mirror of
https://github.com/arcan1s/moldyn.git
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Added documentation for statgen
This commit is contained in:
arcan1s
3
agl/AUTHORS
Normal file
3
agl/AUTHORS
Normal file
@ -0,0 +1,3 @@
|
||||
Current developers:
|
||||
|
||||
Evgeniy Alekseev aka arcanis <esalexeev (at) gmail (dot) com>
|
||||
31
agl/CMakeLists.txt
Normal file
31
agl/CMakeLists.txt
Normal file
@ -0,0 +1,31 @@
|
||||
cmake_minimum_required (VERSION 2.8)
|
||||
|
||||
cmake_policy(SET CMP0011 NEW)
|
||||
cmake_policy(SET CMP0003 OLD)
|
||||
|
||||
# set project name
|
||||
set (PROJECT agl)
|
||||
# set additional cmake file
|
||||
include (${PROJECT}.cmake)
|
||||
|
||||
|
||||
# additional options
|
||||
OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
|
||||
OPTION (ADD_INCLUDE "Add include files" 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 ()
|
||||
|
||||
# additional targets
|
||||
set (TARGETS "")
|
||||
set (HEADERS "")
|
||||
|
||||
add_subdirectory (src)
|
||||
341
agl/COPYING
Normal file
341
agl/COPYING
Normal file
@ -0,0 +1,341 @@
|
||||
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.
|
||||
|
||||
1. You may copy and distribute verbatim copies of the Program's
|
||||
source code as you receive it, in any medium, provided that you
|
||||
conspicuously and appropriately publish on each copy an appropriate
|
||||
copyright notice and disclaimer of warranty; keep intact all the
|
||||
notices that refer to this License and to the absence of any warranty;
|
||||
and give any other recipients of the Program a copy of this License
|
||||
along with the Program.
|
||||
|
||||
You may charge a fee for the physical act of transferring a copy, and
|
||||
you may at your option offer warranty protection in exchange for a fee.
|
||||
|
||||
2. You may modify your copy or copies of the Program or any portion
|
||||
of it, thus forming a work based on the Program, and copy and
|
||||
distribute such modifications or work under the terms of Section 1
|
||||
above, provided that you also meet all of these conditions:
|
||||
|
||||
a) You must cause the modified files to carry prominent notices
|
||||
stating that you changed the files and the date of any change.
|
||||
|
||||
b) You must cause any work that you distribute or publish, that in
|
||||
whole or in part contains or is derived from the Program or any
|
||||
part thereof, to be licensed as a whole at no charge to all third
|
||||
parties under the terms of this License.
|
||||
|
||||
c) If the modified program normally reads commands interactively
|
||||
when run, you must cause it, when started running for such
|
||||
interactive use in the most ordinary way, to print or display an
|
||||
announcement including an appropriate copyright notice and a
|
||||
notice that there is no warranty (or else, saying that you provide
|
||||
a warranty) and that users may redistribute the program under
|
||||
these conditions, and telling the user how to view a copy of this
|
||||
License. (Exception: if the Program itself is interactive but
|
||||
does not normally print such an announcement, your work based on
|
||||
the Program is not required to print an announcement.)
|
||||
|
||||
These requirements apply to the modified work as a whole. If
|
||||
identifiable sections of that work are not derived from the Program,
|
||||
and can be reasonably considered independent and separate works in
|
||||
themselves, then this License, and its terms, do not apply to those
|
||||
sections when you distribute them as separate works. But when you
|
||||
distribute the same sections as part of a whole which is a work based
|
||||
on the Program, the distribution of the whole must be on the terms of
|
||||
this License, whose permissions for other licensees extend to the
|
||||
entire whole, and thus to each and every part regardless of who wrote it.
|
||||
|
||||
Thus, it is not the intent of this section to claim rights or contest
|
||||
your rights to work written entirely by you; rather, the intent is to
|
||||
exercise the right to control the distribution of derivative or
|
||||
collective works based on the Program.
|
||||
|
||||
In addition, mere aggregation of another work not based on the Program
|
||||
with the Program (or with a work based on the Program) on a volume of
|
||||
a storage or distribution medium does not bring the other work under
|
||||
the scope of this License.
|
||||
|
||||
3. You may copy and distribute the Program (or a work based on it,
|
||||
under Section 2) in object code or executable form under the terms of
|
||||
Sections 1 and 2 above provided that you also do one of the following:
|
||||
|
||||
a) Accompany it with the complete corresponding machine-readable
|
||||
source code, which must be distributed under the terms of Sections
|
||||
1 and 2 above on a medium customarily used for software interchange; or,
|
||||
|
||||
b) Accompany it with a written offer, valid for at least three
|
||||
years, to give any third party, for a charge no more than your
|
||||
cost of physically performing source distribution, a complete
|
||||
machine-readable copy of the corresponding source code, to be
|
||||
distributed under the terms of Sections 1 and 2 above on a medium
|
||||
customarily used for software interchange; or,
|
||||
|
||||
c) Accompany it with the information you received as to the offer
|
||||
to distribute corresponding source code. (This alternative is
|
||||
allowed only for noncommercial distribution and only if you
|
||||
received the program in object code or executable form with such
|
||||
an offer, in accord with Subsection b above.)
|
||||
|
||||
The source code for a work means the preferred form of the work for
|
||||
making modifications to it. For an executable work, complete source
|
||||
code means all the source code for all modules it contains, plus any
|
||||
associated interface definition files, plus the scripts used to
|
||||
control compilation and installation of the executable. However, as a
|
||||
special exception, the source code distributed need not include
|
||||
anything that is normally distributed (in either source or binary
|
||||
form) with the major components (compiler, kernel, and so on) of the
|
||||
operating system on which the executable runs, unless that component
|
||||
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
|
||||
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.
|
||||
14
agl/INSTALL
Normal file
14
agl/INSTALL
Normal file
@ -0,0 +1,14 @@
|
||||
CMakeFlags:
|
||||
-DCMAKE_INSTALL_PREFIX= - install prefix (default is '/usr/local')
|
||||
-DADD_INCLUDE=1 - install include files (default is disable)
|
||||
-DWITH_DEBUG_MODE=1 - compile with flag '-g' (default is disable)
|
||||
|
||||
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
|
||||
You may also download compiled executable file for Win_x86.
|
||||
22
agl/agl.cmake
Normal file
22
agl/agl.cmake
Normal file
@ -0,0 +1,22 @@
|
||||
# set directories
|
||||
set (${PROJECT}_BINARY_DIR bin)
|
||||
set (${PROJECT}_SOURCE_DIR src:include)
|
||||
set (${PROJECT}_LIB_DIR lib)
|
||||
|
||||
set (CMAKE_INCLUDE_PATH ${${PROJECT}_SOURCE_DIR})
|
||||
set (CMAKE_LIBRARY_PATH ${${PROJECT}_LIB_DIR})
|
||||
set (EXECUTABLE_OUTPUT_PATH ${${PROJECT}_BINARY_DIR})
|
||||
set (CMAKE_VERBOSE_MAKEFILE ON)
|
||||
|
||||
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 ${ADD_CXX_FLAGS}")
|
||||
set (CMAKE_CXX_FLAGS_DEBUG "-g -O0")
|
||||
set (CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
|
||||
else ()
|
||||
message (STATUS "Flags not enabled")
|
||||
endif ()
|
||||
61
agl/src/CMakeLists.txt
Normal file
61
agl/src/CMakeLists.txt
Normal file
@ -0,0 +1,61 @@
|
||||
set ("${PROJECT}_VERSION_MAJOR" 1)
|
||||
set ("${PROJECT}_VERSION_MINOR" 0)
|
||||
set ("${PROJECT}_VERSION_PATCH" 1)
|
||||
set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
|
||||
|
||||
message (STATUS ${${PROJECT}_VERSION})
|
||||
|
||||
## set files
|
||||
# main files
|
||||
set (MAIN_SOURCES main)
|
||||
# not public srcs
|
||||
set (PRIVATE_CLASSES)
|
||||
# headers only files
|
||||
SET (HEADERS_ONLY)
|
||||
# public srcs
|
||||
set (PUBLIC_CLASSES add_main
|
||||
coords
|
||||
envir_search
|
||||
messages
|
||||
print_struct
|
||||
set_center)
|
||||
# public headers
|
||||
set (PUBLIC_HEADERS)
|
||||
# shared libraries
|
||||
if (CMAKE_COMPILER_IS_GNUCXX)
|
||||
set (ADDITIONAL_LIB m)
|
||||
else ()
|
||||
set (ADDITIONAL_LIB)
|
||||
endif()
|
||||
set (SOURCES)
|
||||
|
||||
# append list
|
||||
foreach (class ${PRIVATE_CLASSES})
|
||||
LIST (APPEND SOURCES ${class}.c)
|
||||
LIST (APPEND HEADERS ${class}.h)
|
||||
endforeach ()
|
||||
|
||||
foreach (class ${HEADERS_ONLY})
|
||||
LIST (APPEND HEADERS ${class}.h)
|
||||
endforeach ()
|
||||
|
||||
foreach (class ${PUBLIC_CLASSES})
|
||||
LIST (APPEND SOURCES ${class}.c)
|
||||
LIST (APPEND HEADERS ../include/${PROJECT}/${class}.h)
|
||||
LIST (APPEND PUBLIC_HEADERS ../include/${PROJECT}/${class}.h)
|
||||
endforeach ()
|
||||
|
||||
# message
|
||||
message (STATUS "SOURCES: ${SOURCES}")
|
||||
|
||||
# link libraries and compile
|
||||
add_executable (${PROJECT} ${MAIN_SOURCES} ${SOURCES})
|
||||
target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
|
||||
|
||||
# install properties
|
||||
INSTALL (TARGETS ${PROJECT}
|
||||
DESTINATION bin)
|
||||
if (ADD_INCLUDE)
|
||||
INSTALL (FILES ${PUBLIC_HEADERS}
|
||||
DESTINATION include/${PROJECT})
|
||||
endif ()
|
||||
21
agl/src/Makefile
Normal file
21
agl/src/Makefile
Normal file
@ -0,0 +1,21 @@
|
||||
PROJECT=AGL
|
||||
|
||||
CC=gcc
|
||||
CFLAGS=-c -Wall -fPIC
|
||||
LDFLAGS=-lm
|
||||
SOURCES_DIR=src
|
||||
SOURCES=main.c add_main.c coords.c messages.c print_struct.c set_center.c read_agl.c
|
||||
OBJECTS=$(SOURCES:.c=.o)
|
||||
EXECUTABLE=agl
|
||||
|
||||
$(PROJECT): $(SOURCES) $(EXECUTABLE)
|
||||
|
||||
$(EXECUTABLE): $(OBJECTS)
|
||||
$(CC) $(LDFLAGS) $(OBJECTS) -o $@
|
||||
|
||||
.c.o:
|
||||
$(CC) $(CFLAGS) $< -o $@
|
||||
|
||||
clean:
|
||||
rm -f *.o
|
||||
|
||||
53
agl/src/add_main.c
Normal file
53
agl/src/add_main.c
Normal file
@ -0,0 +1,53 @@
|
||||
/* Additional library for main.c (agl)
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
|
||||
// #include "messages.h"
|
||||
|
||||
|
||||
int error_checking (const char *aglinp, const float *cell, const char *input,
|
||||
const char *output)
|
||||
{
|
||||
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 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;
|
||||
}
|
||||
|
||||
|
||||
int set_defaults (char aglinp, float *cell, char *input, int *log, int *num_of_mol,
|
||||
char *output, int *quiet, float *rad)
|
||||
{
|
||||
int i;
|
||||
|
||||
aglinp[0] = '#';
|
||||
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;
|
||||
}
|
||||
338
agl/src/coords.c
Normal file
338
