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ftdock.c
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ftdock.c
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/*
This file is part of ftdock, a program for rigid-body protein-protein docking
Copyright (C) 1997-2000 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/
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
#include "structures.h"
#ifdef USE_MPI
#include <mpi.h>
#endif
int main( int argc , char *argv[] ) {
/* index counters */
int i ;
/* Command line options */
char *output_file_name ;
char *static_file_name ;
char *mobile_file_name ;
int global_grid_size ;
int op_global_grid_size ;
float translation_step ;
int angle_step ;
float surface ;
float internal_value ;
int electrostatics ;
int keep_per_rotation ;
int kept_scores ;
int rescue ;
int calculate ;
float reverse_calculated_one_span ;
char *default_global_grid_size ;
char *default_angle_step ;
char *default_surface ;
char *default_internal_value ;
char *default_electrostatics ;
char *default_keep_per_rotation ;
/* File stuff */
FILE *ftdock_file ;
char line_buffer[100] ;
char *scratch_file_name ;
char *static_charge ;
char *mobile_charge ;
char *scratch_max_es_value ;
int id , id2 , SCscore , fflush_ct = 0 ;
float RPscore ;
int x , y , z , z_twist , theta , phi ;
/* Angles stuff */
struct Angle Angles ;
int first_rotation , rotation ;
float fft_scalefac;
/* Structures */
struct Structure Static_Structure , Mobile_Structure ;
struct Structure Origin_Static_Structure , Origin_Mobile_Structure ;
struct Structure Rotated_at_Origin_Mobile_Structure ;
/* Co-ordinates */
int xyz , fx , fy , fz , fxyz ;
/* Grid stuff */
float grid_span , one_span ;
fftw_real *static_grid ;
fftw_real *mobile_grid ;
fftw_real *convoluted_grid ;
fftw_real *static_elec_grid = ( void * ) 0 ;
fftw_real *mobile_elec_grid = ( void * ) 0 ;
fftw_real *convoluted_elec_grid = ( void * ) 0 ;
/* FFTW stuff */
rfftwnd_plan p , pinv ;
fftw_complex *static_fsg ;
fftw_complex *mobile_fsg ;
fftw_complex *multiple_fsg ;
fftw_complex *static_elec_fsg = ( void * ) 0 ;
fftw_complex *mobile_elec_fsg = ( void * ) 0 ;
fftw_complex *multiple_elec_fsg = ( void * ) 0 ;
/* Scores */
struct Score *Scores ;
float max_es_value ;
float tmp_es_value ;
float *max_es_value_array;
/* mpi stuff */
int rank, nproc, iproc ;
/************/
/* 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( "\n Optimized version (FFTW magic numbers) with MPI support enabled\n" ) ;
printf( " Proteins Interactions and Docking Group - Life Sciences\n" ) ;
printf( " Barcelona Supercomputing Center, 2011\n\n" ) ;
printf( "Starting FTDock (v2.0) global search program\n" ) ;
/************/
/* MPI Init */
#ifdef USE_MPI
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &nproc);
#else
rank = 0 ;
nproc = 1 ;
#endif
/* Memory allocation */
if( ( ( output_file_name = ( char * ) malloc ( 500 * sizeof( char ) ) ) == NULL ) ||
( ( scratch_file_name = ( char * ) malloc ( 500 * sizeof( char ) ) ) == NULL ) ||
( ( static_file_name = ( char * ) malloc ( 500 * sizeof( char ) ) ) == NULL ) ||
( ( static_charge = ( char * ) malloc ( 500 * sizeof( char ) ) ) == NULL ) ||
( ( mobile_charge = ( char * ) malloc ( 500 * sizeof( char ) ) ) == NULL ) ||
( ( scratch_max_es_value = ( char * ) malloc ( 500 * sizeof( char ) ) ) == NULL ) ||
( ( max_es_value_array = ( float * ) malloc ( nproc * sizeof( float ) ) ) == NULL ) ||
