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arcan1s
2013-07-28 04:03:28 +04:00
parent 1af86034e7
commit 7cab7c785f
48 changed files with 5349 additions and 297 deletions
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5
agl/CMakeLists.txt
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@ -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 agl)
@ -28,4 +29,4 @@ set (LIBRARIES)
set (TARGETS "")
set (HEADERS "")
add_subdirectory (src)
add_subdirectory (${${PROJECT}_SOURCE_DIR})

15
agl/README Normal file
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@ -0,0 +1,15 @@
agl - program that creates PDB file with chosen aglomerate
Version: 1.0.1
License: GPL
Usage:
agl -a FILENAME -i FILENAME -c X,Y,Z -o FILEMANE [ -l LOGFILE] [ -q ] [ -h ]
Parametrs:
-a - input file with aglomerates (in format statgen)
-i - input file with coordinates
-c - cell size (float), A
-o - output file with coordinates
-l - log enable
-q - quiet enable
-h - show this help and exit

63
agl/about.dox Normal file
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@ -0,0 +1,63 @@
/*!
* @mainpage agl
* @image latex ./logo.png
*
* @section intro_sec Introduction
*
* <b>About this program</b>:
* <ul>
* <li>Program that creates PDB file with chosen aglomerate
* </ul>
*
* <b>Developer</b>:
* <ul>
* <li>Evgeniy Alekseev aka arcanis <pre><esalexeev (at) gmail (dot) com></pre>
*</ul>
* <b>License</b>:
* <ul>
* <li>GPL
* </ul>
*
* @section How-To-Use How to use
* Usage:
* <pre>
* agl -a FILENAME -i FILENAME -c X,Y,Z -o FILEMANE [ -l LOGFILE] [ -q ] [ -h ]
*
* Parametrs:
* -a - input file with aglomerates (in format statgen)
* -i - input file with coordinates
* -c - cell size (float), A
* -o - output file with coordinates
* -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
*/

22
agl/agl.cmake
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@ -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 ()

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48
agl/src/CMakeLists.txt
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@ -3,59 +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
envir_search
messages
print_struct
set_center)
# 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 ()

88
agl/src/coords.c
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@ -1,52 +1,67 @@
/* 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)
* (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
/**
* @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;
@ -61,10 +76,11 @@ 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])
{
@ -85,7 +101,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
break;
case 1:
// for envir and frad
// 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];
@ -104,7 +120,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
*num_atoms = *num_atoms + 1;
break;
case 2:
// for agl
// mode == 2 (selected molecules)
for (j=0; j<type_inter; j++)
if (cur_mol == label_atom[j])
{
@ -126,18 +142,18 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
*num_atoms = *num_atoms + 1;
}
break;
default: return 1;
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];
@ -331,7 +347,7 @@ 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;

2
agl/src/main.c
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@ -46,7 +46,7 @@ int main(int argc, char *argv[])
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, "%sProgram for create PDB file with chosen 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);

24
agl/src/messages.c
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@ -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,

38
agl/src/print_struct.c
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@ -1,3 +1,7 @@
/**
* @file
*/
/* Library for printing structure to pdb file
*
* Usage:
@ -8,23 +12,37 @@
#include <stdio.h>
/**
* @fn print_structure
*/
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
/**
* @brief function that prints structure to pdb file
* @code
* print_structure (output, num_needed_mol, needed_mol, num_atoms, label_mol,
* char_type_atoms, coords);
* @endcode
*
* @param output output file name
* @param num_needed_mol number of needed molecules
* @param needed_mol massive of number of needed molecules
* @param num_atoms number of atoms
* @param label_mol massive of numbers of molecule for atoms
* @param ch_type_atoms massive of char atom types
* @param coords massive of coordinates
*
* @return 0 - exit without errors
*/
{
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 current atom
* cur_atom_num true atom number
* cur_mol current molecule
* f_out output file
*/
cur_atom = 1;

