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/CMakeLists.txt

@@ -46,7 +46,7 @@ if ( CMAKE_COMPILER_IS_GNUCXX )
   set (ADD_CXX_FLAGS  "-Wall")
   set (CMAKE_CXX_FLAGS "-O0 ${ADD_CXX_FLAGS}")
   set (CMAKE_CXX_FLAGS_DEBUG "-g -O0")
-  set (CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
+  set (CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG")
 elseif ( MSVC )
   set (ADD_CXX_FLAGS  "/W4")
   set (CMAKE_CXX_FLAGS "${ADD_CXX_FLAGS}")
@@ -67,4 +67,4 @@ endforeach ()
 # set docs file
 if (ADD_DOCS)
   include (docs.cmake)
-endif ()
+endif ()

mathmech/PKGBUILD

@@ -1,17 +1,17 @@
-# 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=1.2.0
-pkgrel=1
+pkgrel=2
 pkgdesc="Software package for analysis of molecular dynamics trajectories"
-arch=(any)
+arch=('i686' 'x86_64')
 url="http://arcan1s.github.io/projects/moldyn"
 license=('Beerware')
-depends=('qt4' 'qwt')
+depends=('qwt')
 makedepends=('cmake' 'automoc4')
 source=(https://github.com/arcan1s/moldyn/releases/download/mm-${pkgver}/${pkgname}-${pkgver}-src.zip)
-md5sums=('f3f01c7eefdedf23b4eadfbf59058332')
+md5sums=('de893eee2230269b10099c5fd925502b')
 _cmakekeys="-DCMAKE_INSTALL_PREFIX=/usr
             -DQWT_INCLUDE_PATH=/usr/include/qwt
             -DQWT_LIBRARY_PATH=/usr/lib
@@ -25,7 +25,7 @@ prepare() {
   mkdir "${srcdir}/build"
 }
 
-build () {
+build() {
   cd "${srcdir}/build"
   cmake ${_cmakekeys} ../
   make
@@ -34,6 +34,6 @@ build () {
 package() {
   cd "${srcdir}/build"
   make DESTDIR="${pkgdir}" install
-  install -Dm644 "${srcdir}/COPYING" "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
+  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/src/add_main.c

@@ -27,8 +27,6 @@
 int error_checking (const char *aglinp, const system_info _system_info, const char *input, 
                     const char *output)
 {
-  if ((_system_info.cell[0] == 0.0) || (_system_info.cell[1] == 0.0) || (_system_info.cell[2] == 0.0))
-    return 11;
   if (input[0] == '#')
     return 12;
   if (output[0] == '#')

mathmech/agl/src/main.c

@@ -81,11 +81,10 @@ int main(int argc, char *argv[])
       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);
@@ -105,13 +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", &_system_info.cell[0], &_system_info.cell[1], 
-              &_system_info.cell[2]);
-      i++;
-    }
     else if ((argv[i][0] == '-') && (argv[i][1] == 'o') && (argv[i][2] == '\0'))
 // output file
     {

mathmech/envir/src/add_main.c

@@ -27,8 +27,6 @@
 int error_checking (const system_info _system_info, const char *input, 
                     const char *output)
 {
-  if ((_system_info.cell[0] == 0.0) || (_system_info.cell[1] == 0.0) || (_system_info.cell[2] == 0.0))
-    return 11;
   if (input[0] == '#')
     return 12;
   if (output[0] == '#')

mathmech/envir/src/main.c

@@ -81,11 +81,10 @@ int main(int argc, char *argv[])
       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);
@@ -101,12 +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", &_system_info.cell[0], &_system_info.cell[1], &_system_info.cell[2]);
-      i++;
-    }
     else if ((argv[i][0] == '-') && (argv[i][1] == 'o') && (argv[i][2] == '\0'))
 // output file
     {

mathmech/mm/include/mathmech/print_trj.h

@@ -33,12 +33,13 @@
  * @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 *coords, const float *cell);
 
 
 #endif /* PRINT_TRJ_H */

mathmech/mm/src/CMakeLists.txt

@@ -15,12 +15,15 @@ message (STATUS "${SUBPROJECT} HEADERS: ${HEADERS}")
 
