fpocket.h File Reference

#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include <ctype.h>
#include "rpdb.h"
#include "voronoi.h"
#include "pocket.h"
#include "psorting.h"
#include "cluster.h"
#include "refine.h"
#include "descriptors.h"
#include "fparams.h"
#include "memhandler.h"

Go to the source code of this file.

Functions
c_lst_pockets *	search_pocket (s_pdb *pdb, s_fparams *params, s_pdb *pdb_w_lig)

---

Function Documentation

c_lst_pockets* search_pocket	(	s_pdb *	pdb,
		s_fparams *	params,
		s_pdb *	pdb_w_lig
	)

## FUNCTION: pockets search_pocket

## SPECIFICATION: This function will call all functions needed for the pocket finding algorith and will return the list of pockets found on the protein.

## PARAMETRES: @ s_pdb *pdb : The pdb data of the protein to handle. @ s_fparams : Parameters of the algorithm

## RETURN: A chained list of pockets found, sorted according to the current critera (the default is a scoring function)

Definition at line 82 of file fpocket.c.

References s_fparams::asph_max_size, s_fparams::asph_min_size, clusterPockets(), dropSmallNpolarPockets(), load_vvertices(), M_SCORE_SORT_FUNCT, s_fparams::min_apol_neigh, pck_final_clust(), refinePockets(), reIndexPockets(), set_pockets_descriptors(), sort_pockets(), and c_lst_pockets::vertices.

Referenced by check_fpocket(), desc_pocket(), get_actual_pocket(), mdprocess_pdb(), process_pdb(), and test_set().

{
/*
        clock_t b, e ;
        time_t bt, et ;
*/
        c_lst_pockets *pockets = NULL ;

        /* Calculate and read voronoi vertices comming from qhull */
/*
        fprintf(stdout,"========= fpocket algorithm begins =========\n") ;

        fprintf(stdout, "> Calculating vertices ...\n");

        bt = time(NULL) ;
*/
        s_lst_vvertice *lvert = load_vvertices(pdb, params->min_apol_neigh,
                                                                                                params->asph_min_size,
                                                                                                params->asph_max_size) ;
/*
        et = time(NULL) ;
        fprintf(stdout, "> Vertices successfully calculated in apox. %f sec.\n",
                                        (float) (et-bt)) ;
*/
        
        if(lvert == NULL) {
                fprintf(stderr, "! Vertice calculation failed!\n");
                return NULL ;
        }
        /* First clustering */
/*              fprintf(stdout,"> Basic clustering ...\n");

                b = clock() ;
*/
        pockets = clusterPockets(lvert, params);

        
        if(pockets) {
                pockets->vertices = lvert ;
/*
                e = clock() ;
                fprintf(stdout, "> Clustering OK in %f sec.\n",
                                                ((double)e - b) / CLOCKS_PER_SEC) ;
*/

        /* Clustering refinment */

/*
                b = clock() ;
                fprintf(stdout,"> Cluster refinment steps: \n");
*/
                reIndexPockets(pockets) ;

/*
                drop_tiny(pockets) ;    
                reIndexPockets(pockets) ;
*/

/*
                fprintf(stdout,"\t* 2nd refinment step -> clustering : based on barycenters...\n");
*/
                refinePockets(pockets, params) ;        /* Refine clustering (rapid) */
                reIndexPockets(pockets) ;

/*
                fprintf(stdout,"\t* 3rd refinment step -> single linkage clusturing...\n");
*/
                pck_final_clust(pockets, params,pdb,pdb_w_lig); /* Single Linkage Clustering */
                reIndexPockets(pockets) ;

        /* Descriptors calculation */
/*
                fprintf(stdout,"> Calculating descriptors and score...\n");
                b = clock() ;
*/
                
                set_pockets_descriptors(pockets,pdb,params,pdb_w_lig);
                
/*
                e = clock() ;
                fprintf(stdout, "> Descriptors found in %f sec.\n", ((double)e - b) / CLOCKS_PER_SEC) ;

                fprintf(stdout,"> 4th refinment step -> dropping small and polar pockets...\n");
*/

        /* Drop small and too polar binding pockets */
                dropSmallNpolarPockets(pockets, params);
                reIndexPockets(pockets) ;
/*
                e = clock() ;
                fprintf(stdout, "> Refinment OK in %f sec.\n", ((double)e - b) / CLOCKS_PER_SEC) ;
*/

        /* Sorting pockets */
                sort_pockets(pockets, M_SCORE_SORT_FUNCT) ;
                /*sort_pockets(pockets, M_NASPH_SORT_FUNCT) ;*/

                reIndexPockets(pockets) ;
/*
                fprintf(stdout,"===== fpocket algorithm ends =====\n");
*/
        }
        
        return pockets ;
}