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300
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218.495 4.413313
219.495 4.365502
220.495 4.822679
221.495 4.942861
222.495 4.184449
223.495 4.569083
224.495 5.034656
225.495 3.760486
226.495 5.778256
227.495 4.666387
228.495 3.87934
229.495 4.298156
230.495 3.606369
231.495 4.043328
232.495 3.533107
233.495 4.322265
234.495 6.460613
235.495 5.619601
236.495 5.003014
237.495 5.240613
238.495 5.716251
239.495 6.512721
240.495 6.360552
241.495 4.694978
242.495 4.520795
243.495 6.517642
244.495 6.727004
245.495 6.663968
246.495 6.741717
247.495 6.748613
248.495 6.230022
249.495 4.738152
250.495 6.63096
251.495 5.940607
252.495 4.742698
253.495 4.901755
254.495 5.24829
255.495 6.601441
256.495 6.805718
257.495 6.696987
258.495 5.814055
259.495 6.719182
260.495 5.310413
261.495 4.917739
262.495 4.895024
263.495 4.910364
264.495 5.474503
265.495 6.951988
266.495 5.2517
267.495 5.347468
268.495 4.94037
269.495 5.637509
270.495 5.592732
271.495 6.633568
272.495 5.42893
273.495 6.134158
274.495 5.679378
275.495 5.436838
276.495 6.490301
277.495 5.504136
278.495 4.772426
279.495 5.005461
280.495 6.63088
281.495 6.747831
282.495 5.150361
283.495 5.031422
284.495 4.875282
285.495 4.702079
286.495 4.880232
287.495 4.886068
288.495 5.34387
289.495 4.904718
290.495 6.713236
291.495 7.771074
292.495 5.571742
293.495 5.278872
294.495 6.742266
295.495 6.609142
296.495 5.969145
297.495 6.306997
298.495 6.458366
299.495 5.442104

5
envir/CMakeLists.txt
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@ -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 envir)
@ -28,4 +29,4 @@ set (LIBRARIES)
set (TARGETS "")
set (HEADERS "")
add_subdirectory (src)
add_subdirectory (${${PROJECT}_SOURCE_DIR})

2
envir/README
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@ -1,4 +1,4 @@
envir - program for search environment for chosen molecule by geometric criterion
envir - program that searchs environment for chosen molecule by geometric criterion
Version: 1.0.1
License: GPL

65
envir/about.dox Normal file
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@ -0,0 +1,65 @@
/*!
* @mainpage envir
* @image latex ./logo.png
*
* @section intro_sec Introduction
*
* <b>About this program</b>:
* <ul>
* <li>Program that searchs environment for chosen molecule by geometric criterion
* </ul>
*
* <b>Developer</b>:
* <ul>
* <li>Evgeniy Alekseev aka arcanis <pre><esalexeev (at) gmail (dot) com></pre>
*</ul>
* <b>License</b>:
* <ul>
* <li>GPL
* </ul>
*
* @section How-To-Use How to use
* Usage:
* <pre>
* envir -i FILENAME -c X,Y,Z -o FILEMANE [ -n NUM_OF_MOLECULE ] [ -r RADIUS ]
* [ -l LOGFILE] [ -q ] [ -h ]
*
* Parametrs:
* -i - input file with coordinates
* -c - cell size (float), A
* -o - output file with coordinates
* -n - number of molecule for search (integer). Default is 1
* -r - radius of environment (float). Default is 6.0
* -l - log enable
* -q - quiet enable
* -h - show this help and exit
* </pre>
*
* @page Install
*
* @section Requirements Requirements
* The application 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
*/

22
envir/envir.cmake
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@ -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 ()

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48
envir/src/CMakeLists.txt
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@ -3,59 +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 add_main
coords
envir_search
messages
print_struct
set_center)
# headers only files
SET (HEADERS_ONLY)
# public srcs
set (PUBLIC_CLASSES)
# 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 ()