agl/src/coords.c
Normal file
@ -0,0 +1,338 @@
|
||||
/* Library for reading coordinates from input file
|
||||
*
|
||||
* Usage:
|
||||
* reading_coords (mode, filename, type_interaction, labels,
|
||||
* cell, &number_of_molecules, &number_of_atoms, true_label_molecule,
|
||||
* label_molecule, type_atoms, coords, char_type_atoms)
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
|
||||
|
||||
int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
const int *label_atom, const float *cell, int *num_mol,
|
||||
int *num_atoms, int *true_label_mol, int *label_mol,
|
||||
int *type_atoms, float *coords, char *ch_type_atoms)
|
||||
/* filename - name of file with coordinates
|
||||
* type_inter - type interaction (number of molecules for interaction)
|
||||
* (number of molecules in aglomerate for agl)
|
||||
* label_atom - types of atom for interaction
|
||||
* (molecules in aglomerate for agl)
|
||||
* cell - cell dimension
|
||||
* num_mol - number of molecules for writing coordinates
|
||||
* num_atoms - number of atoms for writing coordinates
|
||||
* true_label_mol - massive of true numbers of molecule for atoms
|
||||
* label_mol - massive of numbers of molecule for atoms
|
||||
* type_atoms - massive of atom types for atoms
|
||||
* coords - massive of coordinates
|
||||
* ch_type_atoms - massive of char types for atoms
|
||||
*/
|
||||
{
|
||||
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], *not_tr_coords, ref[3];
|
||||
FILE *inp;
|
||||
/* cur_*, at_symb - temp variables
|
||||
* file_string - temp string variable
|
||||
* atoms - total number of atoms in system
|
||||
* tr_num_atoms - number of translated atoms for writing coordinates (m.b. 8*num_atoms)
|
||||
* ref_mol - number of molecule for reference
|
||||
* not_tr_coords - not translated coordinates
|
||||
* ref - coordinates of reference molecule
|
||||
* inp - file with input data
|
||||
*/
|
||||
|
||||
*num_atoms = 0;
|
||||
*num_mol = 0;
|
||||
|
||||
// Reading file
|
||||
inp = fopen (filename, "r");
|
||||
if (inp == NULL)
|
||||
return 1;
|
||||
|
||||
ref_mol = -1;
|
||||
fscanf (inp, "%i", &atoms);
|
||||
not_tr_coords = (float *) malloc (3 * atoms * sizeof (float));
|
||||
fgets (file_string, 256, inp);
|
||||
for (i=0; i<atoms; i++)
|
||||
{
|
||||
fgets (file_string, 256, inp);
|
||||
sscanf (file_string, "%i%s%f%f%f%i%i", &cur_at_num, at_symb, &cur_coords[0],
|
||||
&cur_coords[1], &cur_coords[2], &cur_at_type, &cur_mol);
|
||||
|
||||
switch (mode)
|
||||
{
|
||||
case 0:
|
||||
// for statgen
|
||||
for (j=0; j<type_inter; j++)
|
||||
if (cur_at_type == label_atom[j])
|
||||
{
|
||||
not_tr_coords[3**num_atoms+0] = cur_coords[0];
|
||||
not_tr_coords[3**num_atoms+1] = cur_coords[1];
|
||||
not_tr_coords[3**num_atoms+2] = cur_coords[2];
|
||||
|
||||
if (ref_mol != cur_mol)
|
||||
{
|
||||
ref_mol = cur_mol;
|
||||
true_label_mol[*num_mol] = ref_mol;
|
||||
*num_mol = *num_mol + 1;
|
||||
}
|
||||
label_mol[*num_atoms] = *num_mol - 1;
|
||||
type_atoms[*num_atoms] = j;
|
||||
|
||||
*num_atoms = *num_atoms + 1;
|
||||
}
|
||||
break;
|
||||
case 1:
|
||||
// for envir and frad
|
||||
not_tr_coords[3**num_atoms+0] = cur_coords[0];
|
||||
not_tr_coords[3**num_atoms+1] = cur_coords[1];
|
||||
not_tr_coords[3**num_atoms+2] = cur_coords[2];
|
||||
ch_type_atoms[2**num_atoms+0] = at_symb[0];
|
||||
ch_type_atoms[2**num_atoms+1] = at_symb[1];
|
||||
|
||||
if (ref_mol != cur_mol)
|
||||
{
|
||||
ref_mol = cur_mol;
|
||||
true_label_mol[*num_mol] = ref_mol;
|
||||
*num_mol = *num_mol + 1;
|
||||
}
|
||||
label_mol[*num_atoms] = *num_mol - 1;
|
||||
type_atoms[*num_atoms] = j;
|
||||
|
||||
*num_atoms = *num_atoms + 1;
|
||||
break;
|
||||
case 2:
|
||||
// for agl
|
||||
for (j=0; j<type_inter; j++)
|
||||
if (cur_mol == label_atom[j])
|
||||
{
|
||||
not_tr_coords[3**num_atoms+0] = cur_coords[0];
|
||||
not_tr_coords[3**num_atoms+1] = cur_coords[1];
|
||||
not_tr_coords[3**num_atoms+2] = cur_coords[2];
|
||||
ch_type_atoms[2**num_atoms+0] = at_symb[0];
|
||||
ch_type_atoms[2**num_atoms+1] = at_symb[1];
|
||||
|
||||
if (ref_mol != cur_mol)
|
||||
{
|
||||
ref_mol = cur_mol;
|
||||
true_label_mol[*num_mol] = ref_mol;
|
||||
*num_mol = *num_mol + 1;
|
||||
}
|
||||
label_mol[*num_atoms] = *num_mol - 1;
|
||||
type_atoms[*num_atoms] = j;
|
||||
|
||||
*num_atoms = *num_atoms + 1;
|
||||
}
|
||||
break;
|
||||
default: return 1;
|
||||
}
|
||||
}
|
||||
fclose (inp);
|
||||
|
||||
// Translation
|
||||
tr_num_atoms = *num_atoms;
|
||||
for (i=0; i<*num_atoms; i++)
|
||||
for (j=0; j<3; j++)
|
||||
coords[3*i+j] = not_tr_coords[3*i+j];
|
||||
|
||||
// Assign initial value to reference coordinates
|
||||
ref_mol = label_mol[0];
|
||||
for (i=0; i<3; i++)
|
||||
ref[i] = coords[3*0+i];
|
||||
|
||||
for (i=0; i<*num_atoms; i++)
|
||||
{
|
||||
if (label_mol[i] != ref_mol)
|
||||
{
|
||||
ref_mol = label_mol[i];
|
||||
for (j=0; j<3; j++)
|
||||
ref[j] = not_tr_coords[3*i+j];
|
||||
}
|
||||
|
||||
for (x=0; x<3; x++)
|
||||
{
|
||||
if (ref[x] >= 0.0)
|
||||
// if xyz >= 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if (j == x)
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
|
||||
else
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
else
|
||||
// if xyz < 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if (j == x)
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
|
||||
else
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
}
|
||||
|
||||
for (x=0; x<3; x++)
|
||||
{
|
||||
for (y=x+1; y<3; y++)
|
||||
{
|
||||
if ((ref[x] >= 0.0) && (ref[y] >= 0.0))
|
||||
// if xyz and xyz >= 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if ((j == x) || (j == y))
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
|
||||
else
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[x] < 0.0) && (ref[y] < 0.0))
|
||||
// if xyz and xyz < 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if ((j == x) || (j == y))
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
|
||||
else
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
}
|
||||
|
||||
for (y=0; y<3; y++)
|
||||
if ((ref[x] < 0.0) && (ref[y] >= 0.0))
|
||||
// if xyz OR xyz >= 0.0
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
{
|
||||
if (j == x)
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
|
||||
if (j == y)
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
|
||||
if ((j != x) && (j != y))
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
}
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
|
||||
// if x and y and z >= 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
|
||||
// if x and y >= 0.0 A and z < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
|
||||
// if x and z >= 0.0 A and y < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
|
||||
// if y and z >= 0.0 A and x < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
|
||||
// if x and y < 0.0 A and z >= 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
|
||||
// if x and z < 0.0 A and y >= 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
|
||||
// if x >= 0.0 A and y and z < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
|
||||
// if x and y and z < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
}
|
||||
|
||||
// free memory
|
||||
free (not_tr_coords);
|
||||
|
||||
return 0;
|
||||
}
|
||||
203
agl/src/main.c
Normal file
203
agl/src/main.c
Normal file
@ -0,0 +1,203 @@
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
|
||||
// #include "add_main.h"
|
||||
// #include "coords.h"
|
||||
// #include "messages.h"
|
||||
// #include "print_struct.h"
|
||||
// #include "read_agl.h"
|
||||
|
||||
|
||||
int main(int argc, char *argv[])
|
||||
{
|
||||
char tmp_str[2048];
|
||||
int error, i, j, *tmp_int;
|
||||
FILE *f_inp, *f_log;
|
||||
|
||||
char aglinp[256], *ch_type_atoms, input[256], logfile[256], output[256];
|
||||
float cell[3], *coords;
|
||||
int *label_mol, log, num_atoms, num_mol, num_needed_mol, *needed_mol, quiet,
|
||||
*true_label_mol;
|
||||
/* ch_type_atoms - massive of char types for atoms
|
||||
* aglinp - input file with aglomerate name
|
||||
* input - input file name
|
||||
* logfile - log file name
|
||||
* output - output file name
|
||||
*
|
||||
* cell - cell dimension
|
||||
* coords - massive of coordinates
|
||||
*
|
||||
* label_mol - massive of numbers of molecule for atoms
|
||||
* log - status of log-mode
|
||||
* num_atoms - number of atoms for writing coordinates
|
||||
* num_mol - number of molecules for writing coordinates
|
||||
* num_needed_mol - number of needed molecules
|
||||
* needed_mol - massive of needed molecules
|
||||
* quiet - status of quiet-mode
|
||||
* true_label_mol - massive of true numbers of molecule for atoms
|
||||
*/
|
||||
|
||||
set_defaults (aglinp, cell, input, &log, &num_of_mol, output, &quiet, &rad);
|
||||
|
||||
for (i=1; i<argc; i++)
|
||||
{
|
||||
if ((argv[i][0] == '-') && (argv[i][1] == 'h'))
|
||||
{
|
||||
sprintf (tmp_str, " agl\n");
|
||||
sprintf (tmp_str, "%sProgram for create PDB file with choosen aglomerate\n", tmp_str);
|
||||
sprintf (tmp_str, "%sVersion : 1.0.1 License : GPL\n", tmp_str);
|
||||
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, "%sagl -a FILENAME -i FILENAME -c X,Y,Z -o FILEMANE [ -l LOGFILE] [ -q ] [ -h ]\n\n", tmp_str);
|
||||
sprintf (tmp_str, "%sParametrs:\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -a - input file with aglomerates (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 with coordinates\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -l - log enable\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -q - quiet enable\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -h - show this help and exit\n", tmp_str);
|
||||
fputs (tmp_str, stdout);
|
||||
return 0;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'a'))
|
||||
// input file
|
||||
{
|
||||
strcpy (aglinp, argv[i+1]);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'i'))
|
||||
// input file
|
||||
{
|
||||
strcpy (input, argv[i+1]);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'c'))
|
||||
// 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'))
|
||||
// output file
|
||||
{
|
||||
strcpy (output, argv[i+1]);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'l'))
|
||||
// log mode
|
||||
{
|
||||
log = 1;
|
||||
strcpy (logfile, argv[i+1]);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'q'))
|
||||
// quiet mode
|
||||
{
|
||||
quiet = 1;
|
||||
}
|
||||
}
|
||||
|
||||
if (log == 1)
|
||||
f_log = fopen (logfile, "w");
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 0, argv[0]);
|
||||
print_message (quiet, stdout, log, f_log, 1, argv[0]);
|
||||
|
||||
// error check
|
||||
error = error_checking (aglinp, cell, input, output);
|
||||
if (error != 0)
|
||||
{
|
||||
print_message (quiet, stderr, log, f_log, 17, argv[0]);
|
||||
return 1;
|
||||
