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centres.c
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centres.c
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/*
Copyright (C) 1997-2000 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 , j ;
int residue , atom , total_atoms ;
int length , atom_serial_number , residue_number ;
/* Command line options */
char *input_file_name ;
char *gf_type ;
char gf_one_letter_code ;
/* File stuff */
FILE *ftdock_file ;
char line_buffer[100] ;
char *static_file_name ;
char *mobile_file_name ;
/* Structures */
struct Structure Static_Structure , Mobile_Structure ;
struct Structure Centres_Structure , Origin_Mobile_Structure ;
struct Structure Rotated_at_Origin_Mobile_Structure , Translated_and_Rotated_at_Origin_Mobile_Structure ;
/* Co-ordinates and Angles */
int x , y , z , z_twist , theta, phi ;
float average_x , average_y , average_z ;
/* Grid stuff */
int grid_size ;
float grid_span , one_span ;
/* ftdock.dat file values */
int complex_id , prev_complex_id , SCscore ;
float RPscore ;
/************/
/* 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 Centres central positions of mobile molecules program\n" ) ;
/************/
/* Memory allocation */
if( ( ( input_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( input_file_name , "ftdock_global.dat" ) ;
strcpy( gf_type , "G_DATA" ) ;
gf_one_letter_code = 'g' ;
/* Command Line parse */
for( i = 1 ; i < argc ; i ++ ) {
if( strcmp( argv[i] , "-in" ) == 0 ) {
i ++ ;
if( ( i == argc ) || ( strncmp( argv[i] , "-" , 1 ) == 0 ) ) {
printf( "Bad command line\n" ) ;
exit( EXIT_FAILURE ) ;
}
strcpy( input_file_name , argv[i] ) ;
} else {
if( strcmp( argv[i] , "-fine" ) == 0 ) {
strcpy( gf_type , "F_DATA" ) ;
gf_one_letter_code = 'f' ;
} else {
printf( "Bad command line\n" ) ;
exit( EXIT_FAILURE ) ;
}
}
}
/************/
/* Read neat data file - headers */
if( ( ftdock_file = fopen( input_file_name , "r" ) ) == NULL ) {
printf( "Could not open %s for reading.\nDying\n\n" , input_file_name ) ;
exit( EXIT_FAILURE ) ;
}
while( fgets( line_buffer, 99, ftdock_file ) ) {
if( strncmp( line_buffer , "Static molecule" , 15 ) == 0 ) sscanf( line_buffer , "Static molecule :: %s" , static_file_name ) ;
if( strncmp( line_buffer , "Mobile molecule" , 15 ) == 0 ) sscanf( line_buffer , "Mobile molecule :: %s" , mobile_file_name ) ;
if( gf_one_letter_code == 'g' ) {
if( strncmp( line_buffer , "Global grid size" , 16 ) == 0 ) sscanf( line_buffer , "Global grid size :: %d" , &grid_size ) ;
} else {
if( strncmp( line_buffer , "Refinement grid size" , 20 ) == 0 ) sscanf( line_buffer , "Refinement grid size :: %d" , &grid_size ) ;
}
if( strncmp( line_buffer , gf_type , 6 ) == 0 ) break ;
}
fclose( ftdock_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 ) ;
/************/
/* Store new structures centered on Origin */
Centres_Structure = translate_structure_onto_origin( Static_Structure ) ;
Origin_Mobile_Structure = translate_structure_onto_origin( Mobile_Structure ) ;
/* Free some 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 ) ;
/************/
/* Calculate Grid stuff */
grid_span = total_span_of_structures( Centres_Structure , Origin_Mobile_Structure ) ;
one_span = grid_span / (float)grid_size ;
/************/
/* Reopen ftdock.dat */
if( ( ftdock_file = fopen( input_file_name , "r" ) ) == NULL ) {
printf( "Could not open %s for reading.\nDying\n\n" , input_file_name ) ;
exit( EXIT_FAILURE ) ;
}
/************/
/* Loop */
length = Centres_Structure.length ;