59
envir/src/add_main.c
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@ -1,4 +1,5 @@
/* Additional library for main.c (envir)
/**
* @file
*/
#include <stdio.h>
@ -6,7 +7,25 @@
#include "messages.h"
/**
* @fn error_checking
*/
int error_checking (const float *cell, const char *input, const char *output)
/**
* @brief function that checks errors in input variables
* @code
* error_checking (cell, input, output);
* @endcode
*
* @param cell massive of cell size
* @param input first trajectory step
* @param output last trajectory step
*
* @return 11 - error in 'cell'
* @return 12 - error in 'input'
* @return 13 - error in 'output'
* @return 0 - exit without errors
*/
{
if ((cell[0] == 0.0) || (cell[1] == 0.0) || (cell[2] == 0.0))
return 11;
@ -19,8 +38,26 @@ int error_checking (const float *cell, const char *input, const char *output)
}
/**
* @fn print_message
*/
int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log,
const int mode, const char *str)
/**
* @brief function that prints message in log and stdout
* @code
* 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);
@ -31,8 +68,28 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
}
/**
* @fn set_defaults
*/
int set_defaults (float *cell, char *input, int *log, int *num_of_mol, char *output,
int *quiet, float *rad)
/**
* @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 input mask of trajectory files
* @param log status of log-mode
* @param num_of_mol number of molecule
* @param output output file name
* @param quiet status of quiet-mode
* @param rad radius of environment sphere
*
* @return 0 - exit without errors
*/
{
int i;

14
envir/src/add_main.h
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@ -1,6 +1,20 @@
/**
* @file
*/
#ifndef ADD_MAIN_H
#define ADD_MAIN_H
/**
* @fn error_checking
*/
/**
* @fn print_message
*/
/**
* @fn set_defaults
*/
int error_checking (const float *, const char *, const char *);
int print_message (const int, FILE *, const int, FILE *, const int, const char *);
int set_defaults (float *, char *, int *, int *, char *, int *, float *);

88
envir/src/coords.c
View File

@ -1,52 +1,67 @@
/* 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)
* (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
/**
* @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;
@ -61,10 +76,11 @@ 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])
{
@ -85,7 +101,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
break;
case 1:
// for envir and frad
// 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];
@ -104,7 +120,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
*num_atoms = *num_atoms + 1;
break;
case 2:
// for agl
// mode == 2 (selected molecules)
for (j=0; j<type_inter; j++)
if (cur_mol == label_atom[j])
{
@ -126,18 +142,18 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
*num_atoms = *num_atoms + 1;
}
break;
default: return 1;
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];
@ -331,7 +347,7 @@ 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;

8
envir/src/coords.h
View File

@ -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 *);

31
envir/src/envir_search.c
View File

@ -1,3 +1,7 @@
/**
* @file
*/
/* Library for search environment
*
* Usage:
@ -8,19 +12,32 @@
#include <math.h>
/**
* @fn search_envir
*/
int search_envir (const int num_of_mol, const int num_mol, const float *centr_coords,
const double rad, int *needed_mol, int *num_needed_mol)
/* num_of_mol - number of molecule for search
* num_mol - number of molecules for writing coordinates
* centr_coords - massive of centered coordinates
* rad - criterion
* needed_mol - massive of needed molecules
* num_needed_mol - number of needed molecules
/**
* @brief function that searchs environment
* @code
* search_envir (number_of_molecule, num_mol, centr_coords, rad, needed_mol,
* &num_needed_mol);
* @endcode
*
* @param num_of_mol number of molecule
* @param num_mol number of molecules
* @param centr_coords massive of centered coordinates
* @param rad radius of environment sphere
* @param needed_mol massive of number of needed molecules
* @param num_needed_mol number of needed molecules
*
* @return 0 - exit without errors
*/
{
float r;
int i;
/* r - radius
/* r radius
*/
*num_needed_mol = 0;

