_03=0.10000).</li></ul>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Operation of the application</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, settings values of variables.<br />Search for interactions that satisfy the specified criteria.<br />The analysis of all connections and specifying to the two molecules that connected, if the conditions are satisfied at least one of these criteria.<br />Adding molecules to agglomerates according to the obtained connectivity matrix.<br />Print agglomerates to the file, adding the summary statistics.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the summary statistic to the file.</li></ol>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Working with GUI</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Agglomeration&quot;. Set the work directory.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of trajectory files.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the first and the last trajectory steps.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set needed atoms.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set interactions. Select type of interaction from the drop down list, change its criterion and press &quot;Save&quot;. Press &quot;Add&quot; after ending of edition. After this the interaction will appear in the special window. To remove an interaction you need select the desired interaction in the special window and press &quot;Remove&quot;.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the maximum depth for search cycles, the log file and the graph generate if this needed.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">For the variation of geometric criteria you need specify the criteria step changes and the number of steps.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html>

mathmech/docs/eng/help_trj.html

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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
+<html><head><meta name="qrichtext" content="1" /><style type="text/css">
+p, li { white-space: pre-wrap; }
+</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;">
+<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">trj</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that generates trajectory files in special format from input trajectory.</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Usage</span><br />mm_trj -i FILE -t TYPE -s NUMBER -a FILE -o MASK [ -tt NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br />	<span style=" text-decoration: underline;">Parametrs</span><br />-i FILE 		– input trajectory file<br />-t TYPE 		– trajectory type. Supported formats: gmx, puma<br />-s NUMBER 		– number of trajectory steps<br />-a FILE 		– file with atom types<br />-o MASK 		– mask of output trajectory files<br />-tt NUMBER 		– maximum number of different atom types. Default is 1024<br />-l FILE 		– print log to specified file<br />-q 		– do not print messages to STDOUT<br />-h 		– show this help and exit</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">File formats</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">	<span style=" font-style:italic;">Trajectory files (*.[0-9])</span></p>
+<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Number of atoms is shown in the title.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Trajectory snapshot (enumeration of all atoms in system). Format<br />00001 СА  1234.000000 1234.000000 1234.000000    01 0001<br />The sequence number of an atom (5 characters), space, character atom type (2 characters), 2 spaces, X coordinate (11 characters, 6 decimal part), Y coordinate (11 characters, 6 decimal part), Z coordinate (11 characters, 6 decimal part), 4 spaces, numerical atom type (2 characters), space, number of molecule (4 characters).</li></ul>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">	<span style=" font-style:italic;">Atom types file (*.types)</span></p>
+<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The number of different molecules (NUMTYPES=1) is shown in the title.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The molecules enumeration block. Variables are the number of molecules (NUMMOL=1), the number of atoms (NUMAT=1).<br />The atoms enumeration block. Format<br />CA=1<br />Character atom type (2 characters), equal sign, numerical atom type.</li></ul>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Operation of the application</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, print results to the specified output file.</li></ol>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Working with GUI</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select Menu -&gt; File creator -&gt; Atom types file.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set atom types. To add a new molecule you need select &quot;Add new molecule&quot; from the drop down list. To change the number of molecules you need change the corresponding numeric value. To add a new atom you need enter 2 character to the special field, set numerical atom type and press &quot;Add&quot;. After this the atom will appear in the special window. To remove an atom you need select the desired atom in the special window and press &quot;Remove&quot;.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Create the atom types file.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate trajectory&quot;. Set the work directory.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select the trajectory type from the drop down list, set the number of trajectory steps.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the atom types file.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of output files.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the maximum number of different atom types and the log file if this needed.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html>

mathmech/docs/eng/help_trj2pdb.html

@@ -0,0 +1,21 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
+<html><head><meta name="qrichtext" content="1" /><style type="text/css">
+p, li { white-space: pre-wrap; }
+</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;">
+<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">trj2pdb</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that creates PDB file from trajetory snapshot.</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Usage</span><br />mm_trj2pdb -i FILE -o FILE [ -l FILE ] [ -q ] [ -h ]<br />	<span style=" text-decoration: underline;">Parametrs</span><br />-i FILE 		– input trajectory file<br />-o FILE 		– output PDB file<br />-l FILE 		– print log to specified file<br />-q 		– do not print messages to STDOUT<br />-h 		– show this help and exit</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">File formats</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">	<span style=" font-style:italic;">Trajectory file (*.pdb)</span></p>
+<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Operation of the application</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.</li></ol>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Working with GUI</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate PDB&quot;. Select &quot;From trajectory snapshot&quot; from the drop down list.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the work directory.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html>

mathmech/docs/rus/help_agl.html

@@ -0,0 +1,31 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
+<html><head><meta name="qrichtext" content="1" /><style type="text/css">
+p, li { white-space: pre-wrap; }
+</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;">
+<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">agl</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Программа для генерации PDB файлов с агломератами.</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Использование</span><br />mm_agl -a ФАЙЛ -i ФАЙЛ -c X,Y,Z -o ФАЙЛ [ -l ФАЙЛ ] [ -q ] [ -h ]<br />	<span style=" text-decoration: underline;">Параметры</span><br />-a ФАЙЛ 		– исходный файл с агломератом<br />-i ФАЙЛ 		– исходный файл с координатами<br />-c X,Y,Z 		– размер элементарной ячейки, А<br />-o ФАЙЛ 		– генерируемый PDB файл с координатами<br />-l ФАЙЛ 		– запись лога в указанный файл<br />-q 		– не выводить сообщения в STDOUT<br />-h 		– показать эту справку и выйти</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Форматы файлов</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">	<span style=" font-style:italic;">Файл с агломератом (*.agl)</span></p>
+<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Заголовок агломерата (AGL=2=1.3.4.) (1 – число молекул в агломерате, 1.3.4. – класс агломерата, если указана проверка изоморфизма).</li>
+<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Перечисление молекул в агломерате (0000001=2,3,4,5,) (1 – номер молекулы (7 символов), знак равенства, перечисление связанных молекул через запятую).</li></ul>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">	<span style=" font-style:italic;">Файл траектории (*.pdb)</span></p>
+<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Работа приложения</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение заголовков исходных файлов, установка начальных переменных.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение исходных файлов.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Поиск оптимальной конфигурации.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Печать результата в файл.</li></ol>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Работа с графическим интерфейсом</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Меню -&gt; Создание файлов -&gt; Файл с агломератом.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать файл, сгенерированный приложением statgen. Нажать &quot;Выбор&quot;.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Выбрать траекторный снимок в выпадающем списке. Выбрать агломерат.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать выходной файл. Создать файл с агломератом.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">5. Перейти во вкладку &quot;Создать PDB&quot;. Из выпадающего списка выбрать &quot;Из агломерата&quot;.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать рабочую директорию.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать файл траектории.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать сгенерированный файл с агломератом.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать размер ячейки в А.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать генерируемый PDB файл.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">При необходимости указать файл лога.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Запустить приложение.</li></ol></body></html>

mathmech/docs/rus/help_envir.html

@@ -0,0 +1,23 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
+<html><head><meta name="qrichtext" content="1" /><style type="text/css">
+p, li { white-space: pre-wrap; }
+</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;">
+<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">envir</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Программа для генерации PDB файла указанной молекулы с окружением указанного радиуса.</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Использование</span><br />mm_envir -i ФАЙЛ -c X,Y,Z -o ФАЙЛ [ -n ЧИСЛО ] [ -r ЧИСЛО ] [ -l ФАЙЛ ] [ -q ] [ -h ]<br />	<span style=" text-decoration: underline;">Параметры</span><br />-i ФАЙЛ 		– исходный файл с координатами<br />-c X,Y,Z 		– размер элементарной ячейки, А<br />-o ФАЙЛ 		– генерируемый PDB файл с координатами<br />-n ЧИСЛО 		– номер молекулы для поиска окружения. По умолчанию 1<br />-r ЧИСЛО 		– радиус окружения, А. По умолчанию 6.0<br />-l ФАЙЛ 		– запись лога в указанный файл<br />-q 		– не выводить сообщения в STDOUT<br />-h 		– показать эту справку и выйти</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Форматы файлов</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">	<span style=" font-style:italic;">Файл траектории (*.pdb)</span></p>
+<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Работа приложения</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение заголовков исходных файлов, установка начальных переменных.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение исходного файла.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Поиск окружения.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Печать окружения в файл.</li></ol>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Работа с графическим интерфейсом</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Перейти во вкладку &quot;Окружение&quot;. Указать рабочую директорию.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать исходный файл.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать размер ячейки в А.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать генерируемый PDB файл.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать молекулу для поиска окружения и радиус окружения в А.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">При необходимости указать файл лога.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Запустить приложение.</li></ol></body></html>

mathmech/docs/rus/help_radf.html

@@ -0,0 +1,27 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
+<html><head><meta name="qrichtext" content="1" /><style type="text/css">
+p, li { white-space: pre-wrap; }
+</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;">
+<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">radf</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Программа для расчета функций радиального (ФРР) и радиально-углового распределения (ФРУР).</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Использование</span><br />mm_radf -i МАСКА -s ЧИСЛО,ЧИСЛО -c X,Y,Z -at ФОРМАТ -o ФАЙЛ [ -r ЧИСЛО,ЧИСЛО ] [ -rs ЧИСЛО ] [ -a ЧИСЛО,ЧИСЛО ] [ -as ЧИСЛО ] [ -m ] [ -l ФАЙЛ ] [ -q ] [ -h ]<br />	<span style=" text-decoration: underline;">Параметры</span><br />-i МАСКА 		– маска снимков траектории<br />-s ЧИСЛО,ЧИСЛО 	– первый и последний шаги траектории<br />-c X,Y,Z 		– размер элементарной ячейки, А<br />-at ФОРМАТ 		– численные типы атомов между которыми строится функция. Формат &quot;1-2&quot; или &quot;1,2,3,-4,5,6&quot; (автоматически включит расчет функции радиального распределения между центрами масс).<br />-o ФАЙЛ 		– генерируемый файл<br />-r ЧИСЛО,ЧИСЛО 	– минимальный и максимальный радиус, А. По умолчанию 2.0 и 15.0<br />-rs ЧИСЛО 		– шаг изменения радиуса, А. По умолчанию 0.2<br />-a ЧИСЛО,ЧИСЛО 	– минимальный и максимальный угол, град. По умолчанию 0.0 и 90.0<br />-as ЧИСЛО 		– шаг изменения угла, град. Эта опция включит расчет функции радиально-углового распределения<br />-m 		– печать в виде матрицы<br />-l ФАЙЛ 		– запись лога в указанный файл<br />-q 		– не выводить сообщения в STDOUT<br />-h 		– показать эту справку и выйти</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Форматы файлов</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">	<span style=" font-style:italic;">Генерируемый файл (*.dat)</span></p>
+<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">В заголовке указывается название программы и ее версия, например &quot;radf ::: V.1.1.0&quot;. Пустая строка.</li>
+<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Блок конфигурации &quot;CONFIGURATION … END&quot;. Печать лога (LOG=1), не выводить сообщения в STDOUT (QUIET=1), матричный вывод (MATRIX=1), файлов (MASK=mask), первый (FIRST=1) и последний (LAST=1)  шаги траектории, размер ячейки (CELL=1.0000,2.0000,3.0000), тип расчета (MODE=0) (0 – для функции радиального распределения, 1 – для функции радиального распределения для центров масс, 2 – для функции радиально-углового распределения), радиальные критерии (R_MIN=0.100) (R_MAX=0.100) (R_STEP=0.100), угловые критерии для функции радиально-углового распределения (ANG_MIN=0.10) (ANG_MAX=0.10) (ANG_STEP=0.10), типы атомов (ATOM=1-2) или (ATOM=1,2,3-4,5,6). Пустая строка.</li>
+<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Блок результатов &quot;SUMMARY STATISTIC … ------------------------------------------------&quot;. После указания блока, если отключен матричный вывод, следует разметка таблицы (2 строки).<br />Формат таблицы для функций радиального распределения (матричный вывод отключен)<br /> 0001.0000 2.0000e-01 000000003 04.000000<br />Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, объем сегмента (10 символов, 4 десятичной части), пробел, число молекул в данном сегменте (9 символов), функция радиального распределения (9 символов, 6 десятичной части).<br />Формат таблицы для функций радиального распределения (матричный вывод включен)<br /> 0001.0000 04.000000<br />Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, функция радиального распределения (9 символов, 6 десятичной части).<br />Формат таблицы для функций радиально-углового распределения (матричный вывод отключен)<br /> 0001.0000 000005.00 2.0000e-01 000000003 04.000000<br />Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, угол (9 символов, 2 десятичной части), пробел, объем сегмента (10 символов, 4 десятичной части), пробел, число молекул в данном сегменте (9 символов), функция радиально-углового распределения (9 символов, 6 десятичной части).<br />Формат таблицы для функций радиально-углового распределения (матричный вывод включен). В заголовке указывается угол (9 символов, 2 десятичной части)<br /> 0001.0000 04.000000 …<br />Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, функция радиально-углового распределения (9 символов, 6 десятичной части) через пробелы, соответствующие данному углу.</li>
+<li style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Конец таблицы.</li></ul>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Работа приложенияn</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение заголовков исходных файлов, установка начальных переменных.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Пошаговое чтение исходных файлов. Установка переменных.<br />Расчет количества пар молекул, находящихся в различных взаимных конфигурациях.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Печать результата в файл.<br />Функция радиального распределения рассчитывается по формуле:<br />RDF(r) = (1 / norm) * sum(d(r_n-r), n),<br />norm(r) = (4*PI*r^2*dr) * ro * N * N_step,<br />где d(r_n-r) – дельта-функция, r – радиус сферы, n – номер молекулы, dr – шаг изменения радиуса, ro – число молекул в единице объема, N – число молекул, N_step – число шагов траектории.<br />Функция радиально-углового распределения рассчитывается по формуле:<br />RADF(r, fi) = (1 / norm) * sum(sum(d(r_n-r)*d(fi_n-fi), n), n),<br />norm(r, fi) = (4*PI*r^2*sin(fi)*dr*dfi) * ro * N * N_step,<br />где d(r_n-r) и d(fi_n-fi) – дельта-функции, r – радиус сферы, fi – угол, n – номер молекулы, dr – шаг изменения радиуса, dfi – шаг изменения угла, ro – число молекул в единице объема, N – число молекул, N_step – число шагов траектории.</li></ol>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Работа с графическим интерфейсом</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Перейти во вкладку &quot;ФРУР&quot;. Указать рабочую директорию.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать маску траекторных файлов.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать первый и последний шаги траектории.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать размер ячейки в А.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать генерируемый файл.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать искомые атомы.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать радиальные параметры функции в А. При необходимости указать угловые параметры функции в градусах.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">При необходимости указать печать в виде матрицы, файл лога и генерацию графика.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Запустить приложение.</li></ol></body></html>

