int main(int argc, char *argv[])
{
/* index counters */
int i, j;
int residue_s, atom_s;
/* Command line options */
char *input_file_name;
int b0, b1, b2;
char *gf_type;
char gf_one_letter_code;
int c_alpha;
/* File stuff */
FILE *ftdock_file;
char line_buffer[100];
char *static_file_name;
char *mobile_file_name;
char *complex_file_name;
/* Structures */
struct Structure Static_Structure, Mobile_Structure;
struct Structure Origin_Static_Structure, Origin_Mobile_Structure;
struct Structure Rotated_at_Origin_Mobile_Structure, Translated_and_Rotated_at_Origin_Mobile_Structure;
struct Structure Complex_Structure, C_Alpha_Complex_Structure;
/* Co-ordinates and Angles */
int x, y, z, z_twist, theta, phi;
/* 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 (March 2001)\n");
printf(" Copyright (C) 1997-2000 Gidon Moont\n");
printf(" This program comes with ABSOLUTELY NO WARRANTY\n");
printf(" for details see license. This program is free software,\n");
printf(" and you may redistribute it under certain conditions.\n\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 3348\n");
printf(" http://www.bmm.icnet.uk/\n\n");
printf("Starting Build 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) || ((complex_file_name = (char *)malloc(500 * sizeof(char))) == NULL)) {
GENERAL_MEMORY_PROBLEM}
/************/
/* Command Line defaults */
strcpy(input_file_name, "ftdock_rpscored.dat");
b0 = 0;
b1 = 1;
b2 = NUMBER_TO_KEEP;
strcpy(gf_type, "G_DATA");
gf_one_letter_code = 'g';
c_alpha = 0;
/* 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], "-b0") == 0) {
i++;
if ((i == argc) || (strncmp(argv[i], "-", 1) == 0)) {
printf("Bad command line\n");
exit(EXIT_FAILURE);
}
sscanf(argv[i], "%d", &b0);
} else {
if (strcmp(argv[i], "-b1") == 0) {
i++;
if ((i == argc) || (strncmp(argv[i], "-", 1) == 0)) {
printf("Bad command line\n");
exit(EXIT_FAILURE);
}
sscanf(argv[i], "%d", &b1);
} else {
if (strcmp(argv[i], "-b2") == 0) {
i++;
if ((i == argc) || (strncmp(argv[i], "-", 1) == 0)) {
printf("Bad command line\n");
exit(EXIT_FAILURE);
}
sscanf(argv[i], "%d", &b2);
} else {
if (strcmp(argv[i], "-fine") == 0) {
strcpy(gf_type, "F_DATA");
gf_one_letter_code = 'f';
} else {
if (strcmp(argv[i], "-c_alpha") == 0) {
c_alpha = 1;
} 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 */
Origin_Static_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(Origin_Static_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);
}
/************/
/* Choose between range to build or specific individual */
if (b0 != 0) {
/* Build individual */
printf("Building complex %s %d only\n", gf_type, b0);
b1 = b0;
b2 = b0;
} else {
/* Build range */
printf("Building complexes %s %d -> %d\n", gf_type, b1, b2);
}
/* Build */
while (fgets(line_buffer, 99, ftdock_file)) {
for (i = b1; i <= b2; i++) {
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);
if (complex_id == i) {
/* 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);
/************/
/* Write Complex */
Complex_Structure = merge_structures(Origin_Static_Structure, Translated_and_Rotated_at_Origin_Mobile_Structure);
sprintf(complex_file_name, "Complex_%d%c.pdb", complex_id, gf_one_letter_code);
/************/
if (c_alpha == 1) {
if ((C_Alpha_Complex_Structure.Residue = (struct Amino_Acid *)malloc((Complex_Structure.length + 1) * sizeof_Amino_Acid)) == NULL) {
GENERAL_MEMORY_PROBLEM}
strcpy(C_Alpha_Complex_Structure.ident, Complex_Structure.ident);
C_Alpha_Complex_Structure.length = Complex_Structure.length;
for (residue_s = 1; residue_s <= Complex_Structure.length; residue_s++) {