}
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 2, argv[0]);
|
||||
|
||||
// processing
|
||||
// initial variables
|
||||
print_message (quiet, stdout, log, f_log, 3, input);
|
||||
f_inp = fopen (input, "r");
|
||||
if (f_inp == NULL)
|
||||
{
|
||||
print_message (quiet, stderr, log, f_log, 18, input);
|
||||
return 1;
|
||||
}
|
||||
fscanf (f_inp, "%i", &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));
|
||||
// error checking
|
||||
if ((ch_type_atoms == NULL) ||
|
||||
(coords == NULL) ||
|
||||
(label_mol == NULL) ||
|
||||
(needed_mol == NULL) ||
|
||||
(tmp_int == NULL) ||
|
||||
(true_label_mol == NULL))
|
||||
{
|
||||
print_message (quiet, stderr, log, f_log, 19, argv[0]);
|
||||
return 17;
|
||||
}
|
||||
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]);
|
||||
print_message (quiet, stdout, log, f_log, 5, tmp_str);
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 6, argv[0]);
|
||||
|
||||
// reading aglomerate
|
||||
print_message (quiet, stdout, log, f_log, 7, aglinp);
|
||||
error = reading_agl (aglinp, &num_needed_mol, tmp_str, needed_mol);
|
||||
|
||||
if (error == 0)
|
||||
{
|
||||
sprintf (tmp_str, "%6cNumber of molecules in aglomerate: %i\n", num_needed_mol);
|
||||
print_message (quiet, stdout, log, f_log, 8, tmp_str);
|
||||
// reading coordinates
|
||||
print_message (quiet, stdout, log, f_log, 7, input);
|
||||
error = reading_coords (1, input, num_needed_mol, needed_mol, cell, &num_mol,
|
||||
&num_atoms, true_label_mol, label_mol, tmp_int, coords,
|
||||
ch_type_atoms);
|
||||
|
||||
// analyze
|
||||
if (error == 0)
|
||||
{
|
||||
sprintf (tmp_str, "%6cNumber of molecules: %i; %6cNumber of atoms: %i\n",
|
||||
' ', num_mol, ' ', num_atoms);
|
||||
print_message (quiet, stdout, log, f_log, 8, tmp_str);
|
||||
error =
|
||||
if (error == 0)
|
||||
{
|
||||
print_message (quiet, stderr, log, f_log, 21, argv[0]);
|
||||
error = print_structure (output, num_needed_mol, needed_mol, num_atoms,
|
||||
label_mol, ch_type_atoms, coords);
|
||||
print_message (quiet, stderr, log, f_log, 12, output);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 13, argv[0]);
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 15, argv[0]);
|
||||
// free memory
|
||||
free (ch_type_atoms);
|
||||
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]);
|
||||
|
||||
if (log == 1)
|
||||
fclose (f_log);
|
||||
return 0;
|
||||
}
|
||||
99
agl/src/messages.c
Normal file
99
agl/src/messages.c
Normal file
@ -0,0 +1,99 @@
|
||||
/* Library for printing messages at output
|
||||
*
|
||||
* Usage:
|
||||
* message (log, mode, text, output)
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
#include <time.h>
|
||||
|
||||
|
||||
int message (const int log, const int mode, const char *text, FILE *output)
|
||||
/* mode - number of message
|
||||
* text - additional text
|
||||
*/
|
||||
{
|
||||
char out[4096];
|
||||
|
||||
if (log == 1)
|
||||
{
|
||||
char time_str[256];
|
||||
time_t t = time (NULL);
|
||||
struct tm* aTm = localtime (&t);
|
||||
sprintf (time_str, "[%04d-%02d-%02d %02d:%02d:%02d] [%2i]: ", aTm->tm_year+1900,
|
||||
aTm->tm_mon+1, aTm->tm_mday, aTm->tm_hour, aTm->tm_min, aTm->tm_sec, mode);
|
||||
fputs (time_str, output);
|
||||
}
|
||||
|
||||
switch (mode)
|
||||
{
|
||||
case 0:
|
||||
sprintf (out, "Starting program: '%s'\n", text);
|
||||
break;
|
||||
case 1:
|
||||
sprintf (out, "Checking errors\n");
|
||||
break;
|
||||
case 2:
|
||||
sprintf (out, "Errors are not detected\n");
|
||||
break;
|
||||
case 3:
|
||||
sprintf (out, "Initialization of variables from file '%s'\n", text);
|
||||
break;
|
||||
case 4:
|
||||
break;
|
||||
case 5:
|
||||
sprintf (out, "Initial parametrs: \n%s", text);
|
||||
break;
|
||||
case 6:
|
||||
sprintf (out, "Processing\n");
|
||||
break;
|
||||
case 7:
|
||||
sprintf (out, "Open file: '%s'\n", text);
|
||||
break;
|
||||
case 8:
|
||||
sprintf (out, "%s", text);
|
||||
break;
|
||||
case 9:
|
||||
sprintf (out, "%6cSize of variables was changed successfully\n", ' ');
|
||||
break;
|
||||
case 10:
|
||||
sprintf (out, "%6cConnectivity matrix was created successfully\n", ' ');
|
||||
break;
|
||||
case 11:
|
||||
sprintf (out, "%6cConnectivity matrix was processed successfully\n", ' ');
|
||||
break;
|
||||
case 12:
|
||||
sprintf (out, "%6cResult was printed to file '%s' successfully\n", ' ', text);
|
||||
break;
|
||||
case 13:
|
||||
sprintf (out, "End of processing\n");
|
||||
break;
|
||||
case 14:
|
||||
sprintf (out, "Printing summary statistic to file '%s'\n", text);
|
||||
break;
|
||||
case 15:
|
||||
sprintf (out, "Free memory\n");
|
||||
break;
|
||||
case 16:
|
||||
sprintf (out, "Exiting without errors\n");
|
||||
break;
|
||||
case 17:
|
||||
sprintf (out, "Something wrong!\nSee '%s -h' for more details\n", text);
|
||||
break;
|
||||
case 18:
|
||||
sprintf (out, "File '%s' not found\nError\n", text);
|
||||
break;
|
||||
case 19:
|
||||
sprintf (out, "Memory error\n");
|
||||
break;
|
||||
case 20:
|
||||
sprintf (out, "%6cCenter of molecules was set successfully\n", ' ');
|
||||
break;
|
||||
case 21:
|
||||
sprintf (out, "%6cEnvironment was selected successfully\n", ' ');
|
||||
break;
|
||||
}
|
||||
|
||||
fputs (out, output);
|
||||
return 0;
|
||||
}
|
||||
58
agl/src/print_struct.c
Normal file
58
agl/src/print_struct.c
Normal file
@ -0,0 +1,58 @@
|
||||
/* Library for printing structure to pdb file
|
||||
*
|
||||
* Usage:
|
||||
* print_structure (output, num_needed_mol, needed_mol, num_atoms,
|
||||
* label_mol, char_type_atoms, coords)
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
|
||||
|
||||
int print_structure (const char *output, const int num_needed_mol, const int *needed_mol,
|
||||
const int num_atoms, const int *label_mol, const char *ch_type_atoms,
|
||||
const float *coords)
|
||||
/* output - output file name
|
||||
* num_needed_mol - number of needed molecules
|
||||
* needed_mol - massive of needed molecules
|
||||
* num_atoms - number of atoms
|
||||
* label_mol - massive of numbers of molecule for atoms
|
||||
* ch_type_atoms - massive of char types for atoms
|
||||
* coords - massive of coordinates
|
||||
*/
|
||||
{
|
||||
int cur_atom, cur_atom_num, cur_mol, i, j;
|
||||
FILE *f_out;
|
||||
/* cur_atom - current atom
|
||||
* cur_atom_num - true atom number
|
||||
* cur_mol - current molecule
|
||||
*/
|
||||
|
||||
cur_atom = 1;
|
||||
f_out = fopen (output, "w");
|
||||
|
||||
for (i=0; i<num_needed_mol; i++)
|
||||
for (j=0; j<8*num_atoms; j++)
|
||||
{
|
||||
if (j < num_atoms)
|
||||
{
|
||||
cur_mol = 0;
|
||||
cur_atom_num = j;
|
||||
}
|
||||
else
|
||||
{
|
||||
cur_mol = ((j - num_atoms) % 7) + 1;
|
||||
cur_atom_num = (j - num_atoms) / 7;
|
||||
}
|
||||
if (needed_mol[i] == (8*label_mol[j]+cur_mol))
|
||||
{
|
||||
fprintf(f_out, "ATOM %5i %c%c MOL %4i %8.3f%8.3f%8.3f\n", cur_atom,
|
||||
ch_type_atoms[2*cur_atom_num+0], ch_type_atoms[2*cur_atom_num+1],
|
||||
i+1, coords[3*j+0], coords[3*j+1], coords[3*j+2]);
|
||||
cur_atom++;
|
||||
}
|
||||
}
|
||||
|
||||
fclose (f_out);
|
||||
|
||||
return 0;
|
||||
}
|
||||
33
agl/src/read_agl.c
Normal file
33
agl/src/read_agl.c
Normal file
@ -0,0 +1,33 @@
|
||||
/* Library for reading aglomerate from statgen-file
|
||||
*
|
||||
* Usage:
|
||||
* reading_agl (aglinput, &num_needed_mol, agl_class, needed_mol)
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
|
||||
|
||||
int reading_agl (const char *aglinp, int *num_needed_mol, char *agl_class, int *needed_mol)
|
||||
/* aglinp - input file with aglomerate
|
||||
* num_needed_mol - number of needed molecules
|
||||
* agl_class - aglomerate class
|
||||
* needed_mol - massive of needed molecules
|
||||
*/
|
||||
{
|
||||
char connect[256], tmp_str[256];
|
||||
int i;
|
||||
FILE *f_agl;
|
||||
|
||||
f_agl = fopen (aglinp, "r");
|
||||
|
||||
fgets (tmp_str, 256, f_agl);
|
||||
sscanf (tmp_str, "AGL=%i=%s", num_needed_mol, agl_class);
|
||||
for (i=0; i<*num_needed_mol; i++)
|
||||
{
|
||||
fgets (tmp_str, 256, f_agl);
|
||||
sscanf (tmp_str, "%i=%s", &needed_mol[i], connect);
|
||||
}
|
||||
fclose (f_agl);
|
||||
|
||||
return 0;
|
||||
}
|
||||
59
agl/src/select_mol.c
Normal file
59
agl/src/select_mol.c
Normal file
@ -0,0 +1,59 @@
|
||||
/* Library for select molecules in translations
|
||||
*
|
||||
* Usage:
|
||||
*
|
||||
*/
|
||||
|
||||
#include <math.h>
|
||||
|
||||
|
||||
int select_molecule (const int num_atoms, const int *label_mol, const int *true_label_mol, const float *coords, const int num_needed_mol, int *needed_mol)
|
||||
{
|
||||
float r, ref[3], rmin;
|
||||
int i, j, k, *old_needed_mol;
|
||||
|
||||
old_needed_mol = (int *) malloc (num_needed_mol * sizeof (int));
|
||||
if (old_needed_mol == NULL)
|
||||
return 1;
|
||||
|
||||
// set first molecule
|
||||
ref_mol = old_needed_mol[0];
|
||||
needed_mol[0] = 0;
|
||||
k = 1;
|
||||
for (i=0; i<3; i++)
|
||||
ref[i] = coords[3*0+i];
|
||||
|
||||
for (i=1; i<num_needed_mol; i++)
|
||||
for (j=0; j<8*num_atoms; j++)
|
||||
if (old_needed_mol[i] == true_label_mol[label_mol[j]])
|
||||
{
|
||||
if (j < num_atoms)
|
||||
cur_mol = 0;
|
||||
else
|
||||
cur_mol = ((j - num_atoms) % 7) + 1;
|
||||
// for (j=0; j<3; j++)
|
||||
// centr_coords[3*(8*label_mol[i]+cur_mol)+j] += coords[3*i+j];
|
||||
}
|
||||
|
||||
for (i=1; i<num_needed_mol; i++)
|
||||
for (j=0; j<num_atoms; j++)
|
||||
if (old_needed_mol[i] == true_label_mol[label_mol[j]])
|
||||
{
|
||||
if (ref_mol != true_label_mol[label_mol[j]])
|
||||
{
|
||||
ref_i = j;
|
||||
rmin = sqrt (pow ((coords[3*j+0] - ref[0]), 2) + \
|
||||
pow ((coords[3*j+1] - ref[1]), 2) + \
|
||||
pow ((coords[3*j+2] - ref[2]), 2));
|
||||
ref_mol = true_label_mol[label_mol[j]];
|
||||
}
|
||||
else
|
||||
{
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
free (old_needed_mol);
|
||||
|
||||
return 0;
|
||||
}
|
||||
@ -9,16 +9,16 @@ message (STATUS ${${PROJECT}_VERSION})
|
||||
# main files
|
||||
set (MAIN_SOURCES main)
|
||||
# not public srcs
|
||||
set (PRIVATE_CLASSES)
|
||||
set (PRIVATE_CLASSES add_main
|
||||
coords
|
||||
envir_search
|
||||
messages
|
||||
print_struct
|
||||
set_center)
|
||||
# headers only files
|
||||
SET (HEADERS_ONLY)
|
||||
# public srcs
|
||||
set (PUBLIC_CLASSES add_main
|
||||
coords
|
||||
envir_search
|
||||
messages
|
||||
print_struct
|
||||
set_center)
|
||||
set (PUBLIC_CLASSES)
|
||||
# public headers
|
||||
set (PUBLIC_HEADERS)
|
||||
# shared libraries
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
|
||||
#include <stdio.h>
|
||||
|
||||
// #include "messages.h"
|
||||
#include "messages.h"
|
||||
|
||||
|
||||
int error_checking (const float *cell, const char *input, const char *output)
|
||||
|
||||
@ -15,8 +15,10 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
int *num_atoms, int *true_label_mol, int *label_mol,
|
||||