 # link libraries and compile
 add_library (${SUBPROJECT} SHARED ${SOURCES} ${HEADERS})
-add_library (${SUBPROJECT} STATIC ${SOURCES} ${HEADERS})
 set_target_properties (${SUBPROJECT} PROPERTIES SOVERSION ${PROJECT_VERSION})
 target_link_libraries (${SUBPROJECT} ${ADDITIONAL_LIB})
+add_library (${SUBPROJECT}_STATIC STATIC ${SOURCES} ${HEADERS})
+set_target_properties(${SUBPROJECT}_STATIC PROPERTIES OUTPUT_NAME ${SUBPROJECT})
+target_link_libraries (${SUBPROJECT} ${ADDITIONAL_LIB})
 
 # install properties
 install (TARGETS ${SUBPROJECT} DESTINATION lib)
+install (TARGETS ${SUBPROJECT}_STATIC DESTINATION lib)
 if (ADD_INCLUDE)
   install (DIRECTORY ${SUBPROJECT_INCLUDE_DIR}/ DESTINATION include/)
 endif ()

mathmech/mm/src/coords.c

@@ -29,7 +29,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
 {
   char at_symb[32], file_string[256];
   int atoms, cur_at_num, cur_at_type, cur_mol, i, j, tr_num_atoms, ref_mol, x, y;
-  float cur_coords[3], ref[3];
+  float cur_coords[3], ref[3], cur_cell[3];
   FILE *inp;
   
 /* cur_*                  temp variables
@@ -132,6 +132,13 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
       default: return 2;
     }
   }
+  // cell sizes
+  fgets (file_string, 256, inp);
+  sscanf (file_string, "%f,%f,%f", &cur_cell[0], &cur_cell[1],
+          &cur_cell[2]);
+  (*_system_info).cell[0] = cur_cell[0];
+  (*_system_info).cell[1] = cur_cell[1];
+  (*_system_info).cell[2] = cur_cell[2];
   fclose (inp);
   
 /// <pre>   translation </pre>

mathmech/mm/src/print_trj.c

@@ -24,7 +24,7 @@
  */
 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 *coords, const float *cell)
 {
   int cur_mol, cur_type[2], i, j, k, l;
   FILE *f_out;
@@ -60,6 +60,8 @@ coords[3*i+1], coords[3*i+2], atom_types[cur_type[1]], cur_mol);
       cur_type[0] += num_atoms[j];
     }
   }
+
+  fprintf (f_out, "%lf,%lf,%lf\n", cell[0], cell[1], cell[2]);
   
   fclose (f_out);
   

mathmech/mm/src/read_gmx.c

@@ -126,7 +126,7 @@ int rw_gmx (const char *input, const int step, const char *output, const int num
     
 // write to output
     printing_trj (filename, atoms, num_types, num_mol, num_atoms, ch_atom_types, 
-                  atom_types, coords);
+                  atom_types, coords, cell);
   }
   
   fclose (f_inp);

mathmech/mm/src/read_puma.c

@@ -78,7 +78,7 @@ int rw_puma (const char *input, const int step, const char *output, const int nu
     
 // write to output
     printing_trj (filename, atoms, num_types, num_mol, num_atoms, ch_atom_types, 
-                  atom_types, coords);
+                  atom_types, coords, cell);
   }
   
   fclose (f_inp);

mathmech/radf/src/add_main.c

@@ -28,8 +28,6 @@
 int error_checking (const char *input, const int num_needed_at, const int *needed_at, 
                     const char *output, const system_info _system_info)
 {
-  if ((_system_info.cell[0] == 0.0) || (_system_info.cell[1] == 0.0) || (_system_info.cell[2] == 0.0))
-    return 11;
   if (input[0] == '#')
     return 12;
   if (output[0] == '#')