mathmech/docs/rus/help_statgen.html

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+p, li { white-space: pre-wrap; }
+</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;">
+<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">statgen</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Программа для анализа снимков молекулярно-динамических траекторий – выделяет молекулы в агломераты согласно указанному геометрическому критерию.</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Использование</span><br />mm_statgen -i МАСКА -s ЧИСЛО,ЧИСЛО -c X,Y,Z -a ФОРМАТ -r ФОРМАТ -o ФАЙЛ [ -g ЧИСЛО ] [ -l ФАЙЛ ] [ -q ] [ -h ]<br />	<span style=" text-decoration: underline;">Параметры</span><br />-i МАСКА 		– маска снимков траектории<br />-s ЧИСЛО,ЧИСЛО 	– первый и последний шаги траектории<br />-c X,Y,Z 		– размер элементарной ячейки, А<br />-a ФОРМАТ 		– численные типы атомов. Максимальное число различных атомов 4. Типы атомов перечисляются через запятую<br />-r ФОРМАТ 		– критерии, А. Этот флаг может быть указан несколько раз. Различные взаимодействия перечисляются через запятую. Указывается тип взаимодействия, двоеточие, критерий. Например, &quot;0-0:2.4,0-1:3.0&quot; означает указание 0-0 взаимодействия &lt;2.4 А и 0-1 &lt;3.0 А.<br />-o ФАЙЛ 		– генерируемый файл<br />-g NUMBER 		– проверять изоморфизм графов. ЧИСЛО – максимальная глубина для проверки числа циклов (&gt;= 3)<br />-l ФАЙЛ 		– запись лога в указанный файл<br />-q 		– не выводить сообщения в STDOUT<br />-h 		– показать эту справку и выйти</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Форматы файлов</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">	<span style=" font-style:italic;">Генерируемый файл (*.dat)</span></p>
+<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">В заголовке указывается название программы и ее версия, например &quot;statgen ::: V.1.1.0&quot;. Пустая строка.</li>
+<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Блок конфигурации &quot;CONFIGURATION … END&quot;. Печать лога (LOG=1), не выводить сообщения в STDOUT (QUIET=1), маска файлов (MASK=mask), первый (FIRST=1) и последний (LAST=1)  шаги траектории, размер ячейки (CELL=1.0000,2.0000,3.0000), типы атомов (ATOMS=1,2,3,4), взаимодействия (INTERACTION=формат), максимальная глубина для проверки числа циклов (DEPTH=0, 0 – не проверять изоморфизм). Пустая строка.</li>
+<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Перечисление статистики по файлам.<br />Имя файла (FILE=mask.001), блок статистики по файлу &quot;STATISTIC … -----------------&quot;. После указания блока следует разметка таблицы (2 строки). Формат таблицы<br /> 0000001 0000001 <br />Пробел, размер агломерата (7 символов), пробел, число агломератов данной стехиометрии в файле (7 символов).<br />Перечисление агломератов, найденных в данном файле. Заголовок агломерата (AGL=2=1.3.4.) (1 – число молекул в агломерате, 1.3.4. – класс агломерата, если указана проверка изоморфизма). Перечисление молекул в агломерате (0000001=2,3,4,5,) (1 – номер молекулы (7 символов), знак равенства, перечисление связанных молекул через запятую).</li>
+<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Общая статистика &quot;.SUMMARY STATISTIC … ------------------------------------------------&quot;..После указания блока следует разметка таблицы (2 строки). Формат таблицы<br /> 0000001 0000002 000003.00 004.00000 0005.00000<br />Пробел, размер агломерата (7 символов), пробел, общее число агломератов данной стехиометрии (7 символов), пробел, средняя концентрация агломератов данной стехиометрии (9 символов, 2 десятичной части), пробел, вероятность нахождения молекулы в агломерате данной стехиометрии (9 символов, 5 десятичной части), пробел, вероятность нахождения молекулы в агломерате данной стехиометрии, умноженная на число молекул в агломерате (10 символов, 5 десятичной части).</li>
+<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Общая статистика агломератов по классам (если указана проверка изоморфизма). Доля линейных (LINEAR=0.10000) и циклических (CYCLE=0.10000) агломератов, пропуск строки, доля неразветвленных (NOT BRANCHED=0.10000) и разветвленных (BRANCHED=0.10000) агломератов, пропуск строки, доля найденных циклов указанного размера (CYCLE_03=0.10000).</li></ul>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Работа приложения</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение заголовков исходных файлов, установка начальных переменных.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Пошаговое чтение исходных файлов, установка переменных.<br />Поиск взаимодействий, удовлетворяющих указанным критериям.<br />Анализ всех связей и указание связи двух молекул, если удовлетворяется условия хотя бы одного из указанных критериев.<br />Добавление молекул в агломераты согласно полученной матрице связанности.<br />Печать агломератов в файл, дополнение общей статистики.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Печать общей статистики в файл.</li></ol>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Работа с графическим интерфейсом</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Перейти во вкладку &quot;Агломерация&quot;. Указать рабочую директорию.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать маску траекторных файлов.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать первый и последний шаги траектории.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать размер ячейки в А.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать искомые атомы.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать взаимодействия. Из выпадающего списка выбрать тип взаимодействия, изменить при его критерий (А) и нажать &quot;Сохранить&quot;. После завершения редактирования нажать &quot;Добавить&quot; – после этого взаимодействие появится в специальном окошке.. Для удаления взаимодействия необходимо выделить нужное взаимодействие в окошке и нажать &quot;Удалить&quot;.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать генерируемый файл.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">При необходимости указать максимальную глубину для проверки числа циклов в агломератах, файл лога и генерацию графика.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Для вариации геометрических критериев необходимо указать шаг изменения критериев и число шагов.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Запустить приложение.</li></ol></body></html>

mathmech/docs/rus/help_trj.html

@@ -0,0 +1,29 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
+<html><head><meta name="qrichtext" content="1" /><style type="text/css">
+p, li { white-space: pre-wrap; }
+</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;">
+<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">trj</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Программа для генерации специальных траекторных файлов из указанных исходных.</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Использование</span><br />mm_trj -i ФАЙЛ -t ТИП -s ЧИСЛО -a ФАЙЛ -o МАСКА [ -tt ЧИСЛО ] [ -l ФАЙЛ ] [ -q ] [ -h ]<br />	<span style=" text-decoration: underline;">Параметры</span><br />-i ФАЙЛ		– исходный траекторный файл<br />-t ТИП 		– тип траектории. Поддерживаемые форматы: gmx, puma<br />-s ЧИСЛО 		– число шагов траектории<br />-a ФАЙЛ 		– файл с указанием типов атомов<br />-o МАСКА 		– маска получаемых траекторных файлов<br />-tt ЧИСЛО 		– максимальное число различных типов атомов. По умолчанию 1024<br />-l ФАЙЛ 		– запись лога в указанный файл<br />-q 		– не выводить сообщения в STDOUT<br />-h 		– показать эту справку и выйти</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Форматы файлов</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">	<span style=" font-style:italic;">Файлы траектории (*.[0-9])</span></p>
+<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">В заголовке указывается число атомов (7 символов).</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Снимок траектории (перечисление всех атомов). Формат<br />00001 СА  1234.000000 1234.000000 1234.000000    01 0001<br />Порядковый номер атома (5 символов), пробел, символьный тип атома (2 символа), 2 пробела, координата X (11 символов, 6 десятичной части), координата Y (11 символов, 6 десятичной части), координата Z (11 символов, 6 десятичной части), 4 пробела, численный тип атома (2 символа), пробел, номер молекулы (4 символа).</li></ul>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">	<span style=" font-style:italic;">Файл с указанием типов атомов (*.types)</span></p>
+<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">В заголовке указывается число молекул (NUMTYPES=1).</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Блок перечисления молекул. Переменные число молекул (NUMMOL=1), число атомов (NUMAT=1).<br />Блок перечисления атомов в молекуле. Формат<br />CA=1<br />Символьный тип атома (2 символа), символ равенства, численный тип атома.</li></ul>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Работа приложения</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение заголовков исходных файлов, установка начальных переменных.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Пошаговое чтение исходных файлов и вывод шагов в указанные файлы.</li></ol>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Работа с графическим интерфейсом</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Выбрать Меню -&gt; Создание файлов -&gt; Файл типов атомов.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать генерируемый файл.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Заполнить типы атомов. Для добавления новой молекулы выбрать из выпадающего списка &quot;Добавить новую молекулу&quot;. Для изменения числа молекул изменить соответствующее числовое значение. Для добавления нового атома необходимо ввести 2 символа в специальное поле, указать численный тип атома и нажать &quot;Добавить&quot; – после этого атом появится в специальном окошке. Для удаления атома необходимо выделить нужный атом в окошке и нажать &quot;Удалить&quot;.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Создать файл типов атомов.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Перейти во вкладку &quot;Создать траекторию&quot;. Указать рабочую директорию.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать исходный траекторный файл.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Выбрать тип траектории из выпадающего списка, указать число шагов траектории.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать созданный ранее файл типов атомов.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать маску генерируемых файлов.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">При необходимости указать максимальное число различных типов атомов и файл лога.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Запустить приложение.</li></ol></body></html>

mathmech/docs/rus/help_trj2pdb.html

@@ -0,0 +1,21 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
+<html><head><meta name="qrichtext" content="1" /><style type="text/css">
+p, li { white-space: pre-wrap; }
+</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;">
+<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">trj2pdb</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Программа для генерации PDB файла из исходных траекторных файлов.</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Использование</span><br />mm_trj2pdb -i ФАЙЛ -o ФАЙЛ [ -l ФАЙЛ ] [ -q ] [ -h ]<br />	<span style=" text-decoration: underline;">Параметры</span><br />-i ФАЙЛ 		– исходный файл с координатами<br />-o ФАЙЛ 		– генерируемый PDB файл с координатами<br />-l ФАЙЛ 		– запись лога в указанный файл<br />-q 		– не выводить сообщения в STDOUT<br />-h 		– показать эту справку и выйти</p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Форматы файлов</span></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">	<span style=" font-style:italic;">Файл траектории (*.pdb)</span></p>
+<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Работа приложения</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение заголовков исходных файлов, установка начальных переменных.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение исходного файла.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Печать в файл.</li></ol>
+<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />	<span style=" text-decoration: underline;">Работа с графическим интерфейсом</span></p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Перейти во вкладку &quot;Создать PDB&quot;. Из выпадающего списка выбрать &quot;Из снимка траектории&quot;.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать рабочую директорию.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать файл траектории.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать генерируемый PDB файл.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">При необходимости указать файл лога.</li>
+<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Запустить приложение.</li></ol></body></html>

mathmech/envir/CMakeLists.txt

@@ -0,0 +1,21 @@
+# set project name
+set (SUBPROJECT envir)
+# set additional cmake file
+include (${SUBPROJECT}.cmake)
+
+# set libraries
+set (LIBRARIES mm)
+foreach (LIBRARY ${LIBRARIES})
+  include_directories (${CMAKE_CURRENT_SOURCE_DIR}/../${LIBRARY}/include/)
+  if (CMAKE_COMPILER_IS_GNUCXX)
+    link_directories (${LIBRARY}/src/lib)
+  elseif (CMAKE_COMPILER_IS_MSVC)
+    link_directories (${LIBRARY}/src/Release)
+  endif ()
+endforeach ()
+
+# additional targets
+set (TARGETS "")
+set (HEADERS "")
+
+add_subdirectory (${SUBPROJECT_SOURCE_DIR})

mathmech/envir/README

@@ -1,9 +1,7 @@
-mm_envir - program that searchs environment for chosen molecule by geometric criterion
-Version: 1.0.3
-License: GPL
+envir - program that searchs environment for chosen molecule by geometric criterion
 
 Usage:
-  mm_envir -i FILENAME -c X,Y,Z -o FILEMANE [ -n NUM_OF_MOLECULE ] [ -r RADIUS ] 
+  envir -i FILENAME -c X,Y,Z -o FILEMANE [ -n NUM_OF_MOLECULE ] [ -r RADIUS ] 
                                                     [ -l LOGFILE ] [ -q ] [ -h ]
 
 Parametrs:

mathmech/envir/envir.cmake

@@ -0,0 +1,10 @@
+# set directories
+set (SUBPROJECT_BINARY_DIR bin)
+set (SUBPROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
+
+# include_path
+include_directories (${SUBPROJECT_SOURCE_DIR}
+                     ${CMAKE_CURRENT_BINARY_DIR}/../)
+
+# executable path
+set (EXECUTABLE_OUTPUT_PATH ${SUBPROJECT_BINARY_DIR})

mathmech/envir/src/CMakeLists.txt

@@ -0,0 +1,23 @@
+# set files
+file (GLOB SOURCES *.c)
+file (GLOB HEADERS *.h)
+
+# set library
+if (CMAKE_COMPILER_IS_GNUCXX)
+  set (ADDITIONAL_LIB m)
+else ()
+  set (ADDITIONAL_LIB)
+endif ()
+
+# message
+message (STATUS "${SUBPROJECT} SOURCES: ${SOURCES}")
+message (STATUS "${SUBPROJECT} HEADERS: ${HEADERS}")
+
+# link libraries and compile
+add_executable (${SUBPROJECT} ${SOURCES} ${HEADERS})
+set_target_properties (${SUBPROJECT} PROPERTIES OUTPUT_NAME ${MM_PREFIX}${SUBPROJECT})
+add_dependencies (${SUBPROJECT} ${LIBRARIES})
+target_link_libraries (${SUBPROJECT} ${ADDITIONAL_LIB} ${LIBRARIES})
+
+# install properties
+install (TARGETS ${SUBPROJECT} DESTINATION bin)

mathmech/envir/src/add_main.c

@@ -0,0 +1,72 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file add_main.c
+ * Source code of envir
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
+#include <stdio.h>
+
+#include "add_main.h"
+#include <mathmech/messages.h>
+#include <mathmech/var_types.h>
+
+
+/**
+ * @fn error_checking
+ */
+int error_checking (const system_info _system_info, const char *input, 
+                    const char *output)
+{
+  if (input[0] == '#')
+    return 12;
+  if (output[0] == '#')
+    return 13;
+  
+  return 0;
+}
+
+
+/**
+ * @fn print_message
+ */
+int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log, 
+                   const int mode, const char *str)
+{
+  if ((quiet != 1) && (std_output != stderr))
+    message (0, mode, str, std_output);
+  if (log == 1)
+    message (1, mode, str, f_log);
+  
+  return 0;
+}
+
+
+/**
+ * @fn set_defaults
+ */
+int set_defaults (system_info *_system_info, char *input, int *log, int *num_of_mol, 
+                  char *output, int *quiet, float *rad)
+{
+  int i;
+  
+  for (i=0; i<3; i++)
+    (*_system_info).cell[i] = 0.0;
+  input[0] = '#';
+  *log = 0;
+  *num_of_mol = 1;
+  output[0] = '#';
+  *quiet = 0;
+  *rad = 6.0;
+  
+  return 0;
+}

mathmech/envir/src/add_main.h

@@ -1,23 +1,32 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
 /**
- * @file
+ * @file add_main.h
+ * Header of envir
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
  */
 
-#include <stdio.h>
+#ifndef ADD_MAIN_H
+#define ADD_MAIN_H
 
-#include "messages.h"
+#include <mathmech/var_types.h>
 
 
-/**
- * @fn error_checking
- */
-int error_checking (const float *cell, const char *input, const char *output)
 /**
  * @brief function that checks errors in input variables
  * @code
- * error_checking (cell, input, output);
+ * error_checking (_system_info, input, output);
  * @endcode
  * 
- * @param cell            massive of cell size
+ * @param _system_info    system information structure
  * @param input           input file name
  * @param output          output file name
  * 
@@ -26,23 +35,10 @@ int error_checking (const float *cell, const char *input, const char *output)
  * @return 13             - error in 'output'
  * @return 0              - exit without errors
  */
-{
-  if ((cell[0] == 0.0) || (cell[1] == 0.0) || (cell[2] == 0.0))
-    return 11;
-  if (input[0] == '#')
-    return 12;
-  if (output[0] == '#')
-    return 13;
-  
-  return 0;
-}
+int error_checking (const system_info _system_info, const char *input, 
+                    const char *output);
 
 
-/**
- * @fn print_message
- */
-int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log, 
-                   const int mode, const char *str)
 /**
  * @brief function that prints message in log and stdout
  * @code
@@ -58,29 +54,18 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
  * 
  * @return 0              - exit without errors
  */
-{
-  if ((quiet != 1) && (std_output != stderr))
-    message (0, mode, str, std_output);
-  if (log == 1)
-    message (1, mode, str, f_log);
-  
-  return 0;
-}
+int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log, 
+                   const int mode, const char *str);
 