( ( mobile_file_name = ( char * ) malloc ( 500 * sizeof( char ) ) ) == NULL ) ) {
GENERAL_MEMORY_PROBLEM
}
/************/
/* Command Line defaults */
strcpy( output_file_name , "ftdock_global.dat" ) ;
strcpy( static_file_name , " --static file name was not provided--" ) ;
strcpy( mobile_file_name , " --mobile file name was not provided--" ) ;
global_grid_size = op_global_grid_size = 128 ;
angle_step = 12 ;
surface = 1.3 ;
internal_value = -15 ;
electrostatics = 1 ;
keep_per_rotation = 3 ;
rescue = 0 ;
calculate = 1 ;
reverse_calculated_one_span = 0.7 ;
default_global_grid_size = "(default calculated)" ;
default_angle_step = "(default)" ;
default_surface = "(default)" ;
default_internal_value = "(default)" ;
default_electrostatics = "(default)" ;
default_keep_per_rotation = "(default)" ;
/* Command Line parse */
for( i = 1 ; i < argc ; i ++ ) {
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 {
if( strcmp( argv[i] , "-static" ) == 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] , "-mobile" ) == 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] , "-grid" ) == 0 ) {
i ++ ;
if( ( i == argc ) || ( strncmp( argv[i] , "-" , 1 ) == 0 ) ) {
printf( "Bad command line\n" ) ;
exit( EXIT_FAILURE ) ;
}
sscanf( argv[i] , "%d" , &global_grid_size ) ;
if( ( global_grid_size % 2 ) != 0 ) {
printf( "Grid size must be even\n" ) ;
exit( EXIT_FAILURE ) ;
}
default_global_grid_size = "(user defined)" ;
calculate = 0 ;
} else {
if( strcmp( argv[i] , "-angle_step" ) == 0 ) {
i ++ ;
if( ( i == argc ) || ( strncmp( argv[i] , "-" , 1 ) == 0 ) ) {
printf( "Bad command line\n" ) ;
exit( EXIT_FAILURE ) ;
}
sscanf( argv[i] , "%d" , &angle_step ) ;
default_angle_step = "(user defined)" ;
} else {
if( strcmp( argv[i] , "-surface" ) == 0 ) {
i ++ ;
if( ( i == argc ) || ( strncmp( argv[i] , "-" , 1 ) == 0 ) ) {
printf( "Bad command line\n" ) ;
exit( EXIT_FAILURE ) ;
}
sscanf( argv[i] , "%f" , &surface ) ;
default_surface = "(user defined)" ;
} else {
if( strcmp( argv[i] , "-internal" ) == 0 ) {
i ++ ;
if( i == argc ) {
printf( "Bad command line\n" ) ;
exit( EXIT_FAILURE ) ;
}
sscanf( argv[i] , "%f" , &internal_value ) ;
default_internal_value = "(user defined)" ;
} else {
if( strcmp( argv[i] , "-noelec" ) == 0 ) {
electrostatics = 0 ;
default_electrostatics = "(user defined)" ;
} else {
if( strcmp( argv[i] , "-keep" ) == 0 ) {
i ++ ;
if( ( i == argc ) || ( strncmp( argv[i] , "-" , 1 ) == 0 ) ) {
printf( "Bad command line\n" ) ;
exit( EXIT_FAILURE ) ;
}
sscanf( argv[i] , "%d" , &keep_per_rotation ) ;
default_keep_per_rotation = "(user defined)" ;
} else {
if( strcmp( argv[i] , "-rescue" ) == 0 ) {
rescue = 1 ;
} else {
if( strcmp( argv[i] , "-calculate_grid" ) == 0 ) {
i ++ ;
if( ( i == argc ) || ( strncmp( argv[i] , "-" , 1 ) == 0 ) ) {
printf( "Bad command line\n" ) ;
exit( EXIT_FAILURE ) ;
}
calculate = 1 ;
default_global_grid_size = "(user defined calculated)" ;
sscanf( argv[i] , "%f" , &reverse_calculated_one_span ) ;
} else {
printf( "Bad command line\n" ) ;
exit( EXIT_FAILURE ) ;
}
}
}
}
}
}
}
}
}
}
}
}
/************/
/* Rescue option */
if( rescue == 1 ) {
printf( "RESCUE mode\n" ) ;
if( ( ftdock_file = fopen( "scratch_parameters.dat" , "r" ) ) == NULL ) {
printf( "Could not open scratch_parameters.dat for reading.\nDying\n\n" ) ;
exit( EXIT_FAILURE ) ;
}
calculate = 0 ;