C_Alpha_Complex_Structure.Residue[residue_s] = Complex_Structure.Residue[residue_s];
C_Alpha_Complex_Structure.Residue[residue_s].size = 1;
if ((C_Alpha_Complex_Structure.Residue[residue_s].Atom = (struct Atom *)malloc(2 * sizeof_Atom)) == NULL) {
GENERAL_MEMORY_PROBLEM}
for (atom_s = 1; atom_s <= Complex_Structure.Residue[residue_s].size; atom_s++) {
if (strcmp(Complex_Structure.Residue[residue_s].Atom[atom_s].atom_name, " CA ") == 0) {
C_Alpha_Complex_Structure.Residue[residue_s].Atom[1] = Complex_Structure.Residue[residue_s].Atom[atom_s];
}
}
}
sprintf(complex_file_name, "CA_Complex_%d%c.pdb", complex_id, gf_one_letter_code);
write_structure_to_pdb(C_Alpha_Complex_Structure, complex_file_name);
} else {
write_structure_to_pdb(Complex_Structure, complex_file_name);
}
/************/
/* 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);
for (j = 1; j <= Complex_Structure.length; j++) {
free(Complex_Structure.Residue[j].Atom);
}
free(Complex_Structure.Residue);
}
}
int main( int argc , char *argv[] ) {
/* index counters */
int i ;
/* Command line options */
char input_file_name[1024] ;
char output_file_name[1024] ;
/* Angles stuff */
int z_twist , theta , phi ;
/* Structures */
struct Structure Input_Structure , Origin_Structure , Spun_Structure ;
/************/
/* Its nice to tell people what going on straight away */
setvbuf( stdout , (char *)NULL , _IONBF , 0 ) ;
printf( "\n 3D-Dock Suite (March 2001)\n" ) ;
printf( " Copyright (C) 1997-2000 Gidon Moont\n" ) ;
printf( " This program comes with ABSOLUTELY NO WARRANTY\n" ) ;
printf( " for details see license. This program is free software,\n");
printf( " and you may redistribute it under certain conditions.\n\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 3348\n" ) ;
printf( " http://www.bmm.icnet.uk/\n\n" ) ;
/************/
printf( "Starting FTDock random spin program (FTDock v2.0)\n" ) ;
/************/
/* Command Line defaults */
strcpy( input_file_name , "unspun.pdb" ) ;
strcpy( output_file_name , "spun.pdb" ) ;
/* 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] , "-out" ) == 0 ) {
i ++ ;
if( ( i == argc ) || ( strncmp( argv[i] , "-" , 1 ) == 0 ) ) {
printf( "Bad command line\n" ) ;
exit( EXIT_FAILURE ) ;
}
strcpy( output_file_name , argv[i] ) ;
} else {
printf( "Bad command line\n" ) ;
exit( EXIT_FAILURE ) ;
}
}
}
/************/
/* Read in Structure from pdb file */
Input_Structure = read_pdb_to_structure( input_file_name ) ;
/* Store new structures centered on Origin */
Origin_Structure = translate_structure_onto_origin( Input_Structure ) ;
/* Free some memory */
for( i = 1 ; i <= Input_Structure.length ; i ++ ) {
free( Input_Structure.Residue[i].Atom ) ;
}
free( Input_Structure.Residue ) ;
/* Spin Structure */
for( i = 0 ; i < 10 ; i ++ ) {
/* Get angles */
srand( (unsigned int)time( NULL ) ) ;
z_twist = (int)( 359 * ( (float)rand() / (float)RAND_MAX ) ) ;
theta = (int)( 179 * ( (float)rand() / (float)RAND_MAX ) ) ;
phi = (int)( 359 * ( (float)rand() / (float)RAND_MAX ) ) ;
Spun_Structure = rotate_structure( Origin_Structure , (long int)z_twist , (long int)theta , (long int)phi ) ;
for( i = 1 ; i <= Origin_Structure.length ; i ++ ) {
free( Origin_Structure.Residue[i].Atom ) ;
}
free( Origin_Structure.Residue ) ;
if( i != 9 ) Origin_Structure = duplicate_structure( Spun_Structure ) ;
}
write_structure_to_pdb( Spun_Structure , output_file_name ) ;
for( i = 1 ; i <= Spun_Structure.length ; i ++ ) {
free( Spun_Structure.Residue[i].Atom ) ;
}
free( Spun_Structure.Residue ) ;
/************/
printf( "\n\nFinished\n\n" ) ;
return( 0 ) ;
} /* end main */
