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rpdock.c
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rpdock.c
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/*
Copyright (C) 1997-2001 Imperial Cancer Research Technology
author: Gidon Moont
Biomolecular Modelling Laboratory
Imperial Cancer Research Fund
44 Lincoln's Inn Fields
London WC2A 3PX
+44 (0)20 7269 3348
http://www.bmm.icnet.uk/
*/
#include "structures.h"
int main( int argc , char *argv[] ) {
/* index counters */
int i ;
/* Command line options */
char *static_file_name ;
char *mobile_file_name ;
char *matrix_file_name ;
char *gf_type ;
char gf_one_letter_code ;
char *default_matrix_file_name ;
/* File stuff */
FILE *matrix_file ;
char line_buffer[200] ;
/* ftdock_*.dat file values */
float RPscore ;
/* Structures */
struct Structure Static_Structure , Mobile_Structure ;
/* Grid stuff */
int static_residue , static_atom ;
int mobile_residue , mobile_atom ;
int prox ;
struct Matrix Matrix ;
/************/
/* Its nice to tell people what going on straight away */
setvbuf( stdout , (char *)NULL , _IONBF , 0 ) ;
printf( "\n 3D-Dock Suite (May 2000)\n" ) ;
printf( " Copyright (C) 1997-2001 Imperial Cancer Research Technology\n" ) ;
printf( " Biomolecular Modelling Laboratory\n" ) ;
printf( " Imperial Cancer Research Fund\n" ) ;
printf( " 44 Lincoln's Inn Fields\n" ) ;
printf( " London WC2A 3PX\n" ) ;
printf( " +44 (0)20 7269 3565\n" ) ;
printf( " http://www.bmm.icnet.uk/\n\n" ) ;
printf( "Starting RPDock residue level pair potential score program\n" ) ;
/************/
/* Memory allocation */
if( ( ( matrix_file_name = ( char * ) malloc ( 500 * sizeof( char ) ) ) == NULL ) ||
( ( gf_type = ( char * ) malloc ( 10 * sizeof( char ) ) ) == NULL ) ||
( ( static_file_name = ( char * ) malloc ( 500 * sizeof( char ) ) ) == NULL ) ||
( ( mobile_file_name = ( char * ) malloc ( 500 * sizeof( char ) ) ) == NULL ) ) {
GENERAL_MEMORY_PROBLEM
}
/************/
/* Command Line defaults */
strcpy( matrix_file_name , "best.matrix" ) ;
strcpy( gf_type , "G_DATA" ) ;
gf_one_letter_code = 'g' ;
default_matrix_file_name = "(default)" ;
/* Command Line parse */
for( i = 1 ; i < argc ; i ++ ) {
if( strcmp( argv[i] , "-p1" ) == 0 ) {
i ++ ;
if( ( i == argc ) || ( strncmp( argv[i] , "-" , 1 ) == 0 ) ) {
printf( "Bad command line\n" ) ;
exit( EXIT_FAILURE ) ;
}
strcpy( static_file_name , argv[i] ) ;
} else {
if( strcmp( argv[i] , "-p2" ) == 0 ) {
i ++ ;
if( ( i == argc ) || ( strncmp( argv[i] , "-" , 1 ) == 0 ) ) {
printf( "Bad command line\n" ) ;
exit( EXIT_FAILURE ) ;
}
strcpy( mobile_file_name , argv[i] ) ;
} else {
if( strcmp( argv[i] , "-matrix" ) == 0 ) {
i ++ ;
if( ( i == argc ) || ( strncmp( argv[i] , "-" , 1 ) == 0 ) ) {
printf( "Bad command line\n" ) ;
exit( EXIT_FAILURE ) ;
}
strcpy( matrix_file_name , argv[i] ) ;
default_matrix_file_name = "(user defined)" ;
} else {
printf( "Bad command line\n" ) ;
exit( EXIT_FAILURE ) ;
}
}
}
}
/************/
/* Read in matrix */
if( ( matrix_file = fopen( matrix_file_name , "r" ) ) == NULL ) {
printf( "Could not open %s for reading.\nDying\n\n" , matrix_file_name ) ;
exit( EXIT_FAILURE ) ;
}
fgets( line_buffer , 199 , matrix_file ) ;
if( strncmp( line_buffer , "Description" , 11 ) == 0 ) {
sscanf( line_buffer , "Description :: %s" , Matrix.description ) ;
} else {
printf( "Error in matrix file\nDying\n" ) ;
exit( EXIT_FAILURE ) ;
}
fgets( line_buffer , 199 , matrix_file ) ;
if( strncmp( line_buffer , "Distance cut off" , 16 ) == 0 ) {
sscanf( line_buffer , "Distance cut off :: %f" , &Matrix.distance ) ;
} else {
printf( "Error in matrix file\nDying\n" ) ;
exit( EXIT_FAILURE ) ;
}