default_global_grid_size = "(read from rescue file)" ;
default_angle_step = "(read from rescue file)" ;
default_surface = "(read from rescue file)" ;
default_internal_value = "(read from rescue file)" ;
default_electrostatics = "(read from rescue file)" ;
while( fgets( line_buffer , 199 , 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( strncmp( line_buffer , "Output file name" , 16 ) == 0 ) sscanf( line_buffer , "Output file name :: %s" , output_file_name ) ;
if( strncmp( line_buffer , "Global grid size" , 16 ) == 0 ) sscanf( line_buffer , "Global grid size :: %d" , &global_grid_size ) ;
if( strncmp( line_buffer , "Global search angle step" , 24 ) == 0 ) sscanf( line_buffer , "Global search angle step :: %d" , &angle_step ) ;
if( strncmp( line_buffer , "Global surface thickness" , 24 ) == 0 ) sscanf( line_buffer , "Global surface thickness :: %f" , &surface ) ;
if( strncmp( line_buffer , "Global internal deterrent value" , 31 ) == 0 ) sscanf( line_buffer , "Global internal deterrent value :: %f" , &internal_value ) ;
if( strncmp( line_buffer , "Electrostatics :: on" , 44 ) == 0 ) electrostatics = 1 ;
if( strncmp( line_buffer , "Electrostatics :: off" , 44 ) == 0 ) electrostatics = 0 ;
if( strncmp( line_buffer , "Global keep per rotation" , 25 ) == 0 ) sscanf( line_buffer , "Global keep per rotation :: %d" , &keep_per_rotation ) ;
}
fclose( ftdock_file ) ;
if( ( ftdock_file = fopen( "scratch_scores.dat" , "r" ) ) == NULL ) {
printf( "Could not open scratch_scores.dat for reading.\nDying\n\n" ) ;
exit( EXIT_FAILURE ) ;
}
fgets( line_buffer , 99 , ftdock_file ) ;
while( fgets( line_buffer , 99 , ftdock_file ) ) {
sscanf( line_buffer , "G_DATA %d " , &first_rotation ) ;
}
fclose( ftdock_file ) ;
first_rotation ++ ;
printf( "Will be starting from rotation %d\n" , first_rotation ) ;
/************/
} else {
first_rotation = 1 ;
}
#ifdef USE_MPI
first_rotation += rank ;
#endif
/************/
/* Do these things first so that bad inputs will be caught soonest */
/* Read in Structures from pdb files */
Static_Structure = read_pdb_to_structure( static_file_name ) ;
Mobile_Structure = read_pdb_to_structure( mobile_file_name ) ;
if( Mobile_Structure.length > Static_Structure.length ) {
printf( "WARNING\n" ) ;
printf( "The mobile molecule has more residues than the static\n" ) ;
printf( "Are you sure you have the correct molecules?\n" ) ;
printf( "Continuing anyway\n" ) ;
}
/************/
/* Get angles */
Angles = generate_global_angles( angle_step ) ;
printf( "Total number of rotations is %d\n" , Angles.n ) ;
/************/
/* Assign charges */
if( electrostatics == 1 ) {
printf( "Assigning charges\n" ) ;
assign_charges( Static_Structure ) ;
assign_charges( Mobile_Structure ) ;
#ifdef DEBUG
printf( "Writing charge files\n" ) ;
sprintf( static_charge , "%s%d%s", "static_pdb_" , rank , ".dat" ) ;
sprintf( mobile_charge , "%s%d%s", "mobile_pdb_" , rank , ".dat" ) ;
write_structure_to_pdb( Static_Structure, static_charge ) ;
write_structure_to_pdb( Mobile_Structure, mobile_charge ) ;
printf( "Done.\n" ) ;
#endif
}
/************/
/* 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 ) ;
if( calculate == 1 ) {
printf( "Using automatic calculation for grid size\n" ) ;
/* Number of grid spans */
global_grid_size = (int)( grid_span / reverse_calculated_one_span ) ;
/* Global grid size */
if( ( global_grid_size % 2 ) != 0 ) global_grid_size ++ ;
