writepocket.c File Reference

#include "../headers/writepocket.h"

Go to the source code of this file.

Functions
void	write_each_pocket_for_DB (const char out_path[], c_lst_pockets *pockets, s_pdb *pdb)
void	write_pocket_pqr_DB (const char out[], s_pocket *pocket)
void	write_pocket_pdb_DB (const char out[], s_pocket *pocket, s_pdb *pdb)
void	write_pockets_single_pdb (const char out[], s_pdb *pdb, c_lst_pockets *pockets)
void	write_pdb_atoms (FILE *f, s_atm *atoms, int natoms)
void	write_pockets_single_pqr (const char out[], c_lst_pockets *pockets)
void	write_mdpockets_concat_pqr (FILE *f, c_lst_pockets *pockets)
void	write_each_pocket (const char out_path[], c_lst_pockets *pockets)
void	write_pocket_pqr (const char out[], s_pocket *pocket)
void	write_pocket_pdb (const char out[], s_pocket *pocket)

---

Function Documentation

void write_each_pocket	(	const char	out_path[],
		c_lst_pockets *	pockets
	)

## FUNCTION: write_each_pocket

## SPECIFICATION: Write each pocket in a single pqr (vertices) and pdb (atoms) file format.

## PARAMETRES: @ const char out[] : Output file path @ c_lst_pockets *pockets : List of pockets

## RETURN:

Definition at line 392 of file writepocket.c.

References c_lst_pockets::first, node_pocket::next, node_pocket::pocket, write_pocket_pdb(), and write_pocket_pqr().

Referenced by write_out_fpocket().

{
        int out_len = strlen(out_path) ;
        char out[out_len+20] ;
        out[0] = '\0' ;

        node_pocket *pcur ;
        
        int i = 0 ;
        if(pockets){
                pcur = pockets->first ;

                while(pcur){
                        sprintf(out, "%s/pocket%d_vert.pqr", out_path, i) ;
                        write_pocket_pqr(out, pcur->pocket) ;

                        sprintf(out, "%s/pocket%d_atm.pdb", out_path, i) ;
                        write_pocket_pdb(out, pcur->pocket) ;

                        pcur = pcur->next ;
                        i++ ;
                }
        }
        else {
                fprintf(stderr, "! The file %s could not be opened!\n", out);
        }
}

void write_each_pocket_for_DB	(	const char	out_path[],
		c_lst_pockets *	pockets,
		s_pdb *	pdb
	)

Definition at line 59 of file writepocket.c.

References c_lst_pockets::first, node_pocket::next, node_pocket::pocket, write_pocket_pdb(), write_pocket_pdb_DB(), and write_pocket_pqr_DB().

Referenced by write_out_fpocket_DB().

{
        int out_len = strlen(out_path) ;
        char out[out_len+20] ;
        out[0] = '\0' ;

        node_pocket *pcur ;

        int i = 0 ;
        if(pockets){
                pcur = pockets->first ;

                while(pcur){
                        sprintf(out, "%s/pocket%d_vert.pqr", out_path, i+1) ;
                        write_pocket_pqr_DB(out, pcur->pocket) ;

                        sprintf(out, "%s/pocket%d_env_atm.pdb", out_path, i+1) ;
                        write_pocket_pdb_DB(out, pcur->pocket,pdb) ;
                        sprintf(out, "%s/pocket%d_atm.pdb", out_path, i+1) ;
                        write_pocket_pdb(out, pcur->pocket) ;

                        pcur = pcur->next ;
                        i++ ;
                }
        }
        else {
                fprintf(stderr, "! The file %s could not be opened!\n", out);
        }
}

void write_mdpockets_concat_pqr	(	FILE *	f,
		c_lst_pockets *	pockets
	)

## FUNCTION: write_mdpockets_concat_pqr

## SPECIFICATION: Write only pockets (alpha sphere) given in argument in the pqr format.

!! No atoms writen here, only all pockets in a single pqr file.

## PARAMETRES: @ File *f : File handle for the output file @ c_lst_pockets *pockets : List of pockets

## RETURN:

Definition at line 347 of file writepocket.c.

