mdpout.c File Reference

#include "../headers/mdpout.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)

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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
	)

## 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");
    
}