 
-/**
- * @fn set_defaults
- */
-int set_defaults (float *cell, char *input, int *log, int *num_of_mol, char *output, 
-                  int *quiet, float *rad)
 /**
  * @brief function that sets default values of variables
  * @code
- * set_defaults (cell, &from, input, &log, &max_depth, &num_of_inter, output, &to, 
+ * set_defaults (&_system_info, &from, input, &log, &max_depth, &num_of_inter, output, &to, 
  *               &type_inter, &quiet);
  * @endcode
  * 
- * @param cell            massive of cell size
+ * @param _system_info    system information structure
  * @param input           mask of trajectory files
  * @param log             status of log-mode
  * @param num_of_mol      number of molecule
@@ -90,17 +75,8 @@ int set_defaults (float *cell, char *input, int *log, int *num_of_mol, char *out
  * 
  * @return 0              - exit without errors
  */
-{
-  int i;
-  
-  for (i=0; i<3; i++)
-    cell[i] = 0.0;
-  input[0] = '#';
-  *log = 0;
-  *num_of_mol = 1;
-  output[0] = '#';
-  *quiet = 0;
-  *rad = 6.0;
-  
-  return 0;
-}
+int set_defaults (system_info *_system_info, char *input, int *log, int *num_of_mol, 
+                  char *output, int *quiet, float *rad);
+
+
+#endif /* ADD_MAIN_H */

mathmech/envir/src/main.c

@@ -1,77 +1,18 @@
-/**
- * @file
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
  */
 /**
- * @mainpage mm_envir
- * @image latex ./logo.png
- *
- * @section intro_sec Introduction
- *
- * <b>About this program</b>:
- * <ul>
- * <li>Program that searchs environment for chosen molecule by geometric criterion
- * </ul>
- *
- * <b>Developer</b>:
- * <ul>
- * <li>Evgeniy Alekseev aka arcanis <pre><esalexeev (at) gmail (dot) com></pre>
- *</ul>
- * <b>License</b>:
- * <ul>
- * <li>GPL
- * </ul>
- *
- * @section How-To-Use How to use
- * Usage:
- * <pre>
- * mm_envir -i INPUT -c X,Y,Z -o OUTPUT [ -n NUM_OF_MOLECULE ] [ -r RADIUS ] 
- *                                           [ -l LOGFILE ] [ -q ] [ -h ]
- *
- * Parametrs:
- *    -i          - input file name
- *    -c          - cell size (float), A
- *    -o          - output file name
- *    -n          - number of molecule for search (integer). Default is 1
- *    -r          - radius of environment (float). Default is 6.0
- *    -l          - log enable
- *    -q          - quiet enable
- *    -h          - show this help and exit
- * </pre>
- * 
- * @page Install
- * 
- * @section Requirements Requirements
- * The application mm_envir requires the following external stuff:
- * - cmake  >= 2.8
- * - gcc    >= 4.8
- *
- * @section How-To How to install
- *
- * @subsection Linux Linux
- * @code
- * mkdir build && cd build
- * cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../
- * make
- * make install
- * @endcode
- * 
- * @subsection Windows Windows
- * @code
- * create project file using 'cmake'
- * compile project
- * @endcode
- * You may also download compiled executable file for Win_x86.
- *
- * @page Changelog
- * V.1.0.3 (2013-08-30)
- * <ul>
- * <li> Bug fixes
- * </ul>
- * V.1.0.1 (2013-07-27)
- * <ul>
- * <li> initial release
- * </ul>
- */ 
+ * @file main.c
+ * Source code of envir
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
 
 #include <math.h>
 #include <stdio.h>
@@ -79,11 +20,13 @@
 #include <string.h>
 
 #include "add_main.h"
-#include "coords.h"
-#include "envir_search.h"
-#include "messages.h"
-#include "print_struct.h"
-#include "set_center.h"
+#include <version.h>
+#include <mathmech/coords.h>
+#include <mathmech/envir_search.h>
+#include <mathmech/messages.h>
+#include <mathmech/print_struct.h>
+#include <mathmech/set_center.h>
+#include <mathmech/var_types.h>
 
 
 /**
@@ -102,33 +45,31 @@ int main(int argc, char *argv[])
   int error, i, *tmp_int;
   FILE *f_inp, *f_log;
   
-  char *ch_type_atoms, input[256], logfile[256], output[256];
-  float cell[3], *centr_coords, *coords, rad;
-  int *label_mol, log, num_atoms, num_mol, num_needed_mol, num_of_mol, 
-      *needed_mol, quiet, *true_label_mol;
+  char input[256], logfile[256], output[256];
+  float *centr_coords, rad;
+  int log, num_needed_mol, num_of_mol, *needed_mol, quiet, *true_label_mol;
+  atom_info *_atom_info;
+  system_info _system_info;
   
-/* ch_type_atoms          massive of char atom types
- * input                  input file name
+/* input                  input file name
  * logfile                log file name
  * output                 output file name
  * 
- * cell                   massive of cell size
  * centr_coords           massive of centered coordinates
- * coords                 massive of coordinates
  * rad                    radius of environment sphere
  * 
- * label_mol              massive of numbers of molecule for atoms
  * log                    status of log-mode
- * num_atoms              number of atoms
- * num_mol                number of molecules
  * num_needed_mol         number of needed molecules
  * num_of_mol             number of molecule
  * needed_mol             massive of number of needed molecules
  * quiet                  status of quiet-mode
  * true_label_mol         massive of true numbers of molecule for atoms
+ * 
+ * _atom_info             atom information file
+ * _system_info           system information file
  */
   
-  set_defaults (cell, input, &log, &num_of_mol, output, &quiet, &rad);
+  set_defaults (&_system_info, input, &log, &num_of_mol, output, &quiet, &rad);
   
   for (i=1; i<argc; i++)
   {
@@ -136,15 +77,14 @@ int main(int argc, char *argv[])
     {
       sprintf (tmp_str, "                                     mm_envir\n");
       sprintf (tmp_str, "%sProgram for search environment for chosen molecule by geometric criterion\n", tmp_str);
-      sprintf (tmp_str, "%sVersion : 1.0.3                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : %s                                               License : Beerware\n", tmp_str, PROJ_VERSION);
       sprintf (tmp_str, "%s                                                    Evgeniy Alekseev aka arcanis\n", tmp_str);
       sprintf (tmp_str, "%s                                                    E-mail : esalexeev@gmail.com\n\n", tmp_str);
       sprintf (tmp_str, "%sUsage:\n", tmp_str);
-      sprintf (tmp_str, "%smm_envir -i INPUT -c X,Y,Z -o OUTPUT [ -n NUM_OF_MOLECULE ] [ -r RADIUS ]\n", tmp_str);
-      sprintf (tmp_str, "%s                                             [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
+      sprintf (tmp_str, "%smm_envir -i INPUT -o OUTPUT [ -n NUM_OF_MOLECULE ] [ -r RADIUS ]\n", tmp_str);
+      sprintf (tmp_str, "%s                                    [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
       sprintf (tmp_str, "%sParametrs:\n", tmp_str);
       sprintf (tmp_str, "%s  -i          - input file name\n", tmp_str);
-      sprintf (tmp_str, "%s  -c          - cell size (float), A\n", tmp_str);
       sprintf (tmp_str, "%s  -o          - output file name\n", tmp_str);
       sprintf (tmp_str, "%s  -n          - number of molecule for search (integer). Default is 1\n", tmp_str);
       sprintf (tmp_str, "%s  -r          - radius of environment (float). Default is 6.0\n", tmp_str);
@@ -160,12 +100,6 @@ int main(int argc, char *argv[])
       strcpy (input, argv[i+1]);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'c') && (argv[i][2] == '\0'))
-// cell size
-    {
-      sscanf (argv[i+1], "%f,%f,%f", &cell[0], &cell[1], &cell[2]);
-      i++;
-    }
     else if ((argv[i][0] == '-') && (argv[i][1] == 'o') && (argv[i][2] == '\0'))
 // output file
     {
@@ -210,7 +144,7 @@ int main(int argc, char *argv[])
   print_message (quiet, stdout, log, f_log, 1, argv[0]);
   
 // error check
-  error = error_checking (cell, input, output);
+  error = error_checking (_system_info, input, output);
   if (error != 0)
   {
     print_message (quiet, stderr, log, f_log, 17, argv[0]);
@@ -228,17 +162,13 @@ int main(int argc, char *argv[])
     print_message (quiet, stderr, log, f_log, 18, input);
     return 2;
   }
-  fscanf (f_inp, "%i", &num_atoms);
+  fscanf (f_inp, "%i", &_system_info.num_atoms);
   fclose (f_inp);
-  ch_type_atoms = (char *) malloc (2 * num_atoms * sizeof (char));
-  coords = (float *) malloc (3 * 8 * num_atoms * sizeof (float));
-  label_mol = (int *) malloc (8 * num_atoms * sizeof (int));
-  tmp_int = (int *) malloc (8 * num_atoms * sizeof (int));
-  true_label_mol = (int *) malloc (num_atoms * sizeof (int));
+  _atom_info = (atom_info *) malloc (8 * _system_info.num_atoms * sizeof (atom_info));
+  tmp_int = (int *) malloc (8 * _system_info.num_atoms * sizeof (int));
+  true_label_mol = (int *) malloc (_system_info.num_atoms * sizeof (int));
 // error checking
-  if ((ch_type_atoms == NULL) ||
-     (coords == NULL) || 
-     (label_mol == NULL) || 
+  if ((_atom_info == NULL) || 
      (tmp_int == NULL) || 
      (true_label_mol == NULL))
   {
@@ -247,8 +177,9 @@ int main(int argc, char *argv[])
   }
   sprintf (tmp_str, "%6cInput file: '%s';\n%6cOutput file: '%s';\n%6cLog: %i;\n\
 %6cQuiet: %i;\n%6cCell size: %.4f, %.4f, %.4f;\n%6cSelect molecule: %i;\n\
-%6cCriterion: %.1f\n", ' ', input, ' ', output, ' ', log, ' ', quiet, ' ', cell[0], 
-           cell[1], cell[2], ' ' , num_of_mol, ' ', rad);
+%6cCriterion: %.1f\n", ' ', input, ' ', output, ' ', log, ' ', quiet, ' ', 
+_system_info.cell[0], _system_info.cell[1], _system_info.cell[2], ' ' , num_of_mol, 
+' ', rad);
   print_message (quiet, stdout, log, f_log, 5, tmp_str);
   
   print_message (quiet, stdout, log, f_log, 6, argv[0]);
@@ -256,14 +187,14 @@ int main(int argc, char *argv[])
 // reading coordinates
   print_message (quiet, stdout, log, f_log, 7, input);
   error = 1;
-  error = reading_coords (1, input, tmp_int[0], tmp_int, cell, &num_mol, &num_atoms, 
-                          true_label_mol, label_mol, tmp_int, coords, ch_type_atoms);
-  centr_coords = (float *) malloc (3 * 8 * num_mol * sizeof (float));
-  needed_mol = (int *) malloc (num_mol * sizeof (int));
+  error = reading_coords (1, input, tmp_int[0], tmp_int, &_system_info, true_label_mol, 
+                          _atom_info);
+  centr_coords = (float *) malloc (3 * 8 * _system_info.num_mol * sizeof (float));
+  needed_mol = (int *) malloc (_system_info.num_mol * sizeof (int));
   if (error == 0)
   {
     sprintf (tmp_str, "%6cNumber of molecules: %i; %6cNumber of atoms: %i\n", 
-             ' ', num_mol, ' ', num_atoms);
+             ' ', _system_info.num_mol, ' ', _system_info.num_atoms);
     print_message (quiet, stdout, log, f_log, 8, tmp_str);
   }
 // error checking
@@ -278,21 +209,21 @@ int main(int argc, char *argv[])
   if (error == 0)
   {
     error = 1;
-    error = set_center (num_atoms, num_mol, label_mol, coords, centr_coords);
+    error = set_center (_system_info, _atom_info, centr_coords);
   }
   if (error == 0)
   {
     print_message (quiet, stderr, log, f_log, 20, argv[0]);
     error = 1;
-    error = search_envir (num_of_mol, num_mol, centr_coords, rad, needed_mol, 
+    error = search_envir (num_of_mol, _system_info, centr_coords, rad, needed_mol, 
                           &num_needed_mol);
   }
   if (error == 0)
   {
     print_message (quiet, stderr, log, f_log, 21, argv[0]);
     error = 1;
-    error = print_structure (output, num_needed_mol, needed_mol, num_atoms, 
-                              label_mol, ch_type_atoms, coords);
+    error = print_structure (output, num_needed_mol, needed_mol, _system_info, 
+                             _atom_info);
   }
   if (error == 0)
     print_message (quiet, stderr, log, f_log, 12, output);
@@ -301,10 +232,8 @@ int main(int argc, char *argv[])
   
   print_message (quiet, stdout, log, f_log, 15, argv[0]);
 // free memory
-  free (ch_type_atoms);
+  free (_atom_info);
   free (centr_coords);
-  free (coords);
-  free (label_mol);
   free (needed_mol);
   free (tmp_int);
   free (true_label_mol);
@@ -314,4 +243,4 @@ int main(int argc, char *argv[])
   if (log == 1)
     fclose (f_log);
   return 0;
-}
+}

mathmech/mathmech/AUTHORS

@@ -1,3 +0,0 @@
-Current developers:
-
-Evgeniy Alekseev aka arcanis <esalexeev (at) gmail (dot) com>

mathmech/mathmech/CMakeLists.txt

@@ -1,31 +1,10 @@
-cmake_minimum_required (VERSION 2.8)
-
-cmake_policy(SET CMP0003 OLD)
-cmake_policy(SET CMP0011 NEW)
-cmake_policy(SET CMP0015 NEW)
-
 # set project name
-set (PROJECT mathmech)
+set (SUBPROJECT mathmech)
 # set additional cmake file
-include (${PROJECT}.cmake)
-
-
-# additional options
-OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
-
-# set libraries
-set (LIBRARIES)
-  foreach (LIBRARY ${LIBRARIES})
-    find_library ("${LIBRARY}_FOUND" ${LIBRARY})
-      message (STATUS "Check the ${LIBRARY} is installed: " ${${LIBRARY}_FOUND})
-      if ("${${LIBRARY}_FOUND}" STREQUAL "${LIBRARY}_FOUND-NOTFOUND")
-        message (STATUS "Adding library sources")
-        add_subdirectory (../${LIBRARY} lib/${LIBRARY})
-      endif ()
-  endforeach ()
+include (${SUBPROJECT}.cmake)
 
 # additional targets
 set (TARGETS "")
 set (HEADERS "")
 
-add_subdirectory (${PROJECT_SOURCE_DIR})
+add_subdirectory (${SUBPROJECT_SOURCE_DIR})