References c_lst_vertices::current, c_lst_pockets::current, c_lst_vertices::first, c_lst_pockets::first, node_pocket::next, node_vertice::next, node_pocket::pocket, s_pocket::v_lst, node_vertice::vertice, and write_pqr_vert().

{
        node_pocket *nextPocket ;
        node_vertice *nextVertice ;

        if(f) {

                if(pockets){
                        pockets->current = pockets->first ;

                        while(pockets->current){
                                pockets->current->pocket->v_lst->current = pockets->current->pocket->v_lst->first ;

                                while(pockets->current->pocket->v_lst->current){
                                        write_pqr_vert(f, pockets->current->pocket->v_lst->current->vertice) ;

                                        nextVertice = pockets->current->pocket->v_lst->current->next;
                                        pockets->current->pocket->v_lst->current = nextVertice;
                                }

                                nextPocket=pockets->current->next;
                                pockets->current=nextPocket;
                        }
                }
        }
        else {
                fprintf(stderr, "! The pqr concat output file is not open!\n");
        }
}

void write_pdb_atoms	(	FILE *	f,
		s_atm *	atoms,
		int	natoms
	)

## FUNCTION: write_pdb_atoms

## SPECIFICATION: Print list of atoms as pdb format in given buffer

## PARAMETRES: @ FILE *f : Buffer to write in. @ s_atm *atoms : List of atoms @ int natoms : Number of atoms

## RETURN:

Definition at line 263 of file writepocket.c.

References s_atm::bfactor, s_atm::chain, s_atm::charge, s_atm::id, s_atm::name, s_atm::occupancy, s_atm::pdb_aloc, s_atm::pdb_insert, s_atm::res_id, s_atm::res_name, s_atm::symbol, s_atm::type, write_pdb_atom_line(), s_atm::x, s_atm::y, and s_atm::z.

Referenced by write_pockets_single_pdb().

{
        s_atm *atom = NULL ;
        int i = 0 ;
        for(i = 0 ; i < natoms ; i++) {
                atom = atoms + i ;
                write_pdb_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc, 
                                                        atom->res_name, atom->chain, atom->res_id, 
                                                        atom->pdb_insert, atom->x, atom->y, atom->z,
                                                        atom->occupancy, atom->bfactor, atom->symbol, 
                                                        atom->charge);
        }
}

void write_pocket_pdb	(	const char	out[],
		s_pocket *	pocket
	)

## FUNCTION: write_pocket_pdb

## SPECIFICATION: Write atoms contacted by vertices of the pocket given in argument in the pdb format.

## PARAMETRES: @ const char out[] : Output file path @ s_pocket *pocket : The pocket to write

## RETURN:

Definition at line 495 of file writepocket.c.

References s_desc::apolar_asphere_prop, s_atm::bfactor, s_atm::chain, s_atm::charge, s_desc::charge_score, s_desc::drug_score, c_lst_vertices::first, s_desc::flex, s_desc::hydrophobicity_score, s_atm::id, is_in_lst_atm(), s_desc::masph_sacc, s_desc::mean_asph_ray, s_desc::mean_loc_hyd_dens, my_free(), my_malloc(), my_realloc(), s_pocket::nAlphaApol, s_atm::name, s_desc::nb_asph, s_vvertice::neigh, node_vertice::next, s_atm::occupancy, s_atm::pdb_aloc, s_atm::pdb_insert, s_pocket::pdesc, s_desc::polarity_score, s_atm::res_id, s_atm::res_name, s_vvertice::resid, s_pocket::score, s_atm::symbol, s_atm::type, s_pocket::v_lst, node_vertice::vertice, s_desc::volume, s_desc::volume_score, write_pdb_atom_line(), s_atm::x, s_atm::y, and s_atm::z.

Referenced by write_each_pocket(), and write_each_pocket_for_DB().

