fpout.c File Reference

#include "../headers/fpout.h"

Go to the source code of this file.

Functions
void	write_out_fpocket (c_lst_pockets *pockets, s_pdb *pdb, char *pdbname)
void	write_out_fpocket_DB (c_lst_pockets *pockets, s_pdb *pdb, char *input_name)
void	write_descriptors_DB (c_lst_pockets *pockets, FILE *f)

---

Function Documentation

void write_descriptors_DB	(	c_lst_pockets *	pockets,
		FILE *	f
	)

Definition at line 212 of file fpout.c.

References s_desc::aa_compo, s_desc::characterChain1, s_desc::characterChain2, s_desc::charge_score, s_desc::drug_score, c_lst_pockets::first, s_desc::flex, s_desc::hydrophobicity_score, s_desc::interChain, s_desc::ligTag, s_desc::masph_sacc, s_desc::mean_asph_ray, s_desc::mean_loc_hyd_dens, s_desc::n_abpa, s_pocket::nAlphaApol, s_desc::nameChain1, s_desc::nameChain2, s_desc::nb_asph, node_pocket::next, s_desc::numResChain1, s_desc::numResChain2, s_pocket::pdesc, node_pocket::pocket, s_desc::polarity_score, s_desc::surf_apol_vdw14, s_desc::surf_apol_vdw22, s_desc::surf_pol_vdw14, s_desc::surf_pol_vdw22, and s_desc::volume_score.

Referenced by process_pdb().

                                                          {

    /*Todo adapt things here*/

     int n=1;
    s_pocket *p;
    node_pocket *npcur;
    npcur=pockets->first;
    int r=1,i;
    fprintf(f,"cav_id drug_score nb_asph inter_chain apol_asph_proportion mean_asph_radius "
            "mean_asph_solv_acc mean_loc_hyd_dens flex hydrophobicity_score volume_score charge_score "
            "polarity_score a0_apol a0_pol af_apol af_pol n_abpa "
            "ala cys asp glu phe gly his ile lys ley met asn pro gln arg ser thr val trp tyr "
            "chain_1_type chain_2_type num_res_chain_1 "
            "num_res_chain_2 lig_het_tag name_chain_1 name_chain_2\n");
    while(npcur){
        p=npcur->pocket;
// python counter part         entry={"pdb_id":pdbFile,"cav_id":int(r[0]),"drug_score":r[1],"nb_asph":int(r[2]),"inter_chain":int(r[3]),"apol_asph_proportion":
        //float(r[4]),"mean_asph_radius":float(r[5]),"mean_asph_solv_acc":float(r[6]),"mean_loc_hyd_dens":float(r[7]),"flex":r[8],"hydrophobicity_score":float(r[9]),
        //"volume_score":float(r[10]),"charge_score":int(r[11]),"polarity_score":int(r[12]),"a0_apol":float(r[13]),"a0_pol":float(r[14]),"af_apol":float(r[15]),
        //"af_pol":float(r[16]),"n_abpa":int(r[17]),"ala":int(r[18]),"cys":int(r[19]),"asp":int(r[20]),"glu":int(r[21]),"phe":int(r[22]),"gly":int(r[23]),
        //"his":int(r[24]),"ile":int(r[25]),"lys":int(r[26]),"leu":int(r[27]),"met":int(r[28]),"asn":int(r[29]),"pro":int(r[30]),"gln":int(r[31]),"arg":int(r[32]),
        //"ser":int(r[33]),"thr":int(r[34]),"val":int(r[35]),"trp":int(r[36]),"tyr":int(r[37])}
        //entry={"pdb_id":pdbFile,"cav_id":int(r[0]),"chain_1_type":int(r[38]), "chain_2_type":int(r[39]), "num_res_chain_1":int(r[40]),"num_res_chain_2":int(r[41])}
        // entry={"pdb_id":pdbFile,"cav_id":int(r[0]),"lig_het_tag":str(r[42])}
           fprintf(f,"%d %.4f %d %d %.4f %.4f",r,p->pdesc->drug_score,\
                   p->pdesc->nb_asph,p->pdesc->interChain,(float)p->nAlphaApol/(float)p->pdesc->nb_asph,p->pdesc->mean_asph_ray);
           fprintf(f," %.4f %.4f %.4f %.4f %.4f %d",p->pdesc->masph_sacc,p->pdesc->mean_loc_hyd_dens,p->pdesc->flex,p->pdesc->hydrophobicity_score,\
                   p->pdesc->volume_score,p->pdesc->charge_score);
           fprintf(f," %d %.4f %.4f %.4f %.4f %d",p->pdesc->polarity_score,p->pdesc->surf_apol_vdw14,p->pdesc->surf_pol_vdw14,\
                   p->pdesc->surf_apol_vdw22,p->pdesc->surf_pol_vdw22,p->pdesc->n_abpa);
           for(i = 0 ; i < 20 ; i++) fprintf(f, " %d", p->pdesc->aa_compo[i]) ;
           fprintf(f," %d %d %d %d %s %s %s",p->pdesc->characterChain1, p->pdesc->characterChain2, p->pdesc->numResChain1, p->pdesc->numResChain2, p->pdesc->ligTag, p->pdesc->nameChain1, p->pdesc->nameChain2);
           //fprintf(f,"%s %s %s",p->pdesc->nameChain1,p->pdesc->nameChain2);
           fprintf(f,"\n");
           fflush(f);


           

       /* sprintf(filename,"pocket_%d.txt",n);
        f=fopen(filename,"w");
        fprintf(f,"probe apolar_surface polar_surface\n");

        int i;
        for(i=0;i<l;i++){
            fprintf(f,"%.3f %.3f %.3f\n",p->probe_size[i], p->apol_asa_probe[i],p->pol_asa_probe[i]);
        }
        fclose(f);*/
        npcur=npcur->next;
        n++;
        r++;
    }

}

void write_out_fpocket	(	c_lst_pockets *	pockets,
		s_pdb *	pdb,
		char *	pdbname
	)

## FUNCTION: write_out_fpocket

## SPECIFICATION: Output routine. See the documentation for more information.

## PARAMETRES: @ c_lst_pockets *pockets : All pockets found and kept. @ c_lst_pockets *pockets : The (input) pdb structure @ char *pdbname : Name of the pdb

## RETURN: void

Definition at line 79 of file fpout.c.