int *type_atoms, float *coords, char *ch_type_atoms)
|
||||
/* filename - name of file with coordinates
|
||||
* type_inter - type interaction (number of molecules for interaction)
|
||||
* label_atom - types of atom for interaction
|
||||
* type_inter - type interaction (number of molecules for interaction)
|
||||
* (number of molecules in aglomerate for agl)
|
||||
* label_atom - types of atom for interaction
|
||||
* (molecules in aglomerate for agl)
|
||||
* cell - cell dimension
|
||||
* num_mol - number of molecules for writing coordinates
|
||||
* num_atoms - number of atoms for writing coordinates
|
||||
@ -83,7 +85,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
}
|
||||
break;
|
||||
case 1:
|
||||
// for envir
|
||||
// for envir and frad
|
||||
not_tr_coords[3**num_atoms+0] = cur_coords[0];
|
||||
not_tr_coords[3**num_atoms+1] = cur_coords[1];
|
||||
not_tr_coords[3**num_atoms+2] = cur_coords[2];
|
||||
@ -101,6 +103,29 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
|
||||
*num_atoms = *num_atoms + 1;
|
||||
break;
|
||||
case 2:
|
||||
// for agl
|
||||
for (j=0; j<type_inter; j++)
|
||||
if (cur_mol == label_atom[j])
|
||||
{
|
||||
not_tr_coords[3**num_atoms+0] = cur_coords[0];
|
||||
not_tr_coords[3**num_atoms+1] = cur_coords[1];
|
||||
not_tr_coords[3**num_atoms+2] = cur_coords[2];
|
||||
ch_type_atoms[2**num_atoms+0] = at_symb[0];
|
||||
ch_type_atoms[2**num_atoms+1] = at_symb[1];
|
||||
|
||||
if (ref_mol != cur_mol)
|
||||
{
|
||||
ref_mol = cur_mol;
|
||||
true_label_mol[*num_mol] = ref_mol;
|
||||
*num_mol = *num_mol + 1;
|
||||
}
|
||||
label_mol[*num_atoms] = *num_mol - 1;
|
||||
type_atoms[*num_atoms] = j;
|
||||
|
||||
*num_atoms = *num_atoms + 1;
|
||||
}
|
||||
break;
|
||||
default: return 1;
|
||||
}
|
||||
}
|
||||
|
||||
@ -22,6 +22,7 @@ int search_envir (const int num_of_mol, const int num_mol, const float *centr_co
|
||||
int i;
|
||||
/* r - radius
|
||||
*/
|
||||
|
||||
*num_needed_mol = 0;
|
||||
|
||||
for (i=0; i<8*num_mol; i++)
|
||||
|
||||
@ -3,12 +3,12 @@
|
||||
#include <stdlib.h>
|
||||
#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 "add_main.h"
|
||||
#include "coords.h"
|
||||
#include "envir_search.h"
|
||||
#include "messages.h"
|
||||
#include "print_struct.h"
|
||||
#include "set_center.h"
|
||||
|
||||
|
||||
int main(int argc, char *argv[])
|
||||
|
||||
@ -1,7 +1,8 @@
|
||||
cmake_minimum_required (VERSION 2.8)
|
||||
|
||||
cmake_policy(SET CMP0011 NEW)
|
||||
cmake_policy(SET CMP0003 OLD)
|
||||
cmake_policy(SET CMP0011 NEW)
|
||||
cmake_policy(SET CMP0015 NEW)
|
||||
|
||||
# set project name
|
||||
set (PROJECT statgen)
|
||||
@ -28,4 +29,4 @@ set (LIBRARIES)
|
||||
set (TARGETS "")
|
||||
set (HEADERS "")
|
||||
|
||||
add_subdirectory (src)
|
||||
add_subdirectory (${${PROJECT}_SOURCE_DIR})
|
||||
61
statgen/about.dox
Normal file
61
statgen/about.dox
Normal file
@ -0,0 +1,61 @@
|
||||
/*! @mainpage statgen
|
||||
*
|
||||
* @section intro_sec Introduction
|
||||
*
|
||||
* <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>
|
||||
* statgen -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -r ... -o OUTPUT [ -g DEPTH ]
|
||||
* [ -l LOGFILE ] [ -q ] [ -h ]
|
||||
*
|
||||
* Parametrs:
|
||||
* -i - mask of input files
|
||||
* -s - trajectory steps (integer)
|
||||
* -c - cell size (float), A
|
||||
* -a - atom types (integer). Format: 'ATOM1' or 'ATOM1,ATOM2' or etc
|
||||
* -r - criteria (float), A. Format: '0-0:2.4,0-1:3.0' means 0-0-interaction
|
||||
* (<2.4 A) and 0-1 (<3.0) are needed. This flag can be used multiple times
|
||||
* -o - output file name
|
||||
* -g - check graph isomorphism. DEPTH is max depth for check cycles (>= 3)
|
||||
* -l - log enable
|
||||
* -q - quiet enable
|
||||
* -h - show this help and exit
|
||||
* </pre>
|
||||
*
|
||||
* @page Install
|
||||
*
|
||||
* @section Requirements Requirements
|
||||
* The application statgen 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.1.0.1 (2013-07-27)
|
||||
* * initial release
|
||||
*/
|
||||
BIN
statgen/logo.png
Executable file
BIN
statgen/logo.png
Executable file
Binary file not shown.
|
After Width: | Height: | Size: 3.4 KiB |
@ -3,62 +3,27 @@ set ("${PROJECT}_VERSION_MINOR" 0)
|
||||
set ("${PROJECT}_VERSION_PATCH" 1)
|
||||
set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
|
||||
|
||||
message (STATUS ${${PROJECT}_VERSION})
|
||||
message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
|
||||
|
||||
## set files
|
||||
# main files
|
||||
set (MAIN_SOURCES main)
|
||||
# not public srcs
|
||||
set (PRIVATE_CLASSES)
|
||||
# headers only files
|
||||
SET (HEADERS_ONLY)
|
||||
# public srcs
|
||||
set (PUBLIC_CLASSES add_main
|
||||
coords
|
||||
graph
|
||||
int2char
|
||||
messages
|
||||
stat_print
|
||||
stat_select
|
||||
stat_sort
|
||||
summary_stat)
|
||||
# public headers
|
||||
set (PUBLIC_HEADERS)
|
||||
# shared libraries
|
||||
# set files
|
||||
aux_source_directory (. SOURCES)
|
||||
|
||||
# set library
|
||||
if (CMAKE_COMPILER_IS_GNUCXX)
|
||||
set (ADDITIONAL_LIB m)
|
||||
else ()
|
||||
set (ADDITIONAL_LIB)
|
||||
endif()
|
||||
set (SOURCES)
|
||||
|
||||
# append list
|
||||
foreach (class ${PRIVATE_CLASSES})
|
||||
LIST (APPEND SOURCES ${class}.c)
|
||||
LIST (APPEND HEADERS ${class}.h)
|
||||
endforeach ()
|
||||
|
||||
foreach (class ${HEADERS_ONLY})
|
||||
LIST (APPEND HEADERS ${class}.h)
|
||||
endforeach ()
|
||||
|
||||
foreach (class ${PUBLIC_CLASSES})
|
||||
LIST (APPEND SOURCES ${class}.c)
|
||||
LIST (APPEND HEADERS ../include/${PROJECT}/${class}.h)
|
||||
LIST (APPEND PUBLIC_HEADERS ../include/${PROJECT}/${class}.h)
|
||||
endforeach ()
|
||||
|
||||
# message
|
||||
message (STATUS "SOURCES: ${SOURCES}")
|
||||
|
||||
# link libraries and compile
|
||||
add_executable (${PROJECT} ${MAIN_SOURCES} ${SOURCES})
|
||||
add_executable (${PROJECT} ${SOURCES})
|
||||
target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
|
||||
|
||||
# install properties
|
||||
INSTALL (TARGETS ${PROJECT}
|
||||
DESTINATION bin)
|
||||
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
|
||||
if (ADD_INCLUDE)
|
||||
INSTALL (FILES ${PUBLIC_HEADERS}
|
||||
DESTINATION include/${PROJECT})
|
||||
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
|
||||
endif ()
|
||||
@ -1,14 +1,43 @@
|
||||
/* Additional library for main.c (statgen)
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
|
||||
// #include "messages.h"
|
||||
#include "messages.h"
|
||||
|
||||
|
||||
/**
|
||||
* @fn error_checking
|
||||
*/
|
||||
int error_checking (const float *cell, const int from, const char *input,
|
||||
const int max_depth, const int num_of_inter, const char *output,
|
||||
const int to, const int type_inter)
|
||||
/**
|
||||
* @brief function that checks errors in input variables
|
||||
* @code
|
||||
* error_checking (cell, from, input, max_depth, num_of_inter, output, to,
|
||||
* type_inter);
|
||||
* @endcode
|
||||
*
|
||||
* @param cell massive of cell size
|
||||
* @param from first trajectory step
|
||||
* @param input mask of trajectory files
|
||||
* @param max_depth max depth for check cycles in graph analyze
|
||||
* @param num_of_inter number of different interactions
|
||||
* @param output output file name
|
||||
* @param to last trajectory step
|
||||
* @param type_inter number of atoms for interactions
|
||||
*
|
||||
* @return 11 - error in 'type_inter'
|
||||
* @return 12 - error in 'cell'
|
||||
* @return 13 - error in 'to' or 'from'
|
||||
* @return 14 - error in 'num_of_inter'
|
||||
* @return 15 - error in 'input'
|
||||
* @return 16 - error in 'output'
|
||||
* @return 19 - error in 'max_depth'
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
if ((type_inter == 0) || (type_inter > 4))
|
||||
return 11;
|
||||
@ -29,10 +58,35 @@ int error_checking (const float *cell, const int from, const char *input,
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* @fn printing_head
|
||||
*/
|
||||
int printing_head (const char *output, const int log, const int quiet,
|
||||
const char *input, const int from, const int to, const float *cell,
|
||||
const int type_inter, const int *label_atom,
|
||||
const int num_of_inter, const float *crit, const int max_depth)
|
||||
/**
|
||||
* @brief function that prints header in output file
|
||||
* @code
|
||||
* printing_head (output, log, quiet, input, from, to, cell, type_inter, label_atom,
|
||||
* num_of_inter, crit, max_depth);
|
||||
* @endcode
|
||||
*
|
||||
* @param output output file nams
|
||||
* @param log status of log-mode
|
||||
* @param quiet status of quiet-mode
|
||||
* @param input mask of trajectory files
|
||||
* @param from first trajectory step
|
||||
* @param to last trajectory step
|
||||
* @param cell massive of cell size
|
||||
* @param type_inter number of atoms for interactions
|
||||
* @param label_atom massive of atom types for interactions
|
||||
* @param num_of_inter number of different interactions
|
||||
* @param crit massive of criteria
|
||||
* @param max_depth maximum depth for check cycles in graph analyze
|
||||
*
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
int i, j;
|
||||
FILE *f_out;
|
||||
@ -65,9 +119,26 @@ int printing_head (const char *output, const int log, const int quiet,
|
||||
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)
|
||||
/**
|
||||
* @brief function that prints message in log and stdout
|
||||
* @code
|
||||
* print_message (quiet, stdout, log, f_log, 0, str);
|
||||
* @endcode
|
||||
*
|
||||
* @param quiet status of quiet-mode
|
||||
* @param std_output stdout
|
||||
* @param log status of log-mode
|
||||
* @param f_log log file
|
||||
* @param mode number of message in "messages.c"
|
||||
* @param str additional text in message
|
||||
*
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
if ((quiet != 1) && (std_output != stderr))
|
||||
message (0, mode, str, std_output);
|
||||
@ -78,8 +149,31 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* @fn set_defaults
|
||||
*/
|
||||
int set_defaults (float *cell, int *from, char *input, int *log, int *max_depth,
|
||||
int *num_of_inter, char *output, int *to, int *type_inter, int *quiet)
|
||||
/**
|
||||
* @brief function for set default values of variables
|
||||
* @code
|
||||
* set_defaults (cell, &from, input, &log, &max_depth, &num_of_inter, output, &to,
|
||||
* &type_inter, &quiet);
|
||||
* @endcode
|
||||
*
|
||||
* @param cell massive of cell size
|
||||
* @param from first trajectory step
|
||||
* @param input mask of trajectory files
|
||||
* @param log status of log-mode
|
||||
* @param max_depth maximum depth for check cycles in graph analyze
|
||||
* @param num_of_inter number of different interactions
|
||||
* @param output output file name
|
||||
* @param to last trajectory step
|
||||
* @param type_inter number of atoms for interactions
|
||||
* @param quiet status of quiet-mode
|
||||