{
        node_vertice *vcur = NULL ;
        int i = 0 ;
        int cur_size = 0,
                cur_allocated = 10 ;

        s_atm **atms = (s_atm**)my_malloc(sizeof(s_atm*)*10) ;
        s_atm *atom = NULL ;

        FILE *f = fopen(out, "w") ;
        if(f && pocket) {

                fprintf(f, "HEADER\n") ;
                fprintf(f, "HEADER This is a pdb format file writen by the programm fpocket.                 \n") ;
                fprintf(f, "HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  \n") ;
                fprintf(f, "HEADER                                                                           \n") ;
                fprintf(f, "HEADER Information about the pocket %5d:\n", pocket->v_lst->first->vertice->resid) ;
                fprintf(f, "HEADER 0  - Pocket Score                      : %.4f\n", pocket->score) ;
                fprintf(f, "HEADER 1  - Drug Score                        : %.4f\n", pocket->pdesc->drug_score) ;
                fprintf(f, "HEADER 2  - Number of V. Vertices             : %5d\n", pocket->pdesc->nb_asph) ;
                fprintf(f, "HEADER 3  - Mean alpha-sphere radius          : %.4f\n", pocket->pdesc->mean_asph_ray) ;
                fprintf(f, "HEADER 4  - Mean alpha-sphere SA              : %.4f\n", pocket->pdesc->masph_sacc) ;
                fprintf(f, "HEADER 5  - Mean B-factor                     : %.4f\n", pocket->pdesc->flex) ;
                fprintf(f, "HEADER 6  - Hydrophobicity Score              : %.4f\n", pocket->pdesc->hydrophobicity_score) ;
                fprintf(f, "HEADER 7  - Polarity Score                    : %5d\n", pocket->pdesc->polarity_score) ;
                fprintf(f, "HEADER 8  - Volume Score                      : %.4f\n", pocket->pdesc->volume_score) ;
                fprintf(f, "HEADER 9  - Real volume (approximation)       : %.4f\n", pocket->pdesc->volume) ;
                fprintf(f, "HEADER 10 - Charge Score                      : %5d\n", pocket->pdesc->charge_score) ;
                fprintf(f, "HEADER 11 - Local hydrophobic density Score   : %.4f\n", pocket->pdesc->mean_loc_hyd_dens) ;
                fprintf(f, "HEADER 12 - Number of apolar alpha sphere     : %5d\n", pocket->nAlphaApol) ;
                fprintf(f, "HEADER 13 - Proportion of apolar alpha sphere : %.4f\n", pocket->pdesc->apolar_asphere_prop) ;

        /* First get the list of atoms */
                vcur = pocket->v_lst->first ;

                while(vcur){
                        for(i = 0 ; i < 4 ; i++) {
                                if(!is_in_lst_atm(atms, cur_size, vcur->vertice->neigh[i]->id)) {
                                        if(cur_size >= cur_allocated-1) {
                                                cur_allocated *= 2 ;
                                                atms = (s_atm**)my_realloc(atms, sizeof(s_atm)*cur_allocated) ;
                                        }
                                        atms[cur_size] = vcur->vertice->neigh[i] ;
                                        cur_size ++ ;
                                }

                        }
                        vcur = vcur->next ;
                }

        /* Then write atoms... */

                for(i = 0 ; i < cur_size ; i++) {
                        atom = atms[i] ;

                        write_pdb_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc, 
                                                                        atom->res_name, atom->chain, atom->res_id, 
                                                                        atom->pdb_insert, atom->x, atom->y, atom->z,
                                                                        atom->occupancy, atom->bfactor, atom->symbol, 
                                                                        atom->charge);
                }
        
                fprintf(f, "TER\nEND\n") ;
                fclose(f) ;
        }
        else {
                if(!f) fprintf(stderr, "! The file %s could not be opened!\n", out);
                else fprintf(stderr, "! Invalid pocket to write in write_pocket_pqr !\n");
        }

        my_free(atms) ;
}

void write_pocket_pdb_DB	(	const char	out[],
		s_pocket *	pocket,
		s_pdb *	pdb
	)

Definition at line 115 of file writepocket.c.