mathmech/mathmech/COPYING

@@ -1,341 +0,0 @@
-                    GNU GENERAL PUBLIC LICENSE
-                       Version 2, June 1991
-
-     Copyright (C) 1989, 1991 Free Software Foundation, Inc.
-     59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
-
-   Everyone is permitted to copy and distribute verbatim copies
-    of this license document, but changing it is not allowed.
-
-                            Preamble
-
-  The licenses for most software are designed to take away your
-freedom to share and change it.  By contrast, the GNU General Public
-License is intended to guarantee your freedom to share and change free
-software--to make sure the software is free for all its users.  This
-General Public License applies to most of the Free Software
-Foundation's software and to any other program whose authors commit to
-using it.  (Some other Free Software Foundation software is covered by
-the GNU Library General Public License instead.)  You can apply it to
-your programs, too.
-
-  When we speak of free software, we are referring to freedom, not
-price.  Our General Public Licenses are designed to make sure that you
-have the freedom to distribute copies of free software (and charge for
-this service if you wish), that you receive source code or can get it
-if you want it, that you can change the software or use pieces of it
-in new free programs; and that you know you can do these things.
-
-  To protect your rights, we need to make restrictions that forbid
-anyone to deny you these rights or to ask you to surrender the rights.
-These restrictions translate to certain responsibilities for you if you
-distribute copies of the software, or if you modify it.
-
-  For example, if you distribute copies of such a program, whether
-gratis or for a fee, you must give the recipients all the rights that
-you have.  You must make sure that they, too, receive or can get the
-source code.  And you must show them these terms so they know their
-rights.
-
-  We protect your rights with two steps: (1) copyright the software, and
-(2) offer you this license which gives you legal permission to copy,
-distribute and/or modify the software.
-
-  Also, for each author's protection and ours, we want to make certain
-that everyone understands that there is no warranty for this free
-software.  If the software is modified by someone else and passed on, we
-want its recipients to know that what they have is not the original, so
-that any problems introduced by others will not reflect on the original
-authors' reputations.
-
-  Finally, any free program is threatened constantly by software
-patents.  We wish to avoid the danger that redistributors of a free
-program will individually obtain patent licenses, in effect making the
-program proprietary.  To prevent this, we have made it clear that any
-patent must be licensed for everyone's free use or not licensed at all.
-
-  The precise terms and conditions for copying, distribution and
-modification follow.
-
-                    GNU GENERAL PUBLIC LICENSE
-   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
-
-  0. This License applies to any program or other work which contains
-a notice placed by the copyright holder saying it may be distributed
-under the terms of this General Public License.  The "Program", below,
-refers to any such program or work, and a "work based on the Program"
-means either the Program or any derivative work under copyright law:
-that is to say, a work containing the Program or a portion of it,
-either verbatim or with modifications and/or translated into another
-language.  (Hereinafter, translation is included without limitation in
-the term "modification".)  Each licensee is addressed as "you".
-
-Activities other than copying, distribution and modification are not
-covered by this License; they are outside its scope.  The act of
-running the Program is not restricted, and the output from the Program
-is covered only if its contents constitute a work based on the
-Program (independent of having been made by running the Program).
-Whether that is true depends on what the Program does.
-
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-source code as you receive it, in any medium, provided that you
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-copyright notice and disclaimer of warranty; keep intact all the
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-along with the Program.
-
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-
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-compelled to copy the source along with the object code.
-
-  4. You may not copy, modify, sublicense, or distribute the Program
-except as expressly provided under this License.  Any attempt
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-  5. You are not required to accept this License, since you have not
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-  6. Each time you redistribute the Program (or any work based on the
-Program), the recipient automatically receives a license from the
-original licensor to copy, distribute or modify the Program subject to
-these terms and conditions.  You may not impose any further
-restrictions on the recipients' exercise of the rights granted herein.
-You are not responsible for enforcing compliance by third parties to
-this License.
-
-  7. If, as a consequence of a court judgment or allegation of patent
-infringement or for any other reason (not limited to patent issues),
-conditions are imposed on you (whether by court order, agreement or
-otherwise) that contradict the conditions of this License, they do not
-excuse you from the conditions of this License.  If you cannot
-distribute so as to satisfy simultaneously your obligations under this
-License and any other pertinent obligations, then as a consequence you
-may not distribute the Program at all.  For example, if a patent
-license would not permit royalty-free redistribution of the Program by
-all those who receive copies directly or indirectly through you, then
-the only way you could satisfy both it and this License would be to
-refrain entirely from distribution of the Program.
-
-If any portion of this section is held invalid or unenforceable under
-any particular circumstance, the balance of the section is intended to
-apply and the section as a whole is intended to apply in other
-circumstances.
-
-It is not the purpose of this section to induce you to infringe any
-patents or other property right claims or to contest validity of any
-such claims; this section has the sole purpose of protecting the
-integrity of the free software distribution system, which is
-implemented by public license practices.  Many people have made
-generous contributions to the wide range of software distributed
-through that system in reliance on consistent application of that
-system; it is up to the author/donor to decide if he or she is willing
-to distribute software through any other system and a licensee cannot
-impose that choice.
-
-This section is intended to make thoroughly clear what is believed to
-be a consequence of the rest of this License.
-
-  8. If the distribution and/or use of the Program is restricted in
-certain countries either by patents or by copyrighted interfaces, the
-original copyright holder who places the Program under this License
-may add an explicit geographical distribution limitation excluding
-those countries, so that distribution is permitted only in or among
-countries not thus excluded.  In such case, this License incorporates
-the limitation as if written in the body of this License.
-
-  9. The Free Software Foundation may publish revised and/or new versions
-of the General Public License from time to time.  Such new versions will
-be similar in spirit to the present version, but may differ in detail to
-address new problems or concerns.
-
-Each version is given a distinguishing version number.  If the Program
-specifies a version number of this License which applies to it and "any
-later version", you have the option of following the terms and conditions
-either of that version or of any later version published by the Free
-Software Foundation.  If the Program does not specify a version number of
-this License, you may choose any version ever published by the Free Software
-Foundation.
-
-  10. If you wish to incorporate parts of the Program into other free
-programs whose distribution conditions are different, write to the author
-to ask for permission.  For software which is copyrighted by the Free
-Software Foundation, write to the Free Software Foundation; we sometimes
-make exceptions for this.  Our decision will be guided by the two goals
-of preserving the free status of all derivatives of our free software and
-of promoting the sharing and reuse of software generally.
-
-                            NO WARRANTY
-
-  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
-FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
-OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
-PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
-OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.  THE ENTIRE RISK AS
-TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU.  SHOULD THE
-PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
-REPAIR OR CORRECTION.
-
-  12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
-WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
-REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
-INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
-OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
-TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
-YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
-PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
-POSSIBILITY OF SUCH DAMAGES.
-
-                     END OF TERMS AND CONDITIONS
-
-            How to Apply These Terms to Your New Programs
-
-  If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
-
-  To do so, attach the following notices to the program.  It is safest
-to attach them to the start of each source file to most effectively
-convey the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
-    <one line to give the program's name and a brief idea of what it does.>
-    Copyright (C) 19yy  <name of author>
-
-    This program is free software; you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation; either version 2 of the License, or
-    (at your option) any later version.
-
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with this program; if not, write to the Free Software
-    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
-
-
-Also add information on how to contact you by electronic and paper mail.
-
-If the program is interactive, make it output a short notice like this
-when it starts in an interactive mode:
-
-    Gnomovision version 69, Copyright (C) 19yy name of author
-    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
-    This is free software, and you are welcome to redistribute it
-    under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License.  Of course, the commands you use may
-be called something other than `show w' and `show c'; they could even be
-mouse-clicks or menu items--whatever suits your program.
-
-You should also get your employer (if you work as a programmer) or your
-school, if any, to sign a "copyright disclaimer" for the program, if
-necessary.  Here is a sample; alter the names:
-
-  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
-  `Gnomovision' (which makes passes at compilers) written by James Hacker.
-
-  <signature of Ty Coon>, 1 April 1989
-  Ty Coon, President of Vice
-
-This General Public License does not permit incorporating your program into
-proprietary programs.  If your program is a subroutine library, you may
-consider it more useful to permit linking proprietary applications with the
-library.  If this is what you want to do, use the GNU Library General
-Public License instead of this License.

mathmech/mathmech/INSTALL

@@ -1,16 +0,0 @@
-CMakeFlags:
-  -DCMAKE_INSTALL_PREFIX=         - install prefix (default is '/usr/local')
-  -DWITH_DEBUG_MODE=1             - compile with flag '-g' (default is disable)
-  -DQWT_INCLUDE_PATH              - path to qwt includes
-  -DQWT_LIBRARY_PATH              - path to qwt library
-
-Install for Linux:
-  mkdir build && cd build
-  cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../
-  make
-  make install
-Install for Windows:
-  create project file using 'cmake'
-  compile project
-  copy QtCore4.dll, QtGui4.dll, QtOpenGL4.dll, QtSvg4.dll, qwt.dll to directory with mathmech
-You may also download compiled executable file for Win_x86.

mathmech/mathmech/README

@@ -1,3 +1 @@
 Mathematical Molecular Mechanics is GUI for "mm" program pack
-Version: 1.0.3
-License: GPL

mathmech/mathmech/mathmech.cmake

@@ -1,31 +1,8 @@
 # set directories
-set (PROJECT_BINARY_DIR bin)
-set (PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
-set (PROJECT_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/include)
-set (PROJECT_LIB_DIR ${CMAKE_CURRENT_SOURCE_DIR}/lib)
-set (PROJECT_RESOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/resources)
-set (PROJECT_TRANSLATION_DIR ${PROJECT_RESOURCE_DIR}/translations)
+set (SUBPROJECT_BINARY_DIR bin)
+set (SUBPROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
+set (SUBPROJECT_RESOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/resources)
+set (SUBPROJECT_TRANSLATION_DIR ${SUBPROJECT_RESOURCE_DIR}/translations)
 
-# library path
-link_directories (${PROJECT_LIB_DIR})
 # executable path
-set (EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR})
-
-# verbose
-set (CMAKE_VERBOSE_MAKEFILE ON)
-
-# flags
-if ( WITH_DEBUG_MODE )
-  add_definitions ( -DDEBUG_MODE=1 )
-endif ()
-if ( CMAKE_COMPILER_IS_GNUCXX )
-  set (ADD_CXX_FLAGS  "-Wall")
-  set (CMAKE_CXX_FLAGS "-O0 ${ADD_CXX_FLAGS}")
-  set (CMAKE_CXX_FLAGS_DEBUG "-g -O0")
-  set (CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
-elseif ( MSVC )
-  set (ADD_CXX_FLAGS  "/W4")
-  set (CMAKE_CXX_FLAGS "${ADD_CXX_FLAGS}")
-else ()
-  message ("Unknown compiler")
-endif ()
+set (EXECUTABLE_OUTPUT_PATH ${SUBPROJECT_BINARY_DIR})

mathmech/mathmech/mathmech.desktop

@@ -1,3 +1,4 @@
+#!/usr/bin/env xdg-open
 [Desktop Entry]
 Name=Mathematical Molecular Mechanics 
 Comment=GUI for mathmech program pack

mathmech/mathmech/src/CMakeLists.txt

@@ -3,7 +3,7 @@ file (GLOB SOURCES *.cpp)
 file (GLOB HEADERS *.h)
 file (GLOB FORMS *.ui)
 if (CMAKE_SYSTEM_NAME MATCHES Windows)
-  set (SOURCES ${SOURCES} ${PROJECT_RESOURCE_DIR}/res_icon.rc)
+  set (SOURCES ${SOURCES} ${SUBPROJECT_RESOURCE_DIR}/res_icon.rc)
 endif ()
 # set library
 if (CMAKE_COMPILER_IS_GNUCXX)
@@ -11,22 +11,18 @@ if (CMAKE_COMPILER_IS_GNUCXX)
 else ()
   set (LIBRARIES qwt)
 endif ()
-set (LANGUAGES
-     eng
-     rus)
-set (RESOURCES ${PROJECT_RESOURCE_DIR}/resources.qrc)
+set (LANGUAGES eng
+               rus)
+set (RESOURCES ${SUBPROJECT_RESOURCE_DIR}/resources.qrc)
 
-message (STATUS "SOURCES: ${SOURCES}")
-message (STATUS "HEADERS: ${HEADERS}")
-message (STATUS "FORMS: ${FORMS}")
+message (STATUS "${SUBPROJECT} SOURCES: ${SOURCES}")
+message (STATUS "${SUBPROJECT} HEADERS: ${HEADERS}")
+message (STATUS "${SUBPROJECT} FORMS: ${FORMS}")
 
 
-# compile
-project (${PROJECT})
 # include_path
 link_directories (${QWT_LIBRARY_PATH})
-include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}
-                     ${PROJECT_SOURCE_DIR}
+include_directories (${SUBPROJECT_SOURCE_DIR}
                      ${CMAKE_CURRENT_BINARY_DIR}
                      ${QWT_INCLUDE_PATH})
 
@@ -36,39 +32,28 @@ qt4_add_resources (QRC_SOURCES ${RESOURCES})
 qt4_wrap_cpp (MOC_SOURCES ${HEADERS})
 qt4_wrap_ui (UI_HEADERS ${FORMS})
 foreach (LANGUAGE ${LANGUAGES})
-    set (TS ${PROJECT_TRANSLATION_DIR}/${LANGUAGE}.ts)
-    set (QM ${PROJECT_TRANSLATION_DIR}/${LANGUAGE}.qm)
+    set (TS ${SUBPROJECT_TRANSLATION_DIR}/${LANGUAGE}.ts)
+    set (QM ${SUBPROJECT_TRANSLATION_DIR}/${LANGUAGE}.qm)
     set (TRANSLATIONS ${TRANSLATIONS} ${TS})
     set (TRANSLATIONS_BINARY ${TRANSLATIONS_BINARY} ${QM})
-    add_custom_command (
-        OUTPUT ${QM}
-        COMMAND ${QT_LRELEASE_EXECUTABLE} ${TS}
-        MAIN_DEPENDENCY ${TS})
+    add_custom_command (OUTPUT ${QM} COMMAND ${QT_LRELEASE_EXECUTABLE} ${TS} MAIN_DEPENDENCY ${TS})
 endforeach ()
-add_custom_target (
-    translations 
-    COMMAND ${QT_LUPDATE_EXECUTABLE} ${HEADERS} ${SOURCES} ${UI_HEADERS} -ts ${TRANSLATIONS})
-add_custom_command (
-    TARGET translations
-    COMMAND ${QT_LRELEASE_EXECUTABLE} ${TRANSLATIONS})
-message (STATUS "TRANSLATIONS: ${TRANSLATIONS_BINARY}")
+add_custom_target (translations COMMAND ${QT_LUPDATE_EXECUTABLE} ${HEADERS} ${SOURCES} ${UI_HEADERS} -ts ${TRANSLATIONS})
+add_custom_command (TARGET translations COMMAND ${QT_LRELEASE_EXECUTABLE} ${TRANSLATIONS})
+message (STATUS "${SUBPROJECT} TRANSLATIONS: ${TRANSLATIONS_BINARY}")
 
 source_group ("Header Files" FILES ${HEADERS})
 source_group ("Source Files" FILES ${SOURCES})
 source_group ("Generated Files" FILES ${MOC_SOURCES})
 source_group ("Resource Files" FILES ${QRC_SOURCES})
 
-add_executable (${PROJECT} WIN32 ${UI_HEADERS} ${HEADERS} ${SOURCES} ${MOC_SOURCES} ${QRC_SOURCES} ${TRANSLATIONS})
-
-target_link_libraries (${PROJECT} ${LIBRARIES} ${QT_LIBRARIES} ${QT_QTMAIN_LIBRARY})
+add_executable (${SUBPROJECT} WIN32 ${UI_HEADERS} ${HEADERS} ${SOURCES} ${MOC_SOURCES} ${QRC_SOURCES} ${TRANSLATIONS})
+target_link_libraries (${SUBPROJECT} ${LIBRARIES} ${QT_LIBRARIES} ${QT_QTMAIN_LIBRARY})
 
 # install properties
-install (TARGETS ${PROJECT} DESTINATION bin)
+install (TARGETS ${SUBPROJECT} DESTINATION bin)
 if (CMAKE_SYSTEM_NAME MATCHES Linux)
-  install (FILES ../mathmech.desktop
-          DESTINATION share/applications/)
-  install (FILES ../mathmech-logo.png
-          DESTINATION share/pixmaps/)
-  install (FILES ../mathmech.png
-          DESTINATION share/icons/hicolor/32x32/apps/)
+  install (FILES ../mathmech.desktop DESTINATION share/applications/)
+  install (FILES ../mathmech-logo.png DESTINATION share/pixmaps/)
+  install (FILES ../mathmech.png DESTINATION share/icons/hicolor/32x32/apps/)
 endif ()

mathmech/mathmech/src/Makefile

@@ -1,6 +1,6 @@
 #############################################################################
 # Makefile for building: mathmech
-# Generated by qmake (2.01a) (Qt 4.8.5) on: ?? ??? 26 15:52:26 2013
+# Generated by qmake (2.01a) (Qt 4.8.5) on: ?? ??? 3 02:36:06 2013
 # Project:  mathmech.pro
 # Template: app
 # Command: /usr/bin/qmake-qt4 -o Makefile mathmech.pro
@@ -54,7 +54,8 @@ SOURCES       = main.cpp \
 		aboutwindow.cpp \
 		statgengraphwindow.cpp \
 		settingswindow.cpp \
-		aglallwindow.cpp moc_mainwindow.cpp \
+		aglallwindow.cpp \
+		helpwindow.cpp moc_mainwindow.cpp \
 		moc_errorwindow.cpp \
 		moc_clear_items.cpp \
 		moc_start_events.cpp \
@@ -64,7 +65,8 @@ SOURCES       = main.cpp \
 		moc_aboutwindow.cpp \
 		moc_statgengraphwindow.cpp \
 		moc_settingswindow.cpp \
-		moc_aglallwindow.cpp
+		moc_aglallwindow.cpp \
+		moc_helpwindow.cpp
 OBJECTS       = main.o \
 		mainwindow.o \
 		errorwindow.o \
@@ -77,6 +79,7 @@ OBJECTS       = main.o \
 		statgengraphwindow.o \
 		settingswindow.o \
 		aglallwindow.o \
+		helpwindow.o \
 		moc_mainwindow.o \
 		moc_errorwindow.o \
 		moc_clear_items.o \
@@ -87,7 +90,8 @@ OBJECTS       = main.o \
 		moc_aboutwindow.o \
 		moc_statgengraphwindow.o \
 		moc_settingswindow.o \
-		moc_aglallwindow.o
+		moc_aglallwindow.o \
+		moc_helpwindow.o
 DIST          = /usr/share/qt4/mkspecs/common/unix.conf \
 		/usr/share/qt4/mkspecs/common/linux.conf \
 		/usr/share/qt4/mkspecs/common/gcc-base.conf \
@@ -146,7 +150,7 @@ first: all
 
 all: Makefile $(TARGET)
 