*
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
int i;
|
||||
|
||||
|
||||
@ -1,6 +1,23 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef ADD_MAIN_H
|
||||
#define ADD_MAIN_H
|
||||
|
||||
/**
|
||||
* @fn error_checking
|
||||
*/
|
||||
/**
|
||||
* @fn printing_head
|
||||
*/
|
||||
/**
|
||||
* @fn print_message
|
||||
*/
|
||||
/**
|
||||
* @fn set_defaults
|
||||
*/
|
||||
|
||||
int error_checking (const float *, const int, const char *, const int, const int,
|
||||
const char *, const int, const int);
|
||||
int printing_head (const char *, const int, const int, const char *, const int,
|
||||
@ -1,50 +1,68 @@
|
||||
/* Library for reading coordinates from input file
|
||||
*
|
||||
* Usage:
|
||||
* reading_coords (mode, filename, type_interaction, labels,
|
||||
* cell, &number_of_molecules, &number_of_atoms, true_label_molecule,
|
||||
* label_molecule, type_atoms, coords, char_type_atoms)
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
|
||||
|
||||
/**
|
||||
* @fn reading_coords
|
||||
*/
|
||||
int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
const int *label_atom, const float *cell, int *num_mol,
|
||||
int *num_atoms, int *true_label_mol, int *label_mol,
|
||||
int *type_atoms, float *coords, char *ch_type_atoms)
|
||||
/* filename - name of file with coordinates
|
||||
* type_inter - type interaction (number of molecules for interaction)
|
||||
* label_atom - types of atom for interaction
|
||||
* cell - cell dimension
|
||||
* num_mol - number of molecules for writing coordinates
|
||||
* num_atoms - number of atoms for writing coordinates
|
||||
* true_label_mol - massive of true numbers of molecule for atoms
|
||||
* label_mol - massive of numbers of molecule for atoms
|
||||
* type_atoms - massive of atom types for atoms
|
||||
* coords - massive of coordinates
|
||||
* ch_type_atoms - massive of char types for atoms
|
||||
/**
|
||||
* @brief function that reads coordinates from special file format
|
||||
* @code
|
||||
* reading_coords (0, filename, type_inter, label_atom, cell, &num_mol,
|
||||
* &num_atoms, true_label_mol, label_mol, type_atoms,
|
||||
* coords, ch_type_atoms);
|
||||
* @endcode
|
||||
*
|
||||
* @param mode mode of reading; '1' is statgen, '2' is envir or
|
||||
* frad, '3' 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 cell massive of cell size
|
||||
* @param num_mol number of molecules
|
||||
* @param num_atoms number of atoms
|
||||
* @param true_label_mol massive of true numbers of molecule for atoms
|
||||
* @param label_mol massive of numbers of molecule for atoms
|
||||
* @param type_atoms massive of atom types
|
||||
* @param coords massive of coordinates
|
||||
* @param ch_type_atoms massive of char atom types
|
||||
*
|
||||
* @return 1 - file $filename does not exist
|
||||
* @return 2 - unknown mode
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
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], *not_tr_coords, ref[3];
|
||||
FILE *inp;
|
||||
/* cur_*, at_symb - temp variables
|
||||
* file_string - temp string variable
|
||||
* atoms - total number of atoms in system
|
||||
* tr_num_atoms - number of translated atoms for writing coordinates (m.b. 8*num_atoms)
|
||||
* ref_mol - number of molecule for reference
|
||||
* not_tr_coords - not translated coordinates
|
||||
* ref - coordinates of reference molecule
|
||||
* inp - file with input data
|
||||
|
||||
/* cur_* temp variables
|
||||
* at_symb temp variable
|
||||
* file_string temp string variable
|
||||
* atoms total number of atoms in system
|
||||
* tr_num_atoms number of translated atoms (must be 8*num_atoms)
|
||||
* ref_mol number of molecule for reference in translation
|
||||
* not_tr_coords massive of not translated coordinates
|
||||
* ref massive of coordinates of reference molecule
|
||||
* inp input file
|
||||
*/
|
||||
|
||||
/// <b>Work blocks</b>
|
||||
|
||||
*num_atoms = 0;
|
||||
*num_mol = 0;
|
||||
|
||||
// Reading file
|
||||
/// <pre> reading file </pre>
|
||||
inp = fopen (filename, "r");
|
||||
if (inp == NULL)
|
||||
return 1;
|
||||
@ -59,10 +77,11 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
sscanf (file_string, "%i%s%f%f%f%i%i", &cur_at_num, at_symb, &cur_coords[0],
|
||||
&cur_coords[1], &cur_coords[2], &cur_at_type, &cur_mol);
|
||||
|
||||
// reading variables according to selected mode
|
||||
switch (mode)
|
||||
{
|
||||
case 0:
|
||||
// for statgen
|
||||
// mode == 0 (selected atoms)
|
||||
for (j=0; j<type_inter; j++)
|
||||
if (cur_at_type == label_atom[j])
|
||||
{
|
||||
@ -83,7 +102,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
}
|
||||
break;
|
||||
case 1:
|
||||
// for envir
|
||||
// mode == 1 (all atoms)
|
||||
not_tr_coords[3**num_atoms+0] = cur_coords[0];
|
||||
not_tr_coords[3**num_atoms+1] = cur_coords[1];
|
||||
not_tr_coords[3**num_atoms+2] = cur_coords[2];
|
||||
@ -101,18 +120,41 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
|
||||
*num_atoms = *num_atoms + 1;
|
||||
break;
|
||||
default: return 1;
|
||||
case 2:
|
||||
// mode == 2 (selected molecules)
|
||||
for (j=0; j<type_inter; j++)
|
||||
if (cur_mol == label_atom[j])
|
||||
{
|
||||
not_tr_coords[3**num_atoms+0] = cur_coords[0];
|
||||
not_tr_coords[3**num_atoms+1] = cur_coords[1];
|
||||
not_tr_coords[3**num_atoms+2] = cur_coords[2];
|
||||
ch_type_atoms[2**num_atoms+0] = at_symb[0];
|
||||
ch_type_atoms[2**num_atoms+1] = at_symb[1];
|
||||
|
||||
if (ref_mol != cur_mol)
|
||||
{
|
||||
ref_mol = cur_mol;
|
||||
true_label_mol[*num_mol] = ref_mol;
|
||||
*num_mol = *num_mol + 1;
|
||||
}
|
||||
label_mol[*num_atoms] = *num_mol - 1;
|
||||
type_atoms[*num_atoms] = j;
|
||||
|
||||
*num_atoms = *num_atoms + 1;
|
||||
}
|
||||
break;
|
||||
default: return 2;
|
||||
}
|
||||
}
|
||||
fclose (inp);
|
||||
|
||||
// Translation
|
||||
/// <pre> translation </pre>
|
||||
tr_num_atoms = *num_atoms;
|
||||
for (i=0; i<*num_atoms; i++)
|
||||
for (j=0; j<3; j++)
|
||||
coords[3*i+j] = not_tr_coords[3*i+j];
|
||||
|
||||
// Assign initial value to reference coordinates
|
||||
// assign initial value to reference coordinates
|
||||
ref_mol = label_mol[0];
|
||||
for (i=0; i<3; i++)
|
||||
ref[i] = coords[3*0+i];
|
||||
@ -129,7 +171,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
for (x=0; x<3; x++)
|
||||
{
|
||||
if (ref[x] >= 0.0)
|
||||
// if xyz >= 0.0 A
|
||||
// if xyz >= 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if (j == x)
|
||||
@ -142,7 +184,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
tr_num_atoms++;
|
||||
}
|
||||
else
|
||||
// if xyz < 0.0 A
|
||||
// if xyz < 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if (j == x)
|
||||
@ -161,7 +203,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
for (y=x+1; y<3; y++)
|
||||
{
|
||||
if ((ref[x] >= 0.0) && (ref[y] >= 0.0))
|
||||
// if xyz and xyz >= 0.0 A
|
||||
// if xyz and xyz >= 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if ((j == x) || (j == y))
|
||||
@ -175,7 +217,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
}
|
||||
|
||||
if ((ref[x] < 0.0) && (ref[y] < 0.0))
|
||||
// if xyz and xyz < 0.0 A
|
||||
// if xyz and xyz < 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if ((j == x) || (j == y))
|
||||
@ -191,7 +233,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
|
||||
for (y=0; y<3; y++)
|
||||
if ((ref[x] < 0.0) && (ref[y] >= 0.0))
|
||||
// if xyz OR xyz >= 0.0
|
||||
// if xyz OR xyz >= 0.0
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
{
|
||||
@ -210,7 +252,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
|
||||
// if x and y and z >= 0.0 A
|
||||
// if x and y and z >= 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
@ -222,7 +264,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
|
||||
// if x and y >= 0.0 A and z < 0.0 A
|
||||
// if x and y >= 0.0 A and z < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
@ -234,7 +276,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
|
||||
// if x and z >= 0.0 A and y < 0.0 A
|
||||
// if x and z >= 0.0 A and y < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
@ -246,7 +288,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
|
||||
// if y and z >= 0.0 A and x < 0.0 A
|
||||
// if y and z >= 0.0 A and x < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
@ -258,7 +300,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
|
||||
// if x and y < 0.0 A and z >= 0.0 A
|
||||
// if x and y < 0.0 A and z >= 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
@ -270,7 +312,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
|
||||
// if x and z < 0.0 A and y >= 0.0 A
|
||||
// if x and z < 0.0 A and y >= 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
@ -282,7 +324,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
|
||||
// if x >= 0.0 A and y and z < 0.0 A
|
||||
// if x >= 0.0 A and y and z < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
@ -294,7 +336,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
|
||||
// if x and y and z < 0.0 A
|
||||
// if x and y and z < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
@ -306,7 +348,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
}
|
||||
}
|
||||
|
||||
// free memory
|
||||
/// <pre> free memory </pre>
|
||||
free (not_tr_coords);
|
||||
|
||||
return 0;
|
||||
|
||||
@ -1,6 +1,14 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef COORDS_H
|
||||
#define COORDS_H
|
||||
|
||||
/**
|
||||
* @fn reading_coords
|
||||
*/
|
||||
|
||||
int reading_coords (const int, const char *, const int, const int *,
|
||||
const float *, int *, int *, int *, int *, int *, float *,
|
||||
char *);
|
||||
@ -1,46 +1,77 @@
|
||||
/* Library for graph structure analyze
|
||||
* Usage:
|
||||
* graph_analyze (N, connect, max_depth, isomorphism_class)
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <math.h>
|
||||
#include <stdlib.h>
|
||||
|
||||
|
||||
/**
|
||||
* @fn check_cycle
|
||||
*/
|
||||
int check_cycle (const int N, const int *pn)
|
||||
// function to return number of cycles
|
||||
/**
|
||||
* @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 cycle, i;
|
||||
/* cycle - number of cycle
|
||||
/* cycle number of cycle
|
||||
*/
|
||||
|
||||
cycle = 0;
|
||||
for (i=1; i<N; i++)
|
||||
cycle += i*pn[i];
|
||||
|
||||
// for linear (0.5*cycle == N-1)
|
||||
// for linear (0.5*cycle == N-1)
|
||||
cycle = 0.5 * cycle - (N - 1);
|
||||
|
||||
return cycle;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* @fn check_cycle_size
|
||||
*/
|
||||
int check_cycle_size (const int N, const int *matrix, const int depth, int *n_cycle)
|
||||
// function to return number of cycles of certain size
|
||||
/**
|
||||
* @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 cur_N, cycle, i, j, k, n, p, *vertex;
|
||||
/* cur_N - current number of elements in submatrix
|
||||
* cycle - if (cycle == 1) that cycle exist