References s_atm::bfactor, s_atm::chain, s_atm::charge, c_lst_vertices::first, get_surrounding_atoms_idx(), s_atm::id, s_pdb::latoms_p, my_free(), my_malloc(), c_lst_vertices::n_vertices, s_atm::name, node_vertice::next, s_atm::occupancy, s_atm::pdb_aloc, s_atm::pdb_insert, s_atm::res_id, s_atm::res_name, s_atm::symbol, s_atm::type, s_pocket::v_lst, node_vertice::vertice, write_pdb_atom_line(), s_atm::x, s_atm::y, and s_atm::z.

Referenced by write_each_pocket_for_DB().

{
        int i = 0,nvert=0 ;
        s_atm **atms = (s_atm **) my_malloc(sizeof(s_atm*)*10) ;
        s_atm *atom = NULL ;
        int n_sa=0;
        int *sa=NULL;    /*surrounding atoms container*/
        s_vvertice **tab_vert =NULL;

        FILE *f = fopen(out, "w") ;
        if(f && pocket) {
        // First get the list of atoms
                        tab_vert = (s_vvertice **) my_malloc(pocket->v_lst->n_vertices*sizeof(s_vvertice*)) ;
                
                        node_vertice *nvcur = pocket->v_lst->first ;

/*
                        fprintf(stdout, "A Pocket:\n") ;
*/
                        while(nvcur) {
/*
                                fprintf(stdout, "Vertice %d: %p %d %f\n", i, nvcur->vertice, nvcur->vertice->id, nvcur->vertice->ray) ;
                                fprintf(stdout, "Atom %s\n", nvcur->vertice->neigh[0]->name) ;
*/

                                tab_vert[nvert] = nvcur->vertice ;
                                nvcur = nvcur->next ;
                                nvert++ ;
                        }
            sa=(int *)get_surrounding_atoms_idx(tab_vert,nvert,pdb, &n_sa);
            for(i=0;i<n_sa;i++){
                        //atom = pocket->sou_atoms[i] ;
                        atom=pdb->latoms_p[sa[i]];
                        write_pdb_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
                                                                        atom->res_name, atom->chain, atom->res_id,
                                                                        atom->pdb_insert, atom->x, atom->y, atom->z,
                                                                        atom->occupancy, atom->bfactor, atom->symbol,
                                                                        atom->charge);
            }
/*
            vcur = pocket->v_lst->first ;

                while(vcur){
                        for(i = 0 ; i < 4 ; i++) {
                                if(!is_in_lst_atm(atms, cur_size, vcur->vertice->neigh[i]->id)) {
                                        if(cur_size >= cur_allocated-1) {
                                                cur_allocated *= 2 ;
                                                atms = (s_atm**) my_realloc(atms, sizeof(s_atm)*cur_allocated) ;
                                        }
                                        atms[cur_size] = vcur->vertice->neigh[i] ;
                                        cur_size ++ ;
                                }

                        }
                        vcur = vcur->next ;
                }
*/
        // Then write atoms...
/*
                for(i = 0 ; i < cur_size ; i++) {
                        atom = atms[i] ;

                        write_pdb_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
                                                                        atom->res_name, atom->chain, atom->res_id,
                                                                        atom->pdb_insert, atom->x, atom->y, atom->z,
                                                                        atom->occupancy, atom->bfactor, atom->symbol,
                                                                        atom->charge);
                }
*/
                fprintf(f, "TER\nEND\n") ;
                fclose(f) ;
        }
        else {
                if(!f) fprintf(stderr, "! The file %s could not be opened!\n", out);
                else fprintf(stderr, "! Invalid pocket to write in write_pocket_pqr !\n");
        }

        my_free(atms) ;
}

void write_pocket_pqr	(	const char	out[],
		s_pocket *	pocket
	)

## FUNCTION: void write_pocket_pqr

## SPECIFICATION: Write vertices of the pocket given in argument in the pqr format.

## PARAMETRES: @ const char out[] : Output file path @ s_pocket *pocket : The pocket to write

## RETURN:

Definition at line 435 of file writepocket.c.