printf("Actual grid size is: %d\n", global_grid_size);
/* Optimiez Global grid size */
op_global_grid_size = (int)getOptimalGridSize(global_grid_size);
printf("Optimized grid size is: %d\n", op_global_grid_size);
/* Cube size */
one_span = grid_span / (float)global_grid_size ;
/* Update grid span */
printf("Actual grid span is: %f\n",grid_span);
grid_span = one_span * (float)op_global_grid_size;
printf("Recalculated grid span is: %f\n",grid_span);
/* Calculate new coordinates if necessary */
if (op_global_grid_size > global_grid_size) {
global_grid_size = op_global_grid_size;
}
} else {
one_span = grid_span / (float)global_grid_size ;
}
printf( "Span = %.3f angstroms\n" , grid_span ) ;
printf( "Grid size = %d\n" , global_grid_size ) ;
printf( "Each Grid cube = %.5f angstroms\n" , one_span ) ;
/************/
/* Memory Allocation */
if( ( Scores = ( struct Score * ) malloc ( ( keep_per_rotation + 2 ) * sizeof( struct Score ) ) ) == NULL ) {
GENERAL_MEMORY_PROBLEM
}
if(
( ( static_grid = ( fftw_real * ) malloc
( global_grid_size * global_grid_size * ( 2 * ( global_grid_size / 2 + 1 ) ) * sizeof( fftw_real ) ) ) == NULL )
||
( ( mobile_grid = ( fftw_real * ) malloc
( global_grid_size * global_grid_size * ( 2 * ( global_grid_size / 2 + 1 ) ) * sizeof( fftw_real ) ) ) == NULL )
||
( ( convoluted_grid = ( fftw_real * ) malloc
( global_grid_size * global_grid_size * ( 2 * ( global_grid_size / 2 + 1 ) ) * sizeof( fftw_real ) ) ) == NULL )
) {
printf( "Not enough memory for surface grids\nUse (sensible) smaller grid size\nDying\n\n" ) ;
exit( EXIT_FAILURE ) ;
}
static_fsg = ( fftw_complex * ) static_grid ;
mobile_fsg = ( fftw_complex * ) mobile_grid ;
multiple_fsg = ( fftw_complex * ) convoluted_grid ;
if( electrostatics == 1 ) {
if(
( ( static_elec_grid = ( fftw_real * ) malloc
( global_grid_size * global_grid_size * ( 2 * ( global_grid_size / 2 + 1 ) ) * sizeof( fftw_real ) ) ) == NULL )
||
( ( mobile_elec_grid = ( fftw_real * ) malloc
( global_grid_size * global_grid_size * ( 2 * ( global_grid_size / 2 + 1 ) ) * sizeof( fftw_real ) ) ) == NULL )
||
( ( convoluted_elec_grid = ( fftw_real * ) malloc
( global_grid_size * global_grid_size * ( 2 * ( global_grid_size / 2 + 1 ) ) * sizeof( fftw_real ) ) ) == NULL )
) {
printf( "Not enough memory for electrostatic grids\nSwitch off electrostatics or use (sensible) smaller grid size\nDying\n\n" ) ;
exit( EXIT_FAILURE ) ;
} else {
/* all ok */
printf( "Electrostatics are on\n" ) ;
}
static_elec_fsg = ( fftw_complex * ) static_elec_grid ;
mobile_elec_fsg = ( fftw_complex * ) mobile_elec_grid ;
multiple_elec_fsg = ( fftw_complex * ) convoluted_elec_grid ;
}
/************/
/* Create FFTW plans */
printf( "Creating plans\n" ) ;
p = rfftw3d_create_plan( global_grid_size , global_grid_size , global_grid_size ,
FFTW_REAL_TO_COMPLEX , FFTW_MEASURE | FFTW_IN_PLACE ) ;
pinv = rfftw3d_create_plan( global_grid_size , global_grid_size , global_grid_size ,
FFTW_COMPLEX_TO_REAL , FFTW_MEASURE | FFTW_IN_PLACE ) ;
/************/
printf( "Setting up Static Structure\n" ) ;
/* Discretise and surface the Static Structure (need do only once) */
discretise_structure( Origin_Static_Structure , grid_span , global_grid_size , static_grid ) ;
printf( " surfacing grid\n" ) ;
surface_grid( grid_span , global_grid_size , static_grid , surface , internal_value ) ;
/* Calculate electic field at all grid nodes (need do only once) */