atom_serial_number = Centres_Structure.Residue[length].Atom[1].serial + 100 ;
residue_number = 0 ;
while( fgets( line_buffer, 99, ftdock_file ) ) {
if( strncmp( line_buffer , gf_type , 6 ) == 0 ) {
sscanf( line_buffer + 1 , "_DATA %d %d %d %f %d %d %d %d %d %d" , &complex_id , &prev_complex_id , &SCscore , &RPscore , &x , &y , &z , &z_twist , &theta , &phi ) ;
/* Rotate Mobile Structure */
Rotated_at_Origin_Mobile_Structure = rotate_structure( Origin_Mobile_Structure , z_twist , theta , phi ) ;
/* Translate Mobile Structure */
Translated_and_Rotated_at_Origin_Mobile_Structure = translate_structure( Rotated_at_Origin_Mobile_Structure , (float)x * one_span , (float)y * one_span , (float)z * one_span ) ;
/* Find current centre of mobile structure */
total_atoms = 0 ;
average_x = 0 ;
average_y = 0 ;
average_z = 0 ;
for( residue = 1 ; residue <= Translated_and_Rotated_at_Origin_Mobile_Structure.length ; residue ++ ) {
for( atom = 1 ; atom <= Translated_and_Rotated_at_Origin_Mobile_Structure.Residue[residue].size ; atom ++ ) {
total_atoms ++ ;
average_x += Translated_and_Rotated_at_Origin_Mobile_Structure.Residue[residue].Atom[atom].coord[1] ;
average_y += Translated_and_Rotated_at_Origin_Mobile_Structure.Residue[residue].Atom[atom].coord[2] ;
average_z += Translated_and_Rotated_at_Origin_Mobile_Structure.Residue[residue].Atom[atom].coord[3] ;
}
}
average_x /= (float)total_atoms ;
average_y /= (float)total_atoms ;
average_z /= (float)total_atoms ;
/* Add centre */
length ++ ;
atom_serial_number ++ ;
residue_number ++ ;
if( ( Centres_Structure.Residue = (struct Amino_Acid * ) realloc ( Centres_Structure.Residue, ( length + 1 ) * sizeof_Amino_Acid ) ) == NULL ) {
GENERAL_MEMORY_PROBLEM
}
strcpy( Centres_Structure.Residue[length].chainID , "X" ) ;
sprintf( Centres_Structure.Residue[length].res_seq_plus_iCode , "%4d " , residue_number ) ;
strcpy( Centres_Structure.Residue[length].olc , "x" ) ;
Centres_Structure.Residue[length].nc = 0 ;
Centres_Structure.Residue[length].size = 1 ;
strcpy( Centres_Structure.Residue[length].res_name , "HOH" ) ;
if( ( Centres_Structure.Residue[length].Atom = ( struct Atom * ) malloc ( 2 * sizeof_Atom ) ) == NULL ) {
GENERAL_MEMORY_PROBLEM
}
Centres_Structure.Residue[length].Atom[1].serial = atom_serial_number ;
strcpy( Centres_Structure.Residue[length].Atom[1].atom_name, " O " ) ;
Centres_Structure.Residue[length].Atom[1].coord[1] = average_x ;
Centres_Structure.Residue[length].Atom[1].coord[2] = average_y ;
Centres_Structure.Residue[length].Atom[1].coord[3] = average_z ;
Centres_Structure.Residue[length].Atom[1].occupancy = 0.0 ;
Centres_Structure.Residue[length].Atom[1].temp_factor = 0.0 ;
/* Free some memory */
for( j = 1 ; j <= Rotated_at_Origin_Mobile_Structure.length ; j ++ ) {
free( Rotated_at_Origin_Mobile_Structure.Residue[j].Atom ) ;
free( Translated_and_Rotated_at_Origin_Mobile_Structure.Residue[j].Atom ) ;
}
free( Rotated_at_Origin_Mobile_Structure.Residue ) ;
free( Translated_and_Rotated_at_Origin_Mobile_Structure.Residue ) ;
}
}
/* End of Loop */
Centres_Structure.length = length ;
/* Write pdb file */
write_structure_to_pdb( Centres_Structure , "centres.pdb" ) ;
/************/
/* Free the memory */
for( i = 1 ; i <= Centres_Structure.length ; i ++ ) {
free( Centres_Structure.Residue[i].Atom ) ;
}
free( Centres_Structure.Residue ) ;
for( i = 1 ; i <= Origin_Mobile_Structure.length ; i ++ ) {
free( Origin_Mobile_Structure.Residue[i].Atom ) ;
}
free( Origin_Mobile_Structure.Residue ) ;
/************/
printf( "Finished\n\n" ) ;
return( 0 ) ;
} /* end main */