References s_desc::apolar_asphere_prop, s_desc::charge_score, s_desc::drug_score, c_lst_vertices::first, s_desc::flex, s_desc::hydrophobicity_score, s_desc::masph_sacc, s_desc::mean_asph_ray, s_desc::mean_loc_hyd_dens, s_pocket::nAlphaApol, s_desc::nb_asph, node_vertice::next, s_pocket::pdesc, s_desc::polarity_score, s_vvertice::resid, s_pocket::score, s_pocket::v_lst, node_vertice::vertice, s_desc::volume, s_desc::volume_score, and write_pqr_vert().

Referenced by write_each_pocket().

{
        node_vertice *vcur = NULL ;

        FILE *f = fopen(out, "w") ;
        if(f && pocket) {
                fprintf(f, "HEADER\n") ;
                fprintf(f, "HEADER This is a pqr format file writen by the programm fpocket.                 \n") ;
                fprintf(f, "HEADER It represent the voronoi vertices of a single pocket found by the         \n") ;
                fprintf(f, "HEADER algorithm.                                                                \n") ;
                fprintf(f, "HEADER                                                                           \n") ;
                fprintf(f, "HEADER Information about the pocket %5d:\n", pocket->v_lst->first->vertice->resid) ;
                fprintf(f, "HEADER 0  - Pocket Score                      : %.4f\n", pocket->score) ;
                fprintf(f, "HEADER 1  - Drug Score                        : %.4f\n", pocket->pdesc->drug_score) ;
                fprintf(f, "HEADER 2  - Number of V. Vertices             : %5d\n", pocket->pdesc->nb_asph) ;
                fprintf(f, "HEADER 3  - Mean alpha-sphere radius          : %.4f\n", pocket->pdesc->mean_asph_ray) ;
                fprintf(f, "HEADER 4  - Mean alpha-sphere SA              : %.4f\n", pocket->pdesc->masph_sacc) ;
                fprintf(f, "HEADER 5  - Mean B-factor                     : %.4f\n", pocket->pdesc->flex) ;
                fprintf(f, "HEADER 6  - Hydrophobicity Score              : %.4f\n", pocket->pdesc->hydrophobicity_score) ;
                fprintf(f, "HEADER 7  - Polarity Score                    : %5d\n", pocket->pdesc->polarity_score) ;
                fprintf(f, "HEADER 8  - Volume Score                      : %.4f\n", pocket->pdesc->volume_score) ;
                fprintf(f, "HEADER 9  - Real volume (approximation)       : %.4f\n", pocket->pdesc->volume) ;
                fprintf(f, "HEADER 10 - Charge Score                      : %5d\n", pocket->pdesc->charge_score) ;
                fprintf(f, "HEADER 11 - Local hydrophobic density Score   : %.4f\n", pocket->pdesc->mean_loc_hyd_dens) ;
                fprintf(f, "HEADER 12 - Number of apolar alpha sphere     : %5d\n", pocket->nAlphaApol) ;
                fprintf(f, "HEADER 13 - Proportion of apolar alpha sphere : %.4f\n", pocket->pdesc->apolar_asphere_prop) ;

                vcur = pocket->v_lst->first ;

                while(vcur){
                        write_pqr_vert(f, vcur->vertice) ;

                        vcur = vcur->next ;
                }

                fprintf(f, "TER\nEND\n") ;
                fclose(f) ;
        }
        else {
                if(!f) fprintf(stderr, "! The file %s could not be opened!\n", out);
                else fprintf(stderr, "! Invalid pocket to write in write_pocket_pqr !\n");
        }
}

void write_pocket_pqr_DB	(	const char	out[],
		s_pocket *	pocket
	)

Definition at line 91 of file writepocket.c.

References c_lst_vertices::first, node_vertice::next, s_pocket::v_lst, node_vertice::vertice, and write_pqr_vert().

Referenced by write_each_pocket_for_DB().