8
envir/src/envir_search.h
View File

@ -1,6 +1,14 @@
/**
* @file
*/
#ifndef ENVIR_SEARCH_H
#define ENVIR_SEARCH_H
/**
* @fn search_envir
*/
int search_envir (const int, const int, const float *, const double, int *, int *);
#endif /* ENVIR_SEARCH_H */

54
envir/src/main.c
View File

@ -1,3 +1,7 @@
/**
* @file
*/
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
@ -11,7 +15,16 @@
#include "set_center.h"
/**
* @fn main
*/
int main(int argc, char *argv[])
/**
* @return 1 - error in error_checking
* @return 2 - input file does not exist
* @return 3 - memory error
* @return 0 - exit without errors
*/
{
char tmp_str[2048];
int error, i, j, *tmp_int;
@ -21,25 +34,26 @@ int main(int argc, char *argv[])
float cell[3], *centr_coords, *coords, rad;
int *label_mol, log, num_atoms, num_mol, num_needed_mol, num_of_mol,
*needed_mol, quiet, *true_label_mol;
/* ch_type_atoms - massive of char types for atoms
* input - input file name
* logfile - log file name
* output - output file name
/* ch_type_atoms massive of char atom types
* input input file name
* logfile log file name
* output output file name
*
* cell - cell dimension
* centr_coords - massive of coordinates of center molecules
* coords - massive of coordinates
* rad - criterion
* cell massive of cell size
* centr_coords massive of centered coordinates
* coords massive of coordinates
* rad radius of environment sphere
*
* label_mol - massive of numbers of molecule for atoms
* log - status of log-mode
* num_atoms - number of atoms for writing coordinates
* num_mol - number of molecules for writing coordinates
* num_needed_mol - number of needed molecules
* num_of_mol - number of molecule for search
* needed_mol - massive of needed molecules
* quiet - status of quiet-mode
* true_label_mol - massive of true numbers of molecule for atoms
* label_mol massive of numbers of molecule for atoms
* log status of log-mode
* num_atoms number of atoms
* num_mol number of molecules
* num_needed_mol number of needed molecules
* num_of_mol number of molecule
* needed_mol massive of number of needed molecules
* quiet status of quiet-mode
* true_label_mol massive of true numbers of molecule for atoms
*/
set_defaults (cell, input, &log, &num_of_mol, output, &quiet, &rad);
@ -134,7 +148,7 @@ int main(int argc, char *argv[])
if (f_inp == NULL)
{
print_message (quiet, stderr, log, f_log, 18, input);
return 1;
return 2;
}
fscanf (f_inp, "%i", &num_atoms);
fclose (f_inp);
@ -151,7 +165,7 @@ int main(int argc, char *argv[])
(true_label_mol == NULL))
{
print_message (quiet, stderr, log, f_log, 19, argv[0]);
return 17;
return 3;
}
sprintf (tmp_str, "%6cInput file: '%s';\n%6cOutput file: '%s';\n%6cLog: %i;\n\
%6cQuiet: %i;\n%6cCell size: %.4f, %.4f, %.4f;\n%6cSelect molecule: %i;\n\
@ -178,7 +192,7 @@ int main(int argc, char *argv[])
(needed_mol == NULL))
{
print_message (quiet, stderr, log, f_log, 19, argv[0]);
return 17;
return 3;
}
// analyze

24
envir/src/messages.c
View File

@ -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,

8
envir/src/messages.h
View File

@ -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 */

38
envir/src/print_struct.c
View File

@ -1,3 +1,7 @@
/**
* @file
*/
/* Library for printing structure to pdb file
*
* Usage:
@ -8,23 +12,37 @@
#include <stdio.h>
/**
* @fn print_structure
*/
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
/**
* @brief function that prints structure to pdb file
* @code
* print_structure (output, num_needed_mol, needed_mol, num_atoms, label_mol,
* char_type_atoms, coords);
* @endcode
*
* @param output output file name
* @param num_needed_mol number of needed molecules
* @param needed_mol massive of number of needed molecules
* @param num_atoms number of atoms
* @param label_mol massive of numbers of molecule for atoms
* @param ch_type_atoms massive of char atom types
* @param coords massive of coordinates
*
* @return 0 - exit without errors
*/
{
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 current atom
* cur_atom_num true atom number
* cur_mol current molecule
* f_out output file
*/
cur_atom = 1;