mathmech/radf/src/main.c

@@ -81,13 +81,12 @@ int main(int argc, char *argv[])
       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_radf -i INPUT -s FIRST,LAST -c X,Y,Z -at ... -o OUTPUT [ -r MIN,MAX ]\n", tmp_str);
-      sprintf (tmp_str, "%s                   [ -rs R_STEP ] [ -a MIN,MAX ] [ -as ANG_STEP ] [ -m ]\n", tmp_str);
-      sprintf (tmp_str, "%s                                            [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
+      sprintf (tmp_str, "%smm_radf -i INPUT -s FIRST,LAST -at ... -o OUTPUT [ -r MIN,MAX ] [ -rs R_STEP ]\n", tmp_str);
+      sprintf (tmp_str, "%s                                        [ -a MIN,MAX ] [ -as ANG_STEP ] [ -m ]\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          - mask of input files\n", tmp_str);
       sprintf (tmp_str, "%s  -s          - trajectory steps (integer)\n", tmp_str);
-      sprintf (tmp_str, "%s  -c          - cell size (float), A\n", tmp_str);
       sprintf (tmp_str, "%s  -at         - atom types (integer). Format: 'AT1-AT2' or 'A1,A2,A3-B1,B2,B3'\n", tmp_str);
       sprintf (tmp_str, "%s                (will enable RDF calculation for center mass automaticaly)\n", tmp_str);
       sprintf (tmp_str, "%s  -o          - output file name\n", tmp_str);
@@ -123,12 +122,6 @@ int main(int argc, char *argv[])
       }
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'c') && (argv[i][2] == '\0'))
-// cell size
-    {
-      sscanf (argv[i+1], "%f,%f,%f", &_system_info.cell[0], &_system_info.cell[1], &_system_info.cell[2]);
-      i++;
-    }
     else if ((argv[i][0] == '-') && (argv[i][1] == 'a') && (argv[i][2] == 't') && (argv[i][3] == '\0'))
 // atom types
     {
@@ -248,12 +241,12 @@ int main(int argc, char *argv[])
   _atom_info = (atom_info *) malloc (8 * _system_info.num_atoms * sizeof (atom_info));
   if (mode == 2)
   {
-    i = (_radf_info.r_max - _radf_info.r_min) / _radf_info.r_step;
-    j = (_radf_info.ang_max - _radf_info.ang_min) / _radf_info.ang_step;
+    i = 1 + (_radf_info.r_max - _radf_info.r_min) / _radf_info.r_step;
+    j = 1 + (_radf_info.ang_max - _radf_info.ang_min) / _radf_info.ang_step;
     i *= j;
   }
   else
-    i = (_radf_info.r_max - _radf_info.r_min) / _radf_info.r_step;
+    i = 1 + (_radf_info.r_max - _radf_info.r_min) / _radf_info.r_step;
   radf = (int *) malloc (i * sizeof (int));
   for (j=0; j<i; j++)
     radf[j] = 0;

mathmech/statgen/src/add_main.c

@@ -30,8 +30,6 @@ int error_checking (const system_info _system_info, const char *input, const int
 {
   if ((type_inter == 0) || (type_inter > 4))
     return 11;
-  if ((_system_info.cell[0] == 0.0) || (_system_info.cell[1] == 0.0) || (_system_info.cell[2] == 0.0))
-    return 12;
   if ((_system_info.to == -1) || (_system_info.from == -1))
     return 13;
   if (num_of_inter == 0)

mathmech/statgen/src/main.c

@@ -107,12 +107,11 @@ int main (int argc, char *argv[])
       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_statgen -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -r ... -o OUTPUT [ -g DEPTH ]\n", tmp_str);
-      sprintf (tmp_str, "%s                                                   [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
+      sprintf (tmp_str, "%smm_statgen -i INPUT -s FIRST,LAST -a ... -r ... -o OUTPUT [ -g DEPTH ]\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          - mask of input files\n", tmp_str);
       sprintf (tmp_str, "%s  -s          - trajectory steps (integer)\n", tmp_str);
-      sprintf (tmp_str, "%s  -c          - cell size (float), A\n", tmp_str);
       sprintf (tmp_str, "%s  -a          - atom types (integer). Format: 'ATOM1' or 'ATOM1,ATOM2' or etc\n", tmp_str);
       sprintf (tmp_str, "%s  -r          - criteria (float), A. Format: '0-0:2.4,0-1:3.0' means 0-0\n", tmp_str);
       sprintf (tmp_str, "%s                interaction (<2.4 A) and 0-1 (<3.0) are needed. This flag can be\n", tmp_str);
@@ -144,12 +143,6 @@ int main (int argc, char *argv[])
       }
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'c') && (argv[i][2] == '\0'))
-// cell size
-    {
-      sscanf (argv[i+1], "%f,%f,%f", &_system_info.cell[0], &_system_info.cell[1], &_system_info.cell[2]);
-      i++;
-    }
     else if ((argv[i][0] == '-') && (argv[i][1] == 'a') && (argv[i][2] == '\0'))
 // atom types
     {