-$(TARGET): ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h $(OBJECTS)  
+$(TARGET): ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h ui_helpwindow.h $(OBJECTS)  
 	$(LINK) $(LFLAGS) -o $(TARGET) $(OBJECTS) $(OBJCOMP) $(LIBS)
 
 Makefile: mathmech.pro  /usr/share/qt4/mkspecs/linux-g++/qmake.conf /usr/share/qt4/mkspecs/common/unix.conf \
@@ -219,7 +223,7 @@ qmake:  FORCE
 
 dist: 
 	@$(CHK_DIR_EXISTS) .tmp/mathmech1.0.0 || $(MKDIR) .tmp/mathmech1.0.0 
-	$(COPY_FILE) --parents $(SOURCES) $(DIST) .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents mainwindow.h errorwindow.h clear_items.h start_events.h update_fields.h atomtypeswindow.h agglwindow.h aboutwindow.h statgengraphwindow.h settingswindow.h aglallwindow.h .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents main.cpp mainwindow.cpp errorwindow.cpp clear_items.cpp start_events.cpp update_fields.cpp atomtypeswindow.cpp agglwindow.cpp aboutwindow.cpp statgengraphwindow.cpp settingswindow.cpp aglallwindow.cpp .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents mainwindow.ui errorwindow.ui atomtypeswindow.ui agglwindow.ui aboutwindow.ui statgengraphwindow.ui settingswindow.ui aglallwindow.ui .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents rus.ts eng.ts .tmp/mathmech1.0.0/ && (cd `dirname .tmp/mathmech1.0.0` && $(TAR) mathmech1.0.0.tar mathmech1.0.0 && $(COMPRESS) mathmech1.0.0.tar) && $(MOVE) `dirname .tmp/mathmech1.0.0`/mathmech1.0.0.tar.gz . && $(DEL_FILE) -r .tmp/mathmech1.0.0
+	$(COPY_FILE) --parents $(SOURCES) $(DIST) .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents mainwindow.h errorwindow.h clear_items.h start_events.h update_fields.h atomtypeswindow.h agglwindow.h aboutwindow.h statgengraphwindow.h settingswindow.h aglallwindow.h helpwindow.h .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents main.cpp mainwindow.cpp errorwindow.cpp clear_items.cpp start_events.cpp update_fields.cpp atomtypeswindow.cpp agglwindow.cpp aboutwindow.cpp statgengraphwindow.cpp settingswindow.cpp aglallwindow.cpp helpwindow.cpp .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents mainwindow.ui errorwindow.ui atomtypeswindow.ui agglwindow.ui aboutwindow.ui statgengraphwindow.ui settingswindow.ui aglallwindow.ui helpwindow.ui .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents rus.ts eng.ts .tmp/mathmech1.0.0/ && (cd `dirname .tmp/mathmech1.0.0` && $(TAR) mathmech1.0.0.tar mathmech1.0.0 && $(COMPRESS) mathmech1.0.0.tar) && $(MOVE) `dirname .tmp/mathmech1.0.0`/mathmech1.0.0.tar.gz . && $(DEL_FILE) -r .tmp/mathmech1.0.0
 
 
 clean:compiler_clean 
@@ -240,9 +244,9 @@ mocclean: compiler_moc_header_clean compiler_moc_source_clean
 
 mocables: compiler_moc_header_make_all compiler_moc_source_make_all
 
-compiler_moc_header_make_all: moc_mainwindow.cpp moc_errorwindow.cpp moc_clear_items.cpp moc_start_events.cpp moc_update_fields.cpp moc_atomtypeswindow.cpp moc_agglwindow.cpp moc_aboutwindow.cpp moc_statgengraphwindow.cpp moc_settingswindow.cpp moc_aglallwindow.cpp
+compiler_moc_header_make_all: moc_mainwindow.cpp moc_errorwindow.cpp moc_clear_items.cpp moc_start_events.cpp moc_update_fields.cpp moc_atomtypeswindow.cpp moc_agglwindow.cpp moc_aboutwindow.cpp moc_statgengraphwindow.cpp moc_settingswindow.cpp moc_aglallwindow.cpp moc_helpwindow.cpp
 compiler_moc_header_clean:
-	-$(DEL_FILE) moc_mainwindow.cpp moc_errorwindow.cpp moc_clear_items.cpp moc_start_events.cpp moc_update_fields.cpp moc_atomtypeswindow.cpp moc_agglwindow.cpp moc_aboutwindow.cpp moc_statgengraphwindow.cpp moc_settingswindow.cpp moc_aglallwindow.cpp
+	-$(DEL_FILE) moc_mainwindow.cpp moc_errorwindow.cpp moc_clear_items.cpp moc_start_events.cpp moc_update_fields.cpp moc_atomtypeswindow.cpp moc_agglwindow.cpp moc_aboutwindow.cpp moc_statgengraphwindow.cpp moc_settingswindow.cpp moc_aglallwindow.cpp moc_helpwindow.cpp
 moc_mainwindow.cpp: mainwindow.h
 	/usr/lib/qt4/bin/moc $(DEFINES) $(INCPATH) mainwindow.h -o moc_mainwindow.cpp
 
@@ -276,6 +280,9 @@ moc_settingswindow.cpp: settingswindow.h
 moc_aglallwindow.cpp: aglallwindow.h
 	/usr/lib/qt4/bin/moc $(DEFINES) $(INCPATH) aglallwindow.h -o moc_aglallwindow.cpp
 
+moc_helpwindow.cpp: helpwindow.h
+	/usr/lib/qt4/bin/moc $(DEFINES) $(INCPATH) helpwindow.h -o moc_helpwindow.cpp
+
 compiler_rcc_make_all:
 compiler_rcc_clean:
 compiler_image_collection_make_all: qmake_image_collection.cpp
@@ -283,9 +290,9 @@ compiler_image_collection_clean:
 	-$(DEL_FILE) qmake_image_collection.cpp
 compiler_moc_source_make_all:
 compiler_moc_source_clean:
-compiler_uic_make_all: ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h
+compiler_uic_make_all: ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h ui_helpwindow.h
 compiler_uic_clean:
-	-$(DEL_FILE) ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h
+	-$(DEL_FILE) ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h ui_helpwindow.h
 ui_mainwindow.h: mainwindow.ui
 	/usr/lib/qt4/bin/uic mainwindow.ui -o ui_mainwindow.h
 
@@ -310,6 +317,9 @@ ui_settingswindow.h: settingswindow.ui
 ui_aglallwindow.h: aglallwindow.ui
 	/usr/lib/qt4/bin/uic aglallwindow.ui -o ui_aglallwindow.h
 
+ui_helpwindow.h: helpwindow.ui
+	/usr/lib/qt4/bin/uic helpwindow.ui -o ui_helpwindow.h
+
 compiler_yacc_decl_make_all:
 compiler_yacc_decl_clean:
 compiler_yacc_impl_make_all:
@@ -327,10 +337,11 @@ mainwindow.o: mainwindow.cpp aboutwindow.h \
 		agglwindow.h \
 		aglallwindow.h \
 		atomtypeswindow.h \
+		helpwindow.h \
 		settingswindow.h \
+		statgengraphwindow.h \
 		clear_items.h \
 		start_events.h \
-		statgengraphwindow.h \
 		update_fields.h \
 		mainwindow.h \
 		ui_mainwindow.h
@@ -386,6 +397,10 @@ aglallwindow.o: aglallwindow.cpp errorwindow.h \
 		ui_aglallwindow.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o aglallwindow.o aglallwindow.cpp
 
+helpwindow.o: helpwindow.cpp helpwindow.h \
+		ui_helpwindow.h
+	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o helpwindow.o helpwindow.cpp
+
 moc_mainwindow.o: moc_mainwindow.cpp 
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o moc_mainwindow.o moc_mainwindow.cpp
 
@@ -419,6 +434,9 @@ moc_settingswindow.o: moc_settingswindow.cpp
 moc_aglallwindow.o: moc_aglallwindow.cpp 
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o moc_aglallwindow.o moc_aglallwindow.cpp
 
+moc_helpwindow.o: moc_helpwindow.cpp 
+	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o moc_helpwindow.o moc_helpwindow.cpp
+
 ####### Install
 
 install:   FORCE

mathmech/mathmech/src/aboutwindow.cpp

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file aboutwindow.cpp
+ * Source code of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #include <QKeyEvent>
 
 #include "aboutwindow.h"

mathmech/mathmech/src/aboutwindow.h

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file aboutwindow.h
+ * Header of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #ifndef ABOUTWINDOW_H
 #define ABOUTWINDOW_H
 

mathmech/mathmech/src/aboutwindow.ui

@@ -25,7 +25,7 @@ p, li { white-space: pre-wrap; }
 <p align="center" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Mathematical Molecular Mechanics</span></p>
 <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p>
 <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Version:</span> 1.0.0</p>
-<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">License:</span> GPL</p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">License:</span> Beerware</p>
 <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p>
 <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Author:</span> Evgeniy Alekseev</p>
 <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">E-mail:</span> esalexeev@gmail.com</p>

mathmech/mathmech/src/agglwindow.cpp

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file agglwindow.cpp
+ * Source code of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #include <QDir>
 #include <QFileDialog>
 #include <QKeyEvent>

mathmech/mathmech/src/agglwindow.h

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file agglwindow.h
+ * Header of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #ifndef AGGLWINDOW_H
 #define AGGLWINDOW_H
 

mathmech/mathmech/src/aglallwindow.cpp

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file aglallwindow.cpp
+ * Source code of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #include <QDir>
 #include <QFileDialog>
 #include <QKeyEvent>

mathmech/mathmech/src/aglallwindow.h

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file aglallwindow.h
+ * Header of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #ifndef AGLALLWINDOW_H
 #define AGLALLWINDOW_H
 

mathmech/mathmech/src/atomtypeswindow.cpp

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file atomtypeswindow.cpp
+ * Source code of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #include <QDir>
 #include <QFileDialog>
 #include <QKeyEvent>

mathmech/mathmech/src/atomtypeswindow.h

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file atomtypeswindow.h
+ * Header of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #ifndef ATOMTYPESWINDOW_H
 #define ATOMTYPESWINDOW_H
 

mathmech/mathmech/src/clear_items.cpp

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file clear_items.cpp
+ * Source code of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #include "clear_items.h"
 
 #include "mainwindow.h"

mathmech/mathmech/src/clear_items.h

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file clear_items.h
+ * Header of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #ifndef CLEAR_ITEMS_H
 #define CLEAR_ITEMS_H
 

mathmech/mathmech/src/errorwindow.cpp

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file errorwindow.cpp
+ * Source code of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #include "errorwindow.h"
 #include "ui_errorwindow.h"
 

mathmech/mathmech/src/errorwindow.h

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file errorwindow.h
+ * Header of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #ifndef ERRORWINDOW_H
 #define ERRORWINDOW_H
 

mathmech/mathmech/src/helpwindow.cpp

@@ -0,0 +1,84 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file helpwindow.cpp
+ * Source code of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
+#include <QDir>
+#include <QFileDialog>
+#include <QKeyEvent>
+#include <QTextStream>
+
+#include "errorwindow.h"
+
+#include "helpwindow.h"
+#include "ui_helpwindow.h"
+
+HelpWindow::HelpWindow(QWidget *parent) :
+  QMainWindow(parent),
+  ui(new Ui::HelpWindow)
+{
+  ui->setupUi(this);
+}
+
+HelpWindow::~HelpWindow()
+{
+  delete ui;
+}
+
+// ESC press event
+void HelpWindow::keyPressEvent(QKeyEvent *pressedKey)
+{
+  if (pressedKey->key() == Qt::Key_Escape)
+    close();
+}
+
+void HelpWindow::on_pushButton_save_clicked()
+{
+  errorwin = new ErrorWindow(this);
+
+  QString filename = QFileDialog::getSaveFileName(
+                     this,
+                     tr("Save file as"),
+                     QDir::currentPath(),
+                     tr("html files (*.html);;All files (*.*)"));
+  if (filename.isEmpty())
+    return;
+  filename = QFileInfo(filename).absoluteFilePath();
+  QFile f_out(filename);
+  if (!f_out.open(QIODevice::WriteOnly | QIODevice::Text))
+  {
+    errorwin->set_message(9);
+    errorwin->show();
+    return;
+  }
+  QTextStream out(&f_out);
+  QString text = QString("");
+  int page = ui->toolBox->currentIndex();
+  if (page == 0)
+    text = ui->textBrowser_trj->toHtml();
+  else if (page == 1)
+    text = ui->textBrowser_statgen->toHtml();
+  else if (page == 2)
+    text = ui->textBrowser_envir->toHtml();
+  else if (page == 3)
+    text = ui->textBrowser_radf->toHtml();
+  else if (page == 4)
+    text = ui->textBrowser_agl->toHtml();
+  else if (page == 5)
+    text = ui->textBrowser_trj2pdb->toHtml();
+  out << text;
+  f_out.close();
+
+  delete errorwin;
+}

mathmech/mathmech/src/helpwindow.h

@@ -0,0 +1,47 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file helpwindow.h
+ * Header of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
+#ifndef HELPWINDOW_H
+#define HELPWINDOW_H
+
+#include <QMainWindow>
+
+class ErrorWindow;
+
+namespace Ui {
+  class HelpWindow;
+}
+
+class HelpWindow : public QMainWindow
+{
+  Q_OBJECT
+
+public:
+  explicit HelpWindow(QWidget *parent = 0);
+  ~HelpWindow();
+
+private slots:
+  void on_pushButton_save_clicked();
+
+private:
+  Ui::HelpWindow *ui;
+  ErrorWindow *errorwin;
+
+// ESC pressed event
+  void keyPressEvent(QKeyEvent *pressedKey);
+};
+
+#endif /* HELPWINDOW_H */