8
envir/src/print_struct.h
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@ -1,6 +1,14 @@
/**
* @file
*/
#ifndef PRINT_STRUCTURE_H
#define PRINT_STRUCTURE_H
/**
* @fn print_structure
*/
int print_structure (const char *, const int, const int *, const int, const int *,
const char *, const float *);

30
envir/src/set_center.c
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@ -1,3 +1,7 @@
/**
* @file
*/
/* Library for search center mass of molecules
*
* Usage:
@ -6,18 +10,30 @@
*/
/**
* @fn set_center
*/
int set_center (const int num_atoms, const int num_mol, const int *label_mol,
const float *coords, float *centr_coords)
/* num_atoms - number of atoms for writing coordinates
* num_mol - number of molecules for writing coordinates
* label_mol - massive of numbers of molecule for atoms
* coords - massive of coordinates
* coords - massive of coordinates of center molecules
/**
* @brief function that searchs center mass of molecules
* @code
* set_center (num_of_atoms, num_of_molecules, label_molecules, coords, centr_coords);
* @endcode
*
* @param num_atoms number of atoms
* @param num_mol number of molecules
* @param label_mol massive of numbers of molecule for atoms
* @param coords massive of coordinates
* @param centr_coords massive of centered coordinates
*
* @return 0 - exit without errors
*/
{
int at_in_mol, cur_mol, i, j, k;
/* at_int_mol - number of atoms in molecule
* cur_mol - current molecule
/* at_int_mol number of atoms in molecule
* cur_mol current molecule
*/
for (i=0; i<8*num_mol; i++)

8
envir/src/set_center.h
View File

@ -1,6 +1,14 @@
/**
* @file
*/
#ifndef SET_CENTER_H
#define SET_CENTER_H
/**
* @fn set_center
*/
int set_center (const int, const int, const int *, const float *, float *);
#endif /* SET_CENTER_H */

2
statgen/README
View File

@ -1,4 +1,4 @@
statgen - program for analyze molecular dynamic trajectories
statgen - program that analyzes molecular dynamic trajectories using topological analysis
Version: 1.0.1
License: GPL

9
statgen/about.dox
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@ -1,7 +1,14 @@
/*! @mainpage statgen
/*!
* @mainpage statgen
* @image latex ./logo.png
*
* @section intro_sec Introduction
*
* <b>About this program</b>:
* <ul>
* <li>Program that analyzes molecular dynamic trajectories using topological analysis
* </ul>
*
* <b>Developer</b>:
* <ul>
* <li>Evgeniy Alekseev aka arcanis <pre><esalexeev (at) gmail (dot) com></pre>

1
statgen/src/add_main.c
View File

@ -119,6 +119,7 @@ int printing_head (const char *output, const int log, const int quiet,
return 0;
}
/**
* @fn print_message
*/

5
statgen/src/coords.c
View File

@ -15,9 +15,8 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
/**
* @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);
* 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

3
statgen/src/graph.c
View File

@ -23,6 +23,7 @@ int check_cycle (const int N, const int *pn)
*/
{
int cycle, i;
/* cycle number of cycle
*/
@ -58,6 +59,7 @@ int check_cycle_size (const int N, const int *matrix, const int depth, int *n_cy
*/
{
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
@ -147,6 +149,7 @@ int graph_analyze (const int N, const int *matrix, const int max_depth, int *iso
*/
{
int depth, i, j, *n_cycle, p, *pn;
/* depth depth of search for check_cycle_size
* n_cycle number of cycle
* p current weight