if( electrostatics == 1 ) {
electric_field( Origin_Static_Structure , grid_span , global_grid_size , static_elec_grid ) ;
electric_field_zero_core( global_grid_size , static_elec_grid , static_grid , internal_value ) ;
}
/* Fourier Transform the static grids (need do only once) */
printf( " one time forward FFT calculations\n" ) ;
rfftwnd_one_real_to_complex( p , static_grid , NULL ) ;
if( electrostatics == 1 ) {
rfftwnd_one_real_to_complex( p , static_elec_grid , NULL ) ;
}
printf( " done\n" ) ;
/************/
/* Store paramaters in case of rescue */
if (rank == 0 ) { /* first proc only if MPI */
if( ( ftdock_file = fopen( "scratch_parameters.dat" , "w" ) ) == NULL ) {
printf( "Could not open scratch_parameters.dat for writing.\nDying\n\n" ) ;
exit( EXIT_FAILURE ) ;
}
fprintf( ftdock_file, "\nGlobal Scan\n" ) ;
fprintf( ftdock_file, "\nCommand line controllable values\n" ) ;
fprintf( ftdock_file, "Static molecule :: %s\n" , static_file_name ) ;
fprintf( ftdock_file, "Mobile molecule :: %s\n" , mobile_file_name ) ;
fprintf( ftdock_file, "Output file name :: %s\n" , output_file_name ) ;
fprintf( ftdock_file, "\n" ) ;
fprintf( ftdock_file, "Global grid size :: %6d %s\n" , global_grid_size , default_global_grid_size ) ;
fprintf( ftdock_file, "Global search angle step :: %6d %s\n" , angle_step , default_angle_step ) ;
fprintf( ftdock_file, "Global surface thickness :: %9.2f %s\n" , surface , default_surface ) ;
fprintf( ftdock_file, "Global internal deterrent value :: %9.2f %s\n" , internal_value , default_internal_value ) ;
if( electrostatics == 1 ) {
fprintf( ftdock_file, "Electrostatics :: on %s\n" , default_electrostatics ) ;
} else {
fprintf( ftdock_file, "Electrostatics :: off %s\n" , default_electrostatics ) ;
}
fprintf( ftdock_file, "Global keep per rotation :: %6d %s\n" , keep_per_rotation , default_keep_per_rotation ) ;
fprintf( ftdock_file, "\nCalculated values\n" ) ;
fprintf( ftdock_file, "Global rotations :: %6d\n" , Angles.n ) ;
fprintf( ftdock_file, "Global total span (angstroms) :: %10.3f\n" , grid_span ) ;
fprintf( ftdock_file, "Global grid cell span (angstroms) :: %10.3f\n" , one_span ) ;
fclose( ftdock_file ) ;
} /* end first proc only */
#ifdef USE_MPI
sprintf(scratch_file_name , "%s%d%s", "scratch_scores" , rank , ".dat" ) ;
#else
strcpy( scratch_file_name , "scratch_scores.dat" ) ;
#endif
/************/
/* Main program loop */
max_es_value = 0 ;
tmp_es_value = 0 ;
printf( "Starting main loop through the rotations\n" ) ; fflush ( stdout ) ;
for( rotation = first_rotation ; rotation <= Angles.n ; rotation += nproc ) {
printf( "." ) ;
fflush_ct ++ ;
/* hard wired low FFLUSH_FREQ here is OK cos ftdock much slower */
if ( ( fflush_ct % 10 ) == 0 ) {
fflush ( stdout ) ;
}
if( ( rotation % 50 ) == 0 ) printf( "\nRotation number %5d\n" , rotation ) ;
/* Rotate Mobile Structure */
Rotated_at_Origin_Mobile_Structure =
rotate_structure( Origin_Mobile_Structure , (int)Angles.z_twist[rotation] , (int)Angles.theta[rotation] , (int)Angles.phi[rotation] ) ;
/* Discretise the rotated Mobile Structure */
discretise_structure( Rotated_at_Origin_Mobile_Structure , grid_span , global_grid_size , mobile_grid ) ;
/* Electic point charge approximation onto grid calculations ( quicker than filed calculations by a long way! ) */
if( electrostatics == 1 ) {
