mirror of
https://github.com/arcan1s/moldyn.git
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271 lines
7.5 KiB
C
271 lines
7.5 KiB
C
/**
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* @file
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*/
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/**
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* @mainpage mm_trj2pdb
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* @image latex ./logo.png
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*
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* @section intro_sec Introduction
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*
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* <b>About this program</b>:
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* <ul>
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* <li>Program that creates PDB file from trajectory snapshot
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* </ul>
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*
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* <b>Developer</b>:
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* <ul>
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* <li>Evgeniy Alekseev aka arcanis <pre><esalexeev (at) gmail (dot) com></pre>
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*</ul>
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* <b>License</b>:
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* <ul>
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* <li>GPL
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* </ul>
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*
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* @section How-To-Use How to use
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* Usage:
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* <pre>
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* mm_trj2pdb -i INPUT -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]
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*
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* Parametrs:
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* -i - input file name
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* -o - output file name
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* -l - log enable
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* -q - quiet enable
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* -h - show this help and exit
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* </pre>
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*
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* @page Install
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*
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* @section Requirements Requirements
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* The application mm_trj2pdb requires the following external stuff:
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* - cmake >= 2.8
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* - gcc >= 4.8
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*
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* @section How-To How to install
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*
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* @subsection Linux Linux
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* @code
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* mkdir build && cd build
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* cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../
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* make
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* make install
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* @endcode
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*
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* @subsection Windows Windows
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* @code
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* create project file using 'cmake'
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* compile project
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* @endcode
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* You may also download compiled executable file for Win_x86.
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*
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* @page Changelog
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* V.1.1.1 (2013-09-03)
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* <ul>
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* <li>optimization
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* </ul>
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* V.1.1.0 (2013-09-02)
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* <ul>
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* <li>added help window
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* <li>added help docs
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* <li>small bug fixes
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* </ul>
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* V.1.0.3 (2013-08-30)
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* <ul>
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* <li>bug fixes
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* </ul>
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* V.1.0.1 (2013-07-27)
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* <ul>
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* <li>initial release
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* </ul>
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*/
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#include <math.h>
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include "add_main.h"
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#include "coords.h"
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#include "messages.h"
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#include "print_struct.h"
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/**
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* @fn main
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*/
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int main(int argc, char *argv[])
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/**
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* @return 1 - error in error_checking
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* @return 2 - input file does not exist
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* @return 3 - memory error
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* @return 4 - unknown flag
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* @return 0 - exit without errors
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*/
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{
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char tmp_str[2048];
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int error, i, *tmp_int;
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FILE *f_inp, *f_log;
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char *ch_type_atoms, input[256], logfile[256], output[256];
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float cell[3], *coords;
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int *label_mol, log, *needed_mol, num_atoms, num_mol, quiet, *true_label_mol;
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/* ch_type_atoms massive of char atom types
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* input input file name
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* logfile log file name
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* output output file name
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*
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* cell sell size
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* coords massive of coordinates
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*
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* label_mol massive of numbers of molecule for atoms
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* log status of log-mode
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* needed_mol massive of numbers of needed molecule
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* num_atoms number of atoms
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* num_mol number of molecules
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* quiet status of quiet-mode
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* true_label_mol massive of true numbers of molecule for atoms
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*/
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set_defaults (input, &log, output, &quiet);
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for (i=1; i<argc; i++)
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{
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if ((argv[i][0] == '-') && (argv[i][1] == 'h') && (argv[i][2] == '\0'))
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{
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sprintf (tmp_str, " mm_trj2pdb\n");
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sprintf (tmp_str, "%sProgram for create PDB file from trajectory snapshot\n", tmp_str);
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sprintf (tmp_str, "%sVersion : 1.1.1 License : GPL\n", tmp_str);
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sprintf (tmp_str, "%s Evgeniy Alekseev aka arcanis\n", tmp_str);
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sprintf (tmp_str, "%s E-mail : esalexeev@gmail.com\n\n", tmp_str);