{
        node_vertice *vcur = NULL ;

        FILE *f = fopen(out, "w") ;
        if(f && pocket) {
                vcur = pocket->v_lst->first ;

                while(vcur){
                        write_pqr_vert(f, vcur->vertice) ;

                        vcur = vcur->next ;
                }

                fprintf(f, "TER\nEND\n") ;
                fclose(f) ;
        }
        else {
                if(!f) fprintf(stderr, "! The file %s could not be opened!\n", out);
                else fprintf(stderr, "! Invalid pocket to write in write_pocket_pqr !\n");
        }
}

void write_pockets_single_pdb	(	const char	out[],
		s_pdb *	pdb,
		c_lst_pockets *	pockets
	)

## FUNCTION: write_single_pdb

## SPECIFICATION: Write atoms and vertices given in argument in the following standard v2.2 pdb format.

## PARAMETRES: @ const char out[] : Output file name @ s_pdb *pdb : PDB infos @ c_lst_pockets *pockets : All pockets

## RETURN:

Definition at line 213 of file writepocket.c.

References c_lst_vertices::current, c_lst_pockets::current, c_lst_vertices::first, c_lst_pockets::first, s_pdb::latoms, s_pdb::natoms, node_pocket::next, node_vertice::next, node_pocket::pocket, s_pocket::v_lst, node_vertice::vertice, write_pdb_atoms(), and write_pdb_vert().

Referenced by write_out_fpocket().

{
        node_pocket *nextPocket ;
        node_vertice *nextVertice ;
        FILE *f = fopen(out, "w") ;
        if(f) {
                if(pdb) {
                        if(pdb->latoms) write_pdb_atoms(f, pdb->latoms, pdb->natoms ) ;
                }

                if(pockets){
                        pockets->current = pockets->first ;

                        while(pockets->current){
                                pockets->current->pocket->v_lst->current = pockets->current->pocket->v_lst->first ;

                                while(pockets->current->pocket->v_lst->current){
                                        write_pdb_vert(f, pockets->current->pocket->v_lst->current->vertice) ;

                                        nextVertice = pockets->current->pocket->v_lst->current->next;
                                        pockets->current->pocket->v_lst->current = nextVertice;
                                }

                                nextPocket=pockets->current->next;
                                pockets->current=nextPocket;
                        }
                }

                fclose(f) ;
        }
        else {
                fprintf(stderr, "! The file %s could not be opened!\n", out);
        }
}

void write_pockets_single_pqr	(	const char	out[],
		c_lst_pockets *	pockets
	)

## FUNCTION: write_pockets_single_pqr

## SPECIFICATION: Write only pockets (alpha sphere) given in argument in the pqr format.

!! No atoms writen here, only all pockets in a single pqr file.

## PARAMETRES: @ const char out[] : Output file path @ c_lst_pockets *pockets : List of pockets

## RETURN:

Definition at line 293 of file writepocket.c.

References c_lst_vertices::current, c_lst_pockets::current, c_lst_vertices::first, c_lst_pockets::first, node_pocket::next, node_vertice::next, node_pocket::pocket, s_pocket::v_lst, node_vertice::vertice, and write_pqr_vert().

Referenced by write_out_fpocket().

{
        node_pocket *nextPocket ;
        node_vertice *nextVertice ;

        FILE *f = fopen(out, "w") ;
        if(f) {

                if(pockets){
                fprintf(f, "HEADER\n") ;
                fprintf(f, "HEADER This is a pqr format file writen by the programm fpocket.                 \n") ;
                fprintf(f, "HEADER It contains all the pockets vertices found by fpocket.                    \n") ;
                        pockets->current = pockets->first ;

                        while(pockets->current){
                                pockets->current->pocket->v_lst->current = pockets->current->pocket->v_lst->first ;

                                while(pockets->current->pocket->v_lst->current){
                                        write_pqr_vert(f, pockets->current->pocket->v_lst->current->vertice) ;

                                        nextVertice = pockets->current->pocket->v_lst->current->next;
                                        pockets->current->pocket->v_lst->current = nextVertice;
                                }

                                nextPocket=pockets->current->next;
                                pockets->current=nextPocket;
                        }
                }

                fprintf(f, "TER\nEND\n") ;
                fclose(f) ;
        }
        else {
                fprintf(stderr, "! The file %s could not be opened!\n", out);
        }
}