electric_point_charge( Rotated_at_Origin_Mobile_Structure , grid_span , global_grid_size , mobile_elec_grid ) ;
}
/* Forward Fourier Transforms */
rfftwnd_one_real_to_complex( p , mobile_grid , NULL ) ;
if( electrostatics == 1 ) {
rfftwnd_one_real_to_complex( p , mobile_elec_grid , NULL ) ;
}
/************/
/* Do convolution of the two sets of grids
convolution is equivalent to multiplication of the complex conjugate of one
fourier grid with other (raw) one
hence the sign changes from a normal complex number multiplication
*/
for( fx = 0 ; fx < global_grid_size ; fx ++ ) {
for( fy = 0 ; fy < global_grid_size ; fy ++ ) {
for( fz = 0 ; fz < global_grid_size/2 + 1 ; fz ++ ) {
fxyz = fz + ( global_grid_size/2 + 1 ) * ( fy + global_grid_size * fx ) ;
multiple_fsg[fxyz].re =
static_fsg[fxyz].re * mobile_fsg[fxyz].re + static_fsg[fxyz].im * mobile_fsg[fxyz].im ;
multiple_fsg[fxyz].im =
static_fsg[fxyz].im * mobile_fsg[fxyz].re - static_fsg[fxyz].re * mobile_fsg[fxyz].im ;
if( electrostatics == 1 ) {
multiple_elec_fsg[fxyz].re =
static_elec_fsg[fxyz].re * mobile_elec_fsg[fxyz].re + static_elec_fsg[fxyz].im * mobile_elec_fsg[fxyz].im ;
multiple_elec_fsg[fxyz].im =
static_elec_fsg[fxyz].im * mobile_elec_fsg[fxyz].re - static_elec_fsg[fxyz].re * mobile_elec_fsg[fxyz].im ;
}
}
}
}
/* Reverse Fourier Transform */
rfftwnd_one_complex_to_real( pinv , multiple_fsg , NULL ) ;
if( electrostatics == 1 ) {
rfftwnd_one_complex_to_real( pinv , multiple_elec_fsg , NULL ) ;
}
/************/
/* Get best scores */
for( i = 0 ; i < keep_per_rotation ; i ++ ) {
Scores[i].score = 0 ;
Scores[i].rpscore = 0.0 ;
Scores[i].coord[1] = 0 ;
Scores[i].coord[2] = 0 ;
Scores[i].coord[3] = 0 ;
}
/* Scale factor from FFTs */
fft_scalefac = ( (one_span/global_grid_size) * (one_span/global_grid_size) * (one_span/global_grid_size) ) ;
for( x = 0 ; x < global_grid_size ; x ++ ) {
fx = x ;
if( fx > ( global_grid_size / 2 ) ) fx -= global_grid_size ;
for( y = 0 ; y < global_grid_size ; y ++ ) {
fy = y ;
if( fy > ( global_grid_size / 2 ) ) fy -= global_grid_size ;
for( z = 0 ; z < global_grid_size ; z ++ ) {
fz = z ;
if( fz > ( global_grid_size / 2 ) ) fz -= global_grid_size ;
xyz = z + ( 2 * ( global_grid_size / 2 + 1 ) ) * ( y + global_grid_size * x ) ;
if( ( electrostatics == 0 ) || ( convoluted_elec_grid[xyz] < 0 ) ) {
/* Scale factor from FFTs */
if( (int)convoluted_grid[xyz] != 0 ) {
convoluted_grid[xyz] /= ( global_grid_size * global_grid_size * global_grid_size ) ;
}
if( (int)convoluted_grid[xyz] > Scores[keep_per_rotation-1].score ) {
i = keep_per_rotation - 2 ;
while( ( (int)convoluted_grid[xyz] > Scores[i].score ) && ( i >= 0 ) ) {
Scores[i+1].score = Scores[i].score ;
Scores[i+1].rpscore = Scores[i].rpscore ;
Scores[i+1].coord[1] = Scores[i].coord[1] ;
Scores[i+1].coord[2] = Scores[i].coord[2] ;
Scores[i+1].coord[3] = Scores[i].coord[3] ;
i -- ;
}
Scores[i+1].score = (int)convoluted_grid[xyz] ;
if( ( electrostatics != 0 ) && ( convoluted_elec_grid[xyz] < 0.1 ) ) {
Scores[i+1].rpscore = (float)convoluted_elec_grid[xyz] ;
} else {
Scores[i+1].rpscore = (float)0 ;
}
Scores[i+1].coord[1] = fx ;
Scores[i+1].coord[2] = fy ;
Scores[i+1].coord[3] = fz ;
}
}
}
}
}
if( ( rotation == first_rotation ) && ( rescue != 1 ) ) {
if( ( ftdock_file = fopen( scratch_file_name , "w" ) ) == NULL ) {
printf( "Could not open scratch_scores.dat for writing.\nDying\n\n" ) ;
exit( EXIT_FAILURE ) ;
}
} else {
