mdpout.h File Reference

#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <string.h>
#include <ctype.h>
#include <limits.h>
#include <assert.h>
#include "fpocket.h"
#include "fpout.h"
#include "writepocket.h"
#include "tpocket.h"
#include "dparams.h"
#include "descriptors.h"
#include "neighbor.h"
#include "pocket.h"
#include "cluster.h"
#include "refine.h"
#include "aa.h"
#include "utils.h"
#include "mdparams.h"
#include "mdpbase.h"
#include "memhandler.h"

Go to the source code of this file.

Functions
void	write_md_grid (s_mdgrid *g, FILE *f, FILE *fiso, s_mdparams *par, float isovalue)
void	write_md_pocket_atoms (FILE *f, int *ids, s_pdb *prot, int nids, int sn)
void	write_first_bfactor_density (FILE *f, s_pdb *prot)

---

Function Documentation

void write_first_bfactor_density	(	FILE *	f,
		s_pdb *	prot
	)

## FUNCTION: write_first_bfactor_density

## SPECIFICATION: writes the protein structure with pocket densities in the bfactor column.

## PARAMETRES: @ FILE *f : output file handle @ s_pdb *prot : protein handle

## RETURN: void

Definition at line 203 of file mdpout.c.

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

Referenced by mdpocket_detect().

                                                     {
    s_atm *cura;
    int i;
    //fprintf(f,"MODEL        %d\n",sn);
    for(i=0;i<prot->natoms;i++){
        cura=prot->latoms_p[i];
        write_pdb_atom_line(f, "ATOM", cura->id, cura->name,
                                                 cura->pdb_aloc, cura->res_name, cura->chain,
                                                 cura->res_id, cura->pdb_insert, cura->x, cura->y, cura->z, cura->occupancy,
                                                 cura->bfactor, cura->symbol, cura->charge);
    }
    fprintf(f,"TER\n");
    fprintf(f,"END\n");

}

void write_md_grid	(	s_mdgrid *	g,
		FILE *	f,
		FILE *	fiso,
		s_mdparams *	par,
		float	isovalue
	)

COPYRIGHT DISCLAIMER

Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery, hereby disclaim all copyright interest in the program “fpocket” (which performs protein cavity detection) written by Vincent Le Guilloux and Peter Schmidtke.

Vincent Le Guilloux 28 November 2008 Peter Schmidtke 28 November 2008 Pierre Tuffery 28 November 2008

GNU GPL

This file is part of the fpocket package.

fpocket 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 3 of the License, or (at your option) any later version.

fpocket 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 fpocket. If not, see <http://www.gnu.org/licenses/>.

## FUNCTION: write_md_grid

## SPECIFICATION: Write the md grid to a file.

## PARAMETRES: @ s_mdgrid g : structure containing the grid @ FILE *f : file handle for output file @ FILE *fiso : file handle for iso pdb output file @ s_mdparams *par : parameters for mdpocket @ float isovalue : isovalue at which one wants to extract the iso PDB

## RETURN: void :

Definition at line 95 of file mdpout.c.

References s_fparams::asph_max_size, s_fparams::asph_min_size, s_fparams::clust_max_dist, s_mdparams::flag_scoring, s_mdparams::fpar, s_mdgrid::gridvalues, s_fparams::min_pock_nb_asph, s_mdgrid::nx, s_mdgrid::ny, s_mdgrid::nz, s_mdgrid::origin, s_fparams::refine_clust_dist, s_mdgrid::resolution, s_fparams::sl_clust_max_dist, and s_fparams::sl_clust_min_nneigh.

Referenced by mdpocket_detect().