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sprintf (tmp_str, "%sUsage:\n", tmp_str);
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sprintf (tmp_str, "%smm_trj2pdb -i INPUT -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
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sprintf (tmp_str, "%sParametrs:\n", tmp_str);
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sprintf (tmp_str, "%s -i - input file name\n", tmp_str);
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sprintf (tmp_str, "%s -o - output file name\n", tmp_str);
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sprintf (tmp_str, "%s -l - log enable\n", tmp_str);
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sprintf (tmp_str, "%s -q - quiet enable\n", tmp_str);
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sprintf (tmp_str, "%s -h - show this help and exit\n", tmp_str);
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fputs (tmp_str, stdout);
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return 0;
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}
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else if ((argv[i][0] == '-') && (argv[i][1] == 'i') && (argv[i][2] == '\0'))
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// input file
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{
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strcpy (input, argv[i+1]);
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i++;
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}
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else if ((argv[i][0] == '-') && (argv[i][1] == 'o') && (argv[i][2] == '\0'))
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// output file
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{
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strcpy (output, argv[i+1]);
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i++;
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}
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else if ((argv[i][0] == '-') && (argv[i][1] == 'l') && (argv[i][2] == '\0'))
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// log mode
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{
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log = 1;
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strcpy (logfile, argv[i+1]);
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i++;
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}
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else if ((argv[i][0] == '-') && (argv[i][1] == 'q') && (argv[i][2] == '\0'))
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// quiet mode
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{
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quiet = 1;
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}
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else
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// unknown flag
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{
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return 4;
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}
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}
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if (log == 1)
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f_log = fopen (logfile, "w");
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print_message (quiet, stdout, log, f_log, 0, argv[0]);
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print_message (quiet, stdout, log, f_log, 1, argv[0]);
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// error check
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error = error_checking (input, output);
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if (error != 0)
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{
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print_message (quiet, stderr, log, f_log, 17, argv[0]);
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return 1;
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}
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print_message (quiet, stdout, log, f_log, 2, argv[0]);
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// processing
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// initial variables
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print_message (quiet, stdout, log, f_log, 3, input);
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f_inp = fopen (input, "r");
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if (f_inp == NULL)
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{
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print_message (quiet, stderr, log, f_log, 18, input);
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return 2;
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}
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fscanf (f_inp, "%i", &num_atoms);
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fclose (f_inp);
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ch_type_atoms = (char *) malloc (2 * num_atoms * sizeof (char));
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coords = (float *) malloc (3 * 8 * num_atoms * sizeof (float));
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label_mol = (int *) malloc (8 * num_atoms * sizeof (int));
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needed_mol = (int *) malloc (num_atoms * sizeof (int));
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tmp_int = (int *) malloc (8 * num_atoms * sizeof (int));
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true_label_mol = (int *) malloc (num_atoms * sizeof (int));
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// error checking
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if ((ch_type_atoms == NULL) ||
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(coords == NULL) ||
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(label_mol == NULL) ||
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(needed_mol == NULL) ||
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(tmp_int == NULL) ||
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(true_label_mol == NULL))
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{
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print_message (quiet, stderr, log, f_log, 19, argv[0]);
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return 3;
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}
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for (i=0; i<3; i++)
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cell[i] = 0.0;
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sprintf (tmp_str, "%6cInput file: '%s';\n%6cOutput file: '%s';\n%6cLog: %i;\n%6cQuiet: %i;\n",
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' ', input, ' ', output, ' ', log, ' ', quiet);
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print_message (quiet, stdout, log, f_log, 5, tmp_str);
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print_message (quiet, stdout, log, f_log, 6, argv[0]);
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// reading coordinates
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print_message (quiet, stdout, log, f_log, 7, input);
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error = 1;
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error = reading_coords (1, input, tmp_int[0], tmp_int, cell, &num_mol, &num_atoms,
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true_label_mol, label_mol, tmp_int, coords, ch_type_atoms);
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// print coordinates
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if (error == 0)
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{
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sprintf (tmp_str, "%6cNumber of molecules: %i; %6cNumber of atoms: %i\n",
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' ', num_mol, ' ', num_atoms);
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for (i=0; i<num_mol; i++)
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needed_mol[i] = 8 * i;
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error = 1;
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error = print_structure (output, num_mol, needed_mol, num_atoms,
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label_mol, ch_type_atoms, coords);
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}
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if (error == 0)
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print_message (quiet, stderr, log, f_log, 12, output);
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print_message (quiet, stderr, log, f_log, 13, argv[0]);
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print_message (quiet, stdout, log, f_log, 15, argv[0]);
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// free memory
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free (ch_type_atoms);
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free (coords);
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free (label_mol);
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free (needed_mol);
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free (tmp_int);
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free (true_label_mol);
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print_message (quiet, stdout, log, f_log, 16, argv[0]);
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if (log == 1)
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fclose (f_log);
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return 0;
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} |