mirror of
https://github.com/arcan1s/moldyn.git
synced 2025-09-08 16:49:58 +00:00
305 lines
9.2 KiB
C
305 lines
9.2 KiB
C
/**
|
|
* @file
|
|
*/
|
|
/**
|
|
* @mainpage mm_agl
|
|
* @image latex ./logo.png
|
|
*
|
|
* @section intro_sec Introduction
|
|
*
|
|
* <b>About this program</b>:
|
|
* <ul>
|
|
* <li>Program that creates PDB file with chosen agglomerate
|
|
* </ul>
|
|
*
|
|
* <b>Developer</b>:
|
|
* <ul>
|
|
* <li>Evgeniy Alekseev aka arcanis <pre><esalexeev (at) gmail (dot) com></pre>
|
|
*</ul>
|
|
* <b>License</b>:
|
|
* <ul>
|
|
* <li>GPL
|
|
* </ul>
|
|
*
|
|
* @section How-To-Use How to use
|
|
* Usage:
|
|
* <pre>
|
|
* mm_agl -a AGL_INP -i INPUT -c X,Y,Z -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]
|
|
*
|
|
* Parametrs:
|
|
* -a - input file with agglomerates (in format statgen)
|
|
* -i - input file with coordinates
|
|
* -c - cell size (float), A
|
|
* -o - output file name
|
|
* -l - log enable
|
|
* -q - quiet enable
|
|
* -h - show this help and exit
|
|
* </pre>
|
|
*
|
|
* @page Install
|
|
*
|
|
* @section Requirements Requirements
|
|
* The application mm_agl requires the following external stuff:
|
|
* - cmake >= 2.8
|
|
* - gcc >= 4.8
|
|
*
|
|
* @section How-To How to install
|
|
*
|
|
* @subsection Linux Linux
|
|
* @code
|
|
* mkdir build && cd build
|
|
* cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../
|
|
* make
|
|
* make install
|
|
* @endcode
|
|
*
|
|
* @subsection Windows Windows
|
|
* @code
|
|
* create project file using 'cmake'
|
|
* compile project
|
|
* @endcode
|
|
* You may also download compiled executable file for Win_x86.
|
|
*
|
|
* @page Changelog
|
|
* V.1.0.2 (2013-07-27)
|
|
* * initial release
|
|
*/
|
|
|
|
#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"
|
|
#include "select_mol.h"
|
|
#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 4 - unknown flag
|
|
* @return 0 - exit without errors
|
|
*/
|
|
{
|
|
char tmp_str[2048];
|
|
int error, i, *tmp_int;
|
|
FILE *f_inp, *f_log;
|
|
|
|
char aglinp[256], *ch_type_atoms, input[256], logfile[256], output[256];
|
|
float cell[3], *centr_coords, *coords;
|
|
int *label_mol, log, num_atoms, num_mol, num_needed_mol, *needed_mol, quiet,
|
|
*true_label_mol;
|
|
|
|
/* aglinp agglomerate file name
|
|
* ch_type_atoms massive of char atom types
|
|
* input input file name
|
|
* logfile log file name
|
|
* output output file name
|
|
*
|
|
* cell massive of cell size
|
|
* centr_coords massive of centered coordinates
|
|
* coords massive of coordinates
|
|
*
|
|
* label_mol massive of numbers of molecule for atoms
|
|
* log status of log-mode
|
|
* num_atoms number of atoms
|
|
* num_mol number of molecules
|
|
* num_needed_mol number of needed molecules
|
|
* needed_mol massive of number of needed molecules
|
|
* quiet status of quiet-mode
|
|
* true_label_mol massive of true numbers of molecule for atoms
|
|
*/
|
|
|
|
set_defaults (aglinp, cell, input, &log, output, &quiet);
|
|
|
|
for (i=1; i<argc; i++)
|
|
{
|
|
if ((argv[i][0] == '-') && (argv[i][1] == 'h') && (argv[i][2] == '\0'))
|
|
{
|
|
sprintf (tmp_str, " mm_agl\n");
|
|
sprintf (tmp_str, "%sProgram for create PDB file with chosen agglomerate\n", tmp_str);
|
|
sprintf (tmp_str, "%sVersion : 1.0.2 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, "%smm_agl -a AGL_INP -i INPUT -c X,Y,Z -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