16
statgen/src/main.c
View File

@ -18,7 +18,16 @@
#include "summary_stat.h"
/**
* @fn main
*/
int main (int argc, char *argv[])
/**
* @return 1 - error in error_checking
* @return 2 - input file does not exist
* @return 3 - memory error
* @return 0 - exit without errors
*/
{
char filename[256], tmp_str[2048];
int error, i, index, j, k, label[2];
@ -30,6 +39,7 @@ 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 trajectory files
* logfile log file name
* output output file name
@ -232,7 +242,7 @@ int main (int argc, char *argv[])
if (f_inp == NULL)
{
print_message (quiet, stderr, log, f_log, 18, filename);
return 1;
return 2;
}
fscanf (f_inp, "%i", &num_atoms);
fclose (f_inp);
@ -260,7 +270,7 @@ int main (int argc, char *argv[])
(stat_all == NULL))
{
print_message (quiet, stderr, log, f_log, 19, argv[0]);
return 17;
return 3;
}
// set type_agl to zero
for (i=0; i<max_depth+2; i++)
@ -327,7 +337,7 @@ int main (int argc, char *argv[])
(stat_all == NULL))
{
print_message (quiet, stderr, log, f_log, 19, argv[0]);
return 18;
return 3;
}
print_message (quiet, stdout, log, f_log, 9, argv[0]);

7
statgen/src/stat_print.c
View File

@ -17,9 +17,9 @@ int printing_agl (const char *input, const char *output, const int *connect,
/**
* @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);
* 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
@ -39,6 +39,7 @@ int printing_agl (const char *input, const char *output, const int *connect,
{
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

5
statgen/src/stat_select.c
View File

@ -15,8 +15,8 @@ int create_matrix (const int num_mol, const int num_atoms, const int *label_mol,
/**
* @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);
* 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
@ -34,6 +34,7 @@ int create_matrix (const int num_mol, const int num_atoms, const int *label_mol,
{
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

5
statgen/src/stat_sort.c
View File

@ -13,8 +13,8 @@ int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *a
/**
* @brief function that processes connectivity matrix
* @code
* proc_matrix (number_of_molecules, connect_matrix,
* num_of_molecules_in_aglomerates, aglomerates, statistic, summary_statistic);
* proc_matrix (number_of_molecules, connect_matrix, num_of_molecules_in_aglomerates,
* aglomerates, statistic, summary_statistic);
* @endcode
*
* @param num_mol number of molecules
@ -29,6 +29,7 @@ int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *a
*/
{
int i, j, k, p, *bin;
/* p weight / graph index
* bin binary massive of labels
*/

1
statgen/src/summary_stat.c
View File

@ -30,6 +30,7 @@ int summary_statistic (const char *filename, const int step, const int num_mol,
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

5
statgen/statgen.doxygen
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@ -38,7 +38,7 @@ PROJECT_NUMBER = V.1.0.1
# for a project that appears at the top of each page and should give viewer
# a quick idea about the purpose of the project. Keep the description short.
PROJECT_BRIEF = "Program for analyze molecular dynamic trajectories"
PROJECT_BRIEF = "Program that analyzes molecular dynamic trajectories using topological analysis"
# With the PROJECT_LOGO tag one can specify an logo or icon that is
# included in the documentation. The maximum height of the logo should not
@ -52,7 +52,7 @@ PROJECT_LOGO = /home/arcanis/Documents/github/moldyn/statgen/logo.png
# If a relative path is entered, it will be relative to the location
# where doxygen was started. If left blank the current directory will be used.
OUTPUT_DIRECTORY = /home/arcanis/Documents/github/moldyn/statgen/docs
OUTPUT_DIRECTORY = ./docs
# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
# 4096 sub-directories (in 2 levels) under the output directory of each output
@ -680,7 +680,6 @@ INPUT_ENCODING = UTF-8
# *.f90 *.f *.for *.vhd *.vhdl
FILE_PATTERNS = *.c \
*.h \
*.dox
# The RECURSIVE tag can be used to turn specify whether or not subdirectories

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