xvg2csv/xvg2csv.py

@@ -0,0 +1,270 @@
+#!/usr/bin/python2
+#    xvg2csv
+#    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, datetime, os
+
+
+def defineType(file):
+    """function to define type of input file"""
+    type = None
+    with open(file, 'r') as input:
+        for line in input:
+            if (line[0] == '@') and (line.find("title") > -1):
+                if (line.find("RMSD") > -1):
+                    type = "rmsd"
+                elif (line.find("istance") > -1):
+                    type = "dist"
+                elif (line.find("Angle") > -1):
+                    type = "angl"
+                elif (line.find("Number") > -1):
+                    type = "num"
+                break
+    return type
+
+
+def getAngleOutput(file, first=True):
+    """function to parse angle file"""
+    data = []
+    with open(file, 'r') as input:
+        for line in input:
+            if ((line[0] == '@') or (line[0] == '#')):
+                continue
+            try:
+                if ((not first) and (float(line.split()[0]) == 0.0)):
+                    continue
+                data.append(float(line.split()[2]))
+            except:
+                pass
+    return data
+
+
+def getDistanceOutput(file, first=True):
+    """function to parse distance file"""
+    data = []
+    with open(file, 'r') as input:
+        for line in input:
+            if ((line[0] == '@') or (line[0] == '#')):
+                continue
+            try:
+                if ((not first) and (float(line.split()[0]) == 0.0)):
+                    continue
+                data.append(float(line.split()[1]) * 10.0)
+            except:
+                pass
+    return data
+
+
+def getNumberOutput(file, first=True):
+    """function to parse distance file"""
+    data = []
+    with open(file, 'r') as input:
+        for line in input:
+            if ((line[0] == '@') or (line[0] == '#')):
+                continue
+            try:
+                if ((not first) and (float(line.split()[0]) == 0.0)):
+                    continue
+                data.append(float(line.split()[1]))
+            except:
+                pass
+    return data
+
+
+def getRmsdOutput(file, first=True):
+    """function to parse rmsd files"""
+    data = []
+    with open(file, 'r') as input:
+        for line in input:
+            if ((line[0] == '@') or (line[0] == '#')):
+                continue
+            try:
+                if ((not first) and (float(line.split()[0]) == 0.0)):
+                    continue
+                data.append(float(line.split()[1]) * 10.0)
+            except:
+                pass
+    return data
+
+
+def getFullFileList(dirs):
+    """function to get full file list"""
+    fileList = {}
+    for dir in dirs:
+        directory = os.path.abspath(dir)
+        if (os.path.exists(directory)) and (os.path.isdir(directory)):
+            newFileList = getFileList(directory)
+            for label in newFileList.keys():
+                if (not fileList.has_key(label)): fileList[label] = {}
+                for system in newFileList[label].keys():
+                    if (not fileList[label].has_key(system)): fileList[label][system] = []
+                    fileList[label][system].append(newFileList[label][system])
+    return fileList
+
+
+def getFileList(directory):
+    """function to get file list"""
+    rawFileList = [file for file in os.listdir(directory) if (os.path.splitext(file)[1] == ".xvg")]
+    rawFileList.sort()
+    return parseFileList(directory, rawFileList)
+
+
+def parseFileList(directory, rawFileList):
+    """function to parse file list"""
+    fileList = {}
+    for file in rawFileList:
+        fullFileName = os.path.join(directory, file)
+        label = os.path.splitext(file)[0].split('_')[-2]
+        system = '_'.join(os.path.splitext(file)[0].split('_')[:-2])
+        if (not fileList.has_key(label)): fileList[label] = {}
+        if (not fileList[label].has_key(system)): fileList[label][system] = []
+        if (fileList[label][system].count(fullFileName) == 0):
+            fileList[label][system].append(fullFileName)
+    return fileList
+
+
+def getAveragingData(rawData, time):
+    """function to get averaging data"""
+    data = {}
+    for system in rawData.keys():
+        if (not data.has_key(system)): data[system] = []
+        count = len(rawData[system]) / time
+        for i in range(count):
+            value = sum(rawData[system][i*time:(i+1)*time]) / float(time)
+            data[system].append(value)
+    return data
+
+
+
+def getData(fileList):
+    """function to get data from files"""
+    rawData = {}
+    for system in fileList.keys():
+        first = True