|
||||
* n - number of samples
|
||||
* vertex - vertexes of subgraph
|
||||
/* cur_N current number of elements in submatrix
|
||||
* cycle if (cycle == 1) that cycle exist
|
||||
* n number of samples
|
||||
* vertex vertexes of subgraph
|
||||
*/
|
||||
|
||||
vertex = (int *) malloc (N * sizeof (int));
|
||||
if (vertex == NULL)
|
||||
return 1;
|
||||
for (i=0; i<depth-2; i++)
|
||||
n_cycle[i] = 0;
|
||||
|
||||
// matrix generation from
|
||||
// http://wincode.org/acm-icpc/subsets-generation
|
||||
// matrix generation from
|
||||
// http://wincode.org/acm-icpc/subsets-generation
|
||||
n = pow (2, N);
|
||||
for (i=0; i<n; i++)
|
||||
{
|
||||
@ -54,7 +85,7 @@ int check_cycle_size (const int N, const int *matrix, const int depth, int *n_cy
|
||||
|
||||
if ((cur_N > 2) && (cur_N <= depth))
|
||||
{
|
||||
// copy connectivity matrix
|
||||
// copy connectivity matrix
|
||||
cycle = 1;
|
||||
for (j=0; j<cur_N; j++)
|
||||
{
|
||||
@ -65,7 +96,7 @@ int check_cycle_size (const int N, const int *matrix, const int depth, int *n_cy
|
||||
cycle = 0;
|
||||
}
|
||||
|
||||
// analyze subgraph
|
||||
// analyze subgraph
|
||||
if (cycle == 1)
|
||||
n_cycle[cur_N-3]++;
|
||||
}
|
||||
@ -77,32 +108,56 @@ int check_cycle_size (const int N, const int *matrix, const int depth, int *n_cy
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* @fn check_tail
|
||||
*/
|
||||
int check_tail (const int *pn)
|
||||
// function to return number of tails
|
||||
/**
|
||||
* @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
|
||||
*/
|
||||
{
|
||||
return pn[1];
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* @fn graph_analyze
|
||||
*/
|
||||
int graph_analyze (const int N, const int *matrix, const int max_depth, int *iso)
|
||||
/* N - number of vertex in graph
|
||||
* matrix - connectivity matrix
|
||||
* max_depth - maximum depth for check_cycle_size
|
||||
* iso - isomorphism class
|
||||
/**
|
||||
* @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 depth, i, j, *n_cycle, p, *pn;
|
||||
/* depth - depth for check_cycle_size
|
||||
* n_cycle - number of cycle
|
||||
* p - current weight
|
||||
* pn - total weight
|
||||
/* depth depth of search for check_cycle_size
|
||||
* n_cycle number of cycle
|
||||
* p current weight
|
||||
* pn massive of number of vertexes with weight equals to i
|
||||
*/
|
||||
|
||||
if (max_depth > N)
|
||||
depth = N;
|
||||
else
|
||||
depth = max_depth;
|
||||
// convert to matrix of weight
|
||||
// convert to matrix of weight
|
||||
pn = (int *) malloc (N * sizeof (int));
|
||||
n_cycle = (int *) malloc ((depth - 2) * sizeof (int));
|
||||
if ((pn == NULL) ||
|
||||
@ -129,6 +184,7 @@ int graph_analyze (const int N, const int *matrix, const int max_depth, int *iso
|
||||
iso[i+2] = n_cycle[i];
|
||||
}
|
||||
|
||||
// free memory
|
||||
free (n_cycle);
|
||||
free (pn);
|
||||
|
||||
|
||||
@ -1,6 +1,23 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef GRAPH_H
|
||||
#define GRAPH_H
|
||||
|
||||
/**
|
||||
* @fn graph_analyze
|
||||
*/
|
||||
/**
|
||||
* @fn check_cycle
|
||||
*/
|
||||
/**
|
||||
* @fn check_cycle_size
|
||||
*/
|
||||
/**
|
||||
* @fn check_tail
|
||||
*/
|
||||
|
||||
int graph_analyze (const int, const int *, const int, int *);
|
||||
int check_cycle (const int, const int *);
|
||||
int check_cycle_size (const int, const int *, const int, int *);
|
||||
@ -1,12 +1,22 @@
|
||||
/* Library for converting integer to string
|
||||
* Usage
|
||||
* char = conv (number, position)
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
|
||||
/**
|
||||
* @fn conv
|
||||
*/
|
||||
char conv (const int fnumb, const int dig_pos)
|
||||
/* fnumb - integer
|
||||
* dig_pos - position
|
||||
/**
|
||||
* @brief function that converts from integer to char
|
||||
* @code
|
||||
* char = conv (N, 0);
|
||||
* @endcode
|
||||
*
|
||||
* @param fnumb integer
|
||||
* @param dig_pos position: ones=1, decimals=2, hundreds=3
|
||||
*
|
||||
* @return char
|
||||
*/
|
||||
{
|
||||
int d, h, o;
|
||||
|
||||
@ -1,6 +1,14 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef INT2CHAR_H
|
||||
#define INT2CHAR_H
|
||||
|
||||
/**
|
||||
* @fn conv
|
||||
*/
|
||||
|
||||
char conv (const int, const int);
|
||||
|
||||
#endif /* INT2CHAR_H */
|
||||
@ -1,17 +1,21 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include <time.h>
|
||||
|
||||
// #include "add_main.h"
|
||||
// #include "coords.h"
|
||||
// #include "int2char.h"
|
||||
// #include "messages.h"
|
||||
// #include "stat_print.h"
|
||||
// #include "stat_select.h"
|
||||
// #include "stat_sort.h"
|
||||
// #include "summary_stat.h"
|
||||
#include "add_main.h"
|
||||
#include "coords.h"
|
||||
#include "int2char.h"
|
||||
#include "messages.h"
|
||||
#include "stat_print.h"
|
||||
#include "stat_select.h"
|
||||
#include "stat_sort.h"
|
||||
#include "summary_stat.h"
|
||||
|
||||
|
||||
int main (int argc, char *argv[])
|
||||
@ -26,40 +30,40 @@ int main (int argc, char *argv[])
|
||||
int *agl, *connect, from, *label_atom, *label_mol, log, max_depth, num_atoms,
|
||||
num_mol, *num_mol_agl, num_of_inter, *stat, *stat_all, step, to,
|
||||
*true_label_mol, *type_agl, *type_atoms, type_inter, quiet;
|
||||
/* input - mask of input files
|
||||
* logfile - log file name
|
||||
* output - output file name
|
||||
/* input mask of trajectory files
|
||||
* logfile log file name
|
||||
* output output file name
|
||||
*
|
||||
* cell - cell dimension
|
||||
* coords - massive of coordinates
|
||||
* crit - massive of criteria
|
||||
* cell massive of cell size
|
||||
* coords massive of coordinates
|
||||
* crit massive of criteria
|
||||
*
|
||||
* agl - massive of aglomerates
|
||||
* connect - connectivity graph for all molecules
|
||||
* from - start point
|
||||
* label_atom - types of atom for interaction
|
||||
* label_mol - massive of numbers of molecule for atoms
|
||||
* log - status of log-mode
|
||||
* max_depth - max depth for check cycles in graph analyze
|
||||
* num_atoms - number of atoms for writing coordinates
|
||||
* num_mol - number of molecules for writing coordinates
|
||||
* num_mol_agl - massive of numbers of molecule in aglomerates
|
||||
* num_of_inter - number of different interactions
|
||||
* stat - massive of statistics
|
||||
* stat_all - massive of summary statistics
|
||||
* step - $(to - from + 1)
|
||||
* to - finish point
|
||||
* true_label_mol - massive of true numbers of molecule for atoms
|
||||
* type_agl - massive of numbers of aglomerate types
|
||||
* type_atoms - massive of atom types for atoms
|
||||
* type_inter - type interaction (number of molecules for interaction)
|
||||
* quiet - status of quiet-mode
|
||||
* agl massive of aglomerates
|
||||
* connect connectivity graph for all molecules
|
||||
* from first trajectory step
|
||||
* label_atom massive of atom types for interactions
|
||||
* label_mol massive of numbers of molecule for atoms
|
||||
* log status of log-mode
|
||||
* max_depth maximum depth for check cycles in graph analyze
|
||||
* num_atoms number of atoms
|
||||
* num_mol number of molecules
|
||||
* num_mol_agl massive of number of molecules in aglomerates
|
||||
* num_of_inter number of different interactions
|
||||
* stat massive of statistic
|
||||
* stat_all massive of summary statistic
|
||||
* step $(to - from + 1)
|
||||
* to last trajectory step
|
||||
* true_label_mol massive of true numbers of molecule for atoms
|
||||
* type_agl massive of number of aglomerate types
|
||||
* type_atoms massive of atom types
|
||||
* type_inter number of atoms for interactions
|
||||
* quiet status of quiet-mode
|
||||
*/
|
||||
|
||||
set_defaults (cell, &from, input, &log, &max_depth, &num_of_inter, output, &to,
|
||||
&type_inter, &quiet);
|
||||
|
||||
// reading number of interactions
|
||||
// reading number of interactions
|
||||
for (i=1; i<argc; i++)
|
||||
if ((argv[i][0] == '-') && (argv[i][1] == 'r'))
|
||||
num_of_inter++;
|
||||
@ -71,7 +75,7 @@ int main (int argc, char *argv[])
|
||||
num_of_inter = 0;
|
||||
}
|
||||
|
||||
// reading arguments
|
||||
// reading arguments
|
||||
for (i=1; i<argc; i++)
|
||||
{
|
||||
if ((argv[i][0] == '-') && (argv[i][1] == 'h'))
|
||||
@ -99,13 +103,13 @@ int main (int argc, char *argv[])
|
||||
return 0;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'i'))
|
||||
// mask of input files
|
||||
// mask of input files
|
||||
{
|
||||
strcpy (input, argv[i+1]);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 's'))
|
||||
// steps
|
||||
// steps
|
||||
{
|
||||
sscanf (argv[i+1], "%i,%i", &from, &to);
|
||||
if (from > to)
|
||||
@ -118,13 +122,13 @@ int main (int argc, char *argv[])
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'c'))
|
||||
// cell size
|
||||
// cell size
|
||||
{
|
||||
sscanf (argv[i+1], "%f,%f,%f", &cell[0], &cell[1], &cell[2]);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'a'))
|
||||
// atom types
|
||||
// atom types
|
||||
{
|
||||
type_inter = 1;
|
||||
for (j=0; j<strlen(argv[i+1]); j++)
|
||||
@ -153,7 +157,7 @@ int main (int argc, char *argv[])
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'r'))
|
||||
// criteria
|
||||
// criteria
|
||||
{
|
||||
index = 0;
|
||||
sscanf (&argv[i+1][index], "%i-%i:%f%s", &label[0], &label[1], &label_fl, tmp_str);
|
||||
@ -172,26 +176,26 @@ int main (int argc, char *argv[])
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'o'))
|
||||
// output file
|
||||
// output file
|
||||
{
|
||||
strcpy (output, argv[i+1]);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'g'))
|
||||
// graph isomorphism scan
|
||||
// graph isomorphism scan
|
||||
{
|
||||
sscanf (argv[i+1], "%i", &max_depth);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'l'))
|
||||
// log mode
|
||||
// log mode
|
||||
{
|
||||
log = 1;
|
||||
strcpy (logfile, argv[i+1]);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'q'))
|
||||
// quiet mode
|
||||
// quiet mode
|
||||
{
|
||||
quiet = 1;
|
||||
}
|
||||
@ -203,7 +207,7 @@ int main (int argc, char *argv[])
|
||||
print_message (quiet, stdout, log, f_log, 0, argv[0]);
|
||||
print_message (quiet, stdout, log, f_log, 1, argv[0]);
|
||||
|
||||
// error checking
|
||||
// error checking
|
||||
error = error_checking (cell, from, input, max_depth, num_of_inter, output, to,
|
||||
type_inter);
|
||||
if (error != 0)
|
||||
@ -214,8 +218,8 @@ int main (int argc, char *argv[])
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 2, argv[0]);
|
||||
|
||||
// processing
|
||||
// initial variables
|
||||
// processing
|
||||
// initial variables
|
||||
k = strlen (input);
|
||||
strcpy (filename, input);
|
||||
filename[k] = '.';
|
||||
@ -237,13 +241,13 @@ int main (int argc, char *argv[])
|
||||
true_label_mol = (int *) malloc (num_atoms * sizeof (int));
|
||||
type_agl = (int *) malloc ((max_depth + 2) * sizeof (int));