if( ( ftdock_file = fopen( scratch_file_name , "a" ) ) == NULL ) {
printf( "Could not open scratch_scores.dat for writing.\nDying\n\n" ) ;
exit( EXIT_FAILURE ) ;
}
}
for( i = 0 ; i < keep_per_rotation ; i ++ ) {
max_es_value = min( max_es_value , Scores[i].rpscore ) ;
fprintf( ftdock_file, "G_DATA %6d %6d %7d %.0f %4d %4d %4d %4d%4d%4d\n" ,
rotation , 0 , Scores[i].score , (double)Scores[i].rpscore , Scores[i].coord[1] , Scores[i].coord[2] , Scores[i].coord[3 ] ,
Angles.z_twist[rotation] , Angles.theta[rotation] , Angles.phi[rotation] ) ;
}
fclose( ftdock_file ) ;
/* Free some memory */
for( i = 1 ; i <= Rotated_at_Origin_Mobile_Structure.length ; i ++ ) {
free( Rotated_at_Origin_Mobile_Structure.Residue[i].Atom ) ;
}
free( Rotated_at_Origin_Mobile_Structure.Residue ) ;
}
/* Save current max_es_value for a given task */
printf( "Writing max charge files\n" ) ;
//sprintf( scratch_max_es_value , "%s%d%s", "max_es_value" , rank , ".dat" ) ;
sprintf(scratch_file_name , "%s%d%s", "scratch_scores" , rank , ".dat" ) ;
max_es_value_array[rank] = max_es_value ;
if( ( ftdock_file = fopen( scratch_file_name , "a+" ) ) == NULL ) {
printf( "Could not open scratch_file.dat for writing.\nDying\n\n" ) ;
exit( EXIT_FAILURE ) ;
}
fprintf( ftdock_file, "MAX_ES %f\n",max_es_value ) ;
fclose( ftdock_file ) ;
printf( "Done.\n" ) ;
/* Finished main loop */
#ifdef USE_MPI
/* so if parallel make sure all have finished before reloading scores */
MPI_Barrier(MPI_COMM_WORLD);
#endif
/************/
/* Free the memory */
rfftwnd_destroy_plan( p ) ;
rfftwnd_destroy_plan( pinv ) ;
free( static_grid ) ;
free( mobile_grid ) ;
free( convoluted_grid ) ;
if( electrostatics == 1 ) {
free( static_elec_grid ) ;
free( mobile_elec_grid ) ;
free( convoluted_elec_grid ) ;
}
for( i = 1 ; i <= Origin_Static_Structure.length ; i ++ ) {
free( Origin_Static_Structure.Residue[i].Atom ) ;
}
free( Origin_Static_Structure.Residue ) ;
for( i = 1 ; i <= Origin_Mobile_Structure.length ; i ++ ) {
free( Origin_Mobile_Structure.Residue[i].Atom ) ;
}
free( Origin_Mobile_Structure.Residue ) ;
/************/
#ifdef USE_MPI
MPI_Barrier(MPI_COMM_WORLD);
#endif
/* Read in all the scores */
if (rank == 0 ) { /* first proc only if MPI */
fflush ( stdout ) ;
printf( "\nReloading all the scores\n" ) ;
kept_scores = 0;
#ifdef USE_MPI
for (iproc = 0 ; iproc < nproc ; iproc ++ ) {
sprintf(scratch_file_name , "%s%d%s", "scratch_scores" , iproc , ".dat" ) ;
#else
iproc = 0 ; /* shut up, compiler */
strcpy( scratch_file_name , "scratch_scores.dat" ) ;
#endif
if( ( ftdock_file = fopen( scratch_file_name , "r" ) ) == NULL ) {
printf( "Could not open scratch_scores.dat for reading.\nDying\n\n" ) ;
exit( EXIT_FAILURE ) ;
}
if( ( Scores = ( struct Score * ) realloc ( Scores , ( 1 + keep_per_rotation ) * Angles.n * sizeof( struct Score ) ) ) == NULL ) {
printf( "Not enough memory left for storing scores\nProbably keeping too many per rotation\nDying\n\n" ) ;
exit( EXIT_FAILURE ) ;
}
while( fgets( line_buffer , 99 , ftdock_file ) ) {
if( line_buffer[0] == 'G' )
sscanf( line_buffer , "G_DATA %d %d %d %f %d %d %d %d %d %d" , &id , &id2 , &SCscore , &RPscore ,
&x , &y , &z , &z_twist , &theta , &phi ) ;
else
sscanf( line_buffer , "MAX_ES %f", &tmp_es_value ) ;
Scores[kept_scores].score = SCscore ;
Scores[kept_scores].rpscore = RPscore ;
Scores[kept_scores].coord[1] = x ;
Scores[kept_scores].coord[2] = y ;