+        type = None
+        if (not rawData.has_key(system)): rawData[system] = []
+        for files in fileList[system]:
+            for file in files:
+                if (first):
+                    type = defineType(file)
+                if (type == "rmsd"):
+                    rawData[system] = rawData[system] + getRmsdOutput(file, first)
+                elif (type == "dist"):
+                    rawData[system] = rawData[system] + getDistanceOutput(file, first)
+                elif (type == "angl"):
+                    rawData[system] = rawData[system] + getAngleOutput(file, first)
+                elif (type == "num"):
+                    rawData[system] = rawData[system] + getNumberOutput(file, first)
+                if (first):
+                    first = False
+    return rawData
+
+
+def createCsv(directory, label, data, timeStep):
+    """function to create *.csv file"""
+    file = os.path.join(directory, label + ".csv")
+    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("t\t%s\n" % ('\t'.join(data.keys())))
+        count = max([len(data[system]) for system in data.keys()])
+        for i in range(count):
+            line = "%.3f" % (i * timeStep + timeStep / 2.0)
+            for system in data.keys():
+                if (len(data[system]) > i):
+                    line = "%s\t%.5f" % (line, data[system][i])
+                else:
+                    line = "%s\t" % (line)
+            output.write(line + "\n")
+
+
+def createQti(directory, label, data, timeStep):
+    """function to create *.qti file"""
+    file = os.path.join(directory, label + ".qti")
+    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:
+        count = max([len(data[system]) for system in data.keys()])
+        timestamp = datetime.datetime.now().strftime("%d.%m.%y %H:%M")
+        output.write("QtiPlot 0.9.8 project file\n")
+        output.write("<scripting-lang>\tPython\n")
+        output.write("<windows>\t1\n")
+        output.write("<table>\n")
+        output.write("%s\t%i\t%i\t%s\n" % (label, count, len(data.keys()) + 1, timestamp))
+        output.write("geometry\t0\t0\t445\t220\t\n")
+        output.write("header\tt[X]\t%s[Y]\n" % ('[Y]\t'.join(data.keys())))
+        output.write("ColWidth\t100")
+        for system in data.keys(): output.write("\t100")
+        output.write("\n<com>\n</com>\n")
+        output.write("ColType\t0;0/13")
+        for system in data.keys(): output.write("\t0;0/13")
+        output.write("\nReadOnlyColumn\t0")
+        for system in data.keys(): output.write("\t0")
+        output.write("\nHiddenColumn\t0")
+        for system in data.keys(): output.write("\t0")
+        output.write("\nComments\t\t")
+        for system in data.keys(): output.write("\t")
+        output.write("\nWindowLabel\t\t2\n<data>\n")
+        for i in range(count):
+            line = "%i\t%.3f" % (i, i * timeStep + timeStep / 2.0)
+            for system in data.keys():
+                if (len(data[system]) > i):
+                    line = "%s\t%.8f" % (line, data[system][i])
+                else:
+                    line = "%s\t" % (line)
+            output.write(line + "\n")
+        output.write("</data>\n</table>\n")
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description = 'Convert GROMACS *.xvg files to *.csv and *.qti. Example filename is "system_label_number.xvg"')
+    parser.add_argument('-d', '--directories', dest = 'dirs',
+        help = 'Directories, comma separared', action = 'store', default = ".")
+    parser.add_argument('-o', '--output', dest = 'output',
+        help = 'Output directory', action = 'store', default = ".")
+    parser.add_argument('-nc', '--nocsv', dest = 'nocsv',
+        help = 'Do not create *.csv file', action = 'store_true', default = False)
+    parser.add_argument('-nq', '--noqti', dest = 'noqti',
+        help = 'Do not create *.qti file', action = 'store_true', default = False)
+    parser.add_argument('-t', '--time', dest = 'time', type = int,
+        help = 'Averaging time', action = 'store', default = 1)
+    parser.add_argument('-s', '--step', dest = 'step', type = float,
+        help = 'Time step', action = 'store', default = 1.0)
+    args = parser.parse_args()
+
+    dirs = args.dirs.split(',')
+    output = os.path.abspath(args.output)
+    if not os.path.exists(output): os.makedirs(output)
+
+    fileList = getFullFileList(dirs)
+    for label in fileList.keys():
+        rawData = getData(fileList[label])
+        data = getAveragingData(rawData, args.time)
+        if (not args.nocsv):
+            createCsv(output, label, data, args.step)
+        if (not args.noqti):
+            createQti(output, label, data, args.step)