|
||||
type_atoms = (int *) malloc (8 * num_atoms * sizeof (int));
|
||||
// temporary declaration of variables
|
||||
// temporary declaration of variables
|
||||
agl = (int *) malloc (2 * 2 * sizeof (int));
|
||||
connect = (int *) malloc (2 * 2 * sizeof (int));
|
||||
num_mol_agl = (int *) malloc (2 * sizeof (int));
|
||||
stat = (int *) malloc (2 * sizeof (int));
|
||||
stat_all = (int *) malloc (2 * sizeof (int));
|
||||
// error checking
|
||||
// error checking
|
||||
if ((coords == NULL) ||
|
||||
(label_mol == NULL) ||
|
||||
(true_label_mol == NULL) ||
|
||||
@ -258,7 +262,7 @@ int main (int argc, char *argv[])
|
||||
print_message (quiet, stderr, log, f_log, 19, argv[0]);
|
||||
return 17;
|
||||
}
|
||||
// set type_agl to zero
|
||||
// set type_agl to zero
|
||||
for (i=0; i<max_depth+2; i++)
|
||||
type_agl[i] = 0;
|
||||
sprintf (tmp_str, "%6cOutput file: '%s';\n%6cLog: %i;\n%6cQuiet: %i;\n\
|
||||
@ -280,15 +284,15 @@ int main (int argc, char *argv[])
|
||||
sprintf (tmp_str, "%s%6cIsomorphism check: %i\n", tmp_str, ' ', max_depth);
|
||||
print_message (quiet, stdout, log, f_log, 5, tmp_str);
|
||||
|
||||
// head
|
||||
// head
|
||||
printing_head (output, log, quiet, input, from, to, cell, type_inter, label_atom,
|
||||
num_of_inter, crit, max_depth);
|
||||
|
||||
// main cycle
|
||||
// main cycle
|
||||
print_message (quiet, stdout, log, f_log, 6, argv[0]);
|
||||
for (i=from; i<to+1; i++)
|
||||
{
|
||||
// reading coordinates
|
||||
// reading coordinates
|
||||
filename[k+1] = conv (i, 3);
|
||||
filename[k+2] = conv (i, 2);
|
||||
filename[k+3] = conv (i, 1);
|
||||
@ -304,7 +308,7 @@ int main (int argc, char *argv[])
|
||||
print_message (quiet, stdout, log, f_log, 8, tmp_str);
|
||||
}
|
||||
|
||||
// resize dynamic arrays
|
||||
// resize dynamic arrays
|
||||
agl = (int *) realloc (agl, num_mol * num_mol * sizeof (int));
|
||||
connect = (int *) realloc (connect, num_mol * num_mol * sizeof (int));
|
||||
num_mol_agl = (int *) realloc (num_mol_agl, num_mol * sizeof (int));
|
||||
@ -315,7 +319,7 @@ int main (int argc, char *argv[])
|
||||
for (j=0; j<num_mol; j++)
|
||||
stat_all[j] = 0;
|
||||
}
|
||||
// error checking
|
||||
// error checking
|
||||
if ((agl == NULL) ||
|
||||
(connect == NULL) ||
|
||||
(num_mol_agl == NULL) ||
|
||||
@ -327,7 +331,7 @@ int main (int argc, char *argv[])
|
||||
}
|
||||
print_message (quiet, stdout, log, f_log, 9, argv[0]);
|
||||
|
||||
// analyze
|
||||
// analyze
|
||||
if (error == 0)
|
||||
{
|
||||
error = 1;
|
||||
@ -352,11 +356,11 @@ int main (int argc, char *argv[])
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 13, argv[0]);
|
||||
print_message (quiet, stdout, log, f_log, 14, output);
|
||||
// tail
|
||||
// tail
|
||||
summary_statistic (output, step, num_mol, max_depth, type_agl, stat_all);
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 15, argv[0]);
|
||||
// free memory
|
||||
// free memory
|
||||
free (agl);
|
||||
free (connect);
|
||||
free (coords);
|
||||
|
||||
@ -1,16 +1,27 @@
|
||||
/* Library for printing messages at output
|
||||
*
|
||||
* Usage:
|
||||
* message (log, mode, text, output)
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
#include <time.h>
|
||||
|
||||
|
||||
/**
|
||||
* @fn message
|
||||
*/
|
||||
int message (const int log, const int mode, const char *text, FILE *output)
|
||||
/* mode - number of message
|
||||
* text - additional text
|
||||
/**
|
||||
* @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 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
char out[4096];
|
||||
@ -18,6 +29,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
|
||||
if (log == 1)
|
||||
{
|
||||
char time_str[256];
|
||||
|
||||
time_t t = time (NULL);
|
||||
struct tm* aTm = localtime (&t);
|
||||
sprintf (time_str, "[%04d-%02d-%02d %02d:%02d:%02d] [%2i]: ", aTm->tm_year+1900,
|
||||
|
||||
@ -1,6 +1,14 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef MESSAGES_H
|
||||
#define MESSAGES_H
|
||||
|
||||
/**
|
||||
* @fn message
|
||||
*/
|
||||
|
||||
int message (const int, const int, const char *, FILE *);
|
||||
|
||||
#endif /* MESSAGES_H */
|
||||
@ -1,57 +1,69 @@
|
||||
/* Library for printing aglomerates
|
||||
*
|
||||
* Usage:
|
||||
* printing_agl (input_file, output_file, number_of_molecules,
|
||||
* true_label_molecules, num_of_molecules_in_aglomerates, aglomerates,
|
||||
* statistic, max_depth, type_of_aglomerate)
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
|
||||
// #include "graph.h"
|
||||
#include "graph.h"
|
||||
|
||||
|
||||
/**
|
||||
* @fn printing_agl
|
||||
*/
|
||||
int printing_agl (const char *input, const char *output, const int *connect,
|
||||
const int num_mol, const int *true_label_mol, const int *num_mol_agl,
|
||||
const int *agl, const int *stat, const int max_depth, int *type_agl)
|
||||
/* input - name of file with coordinates
|
||||
* output - name of output file
|
||||
* connect - connectivity graph for all molecules
|
||||
* num_mol - number of molecules
|
||||
* true_label_mol - massive of true numbers of molecule for atoms
|
||||
* num_mol_agl - massive of numbers of molecule in aglomerates
|
||||
* agl - massive of aglomerates
|
||||
* stat - massive of statistics
|
||||
* max_depth - max depth for check cycles in graph analyze
|
||||
* type_agl - massive of numbers of aglomerate types
|
||||
/**
|
||||
* @brief function that prints aglomerates to output file
|
||||
* @code
|
||||
* printing_agl (input_file, output_file, number_of_molecules,
|
||||
* true_label_molecules, num_of_molecules_in_aglomerates, aglomerates,
|
||||
* statistic, max_depth, type_of_aglomerate);
|
||||
* @endcode
|
||||
*
|
||||
* @param input input file name
|
||||
* @param output output file name
|
||||
* @param connect connectivity graph for all molecules
|
||||
* @param num_mol number of molecules
|
||||
* @param true_label_mol massive of true numbers of molecule for atoms
|
||||
* @param num_mol_agl massive of number of molecules in aglomerates
|
||||
* @param agl massive of aglomerates
|
||||
* @param stat massive of statistic
|
||||
* @param max_depth maximum depth for check cycles in graph analyze
|
||||
* @param type_agl massive of number of aglomerate types
|
||||
*
|
||||
* @return 1 - memory error
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
int error, i, *iso, j, k, *label_matrix, *matrix;
|
||||
FILE *f_out;
|
||||
/* iso - isomorphic graph in database
|
||||
* label_matrix - massive of indexes of molecule
|
||||
* matrix - connectivity graph
|
||||
* f_out - output file
|
||||
/* iso isomorphic graph in database
|
||||
* label_matrix massive of indexes of molecule
|
||||
* matrix connectivity graph
|
||||
* f_out output file
|
||||
*/
|
||||
|
||||
/// <b>Work blocks</b>
|
||||
|
||||
iso = (int *) malloc (max_depth * sizeof (int));
|
||||
if (iso == NULL)
|
||||
return 1;
|
||||
f_out = fopen (output, "a");
|
||||
|
||||
// head
|
||||
/// <pre> print header </pre>
|
||||
fprintf (f_out, "FILE=%s\nSTATISTIC\n| n | N |\n-----------------\n", input);
|
||||
for (i=0; i<num_mol; i++)
|
||||
if (stat[i] != 0)
|
||||
fprintf (f_out, " %7i %7i \n", i+1, stat[i]);
|
||||
fprintf (f_out, "-----------------\n");
|
||||
|
||||
// body
|
||||
/// <pre> print body </pre>
|
||||
for (i=0; i<num_mol; i++)
|
||||
if (num_mol_agl[i] > 0)
|
||||
{
|
||||
// creating connectivity graph
|
||||
/// <pre> creating connectivity graph </pre>
|
||||
label_matrix = (int *) malloc (num_mol * sizeof (int));
|
||||
matrix = (int *) malloc (num_mol_agl[i] * num_mol_agl[i] * sizeof (int));
|
||||
if ((matrix == NULL) ||
|
||||
@ -71,34 +83,34 @@ int printing_agl (const char *input, const char *output, const int *connect,
|
||||
matrix[label_matrix[agl[num_mol*i+k]]*num_mol_agl[i]+label_matrix[agl[num_mol*i+j]]] = 1;
|
||||
}
|
||||
|
||||
// graph topology analyze
|
||||
/// <pre> graph topology analyze </pre>
|
||||
if (max_depth > 0)
|
||||
error = graph_analyze (num_mol_agl[i], matrix, max_depth, iso);
|
||||
if (error > 0)
|
||||
return 1;
|
||||
|
||||
// printing class of aglomerate
|
||||
// print class of aglomerate
|
||||
fprintf (f_out, "AGL=%i=", num_mol_agl[i]);
|
||||
for (j=0; j<max_depth; j++)
|
||||
{
|
||||
// number of tails
|
||||
// number of tails
|
||||
if (j == 0)
|
||||
if (iso[j] > 2)
|
||||
// branched
|
||||
// branched
|
||||
type_agl[3]++;
|
||||
else
|
||||
// not branched
|
||||
// not branched
|
||||
type_agl[2]++;
|
||||
// number of cycles
|
||||
// number of cycles
|
||||
else if (j == 1)
|
||||
if (iso[j] > 0)
|
||||
// cycle
|
||||
// cycle
|
||||
type_agl[1]++;
|
||||
else
|
||||
// linear
|
||||
// linear
|
||||
type_agl[0]++;
|
||||
else if (j > 1)
|
||||
// number of n_cycles
|
||||
// number of n_cycles
|
||||
type_agl[j+2] += iso[j];
|
||||
|
||||
fprintf (f_out, "%i.", iso[j]);
|
||||
@ -108,20 +120,21 @@ int printing_agl (const char *input, const char *output, const int *connect,
|
||||
{
|
||||
fprintf (f_out, "%7i=", true_label_mol[agl[num_mol*i+j]]);
|
||||
for (k=0; k<num_mol_agl[i]; k++)
|
||||
{
|
||||
if (matrix[j*num_mol_agl[i]+k] == 1)
|
||||
fprintf (f_out, "%i,", true_label_mol[agl[num_mol*i+k]]);
|
||||
}
|
||||
fprintf (f_out, "\n");
|
||||
}
|
||||
|
||||
// free memory
|
||||
/// <pre> free memory </pre>
|
||||
free (matrix);
|
||||
free (label_matrix);
|
||||
}
|
||||
|
||||
fprintf (f_out, "---------------------------------------------------\n");
|
||||
fclose (f_out);
|
||||
|
||||
/// <pre> free memory </pre>
|
||||
free (iso);
|
||||
|
||||
return 0;
|
||||
}
|
||||
@ -1,6 +1,14 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef STAT_PRINT_H
|
||||
#define STAT_PRINT_H
|
||||
|
||||
/**
|
||||
* @fn printing_agl
|
||||
*/
|
||||
|
||||
int printing_agl (const char *, const char *, const int *, const int, const int *,
|
||||
const int *, const int *, const int *, const int,int *);
|
||||
|
||||
@ -1,35 +1,47 @@
|
||||
/* Library for creating connectivity matrix
|
||||
*
|
||||
* Usage:
|
||||
* create_matrix (number_of_molecules, number_of_atoms, label_molecule,
|
||||
* type_atoms, coords, number_of_interactions, criteria, connect_matrix)
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <math.h>
|
||||
#include <stdlib.h>
|
||||
|
||||
|
||||
/**
|
||||
* @fn create_matrix
|
||||
*/
|
||||
int create_matrix (const int num_mol, const int num_atoms, const int *label_mol,
|
||||
const int *type_atoms, const float *coords, const int num_of_inter,
|
||||
const float *crit, int *connect)
|
||||
/* num_mol - number of molecules
|
||||
* num_atoms - number of atoms
|
||||
* label_mol - massive of numbers of molecule for atoms
|
||||
* type_atoms - massive of atom types for atoms
|
||||
* coords - massive of coordinates
|
||||
* num_of_inter - number of different interactions
|
||||
* crit - massive of criteria
|
||||