mathmech/mathmech/src/helpwindow.ui

@@ -0,0 +1,416 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>HelpWindow</class>
+ <widget class="QMainWindow" name="HelpWindow">
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>598</width>
+    <height>456</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>Help</string>
+  </property>
+  <widget class="QWidget" name="centralwidget">
+   <layout class="QGridLayout" name="gridLayout">
+    <item row="0" column="0">
+     <widget class="QToolBox" name="toolBox">
+      <property name="currentIndex">
+       <number>0</number>
+      </property>
+      <widget class="QWidget" name="page_trj">
+       <property name="geometry">
+        <rect>
+         <x>0</x>
+         <y>0</y>
+         <width>580</width>
+         <height>233</height>
+        </rect>
+       </property>
+       <property name="toolTip">
+        <string>Help about trj</string>
+       </property>
+       <attribute name="label">
+        <string>trj</string>
+       </attribute>
+       <layout class="QGridLayout" name="gridLayout_3">
+        <item row="0" column="0">
+         <widget class="QTextBrowser" name="textBrowser_trj">
+          <property name="html">
+           <string>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
+&lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
+p, li { white-space: pre-wrap; }
+&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;&quot;&gt;
+&lt;p align=&quot;center&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;trj&lt;/span&gt;&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;Program that generates trajectory files in special format from input trajectory.&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_trj -i FILE -t TYPE -s NUMBER -a FILE -o MASK [ -tt NUMBER ] [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-i FILE 		– input trajectory file&lt;br /&gt;-t TYPE 		– trajectory type. Supported formats: gmx, puma&lt;br /&gt;-s NUMBER 		– number of trajectory steps&lt;br /&gt;-a FILE 		– file with atom types&lt;br /&gt;-o MASK 		– mask of output trajectory files&lt;br /&gt;-tt NUMBER 		– maximum number of different atom types. Default is 1024&lt;br /&gt;-l FILE 		– print log to specified file&lt;br /&gt;-q 		– do not print messages to STDOUT&lt;br /&gt;-h 		– show this help and exit&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;	&lt;span style=&quot; font-style:italic;&quot;&gt;Trajectory files (*.[0-9])&lt;/span&gt;&lt;/p&gt;
+&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Number of atoms is shown in the title.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Trajectory snapshot (enumeration of all atoms in system). Format&lt;br /&gt;00001 СА  1234.000000 1234.000000 1234.000000    01 0001&lt;br /&gt;The sequence number of an atom (5 characters), space, character atom type (2 characters), 2 spaces, X coordinate (11 characters, 6 decimal part), Y coordinate (11 characters, 6 decimal part), Z coordinate (11 characters, 6 decimal part), 4 spaces, numerical atom type (2 characters), space, number of molecule (4 characters).&lt;/li&gt;&lt;/ul&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;	&lt;span style=&quot; font-style:italic;&quot;&gt;Atom types file (*.types)&lt;/span&gt;&lt;/p&gt;
+&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The number of different molecules (NUMTYPES=1) is shown in the title.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The molecules enumeration block. Variables are the number of molecules (NUMMOL=1), the number of atoms (NUMAT=1).&lt;br /&gt;The atoms enumeration block. Format&lt;br /&gt;CA=1&lt;br /&gt;Character atom type (2 characters), equal sign, numerical atom type.&lt;/li&gt;&lt;/ul&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Operation of the application&lt;/span&gt;&lt;/p&gt;
+&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Reading titles of source files, setting values of initial variables.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Step by step reading of source files, print results to the specified output file.&lt;/li&gt;&lt;/ol&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Working with GUI&lt;/span&gt;&lt;/p&gt;
+&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Select Menu -&amp;gt; File creator -&amp;gt; Atom types file.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the output file.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set atom types. To add a new molecule you need select &amp;quot;Add new molecule&amp;quot; from the drop down list. To change the number of molecules you need change the corresponding numeric value. To add a new atom you need enter 2 character to the special field, set numerical atom type and press &amp;quot;Add&amp;quot;. After this the atom will appear in the special window. To remove an atom you need select the desired atom in the special window and press &amp;quot;Remove&amp;quot;.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Create the atom types file.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Go to the tab &amp;quot;Generate trajectory&amp;quot;. Set the work directory.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the input trajectory file.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Select the trajectory type from the drop down list, set the number of trajectory steps.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the atom types file.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the mask of output files.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the maximum number of different atom types and the log file if this needed.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Run application.&lt;/li&gt;&lt;/ol&gt;&lt;/body&gt;&lt;/html&gt;</string>
+          </property>
+         </widget>
+        </item>
+       </layout>
+      </widget>
+      <widget class="QWidget" name="page_statgen">
+       <property name="geometry">
+        <rect>
+         <x>0</x>
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+         <width>98</width>
+         <height>88</height>
+        </rect>
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+       <property name="toolTip">
+        <string>Help about statgen</string>
+       </property>
+       <attribute name="label">
+        <string>statgen</string>
+       </attribute>
+       <layout class="QGridLayout" name="gridLayout_4">
+        <item row="0" column="0">
+         <widget class="QTextBrowser" name="textBrowser_statgen">
+          <property name="html">
+           <string>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
+&lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
+p, li { white-space: pre-wrap; }
+&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;&quot;&gt;
+&lt;p align=&quot;center&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;statgen&lt;/span&gt;&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;Program that analyzes molecular dynamics trajectories using topological analysis.&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-i MASK 		– mask of trajectory files&lt;br /&gt;-s NUMBER,NUMBER 	– first and last trajectory steps&lt;br /&gt;-c X,Y,Z 		– cell size, A&lt;br /&gt;-a FORMAT 		– numerical atom types. Maximum number of different atom types is 4. Types are comma separated&lt;br /&gt;-r FORMAT 		– criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &amp;quot;0-0:2.4,0-1:3.0&amp;quot; means set 0-0 interaction as &amp;lt;2.4 А and 0-1 interaction as &amp;lt;3.0 A&lt;br /&gt;-o FILE 		– output file&lt;br /&gt;-g NUMBER 		– chech graph isomorphism. NUMBER is a maximum depth for search cycles (&amp;gt;= 3)&lt;br /&gt;-l FILE 		– print log to specified file&lt;br /&gt;-q 		– do not print messages to STDOUT&lt;br /&gt;-h 		– show this help and exit&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;	&lt;span style=&quot; font-style:italic;&quot;&gt;Output file (*.dat)&lt;/span&gt;&lt;/p&gt;
+&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;statgen ::: V.1.1.0&amp;quot;. Blank line.&lt;/li&gt;
+&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The configuration block &amp;quot;CONFIGURATION ... END&amp;quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), atom types (ATOMS=1,2,3,4), interactions (INTERACTION=format), maximum depth for check cycle number (DEPTH=0, 0 - do not check graph isomorphism). Blank line.&lt;/li&gt;
+&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The enumeration of statistics on individual files.&lt;br /&gt;File name (FILE=mask.001), the statistic block for file &amp;quot;STATISTIC ... -----------------&amp;quot;. Table layout (2 rows) follows after specifying the block. The table format&lt;br /&gt; 0000001 0000001 &lt;br /&gt;Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).&lt;br /&gt;The enumeration of agglomerates in the file. Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified). The enumeration of molecules in the agglomerate. (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).&lt;/li&gt;
+&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The summary statistic block &amp;quot;SUMMARY STATISTIC … ------------------------------------------------&amp;quot;. Table layout (2 rows) follows after specifying the block. The table format&lt;br /&gt; 0000001 0000002 000003.00 004.00000 0005.00000&lt;br /&gt;Space, agglomerate size (7 characters), space, total number of agglomerates of this size (7 characters), space, average concentration of agglomerates of this size (9 characters, 2 decimal part), space, probability of finding molecules in agglomerates of this size (9 characters, 5 decimal part), space, probability of finding molecules in agglomerates of this size multiplied by the size (10 characters, 5 decimal part).&lt;/li&gt;
+&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Summary statistic of agglomerates on classes (if verification of isomorphism is specified). The proportion of linear (LINEAR=0.10000) and cyclic (CYCLE=0.10000) agglomerates, blank line, the proportion of not branched (NOT BRANCHED=0.10000) and branched (BRANCHED=0.10000) agglomerates, blank line, the proportion of found cycles of the specified size (CYCLE_03=0.10000).&lt;/li&gt;&lt;/ul&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Operation of the application&lt;/span&gt;&lt;/p&gt;
+&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Reading titles of source files, setting values of initial variables.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Step by step reading of source files, settings values of variables.&lt;br /&gt;Search for interactions that satisfy the specified criteria.&lt;br /&gt;The analysis of all connections and specifying to the two molecules that connected, if the conditions are satisfied at least one of these criteria.&lt;br /&gt;Adding molecules to agglomerates according to the obtained connectivity matrix.&lt;br /&gt;Print agglomerates to the file, adding the summary statistics.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Print the summary statistic to the file.&lt;/li&gt;&lt;/ol&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Working with GUI&lt;/span&gt;&lt;/p&gt;
+&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Go to the tab &amp;quot;Agglomeration&amp;quot;. Set the work directory.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the mask of trajectory files.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the first and the last trajectory steps.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the cell size, A.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set needed atoms.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set interactions. Select type of interaction from the drop down list, change its criterion and press &amp;quot;Save&amp;quot;. Press &amp;quot;Add&amp;quot; after ending of edition. After this the interaction will appear in the special window. To remove an interaction you need select the desired interaction in the special window and press &amp;quot;Remove&amp;quot;.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the output file.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the maximum depth for search cycles, the log file and the graph generate if this needed.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;For the variation of geometric criteria you need specify the criteria step changes and the number of steps.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Run application.&lt;/li&gt;&lt;/ol&gt;&lt;/body&gt;&lt;/html&gt;</string>
+          </property>
+         </widget>
+        </item>
+       </layout>
+      </widget>
+      <widget class="QWidget" name="page_envir">
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+        <rect>
+         <x>0</x>
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+       <property name="toolTip">
+        <string>Help about envir</string>
+       </property>
+       <attribute name="label">
+        <string>envir</string>
+       </attribute>
+       <layout class="QGridLayout" name="gridLayout_5">
+        <item row="0" column="0">
+         <widget class="QTextBrowser" name="textBrowser_envir">
+          <property name="html">
+           <string>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
+&lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
+p, li { white-space: pre-wrap; }
+&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;&quot;&gt;
+&lt;p align=&quot;center&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;envir&lt;/span&gt;&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;Program that searchs environment for chosen molecule by geometric criterion.&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_envir -i FILE -c X,Y,Z -o FILE [ -n NUMBER ] [ -r NUMBER ] [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-i FILE 		– input trajectory file&lt;br /&gt;-c X,Y,Z 		– cell size, A&lt;br /&gt;-o FILE 		– output PDB file&lt;br /&gt;-n NUMBER 		– number of molecule for search. Default is 1&lt;br /&gt;-r NUMBER 		– radius of environment. Default is 6.0&lt;br /&gt;-l FILE 		– print log to specified file&lt;br /&gt;-q 		– do not print messages to STDOUT&lt;br /&gt;-h 		– show this help and exit&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;	&lt;span style=&quot; font-style:italic;&quot;&gt;Trajectory file (*.pdb)&lt;/span&gt;&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;a href=&quot;http://www.wwpdb.org/documentation/format33/sect9.html&quot;&gt;&lt;span style=&quot; text-decoration: underline; color:#0000ff;&quot;&gt;http://www.wwpdb.org/documentation/format33/sect9.html&lt;/span&gt;&lt;/a&gt;&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Operation of the application&lt;/span&gt;&lt;/p&gt;
+&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Reading titles of source files, setting values of initial variables.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Reading of source file.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Search for the environment.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Print the environment to the file.&lt;/li&gt;&lt;/ol&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Working with GUI&lt;/span&gt;&lt;/p&gt;
+&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Go to the tab &amp;quot;Environment&amp;quot;. Set the work directory.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the input trajectory file.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the cell size, A.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the output PDB file.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the number of molecule for search and the radius of environment.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the log file if this needed.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Run application.&lt;/li&gt;&lt;/ol&gt;&lt;/body&gt;&lt;/html&gt;</string>
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+       </property>
+       <property name="toolTip">
+        <string>Help about radf</string>
+       </property>
+       <attribute name="label">
+        <string>radf</string>
+       </attribute>
+       <layout class="QGridLayout" name="gridLayout_6">
+        <item row="0" column="0">
+         <widget class="QTextBrowser" name="textBrowser_radf">
+          <property name="html">
+           <string>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
+&lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
+p, li { white-space: pre-wrap; }
+&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;&quot;&gt;
+&lt;p align=&quot;center&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;radf&lt;/span&gt;&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;Program that calculates radial distribution function (RDF) or radial-angles distribution function (RADF).&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_radf -i MASK -s NUMBER,NUMBER -c X,Y,Z -at FORMAT -o FILE [ -r NUMBER,NUMBER ] [ -rs NUMBER ] [ -a NUMBER,NUMBER ] [ -as NUMBER ] [ -m ] [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-i MASK 		– mask of trajectory files&lt;br /&gt;-s NUMBER,NUMBER 	– first and last trajectory steps&lt;br /&gt;-c X,Y,Z 		– cell size, A&lt;br /&gt;-at FORMAT 		– numerical atom types between which the function is calculated. Format is &amp;quot;1-2&amp;quot; or &amp;quot;1,2,3-4,5,6&amp;quot; (automatically enable calculation of radial distribution function between centers of mass)&lt;br /&gt;-o FILE 		– output file&lt;br /&gt;-r NUMBER,NUMBER 	– radial criteria, A. Default is 2.0 and 15.0&lt;br /&gt;-rs NUMBER 		– radius change step, A. Default is 0.2&lt;br /&gt;-a NUMBER,NUMBER 	– angular criteria, deg. Default is 0.0 and 90.0&lt;br /&gt;-as NUMBER 		– angle change step, deg. This option will enable calculation of radial-angles distribution function&lt;br /&gt;-as 		– enable matrix output&lt;br /&gt;-l FILE 		– print log to specified file&lt;br /&gt;-q 		– do not print messages to STDOUT&lt;br /&gt;-h 		– show this help and exit&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;	&lt;span style=&quot; font-style:italic;&quot;&gt;Output file (*.dat)&lt;/span&gt;&lt;/p&gt;
+&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;radf ::: V.1.1.0&amp;quot;. Blank line.&lt;/li&gt;
+&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The configuration block &amp;quot;CONFIGURATION ... END&amp;quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), matrix output (MATRIX=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), mode (MODE=0) (0 – radial distribution function, 1 – radial distribution function between centers of mass, 2 – radial-angles distribution function), radial criteria (R_MIN=0.100) (R_MAX=0.100) (R_STEP=0.100), angular criteria for radial-angles distribution function (ANG_MIN=0.10) (ANG_MAX=0.10) (ANG_STEP=0.10), atom types (ATOM=1-2) or (ATOM=1,2,3-4,5,6). Blank line.&lt;/li&gt;
+&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.&lt;br /&gt;The table format for radial distribution function (matrix output disables)&lt;br /&gt; 0001.0000 2.0000e-01 000000003 04.000000&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, segment volume (10 characters, 4 decimal part), space, number of molecules in this radius (9 characters), space, radial distribution function (9 characters, 6 decimal part).&lt;br /&gt;The table format for radial distribution function (matrix output enables)&lt;br /&gt; 0001.0000 04.000000&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).&lt;br /&gt;The table format for radial-angles distribution function (matrix output disables)&lt;br /&gt; 0001.0000 000005.00 2.0000e-01 000000003 04.000000&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, segment angle (9 characters, 2 decimal part), segment volume (10 characters, 4 decimal part), space, number of molecules in this segment (9 characters), space, radial-angles distribution function (9 characters, 6 decimal part).&lt;br /&gt;The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title&lt;br /&gt; 0001.0000 04.000000 ...&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.&lt;/li&gt;
+&lt;li style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;End of the table&lt;/li&gt;&lt;/ul&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Operation of the application&lt;/span&gt;&lt;/p&gt;
+&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Reading titles of source files, setting values of initial variables.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Step by step reading of source files, settings values of variables.&lt;br /&gt;Calculating of the number of pairs of molecules in various relative configurations.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Print the result to the file.&lt;br /&gt;Radial distribution function calculated by:&lt;br /&gt;RDF(r) = (1 / norm) * sum(d(r_n-r), n),&lt;br /&gt;norm(r) = (4*PI*r^2*dr) * ro * N * N_step,&lt;br /&gt;where d(r_n-r) is the delta function, r is a shpere radius, n is a number of molecule, dr is the radius change step, ro is the number of molecules per volume unit, N is the number of molecules, N_step is a number of trajectory step.&lt;br /&gt;Radial-angles distribution function calculated by:&lt;br /&gt;RADF(r, fi) = (1 / norm) * sum(sum(d(r_n-r)*d(fi_n-fi), n), n),&lt;br /&gt;norm(r, fi) = (4*PI*r^2*sin(fi)*dr*dfi) * ro * N * N_step,&lt;br /&gt;where d(r_n-r) and d(fi_n-fi) are the delta functions, r is a shpere radius, fi is a segment angle, n is a number of molecule, dr is the radius change step, dfi is the angle change step, ro is the number of molecules per volume unit, N is the number of molecules, N_step is a number of trajectory step.&lt;/li&gt;&lt;/ol&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Working with GUI&lt;/span&gt;&lt;/p&gt;
+&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Go to the tab &amp;quot;RADF&amp;quot;. Set the work directory.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the mask of trajectory files.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the first and the last trajectory steps.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the cell size, A.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the output file.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set needed atoms.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set radial criteria. Set angular criteria if this needed.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the matrix output, the log file and the graph generate if this needed.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Run application.&lt;/li&gt;&lt;/ol&gt;&lt;/body&gt;&lt;/html&gt;</string>
+          </property>
+         </widget>
+        </item>
+       </layout>
+      </widget>
+      <widget class="QWidget" name="page_agl">
+       <property name="geometry">
+        <rect>
+         <x>0</x>
+         <y>0</y>
+         <width>98</width>
+         <height>88</height>
+        </rect>
+       </property>
+       <property name="toolTip">
+        <string>Help about agl</string>
+       </property>
+       <attribute name="label">
+        <string>agl</string>
+       </attribute>
+       <layout class="QGridLayout" name="gridLayout_2">
+        <item row="0" column="0">
+         <widget class="QTextBrowser" name="textBrowser_agl">
+          <property name="html">
+           <string>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
+&lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
+p, li { white-space: pre-wrap; }
+&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;&quot;&gt;
+&lt;p align=&quot;center&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;agl&lt;/span&gt;&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;Program that creates PDB file with chosen agglomerate.&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_agl -a FILE -i FILE -c X,Y,Z -o FILE [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-a FILE 		– input file with agglomerate&lt;br /&gt;-i FILE 		– input trajectory file&lt;br /&gt;-c X,Y,Z 		– cell size, A&lt;br /&gt;-o FILE 		– output PDB file&lt;br /&gt;-l FILE 		– print log to specified file&lt;br /&gt;-q 		– do not print messages to STDOUT&lt;br /&gt;-h 		– show this help and exit&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;	&lt;span style=&quot; font-style:italic;&quot;&gt;Agglomerate file (*.agl)&lt;/span&gt;&lt;/p&gt;
+&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified).&lt;/li&gt;
+&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The enumeration of molecules in the agglomerate (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).&lt;/li&gt;&lt;/ul&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;	&lt;span style=&quot; font-style:italic;&quot;&gt;Trajectory file (*.pdb)&lt;/span&gt;&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;a href=&quot;http://www.wwpdb.org/documentation/format33/sect9.html&quot;&gt;&lt;span style=&quot; text-decoration: underline; color:#0000ff;&quot;&gt;http://www.wwpdb.org/documentation/format33/sect9.html&lt;/span&gt;&lt;/a&gt;&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Operation of the application&lt;/span&gt;&lt;/p&gt;
+&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Reading titles of source files, setting values of initial variables.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Reading of source file.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Search for the best configuration.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Print the result to the file.&lt;/li&gt;&lt;/ol&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Working with GUI&lt;/span&gt;&lt;/p&gt;
+&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Select Menu -&amp;gt; File creator -&amp;gt; Agglomerate file.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the file generated by statgen. Push &amp;quot;Select&amp;quot;.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Select the trajectory file from the drop down list. Select the agglomerate.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the output file. Create file.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Go to the tab &amp;quot;Generate PDB&amp;quot;. Select &amp;quot;From agglomerate&amp;quot; from the drop down list.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the work directory.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the input trajectory file.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the agglomerate file.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the cell size, A.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the output PDB file.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the log file if this needed.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Run application.&lt;/li&gt;&lt;/ol&gt;&lt;/body&gt;&lt;/html&gt;</string>
+          </property>
+         </widget>
+        </item>
+       </layout>
+      </widget>
+      <widget class="QWidget" name="page_trj2pdb">
+       <property name="geometry">
+        <rect>
+         <x>0</x>
+         <y>0</y>
+         <width>98</width>
+         <height>88</height>
+        </rect>
+       </property>
+       <property name="toolTip">
+        <string>Help about trj2pdb</string>
+       </property>
+       <attribute name="label">
+        <string>trj2pdb</string>
+       </attribute>
+       <layout class="QGridLayout" name="gridLayout_7">
+        <item row="0" column="0">
+         <widget class="QTextBrowser" name="textBrowser_trj2pdb">
+          <property name="html">
+           <string>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
+&lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
+p, li { white-space: pre-wrap; }
+&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;&quot;&gt;
+&lt;p align=&quot;center&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;trj2pdb&lt;/span&gt;&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;Program that creates PDB file from trajetory snapshot.&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_trj2pdb -i FILE -o FILE [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-i FILE 		– input trajectory file&lt;br /&gt;-o FILE 		– output PDB file&lt;br /&gt;-l FILE 		– print log to specified file&lt;br /&gt;-q 		– do not print messages to STDOUT&lt;br /&gt;-h 		– show this help and exit&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;	&lt;span style=&quot; font-style:italic;&quot;&gt;Trajectory file (*.pdb)&lt;/span&gt;&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;a href=&quot;http://www.wwpdb.org/documentation/format33/sect9.html&quot;&gt;&lt;span style=&quot; text-decoration: underline; color:#0000ff;&quot;&gt;http://www.wwpdb.org/documentation/format33/sect9.html&lt;/span&gt;&lt;/a&gt;&lt;/p&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Operation of the application&lt;/span&gt;&lt;/p&gt;
+&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Reading titles of source files, setting values of initial variables.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Reading of source file.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Print the result to the file.&lt;/li&gt;&lt;/ol&gt;
+&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;	&lt;span style=&quot; text-decoration: underline;&quot;&gt;Working with GUI&lt;/span&gt;&lt;/p&gt;
+&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Go to the tab &amp;quot;Generate PDB&amp;quot;. Select &amp;quot;From trajectory snapshot&amp;quot; from the drop down list.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the work directory.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the input trajectory file.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the output PDB file.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the log file if this needed.&lt;/li&gt;
+&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Run application.&lt;/li&gt;&lt;/ol&gt;&lt;/body&gt;&lt;/html&gt;</string>
+          </property>
+         </widget>
+        </item>
+       </layout>
+      </widget>
+     </widget>
+    </item>
+    <item row="1" column="0">
+     <layout class="QHBoxLayout" name="horizontalLayout">
+      <item>
+       <spacer name="horizontalSpacer">
+        <property name="orientation">
+         <enum>Qt::Horizontal</enum>
+        </property>
+        <property name="sizeHint" stdset="0">
+         <size>
+          <width>40</width>
+          <height>20</height>
+         </size>
+        </property>
+       </spacer>
+      </item>
+      <item>
+       <widget class="QPushButton" name="pushButton_save">
+        <property name="minimumSize">
+         <size>
+          <width>80</width>
+          <height>23</height>
+         </size>
+        </property>
+        <property name="toolTip">
+         <string>Save help to html</string>
+        </property>
+        <property name="text">
+         <string>Save html</string>
+        </property>
+        <property name="autoDefault">
+         <bool>true</bool>
+        </property>
+       </widget>
+      </item>
+      <item>
+       <widget class="QPushButton" name="pushButton_close">
+        <property name="minimumSize">
+         <size>
+          <width>80</width>
+          <height>23</height>
+         </size>
+        </property>
+        <property name="toolTip">
+         <string>Close window</string>
+        </property>
+        <property name="text">
+         <string>Close</string>
+        </property>
+        <property name="autoDefault">
+         <bool>true</bool>
+        </property>
+       </widget>
+      </item>
+     </layout>
+    </item>
+   </layout>
+  </widget>
+ </widget>
+ <tabstops>
+  <tabstop>textBrowser_trj</tabstop>
+  <tabstop>textBrowser_statgen</tabstop>
+  <tabstop>textBrowser_envir</tabstop>
+  <tabstop>textBrowser_radf</tabstop>
+  <tabstop>textBrowser_agl</tabstop>
+  <tabstop>textBrowser_trj2pdb</tabstop>
+  <tabstop>pushButton_save</tabstop>
+  <tabstop>pushButton_close</tabstop>
+ </tabstops>
+ <resources/>
+ <connections>
+  <connection>
+   <sender>pushButton_close</sender>
+   <signal>clicked()</signal>
+   <receiver>HelpWindow</receiver>
+   <slot>close()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>545</x>
+     <y>431</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>598</x>
+     <y>414</y>
+    </hint>
+   </hints>
+  </connection>
+ </connections>
+</ui>