References extract_path(), remove_ext(), remove_path(), write_each_pocket(), write_pockets_single_pdb(), write_pockets_single_pqr(), and write_visualization().

Referenced by check_fpocket(), process_pdb(), and test_set().

{
        char pdb_code[350] = "" ;
        char pdb_path[350] = "" ;
        char out_path[350] = "" ;
        char pdb_out_path[350] = "" ;
        char fout[350] = "" ;
        char command[370] = "" ;
        int status ;
        
        if(pockets) {
        /* Extract path, pdb code... */
                strcpy(pdb_code, pdbname) ;
                extract_path(pdbname, pdb_path) ;
                remove_ext(pdb_code) ;
                remove_path(pdb_code) ;

                if(strlen(pdb_path) > 0) sprintf(out_path, "%s/%s_out", pdb_path, pdb_code) ;
                else sprintf(out_path, "%s_out", pdb_code) ;
                
                sprintf(command, "mkdir %s", out_path) ;
                status = system(command) ;
                /*if(status != 0) {
                        return ;
                }*/
                
                sprintf(out_path, "%s/%s", out_path, pdb_code) ;
                sprintf(pdb_out_path, "%s_out.pdb", out_path) ;
                
        /* Write vmd and pymol scripts */
                sprintf(fout, "%s_out.pdb", pdb_code) ;
                write_visualization(out_path, fout);

        /* Writing full pdb */
                sprintf(pdb_out_path, "%s_out.pdb", out_path) ;

                write_pockets_single_pdb(pdb_out_path, pdb, pockets) ;
        
        /* Writing pockets as a single pqr */
                sprintf(fout, "%s_pockets.pqr", out_path) ;
                write_pockets_single_pqr(fout, pockets) ;

        /* Writing individual pockets pqr */
                if(strlen(pdb_path) > 0) sprintf(out_path, "%s/%s_out", pdb_path, pdb_code) ;
                else sprintf(out_path, "%s_out", pdb_code) ;
                
                sprintf(out_path, "%s/pockets", out_path) ;
                sprintf(command, "mkdir %s", out_path) ;
                status = system(command) ;
                /*if(status != 0) {
                        return ;
                }*/

                write_each_pocket(out_path, pockets) ;
        }
}

void write_out_fpocket_DB	(	c_lst_pockets *	pockets,
		s_pdb *	pdb,
		char *	input_name
	)

----------------------------------------------------------------------------- ## FUNCTION: void write_out(c_lst_pockets *pockets) ----------------------------------------------------------------------------- ## SPECIFICATION: Output routine. -----------------------------------------------------------------------------

Definition at line 145 of file fpout.c.

References extract_path(), remove_ext(), remove_path(), and write_each_pocket_for_DB().

Referenced by process_pdb().

{
        char pdb_code[350] = "" ;
        char pdb_path[350] = "" ;
        char out_path[350] = "" ;
        char pdb_out_path[350] = "" ;
        char command[370] = "" ;

        if(pockets) {
        // Extract path, pdb code...
                strcpy(pdb_code, input_name) ;
                extract_path(input_name, pdb_path) ;
                remove_ext(pdb_code) ;
                remove_path(pdb_code) ;
                /*sprintf(out_path, "%s/%s_out", pdb_path, pdb_code) ;*/
                if(strlen(pdb_path) > 0) sprintf(out_path, "%s/%s_out", pdb_path, pdb_code) ;
                else sprintf(out_path, "%s_out", pdb_code) ;
                sprintf(command, "mkdir %s", out_path) ;
                system(command) ;
/*
                sprintf(out_path, "%s/%s_out/%s", pdb_path, pdb_code, pdb_code) ;
                sprintf(pdb_out_path, "%s_out.pdb", out_path) ;
*/
        //Write vmd and pymol scripts
/*
                sprintf(fout, "%s_out.pdb", pdb_code) ;
                write_visualization(out_path, fout);
        // Print the whole pockets informations in a single file
*/
                /*sprintf(fout, "%s_pockets.info", out_path) ;
                FILE *f = fopen(fout, "w") ;
                if(f) {
                        print_pockets(f, pockets) ;
                        fclose(f) ;
                }
*/
        // Writing full pdb
                sprintf(pdb_out_path, "%s_out.pdb", out_path) ;

                //write_pockets_single_pdb(pdb_out_path, pdb, pockets) ;

        // Writing topology clusters
               /* sprintf(pdb_out_path, "%s_topo_connect.pdb", out_path) ;

                write_topology_pdb(pdb_out_path,pockets) ;*/
        // Writing pockets as a single pqr
                /*sprintf(fout, "%s_pockets.pqr", out_path) ;
                write_pockets_single_pqr(fout, pockets) ;*/

        // Writing pocket distance matrix to a file
                //  sprintf(fout, "%s_dist_mat.txt", out_path) ;


        // Writing individual pockets pqr

/*              sprintf(out_path, "%s/%s_out/", pdb_path, pdb_code) ;
                sprintf(command, "mkdir %s", out_path) ;
                system(command) ;*/

                write_each_pocket_for_DB(out_path, pockets,pdb) ;
                //write_each_matrix(out_path,pockets);
        }
}