* connect - connectivity graph for all molecules
|
||||
/**
|
||||
* @brief function that creates connectivity matrix
|
||||
* @code
|
||||
* create_matrix (number_of_molecules, number_of_atoms, label_molecule,
|
||||
* type_atoms, coords, number_of_interactions, criteria, connect_matrix);
|
||||
* @endcode
|
||||
*
|
||||
* @param num_mol number of molecules
|
||||
* @param num_atoms number of atoms
|
||||
* @param label_mol massive of numbers of molecule for atoms
|
||||
* @param type_atoms massive of atom types
|
||||
* @param coords massive of coordinates
|
||||
* @param num_of_inter number of different interactions
|
||||
* @param crit massive of criteria
|
||||
* @param connect connectivity graph for all molecules
|
||||
*
|
||||
* @return 1 - memory error
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
float r;
|
||||
int cur_num_inter, i, j, k, l, num_inter, ***label_inter;
|
||||
/* r - radius
|
||||
* cur_num_inter - current number of true interactions
|
||||
* num_inter - needed number of true interactions
|
||||
* label_inter - temporary massive of true interactions
|
||||
/* r radius
|
||||
* cur_num_inter current number of true interactions
|
||||
* num_inter needed number of true interactions
|
||||
* label_inter temporary massive of true interactions
|
||||
*/
|
||||
|
||||
/// <b>Work blocks</b>
|
||||
|
||||
label_inter = (int ***) malloc (num_mol * sizeof (int **));
|
||||
for (i=0; i<num_mol; i++)
|
||||
{
|
||||
@ -44,10 +56,10 @@ int create_matrix (const int num_mol, const int num_atoms, const int *label_mol,
|
||||
if (label_inter == NULL)
|
||||
return 1;
|
||||
|
||||
// creating initial connectivity matrix
|
||||
/// <pre> creating initial connectivity matrix </pre>
|
||||
for (i=0; i<num_atoms*8; i++)
|
||||
for (j=i+1; j<num_atoms*8; j++)
|
||||
// if atoms from different molecules
|
||||
// if atoms from different molecules
|
||||
if (label_mol[i] != label_mol[j])
|
||||
{
|
||||
r = sqrt (pow ((coords[3*i+0]-coords[3*j+0]), 2) +
|
||||
@ -68,10 +80,10 @@ int create_matrix (const int num_mol, const int num_atoms, const int *label_mol,
|
||||
for (j=0; j<num_mol; j++)
|
||||
connect[i*num_mol+j] = 0;
|
||||
|
||||
// processing of initial connectivity matrix
|
||||
/// <pre> processing of initial connectivity matrix </pre>
|
||||
for (k=0; k<num_of_inter; k++)
|
||||
{
|
||||
// determination of the number of interactions
|
||||
// determination of the number of interactions
|
||||
num_inter = 0;
|
||||
for (l=0; l<16; l++)
|
||||
if (crit[16*k+l] != 0.0)
|
||||
@ -92,7 +104,7 @@ int create_matrix (const int num_mol, const int num_atoms, const int *label_mol,
|
||||
}
|
||||
}
|
||||
|
||||
// free memory
|
||||
/// <pre> free memory</pre>
|
||||
for (i=0; i<num_mol; i++)
|
||||
{
|
||||
for (j=0; j<num_mol; j++)
|
||||
|
||||
@ -1,6 +1,14 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef STAT_SELECT_H
|
||||
#define STAT_SELECT_H
|
||||
|
||||
/**
|
||||
* @fn create_matrix
|
||||
*/
|
||||
|
||||
int create_matrix (const int, const int, const int *, const int *, const float *,
|
||||
const int, const float *, int *);
|
||||
|
||||
@ -1,29 +1,41 @@
|
||||
/* Library for processing connectivity matrix
|
||||
*
|
||||
* Usage:
|
||||
* proc_matrix (number_of_molecules, connect_matrix,
|
||||
* num_of_molecules_in_aglomerates, aglomerates, statistic, summary_statistic)
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <stdlib.h>
|
||||
|
||||
|
||||
/**
|
||||
* @fn proc_matrix
|
||||
*/
|
||||
int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *agl,
|
||||
int *stat, int *stat_all)
|
||||
/* num_mol - number of molecules
|
||||
* connect - connectivity graph for all molecules
|
||||
* num_mol_agl - massive of numbers of molecule in aglomerates
|
||||
* agl - massive of aglomerates
|
||||
* stat - massive of statistics
|
||||
* stat_all - massive of summary statistics
|
||||
/**
|
||||
* @brief function that processes connectivity matrix
|
||||
* @code
|
||||
* proc_matrix (number_of_molecules, connect_matrix,
|
||||
* num_of_molecules_in_aglomerates, aglomerates, statistic, summary_statistic);
|
||||
* @endcode
|
||||
*
|
||||
* @param num_mol number of molecules
|
||||
* @param connect connectivity graph for all molecules
|
||||
* @param num_mol_agl massive of number of molecules in aglomerates
|
||||
* @param agl massive of aglomerates
|
||||
* @param stat massive of statistic
|
||||
* @param stat_all massive of summary statistic
|
||||
*
|
||||
* @return 1 - memory error
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
int i, j, k, p, *bin;
|
||||
/* p - weight / graph index
|
||||
* bin - binary massive of labels
|
||||
/* p weight / graph index
|
||||
* bin binary massive of labels
|
||||
*/
|
||||
|
||||
// definition and zeroing
|
||||
/// <b>Work blocks</b>
|
||||
|
||||
// definition and zeroing
|
||||
bin = (int *) malloc (num_mol * sizeof (int));
|
||||
if (bin == NULL)
|
||||
return 1;
|
||||
@ -36,7 +48,7 @@ int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *a
|
||||
agl[num_mol*i+j] = 0;
|
||||
}
|
||||
|
||||
// select non-bonded molecules
|
||||
/// <pre> select non-bonded molecules </pre>
|
||||
for (i=0; i<num_mol; i++)
|
||||
{
|
||||
p = 0;
|
||||
@ -50,7 +62,7 @@ int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *a
|
||||
}
|
||||
}
|
||||
|
||||
// unwraping of connectivity matrix
|
||||
/// <pre> unwraping of connectivity matrix </pre>
|
||||
p = 0;
|
||||
for (i=0; i<num_mol; i++)
|
||||
if (bin[i] == 1)
|
||||
@ -71,7 +83,7 @@ int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *a
|
||||
p++;
|
||||
}
|
||||
|
||||
// filling statistic array
|
||||
/// <pre> filling statistic array </pre>
|
||||
i = 0;
|
||||
while (num_mol_agl[i] > 0)
|
||||
{
|
||||
@ -80,6 +92,7 @@ int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *a
|
||||
i++;
|
||||
}
|
||||
|
||||
/// <pre> free memory </pre>
|
||||
free (bin);
|
||||
|
||||
return 0;
|
||||
|
||||
@ -1,6 +1,14 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef STAT_SORT_H
|
||||
#define STAT_SORT_H
|
||||
|
||||
/**
|
||||
* @fn proc_matrix
|
||||
*/
|
||||
|
||||
int proc_matrix (const int, const int *, int *, int *, int *, int *);
|
||||
|
||||
#endif /* STAT_SORT_H */
|
||||
@ -1,29 +1,39 @@
|
||||
/* Library for summary statistic
|
||||
* Usage:
|
||||
* summary_statistic (filename, number_of_step, number_of_molecules,
|
||||
* max_depth, type_of_aglomerate, summary_statistic)
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
|
||||
|
||||
/**
|
||||
* @fn summary_statistic
|
||||
*/
|
||||
int summary_statistic (const char *filename, const int step, const int num_mol,
|
||||
const int max_depth, const int *type_agl, const int *stat_all)
|
||||
/* filename - name of output file
|
||||
* step - number of steps
|
||||
* num_mol - number of molecules
|
||||
* max_depth - max depth for check cycles in graph analyze
|
||||
* type_agl - massive of numbers of aglomerate types
|
||||
* stat_all - massive of summary statistics
|
||||
/**
|
||||
* @brief function that prints summary statistic
|
||||
* @code
|
||||
* summary_statistic (filename, number_of_step, number_of_molecules, max_depth,
|
||||
* type_of_aglomerate, summary_statistic);
|
||||
* @endcode
|
||||
*
|
||||
* @param filename output file name
|
||||
* @param step number of steps
|
||||
* @param num_mol number of molecules
|
||||
* @param max_depth maximum depth for check cycles in graph analyze
|
||||
* @param type_agl massive of number of aglomerate types
|
||||
* @param stat_all massive of summary statistic
|
||||
*
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
float conc, p, pn, type[2], x, y;
|
||||
int i, index;
|
||||
FILE *f_out;
|
||||
/* conc - concentrate of aglomerates
|
||||
* p - probability of aglomerates
|
||||
* pn - weight probability of aglomerates
|
||||
* f_out - output file
|
||||
/* conc concentrate of aglomerates
|
||||
* p probability of aglomerates
|
||||
* pn weight probability of aglomerates
|
||||
* f_out output file
|
||||
*/
|
||||
|
||||
index = 0;
|
||||
@ -31,19 +41,19 @@ int summary_statistic (const char *filename, const int step, const int num_mol,
|
||||
if (stat_all[i] != 0)
|
||||
index = i;
|
||||
|
||||
// head
|
||||
// head
|
||||
f_out = fopen (filename, "a");
|
||||
fprintf (f_out, "SUMMARY STATISTIC\n");
|
||||
fprintf (f_out, "| n | N | C | p | pn |\n------------------------------------------------\n");
|
||||
|
||||
for (i=0; i<index+1; i++)
|
||||
{
|
||||
// calculating concentrates
|
||||
// calculating concentrates
|
||||
x = stat_all[i];
|
||||
y = step;
|
||||
conc = x / y;
|
||||
|
||||
// calculating probabilityes
|
||||
// calculating probabilityes
|
||||
x = (i + 1) * stat_all[i];
|
||||
y = step * num_mol;
|
||||
p = x / y;
|
||||
@ -54,18 +64,18 @@ int summary_statistic (const char *filename, const int step, const int num_mol,
|
||||
|
||||
if (max_depth > 0)
|
||||
{
|
||||
// types of aglomerates
|
||||
// types of aglomerates
|
||||
fprintf (f_out, "------------------------------------------------\n");
|
||||
// linear and cycle
|
||||
// linear and cycle
|
||||
x = type_agl[0] + type_agl[1];
|
||||
type[0] = type_agl[0];
|
||||
type[1] = type_agl[1];
|
||||
fprintf (f_out, "LINEAR=%7.5f\nCYCLE=%7.5f\n--------------------\n", type[0]/x, type[1]/x);
|
||||
// branched
|
||||
// branched
|
||||
type[0] = type_agl[2];
|
||||
type[1] = type_agl[3];
|
||||
fprintf (f_out, "NOT BRANCHED=%7.5f\nBRANCHED=%7.5f\n--------------------\n", type[0]/x, type[1]/x);
|
||||
// n_cycle
|
||||
// n_cycle
|
||||
x = 0;
|
||||
for (i=4; i<max_depth+2; i++)
|
||||
x += type_agl[i];
|
||||
|
||||
@ -1,6 +1,14 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef SUMMARY_STAT_H
|
||||
#define SUMMARY_STAT_H
|
||||
|
||||
/**
|
||||
* @fn summary_statistic
|
||||
*/
|
||||
|
||||
int summary_statistic (const char *, const int, const int, const int, const int *,
|
||||
const int *);
|
||||
|
||||
@ -1,22 +1,32 @@
|
||||
# set directories
|
||||
set (${PROJECT}_BINARY_DIR bin)
|
||||
set (${PROJECT}_SOURCE_DIR src:include)
|
||||
set (${PROJECT}_SOURCE_DIR src)
|
||||
set (${PROJECT}_INCLUDE_DIR include)
|
||||
set (${PROJECT}_LIB_DIR lib)
|
||||
|
||||
set (CMAKE_INCLUDE_PATH ${${PROJECT}_SOURCE_DIR})
|
||||
set (CMAKE_LIBRARY_PATH ${${PROJECT}_LIB_DIR})
|
||||
# include_path
|
||||
include_directories (${${PROJECT}_INCLUDE_DIR}/${PROJECT}
|
||||
${${PROJECT}_SOURCE_DIR})
|
||||
# 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 )
|
||||
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 (STATUS "Flags not enabled")
|
||||
message ("Unknown compiler")
|
||||
endif ()
|
||||
1890
statgen/statgen.doxygen
Normal file
1890
statgen/statgen.doxygen
Normal file
File diff suppressed because it is too large
Load Diff
BIN
statgen/statgen.pdf
Normal file
BIN
statgen/statgen.pdf
Normal file
Binary file not shown.
Reference in New Issue
Block a user