mathmech/mathmech/src/main.cpp

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file main.cpp
+ * Source code of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #include "mainwindow.h"
 #include <QApplication>
 #include <QDir>

mathmech/mathmech/src/mainwindow.cpp

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file mainwindow.cpp
+ * Source code of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #include <QFileDialog>
 #include <QDir>
 
@@ -5,10 +21,11 @@
 #include "agglwindow.h"
 #include "aglallwindow.h"
 #include "atomtypeswindow.h"
+#include "helpwindow.h"
 #include "settingswindow.h"
+#include "statgengraphwindow.h"
 #include "clear_items.h"
 #include "start_events.h"
-#include "statgengraphwindow.h"
 #include "update_fields.h"
 
 #include "mainwindow.h"
@@ -928,9 +945,10 @@ void MainWindow::createActions()
 {
   connect(ui->actionAtom_types_file, SIGNAL(triggered()), this, SLOT(createAtomTypes()));
   connect(ui->actionAgglomerate_file, SIGNAL(triggered()), this, SLOT(createAgglFile()));
-  connect(ui->actionAbout, SIGNAL(triggered()), this, SLOT(aboutWin()));
-  connect(ui->actionSettings, SIGNAL(triggered()), this, SLOT(settingsWinShow()));
   connect(ui->actionAgl_all, SIGNAL(triggered()), this, SLOT(aglallWinShow()));
+  connect(ui->actionHelp, SIGNAL(triggered()), this, SLOT(helpWindow()));
+  connect(ui->actionSettings, SIGNAL(triggered()), this, SLOT(settingsWinShow()));
+  connect(ui->actionAbout, SIGNAL(triggered()), this, SLOT(aboutWin()));
 }
 
 void MainWindow::createAtomTypes()
@@ -967,3 +985,10 @@ void MainWindow::aglallWinShow()
   aglallWin = new AglAllWindow(this, mm_agl_path);
   aglallWin->show();
 }
+
+void MainWindow::helpWindow()
+{
+  HelpWindow *helpWindow;
+  helpWindow = new HelpWindow(this);
+  helpWindow->show();
+}

mathmech/mathmech/src/mainwindow.h

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file mainwindow.h
+ * Header of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #ifndef MAINWINDOW_H
 #define MAINWINDOW_H
 
@@ -86,11 +102,12 @@ private slots:
 // completion
   void on_tabWidget_currentChanged(int index);
 // window signals
-  void createAtomTypes();
-  void createAgglFile();
   void aboutWin();
-  void settingsWinShow();
   void aglallWinShow();
+  void createAgglFile();
+  void createAtomTypes();
+  void settingsWinShow();
+  void helpWindow();
 
 private:
   Ui::MainWindow *ui;

mathmech/mathmech/src/mainwindow.ui

@@ -1352,6 +1352,9 @@
             <property name="toolTip">
              <string>Number of steps of analysis</string>
             </property>
+            <property name="alignment">
+             <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
+            </property>
             <property name="minimum">
              <number>1</number>
             </property>
@@ -3710,6 +3713,7 @@
     <property name="title">
      <string>Help</string>
     </property>
+    <addaction name="actionHelp"/>
     <addaction name="actionAbout"/>
    </widget>
    <addaction name="menuMenu"/>
@@ -3755,6 +3759,14 @@
     <string>agl_all</string>
    </property>
   </action>
+  <action name="actionHelp">
+   <property name="text">
+    <string>&amp;Help</string>
+   </property>
+   <property name="shortcut">
+    <string>F1</string>
+   </property>
+  </action>
  </widget>
  <layoutdefault spacing="6" margin="11"/>
  <tabstops>

mathmech/mathmech/src/mathmech.pro

@@ -19,7 +19,8 @@ HEADERS += mainwindow.h \
     aboutwindow.h \
     statgengraphwindow.h \
     settingswindow.h \
-    aglallwindow.h
+    aglallwindow.h \
+    helpwindow.h
 FORMS += mainwindow.ui \
     errorwindow.ui \
     atomtypeswindow.ui \
@@ -27,7 +28,8 @@ FORMS += mainwindow.ui \
     aboutwindow.ui \
     statgengraphwindow.ui \
     settingswindow.ui \
-    aglallwindow.ui
+    aglallwindow.ui \
+    helpwindow.ui
 SOURCES += main.cpp mainwindow.cpp \
     errorwindow.cpp \
     clear_items.cpp \
@@ -38,7 +40,8 @@ SOURCES += main.cpp mainwindow.cpp \
     aboutwindow.cpp \
     statgengraphwindow.cpp \
     settingswindow.cpp \
-    aglallwindow.cpp
+    aglallwindow.cpp \
+    helpwindow.cpp
 TRANSLATIONS += rus.ts \
     eng.ts
 

mathmech/mathmech/src/mathmech.pro.user

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE QtCreatorProject>
-<!-- Written by QtCreator 2.8.1, 2013-08-30T19:09:45. -->
+<!-- Written by QtCreator 2.8.1, 2013-09-03T05:28:10. -->
 <qtcreator>
  <data>
   <variable>ProjectExplorer.Project.ActiveTarget</variable>

mathmech/mathmech/src/settingswindow.cpp

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file settingswindow.cpp
+ * Source code of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #include <QApplication>
 #include <QDir>
 #include <QKeyEvent>

mathmech/mathmech/src/settingswindow.h

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file settingswindow.h
+ * Header of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #ifndef SETTINGSWINDOW_H
 #define SETTINGSWINDOW_H
 

mathmech/mathmech/src/start_events.cpp

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file start_events.cpp
+ * Source code of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #include <QDir>
 #include <math.h>
 

mathmech/mathmech/src/start_events.h

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file start_events.h
+ * Header of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #ifndef START_EVENTS_H
 #define START_EVENTS_H
 

mathmech/mathmech/src/statgengraphwindow.cpp

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file statgengraphwindow.cpp
+ * Source code of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #include <QDir>
 #include <QFileDialog>
 #include <QKeyEvent>

mathmech/mathmech/src/statgengraphwindow.h

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file statgengraphwindow.h
+ * Header of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #ifndef STATGENGRAPHWINDOW_H
 #define STATGENGRAPHWINDOW_H
 

mathmech/mathmech/src/update_fields.cpp

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file update_fields.cpp
+ * Source code of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #include <QDir>
 #include <math.h>
 

mathmech/mathmech/src/update_fields.h

@@ -1,3 +1,19 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file update_fields.h
+ * Header of mathmech
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
 #ifndef UPDATE_FIELDS_H
 #define UPDATE_FIELDS_H
 

mathmech/mm/CMakeLists.txt

@@ -0,0 +1,10 @@
+# set project name
+set (SUBPROJECT mm)
+# set additional cmake file
+include (${SUBPROJECT}.cmake)
+
+# additional targets
+set (TARGETS "")
+set (HEADERS "")
+
+add_subdirectory (${SUBPROJECT_SOURCE_DIR})

mathmech/mm/README

@@ -0,0 +1 @@
+libmm is a library for "mm" project

mathmech/mm/include/mathmech/atom_types.h

@@ -0,0 +1,45 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file atom_types.h
+ * Header of mathmech library
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
+#ifndef ATOM_TYPES_H
+#define ATOM_TYPES_H
+
+
+/**
+ * @brief function that reads atom types from input file
+ * @code
+ * reading_atoms (input_at, &num_types, num_mol, num_atoms, ch_atom_types, atom_types, 
+ *                total_types);
+ * @endcode
+ * 
+ * @param input_at        input file name with atom types
+ * @param num_types       number of molecule types
+ * @param num_mol         massive of number of molecules of selected type
+ * @param num_atoms       massive of number of atoms of selected molecule
+ * @param ch_atom_types   massive of char atom types
+ * @param atom_types      massive of atom types
+ * @param total_types     number of different atom types
+ * 
+ * @return 1              - error in opening file
+ * @return 2              - error in file format
+ * @return 3              - memory error
+ * @return 0              - exit without errors
+ */
+int reading_atoms (const char *input_at, int *num_types, int *num_mol, int *num_atoms, 
+                   char *ch_atom_types, int *atom_types, const int total_types);
+
+
+#endif /* ATOM_TYPES_H */