for( i = 1 ; i <= 20 ; i ++ ) {
fgets( line_buffer , 199 , matrix_file ) ;
sscanf( line_buffer , "%8f" , &Matrix.score[i][1] ) ;
sscanf( line_buffer + 8 , "%8f" , &Matrix.score[i][2] ) ;
sscanf( line_buffer + 16 , "%8f" , &Matrix.score[i][3] ) ;
sscanf( line_buffer + 24 , "%8f" , &Matrix.score[i][4] ) ;
sscanf( line_buffer + 32 , "%8f" , &Matrix.score[i][5] ) ;
sscanf( line_buffer + 40 , "%8f" , &Matrix.score[i][6] ) ;
sscanf( line_buffer + 48 , "%8f" , &Matrix.score[i][7] ) ;
sscanf( line_buffer + 56 , "%8f" , &Matrix.score[i][8] ) ;
sscanf( line_buffer + 64 , "%8f" , &Matrix.score[i][9] ) ;
sscanf( line_buffer + 72 , "%8f" , &Matrix.score[i][10] ) ;
sscanf( line_buffer + 80 , "%8f" , &Matrix.score[i][11] ) ;
sscanf( line_buffer + 88 , "%8f" , &Matrix.score[i][12] ) ;
sscanf( line_buffer + 96 , "%8f" , &Matrix.score[i][13] ) ;
sscanf( line_buffer + 104 , "%8f" , &Matrix.score[i][14] ) ;
sscanf( line_buffer + 112 , "%8f" , &Matrix.score[i][15] ) ;
sscanf( line_buffer + 120 , "%8f" , &Matrix.score[i][16] ) ;
sscanf( line_buffer + 128 , "%8f" , &Matrix.score[i][17] ) ;
sscanf( line_buffer + 136 , "%8f" , &Matrix.score[i][18] ) ;
sscanf( line_buffer + 144 , "%8f" , &Matrix.score[i][19] ) ;
sscanf( line_buffer + 152 , "%8f" , &Matrix.score[i][20] ) ;
}
fclose( matrix_file ) ;
/************/
/* Read in Structures from pdb files */
Static_Structure = read_pdb_to_structure( static_file_name ) ;
Mobile_Structure = read_pdb_to_structure( mobile_file_name ) ;
/************/
/* Main program loop */
/* No buffering at all */
setvbuf( stdout , (char *)NULL , _IONBF , 0 ) ;
RPscore = 0 ;
for( static_residue = 1 ; static_residue <= Static_Structure.length ; static_residue ++ ) {
if( Static_Structure.Residue[static_residue].nc > 20 ) break ;
for( mobile_residue = 1 ; mobile_residue <= Mobile_Structure.length ; mobile_residue ++ ) {
if( Mobile_Structure.Residue[mobile_residue].nc > 20 ) break ;
prox = 0 ;
for( static_atom = 1 ; static_atom <= Static_Structure.Residue[static_residue].size ; static_atom ++ ) {
for( mobile_atom = 1 ; mobile_atom <= Mobile_Structure.Residue[mobile_residue].size ; mobile_atom ++ ) {
if( ( ( Static_Structure.Residue[static_residue].Atom[static_atom].coord[1] - Mobile_Structure.Residue[mobile_residue].Atom[mobile_atom].coord[1] ) * ( Static_Structure.Residue[static_residue].Atom[static_atom].coord[1] - Mobile_Structure.Residue[mobile_residue].Atom[mobile_atom].coord[1] ) ) + ( ( Static_Structure.Residue[static_residue].Atom[static_atom].coord[2] - Mobile_Structure.Residue[mobile_residue].Atom[mobile_atom].coord[2] ) * ( Static_Structure.Residue[static_residue].Atom[static_atom].coord[2] - Mobile_Structure.Residue[mobile_residue].Atom[mobile_atom].coord[2] ) ) + ( ( Static_Structure.Residue[static_residue].Atom[static_atom].coord[3] - Mobile_Structure.Residue[mobile_residue].Atom[mobile_atom].coord[3] ) * ( Static_Structure.Residue[static_residue].Atom[static_atom].coord[3] - Mobile_Structure.Residue[mobile_residue].Atom[mobile_atom].coord[3] ) ) < ( Matrix.distance * Matrix.distance ) ) prox = 1 ;
}
}
if( prox == 1 ) RPscore += Matrix.score[Static_Structure.Residue[static_residue].nc][Mobile_Structure.Residue[mobile_residue].nc] ;
}
}
fprintf( stdout, "%6s %8.3f\n" , gf_type , RPscore ) ;
printf( "\n" ) ;
/************/
/* Free the memory */
for( i = 1 ; i <= Static_Structure.length ; i ++ ) {
free( Static_Structure.Residue[i].Atom ) ;
}
free( Static_Structure.Residue ) ;
for( i = 1 ; i <= Mobile_Structure.length ; i ++ ) {
free( Mobile_Structure.Residue[i].Atom ) ;
}
free( Mobile_Structure.Residue ) ;
/************/
printf( "Finished\n\n" ) ;
return( 0 ) ;
} /* end main */