|
|
sprintf (tmp_str, "%sParametrs:\n", tmp_str);
|
|
sprintf (tmp_str, "%s -a - input file with agglomerates (in format statgen)\n", tmp_str);
|
|
sprintf (tmp_str, "%s -i - input file with coordinates\n", tmp_str);
|
|
sprintf (tmp_str, "%s -c - cell size (float), A\n", tmp_str);
|
|
sprintf (tmp_str, "%s -o - output file name\n", tmp_str);
|
|
sprintf (tmp_str, "%s -l - log enable\n", tmp_str);
|
|
sprintf (tmp_str, "%s -q - quiet enable\n", tmp_str);
|
|
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') && (argv[i][2] == '\0'))
|
|
// input file
|
|
{
|
|
strcpy (aglinp, argv[i+1]);
|
|
i++;
|
|
}
|
|
else if ((argv[i][0] == '-') && (argv[i][1] == 'i') && (argv[i][2] == '\0'))
|
|
// input file
|
|
{
|
|
strcpy (input, argv[i+1]);
|
|
i++;
|
|
}
|
|
else if ((argv[i][0] == '-') && (argv[i][1] == 'c') && (argv[i][2] == '\0'))
|
|
// cell size
|
|
{
|
|
sscanf (argv[i+1], "%f,%f,%f", &cell[0], &cell[1], &cell[2]);
|
|
i++;
|
|
}
|
|
else if ((argv[i][0] == '-') && (argv[i][1] == 'o') && (argv[i][2] == '\0'))
|
|
// output file
|
|
{
|
|
strcpy (output, argv[i+1]);
|
|
i++;
|
|
}
|
|
else if ((argv[i][0] == '-') && (argv[i][1] == 'l') && (argv[i][2] == '\0'))
|
|
// log mode
|
|
{
|
|
log = 1;
|
|
strcpy (logfile, argv[i+1]);
|
|
i++;
|
|
}
|
|
else if ((argv[i][0] == '-') && (argv[i][1] == 'q') && (argv[i][2] == '\0'))
|
|
// quiet mode
|
|
{
|
|
quiet = 1;
|
|
}
|
|
else
|
|
// unknown flag
|
|
{
|
|
return 4;
|
|
}
|
|
}
|
|
|
|
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 2;
|
|
}
|
|
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 3;
|
|
}
|
|
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 agglomerate
|
|
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 agglomerate: %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 = 1;
|
|
error = reading_coords (2, input, num_needed_mol, needed_mol, cell, &num_mol,
|
|
&num_atoms, true_label_mol, label_mol, tmp_int, coords,
|
|
ch_type_atoms);
|
|
centr_coords = (float *) malloc (3 * 8 * num_mol * sizeof (float));
|
|
if (centr_coords == NULL)
|
|
{
|
|
print_message (quiet, stderr, log, f_log, 19, argv[0]);
|
|
return 3;
|
|
}
|
|
}
|
|
|
|
// 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 = 1;
|
|
error = set_center (num_atoms, num_mol, label_mol, coords, centr_coords);
|
|
}
|
|
if (error == 0)
|
|
{
|
|
print_message (quiet, stderr, log, f_log, 20, argv[0]);
|
|
error = 1;
|
|
error = select_molecule (centr_coords, num_needed_mol, needed_mol);
|
|
}
|
|
if (error == 0)
|
|
{
|
|
print_message (quiet, stderr, log, f_log, 4, argv[0]);
|
|
error = 1;
|
|
error = print_structure (output, num_needed_mol, needed_mol, num_atoms,
|
|
label_mol, ch_type_atoms, coords);
|
|
}
|
|
if (error == 0)
|
|
print_message (quiet, stderr, log, f_log, 12, output);
|
|
|
|
print_message (quiet, stderr, log, f_log, 13, argv[0]);
|
|
|
|
print_message (quiet, stdout, log, f_log, 15, argv[0]);
|
|
// free memory
|
|
free (ch_type_atoms);
|
|
free (centr_coords);
|
|
free (coords);
|
|
free (label_mol);
|
|
free (needed_mol);
|
|
free (tmp_int);
|
|
free (true_label_mol);
|
|
|
|
print_message (quiet, stdout, log, f_log, 16, argv[0]);
|
|
|
|
if (log == 1)
|
|
fclose (f_log);
|
|
return 0;
|
|
} |