mathmech/mm/include/mathmech/coords.h

@@ -0,0 +1,51 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file coords.h
+ * Header of mathmech library
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
+#ifndef COORDS_H
+#define COORDS_H
+
+#include <mathmech/var_types.h>
+
+
+/**
+ * @brief function that reads coordinates from special file format
+ * @code
+ * reading_coords (0, filename, type_inter, label_atom, &_system_info, 
+ *                 true_label_mol, _atom_info);
+ * @endcode
+ * 
+ * @param mode            mode of reading; '0' is statgen, '1' is envir or 
+ *                        frad, '2' is agl
+ * @param filename        input file name
+ * @param type_inter      number of needed atoms
+ *                        (number of needed molecules)
+ * @param label_atom      massive of needed atom types
+ *                        (massive of needed molecules)
+ * @param _system_info    system information structure
+ * @param true_label_mol  massive of true numbers of molecule for atoms
+ * @param _atom_info      atom information structure
+ * 
+ * @return 1              - file $filename does not exist
+ * @return 2              - unknown mode
+ * @return 3              - memory error
+ * @return 0              - exit without errors
+ */
+int reading_coords (const int mode, const char *filename, const int type_inter, 
+                    const int *label_atom, system_info *_system_info, 
+                    int *true_label_mol, atom_info *_atom_info);
+
+
+#endif /* COORDS_H */

mathmech/mm/include/mathmech/envir_search.h

@@ -0,0 +1,43 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file envir_search.h
+ * Header of mathmech library
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
+#ifndef ENVIR_SEARCH_H
+#define ENVIR_SEARCH_H
+
+#include <mathmech/var_types.h>
+
+
+/**
+ * @brief function that searchs environment
+ * @code
+ * search_envir (number_of_molecule, _system_info, centr_coords, rad, needed_mol, 
+ *               &num_needed_mol);
+ * @endcode
+ * 
+ * @param num_of_mol      number of molecule
+ * @param _system_info    system information structure
+ * @param centr_coords    massive of centered coordinates
+ * @param rad             radius of environment sphere
+ * @param needed_mol      massive of number of needed molecules
+ * @param num_needed_mol  number of needed molecules
+ * 
+ * @return 0              - exit without errors
+ */
+int search_envir (const int num_of_mol, const system_info _system_info, const float *centr_coords, 
+                  const double rad, int *needed_mol, int *num_needed_mol);
+
+
+#endif /* ENVIR_SEARCH_H */

mathmech/mm/include/mathmech/graph.h

@@ -0,0 +1,83 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file graph.h
+ * Header of mathmech library
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
+#ifndef GRAPH_H
+#define GRAPH_H
+
+
+/**
+ * @brief function that calculates number of cycles in graph
+ * @code
+ * cycle = check_cycle (N, pn);
+ * @endcode
+ * 
+ * @param N               number of vertexes
+ * @param pn              massive of number of vertexes with weight equals to i
+ * 
+ * @return number of cycles
+ */
+int check_cycle (const int N, const int *pn);
+
+
+/**
+ * @brief function that returns number of cycles different size
+ * @code
+ * check_cycle_size (N, matrix, depth, n_cycle);
+ * @endcode
+ * 
+ * @param N               number of vertexes
+ * @param matrix          connectivity matrix
+ * @param depth           depth of search (maximum number of vertexes in cycle)
+ * @param n_cycle         massive of number of cycle with number of vertexes 
+ *                        equals to i
+ * 
+ * @return 1              - memory error
+ * @return 0              - exit without errors
+ */
+int check_cycle_size (const int N, const int *matrix, const int depth, int *n_cycle);
+
+
+/**
+ * @brief function that calculates number of tails
+ * @code
+ * tails = check_tail (pn);
+ * @endcode
+ * 
+ * @param pn              massive of number of vertexes with weight equals to i
+ * 
+ * @return number of tails
+ */
+int check_tail (const int *pn);
+
+
+/**
+ * @brief function that analyzes graph isomorhic class
+ * @code
+ * graph_analyze (N, matrix, max_depth, iso);
+ * @endcode
+ * 
+ * @param N               number of vertexes
+ * @param matrix          connectivity matrix
+ * @param max_depth       maximum depth of search for check_cycle_size
+ * @param iso             isomorphism class
+ * 
+ * @return 1              - memory error
+ * @return 0              - exit without errors
+ */
+int graph_analyze (const int N, const int *matrix, const int max_depth, int *iso);
+
+
+#endif /* GRAPH_H */

mathmech/mm/include/mathmech/messages.h

@@ -0,0 +1,38 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file messages.h
+ * Header of mathmech library
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
+#ifndef MESSAGES_H
+#define MESSAGES_H
+
+
+/**
+ * @brief function that prints messages to output
+ * @code
+ * message (log, mode, text, output);
+ * @endcode
+ * 
+ * @param log             equal to 1 if print to logfile
+ * @param mode            number of message
+ * @param text            additional text
+ * @param output          output file (may be stdout)
+ * 
+ * @return 1              - unknown mode
+ * @return 0              - exit without errors
+ */
+int message (const int log, const int mode, const char *text, FILE *output);
+
+
+#endif /* MESSAGES_H */

mathmech/mm/include/mathmech/print_struct.h

@@ -0,0 +1,41 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file print_struct.h
+ * Header of mathmech library
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
+#ifndef PRINT_STRUCT_H
+#define PRINT_STRUCT_H
+
+#include <mathmech/var_types.h>
+
+
+/**
+ * @brief function that prints structure to pdb file
+ * @code
+ * print_structure (output, num_needed_mol, needed_mol, _system_info, _atom_info);
+ * @endcode
+ * 
+ * @param output          output file name
+ * @param num_needed_mol  number of needed molecules
+ * @param needed_mol      massive of number of needed molecules
+ * @param _system_info    system information structure
+ * @param _atom_info      atom information structure
+ * 
+ * @return 0              - exit without errors
+ */
+int print_structure (const char *output, const int num_needed_mol, const int *needed_mol, 
+                     const system_info _system_info, const atom_info *_atom_info);
+
+
+#endif /* PRINT_STRUCT_H */

mathmech/mm/include/mathmech/print_trj.h

@@ -0,0 +1,45 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file print_trj.h
+ * Header of mathmech library
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
+#ifndef PRINT_TRJ_H
+#define PRINT_TRJ_H
+
+
+/**
+ * @brief function that prints trajectory snapshots
+ * @code
+ * printing_trj (filename, atoms, num_types, num_mol, num_atoms, ch_atom_types, 
+ *               atom_types, coords);
+ * @endcode
+ * 
+ * @param filename        output file name
+ * @param atoms           number of atoms in system
+ * @param num_types       number of molecule types
+ * @param num_mol         massive of number of molecule of selected type
+ * @param num_atoms       massive of number of atoms of selected molecule
+ * @param ch_atom_types   massive of char atom types
+ * @param atom_types      massive of atom types
+ * @param coords          massive of coordinates
+ * @param cell            cell size
+ * 
+ * @return 0              - exit without errors
+ */
+int printing_trj (const char *filename, const int atoms, const int num_types, const int *num_mol, 
+                  const int *num_atoms, const char *ch_atom_types, const int *atom_types,
+                  const float *coords, const float *cell);
+
+
+#endif /* PRINT_TRJ_H */

mathmech/mm/include/mathmech/radf.h

@@ -0,0 +1,76 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file radf.h
+ * Header of mathmech library
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
+#ifndef RADF_H
+#define RADF_H
+
+#include <mathmech/var_types.h>
+
+
+/**
+ * @brief function that searchs molecule for rdf massive
+ * @code
+ * search_rdf (_system_info, _atom_info, _radf_info, radf);
+ * @endcode
+ * 
+ * @param _system_info    system information structure
+ * @param _atom_info      atom information structure
+ * @param _radf_info      radf information structure
+ * @param radf            not normed RDF
+ * 
+ * @return 0              - exit without errors
+ */
+int search_rdf (const system_info _system_info, const atom_info *_atom_info, 
+                const radf_info _radf_info, int *radf);
+
+
+/**
+ * @brief function that searchs molecule for rdf massive by centered coordinates
+ * @code
+ * search_rdf_centr (_system_info, _atom_info, _radf_info, radf);
+ * @endcode
+ * 
+ * @param _system_info    system information structure
+ * @param _atom_info      atom information structure
+ * @param _radf_info      radf information structure
+ * @param radf            not normed RDF
+ * 
+ * @return 0              - exit without errors
+ * @return 1              - error in set center (missing atoms)
+ */
+int search_rdf_centr (const system_info _system_info, const atom_info *_atom_info, 
+                      const radf_info _radf_info, int *radf);
+
+
+/**
+ * @brief function that searchs molecule for radf massive
+ * @code
+ * search_radf (_system_info, _atom_info, _radf_info, radf);
+ * @endcode
+ * 
+ * @param _system_info    system information structure
+ * @param _atom_info      atom information structure
+ * @param _radf_info      radf information structure
+ * @param radf            not normed RDF
+ * 
+ * @return 0              - exit without errors
+ * @return 1              - error in set center (missing atoms)
+ */
+int search_radf (const system_info _system_info, const atom_info *_atom_info, 
+                 const radf_info _radf_info, int *radf);
+
+
+#endif /* RADF_H */

mathmech/mm/include/mathmech/radf_proc.h

@@ -0,0 +1,43 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file radf_proc.h
+ * Header of mathmech library
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
+#ifndef RADF_PROC_H
+#define RADF_PROC_H
+
+#include <mathmech/var_types.h>
+
+
+/**
+ * @brief function that print result to output file
+ * @code
+ * print_result (output, matrix, mode, _system_info, _radf_info, radf);
+ * @endcode
+ * 
+ * @param output          output file name
+ * @param matrix          status of matrix-mode
+ * @param mode            1 - if RDF, 2 - if RDF for center mass, 3 - if RADF
+ * @param _system_info    system information structure
+ * @param _radf_info      radf information structure
+ * @param radf            not normed RADF
+ * 
+ * @return 0              - exit without errors
+ */
+int print_result (const char *output, const int matrix, const int mode, 
+                  const system_info _system_info, const radf_info _radf_info,
+                  const int *radf);
+
+
+#endif /* RADF_PROC_H */

mathmech/mm/include/mathmech/read_agl.h

@@ -0,0 +1,37 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file read_agl.h
+ * Header of mathmech library
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
+#ifndef READ_AGL_H
+#define READ_AGL_H
+
+
+/**
+ * @brief function that reads agglomerate from statgen-formated file
+ * @code
+ * reading_agl (aglinput, &num_needed_mol, agl_class, needed_mol);
+ * @endcode
+ * 
+ * @param aglinp          agglomerate file name
+ * @param num_needed_mol  number of needed molecules
+ * @param agl_class       agglomerate class
+ * @param needed_mol      massive of numbed of needed molecules
+ * 
+ * @return 0              - exit without errors
+ */
+int reading_agl (const char *aglinp, int *num_needed_mol, char *agl_class, int *needed_mol);
+
+
+#endif /* READ_AGL_H */

mathmech/mm/include/mathmech/read_gmx.h

@@ -0,0 +1,61 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file read_gmx.h
+ * Header of mathmech library
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
+#ifndef READ_GMX_H
+#define READ_GMX_H
+
+
+/**
+ * @brief funtion that translates coordinate
+ * @code
+ * translate_coords (coords[3*i+j], cell[j], trans);
+ * @endcode
+ * 
+ * @param coords          coordinate
+ * @param cell            cell size
+ * @param trans           massive of translated coordinates
+ * 
+ * @return 0              - exit without errors
+ */
+int translate_coords (const float coords, const float cell, float *trans);
+
+
+/**
+ * @brief function that read GROMACS trajectory file and write to output
+ * @code
+ * rw_gmx (input, step, output, num_types, num_mol, num_atoms, ch_atom_types, 
+ *         atom_types, coords);
+ * @endcode
+ * 
+ * @param input           input file name
+ * @param step            number of trajectory steps
+ * @param output          mask of output files
+ * @param num_types       number of molecule types
+ * @param num_mol         massive of number of molecule of selected type
+ * @param num_atoms       massive of number of atoms of selected molecule
+ * @param ch_atom_types   massive of char atom types
+ * @param atom_types      massive of atom types
+ * @param coords          massive of coordinates
+ * 
+ * @return 1              - file does not exist
+ * @return 0              - exit without errors
+ */
+int rw_gmx (const char *input, const int step, const char *output, const int num_types, 
+            const int *num_mol, const int *num_atoms, const char *ch_atom_types, 
+            const int *atom_types, float *coords);
+
+
+#endif /* READ_GMX_H */

mathmech/mm/include/mathmech/read_puma.h

@@ -0,0 +1,46 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file read_puma.h
+ * Header of mathmech library
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
+#ifndef READ_PUMA_H
+#define READ_PUMA_H
+
+
+/**
+ * @brief function that read PUMA trajectory file and write to output
+ * @code
+ * rw_puma (input, step, output, num_types, num_mol, num_atoms, ch_atom_types, 
+ *          atom_types, coords);
+ * @endcode
+ * 
+ * @param input           input file name
+ * @param step            number of trajectory steps
+ * @param output          mask of output files
+ * @param num_types       number of molecule types
+ * @param num_mol         massive of number of molecule of selected type
+ * @param num_atoms       massive of number of atoms of selected molecule
+ * @param ch_atom_types   massive of char atom types
+ * @param atom_types      massive of atom types
+ * @param coords          massive of coordinates
+ * 
+ * @return 1              - file does not exist
+ * @return 0              - exit without errors
+ */
+int rw_puma (const char *input, const int step, const char *output, const int num_types, 
+             const int *num_mol, const int *num_atoms, const char *ch_atom_types, 
+             const int *atom_types, float *coords);
+
+
+#endif /* READ_PUMA_H */

mathmech/mm/include/mathmech/select_mol.h

@@ -0,0 +1,36 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file select_mol.h
+ * Header of mathmech library
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
+#ifndef SELECT_MOL_H
+#define SELECT_MOL_H
+
+
+/**
+ * @brief function that selects molecules from array of translated molecules
+ * @code
+ * select_molecule (centr_coords, num_needed_mol, needed_mol);
+ * @endcode
+ * 
+ * @param centr_coords    massive of centered coordinates
+ * @param num_needed_mol  number of needed molecules
+ * @param needed_mol      massive of number of needed molecules
+ * 
+ * @return 0              - exit without errors
+ */
+int select_molecule (const float *centr_coords, const int num_needed_mol, int *needed_mol);
+
+
+#endif /* SELECT_MOL_H */

mathmech/mm/include/mathmech/set_center.h

@@ -0,0 +1,39 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file set_center.h
+ * Header of mathmech library
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
+#ifndef SET_CENTER_H
+#define SET_CENTER_H
+
+#include <mathmech/var_types.h>
+
+
+/**
+ * @brief function that searchs center mass of molecules
+ * @code
+ * set_center (_system_info, _atom_info, centr_coords);
+ * @endcode
+ * 
+ * @param _system_info    system information structure
+ * @param _atom_info      atom information structure
+ * @param centr_coords    massive of centered coordinates
+ * 
+ * @return 0              - exit without errors
+ */
+int set_center (const system_info _system_info, const atom_info *_atom_info, 
+                float *centr_coords);
+
+
+#endif /* SET_CENTER_H */

mathmech/mm/include/mathmech/stat_print.h

@@ -0,0 +1,50 @@
+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * Evgeniy Alekseev wrote this file. As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @file stat_print.h
+ * Header of mathmech library
+ * @author Evgeniy Alekseev (arcanis)
+ * @copyright Beerware
+ * @bug No known bugs
+ */
+
+#ifndef STAT_PRINT_H
+#define STAT_PRINT_H
+
+#include <mathmech/var_types.h>
+
+
+/**
+ * @brief function that prints agglomerates to output file
+ * @code
+ * printing_agl (input, output, connect, _system_info, true_label_mol, num_mol_agl, 
+ *               agl, stat, max_depth, type_agl);
+ * @endcode
+ * 
+ * @param input           input file name
+ * @param output          output file name
+ * @param connect         connectivity graph for all molecules
+ * @param _system_info    system information structure
+ * @param true_label_mol  massive of true numbers of molecule for atoms
+ * @param num_mol_agl     massive of number of molecules in agglomerates
+ * @param agl             massive of agglomerates
+ * @param stat            massive of statistic
+ * @param max_depth       maximum depth for check cycles in graph analyze
+ * @param type_agl        massive of number of agglomerate types
+ * 
+ * @return 1              - memory error
+ * @return 0              - exit without errors
+ */
+int printing_agl (const char *input, const char *output, const int *connect, 
+                  const system_info _system_info, const int *true_label_mol, 
+                  const int *num_mol_agl, const int *agl, const int *stat, 
+                  const int max_depth, int *type_agl);
+
+
+#endif /* STAT_PRINT_H */