{
    int cx,cy,cz;
    float cv;
    float rx,ry,rz;
    size_t cnt=0;
    /*write the header of the dx file*/
    fprintf(f,"# Data calculated by mdpocket, part of the fpocket package\n");
    fprintf(f,"# This is a standard DX file of occurences of cavities within MD trajectories.\n");
    fprintf(f,"# The file can be visualised using the freely available VMD software\n");
    fprintf(f,"# fpocket parameters used to create this dx file : \n");
    fprintf(f,"# \t-m %2.f (min alpha sphere size) -M %.2f (max alpha sphere size)\n",par->fpar->asph_min_size, par->fpar->asph_max_size);
    fprintf(f,"# \t-i %d (min number of alpha spheres per pocket)\n",par->fpar->min_pock_nb_asph);
    fprintf(f,"# \t-D %.2f (Max distance for 1st clustering algo)\n#\t-r %.2f (Max dist for 2nd clustering algo)\n#\t-s %.2f (Max dist for third clustering algo)\n",par->fpar->clust_max_dist, par->fpar->refine_clust_dist, par->fpar->sl_clust_max_dist);
    fprintf(f,"# \t-n %d (Min neighbour atoms for multi linkage clustering)\n",par->fpar->sl_clust_min_nneigh);
    if(par->flag_scoring) fprintf(f,"# \t-S (Map drug score to density map!)\n");
    fprintf(f,"object 1 class gridpositions counts %d %d %d\n",g->nx,g->ny,g->nz);
    fprintf(f,"origin %.2f %.2f %.2f\n",g->origin[0],g->origin[1],g->origin[2]);
    fprintf(f,"delta %.2f 0 0\n",g->resolution);
    fprintf(f,"delta 0 %.2f 0\n",g->resolution);
    fprintf(f,"delta 0 0 %.2f\n",g->resolution);
    fprintf(f,"object 2 class gridconnections counts %d %d %d\n",g->nx,g->ny,g->nz);
    fprintf(f,"object 3 class array type double rank 0 items %d data follows\n",g->nx*g->ny*g->nz);
    int i=0;
    for(cx=0;cx<g->nx;cx++){
        for(cy=0;cy<g->ny;cy++){
            for(cz=0;cz<g->nz;cz++){
                if(i==3) {
                    i=0;
                    fprintf(f,"\n");
                }
                cv=g->gridvalues[cx][cy][cz];
                fprintf(f,"%.3f ",cv);
                if(cv>=isovalue){
                    cnt++;
                    rx=g->origin[0]+cx*g->resolution;
                    ry=g->origin[1]+cy*g->resolution;
                    rz=g->origin[2]+cz*g->resolution;
                    fprintf(fiso,"ATOM  %5d  C   PTH     1    %8.3f%8.3f%8.3f%6.2f%6.2f\n",(int)cnt,rx,ry,rz,0.0,0.0);
                }
                i++;
            }
        }
    }
}

void write_md_pocket_atoms	(	FILE *	f,
		int *	ids,
		s_pdb *	prot,
		int	nids,
		int	sn
	)

## FUNCTION: write_md_pocket_atoms

## SPECIFICATION: writes a pdb file containing all pocket atoms at each snapshot in distinct models

## PARAMETRES: @ FILE *f : output file handle @ int *ids : list of atom identifiers @ s_pdb *prot : the protein handle @ int nids : number of ids in ids list @ int sn : number of snapshots

## RETURN: void

Definition at line 162 of file mdpout.c.

References s_atm::bfactor, s_atm::chain, s_atm::charge, s_atm::id, s_pdb::latoms_p, 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, write_pdb_atom_line(), s_atm::x, s_atm::y, and s_atm::z.

Referenced by mdpocket_characterize().

                                                                          {
    s_atm *cura;
    int i,j,flag;
    i=0;
    j=0;
    fprintf(f,"MODEL        %d\n",sn);
    for(i=0;i<nids;i++){
        flag=0;
        while(flag==0 && j<prot->natoms){
            cura=prot->latoms_p[j];
            if(cura->id==ids[i]){
                flag=1;
                write_pdb_atom_line(f, "ATOM", cura->id, cura->name,
                                                 cura->pdb_aloc, cura->res_name, cura->chain,
                                                 cura->res_id, cura->pdb_insert, cura->x, cura->y, cura->z, cura->occupancy,
                                                 cura->bfactor, cura->symbol, cura->charge);
            }
            j++;
        }
    }
    fprintf(f,"ENDMDL\n");
    
}