Scores[kept_scores].coord[3] = z ;
Scores[kept_scores].angle[1] = z_twist ;
Scores[kept_scores].angle[2] = theta ;
Scores[kept_scores].angle[3] = phi ;
max_es_value = min( max_es_value, tmp_es_value ) ;
#ifdef DEBUG
printf("Score: %d RPscore: %f \n", SCscore, RPscore );
#endif
kept_scores ++ ;
}
fclose( ftdock_file ) ;
#ifdef USE_MPI
} /* end the for iproc loop over the various processors' output files */
#endif
kept_scores -- ;
qsort_scores( Scores , 0 , kept_scores ) ;
/************/
/* Writing data file */
if( ( ftdock_file = fopen( output_file_name , "w" ) ) == NULL ) {
printf( "Could not open %s for writing.\nDying\n\n" , output_file_name ) ;
exit( EXIT_FAILURE ) ;
}
fprintf( ftdock_file, "FTDOCK data file\n" ) ;
fprintf( ftdock_file, "\nGlobal Scan\n" ) ;
fprintf( ftdock_file, "\nCommand line controllable values\n" ) ;
fprintf( ftdock_file, "Static molecule :: %s\n" , static_file_name ) ;
fprintf( ftdock_file, "Mobile molecule :: %s\n" , mobile_file_name ) ;
fprintf( ftdock_file, "\n" ) ;
fprintf( ftdock_file, "Global grid size :: %6d %s\n" , global_grid_size , default_global_grid_size ) ;
fprintf( ftdock_file, "Global search angle step :: %6d %s\n" , angle_step , default_angle_step ) ;
fprintf( ftdock_file, "Global surface thickness :: %9.2f %s\n" , surface , default_surface ) ;
fprintf( ftdock_file, "Global internal deterrent value :: %9.2f %s\n" , internal_value , default_internal_value ) ;
if( electrostatics == 1 ) {
fprintf( ftdock_file, "Electrostatics :: on %s\n" , default_electrostatics ) ;
} else {
fprintf( ftdock_file, "Electrostatics :: off %s\n" , default_electrostatics ) ;
}
fprintf( ftdock_file, "Global keep per rotation :: %6d %s\n" , keep_per_rotation , default_keep_per_rotation ) ;
fprintf( ftdock_file, "\nCalculated values\n" ) ;
fprintf( ftdock_file, "Global rotations :: %6d\n" , Angles.n ) ;
fprintf( ftdock_file, "Global total span (angstroms) :: %10.3f\n" , grid_span ) ;
fprintf( ftdock_file, "Global grid cell span (angstroms) :: %10.3f\n" , one_span ) ;
fprintf( ftdock_file, "\nData\n" ) ;
fprintf( ftdock_file , "Type ID prvID SCscore ESratio Coordinates Angles\n\n" ) ;
if( electrostatics == 1 ) {
/*
for( i = 0 ; i < nproc ; ++i ) {
max_es_value = min(max_es_value,max_es_value_array[i]);
printf("Nproc: %d Max_es_value_array: %f MAX: %f\n",i,max_es_value_array[i],max_es_value);
}
*/
for( i = 0 ; i <= min( kept_scores , ( NUMBER_TO_KEEP - 1 ) ) ; i ++ ) {
#ifdef DEBUG
printf("Score: %d RPscore: %f Max_es_value: %f Final: %8.3f \n", Scores[i].score , Scores[i].rpscore, max_es_value, 100 * ( Scores[i].rpscore / max_es_value ) ) ;
#endif
fprintf( ftdock_file, "G_DATA %6d %6d %7d %8.3f %4d %4d %4d %4d%4d%4d\n" ,
i + 1 , 0 , Scores[i].score , 100 * ( Scores[i].rpscore / max_es_value ) ,
Scores[i].coord[1] , Scores[i].coord[2] , Scores[i].coord[3] ,
Scores[i].angle[1] , Scores[i].angle[2] , Scores[i].angle[3] ) ;
}
} else {
for( i = 0 ; i <= min( kept_scores , ( NUMBER_TO_KEEP - 1 ) ) ; i ++ ) {
fprintf( ftdock_file, "G_DATA %6d %6d %7d %8.3f %4d %4d %4d %4d%4d%4d\n" ,
i + 1 , 0 , Scores[i].score , 0.0 ,
Scores[i].coord[1] , Scores[i].coord[2] , Scores[i].coord[3] ,
Scores[i].angle[1] , Scores[i].angle[2] , Scores[i].angle[3] ) ;
}
}
fclose( ftdock_file ) ;
/************/
printf( "\n\nFinished\n\n" ) ;
} /* end first proc */
#ifdef USE_MPI
MPI_Finalize();
#endif
return( 0 ) ;
} /* end main */