asa.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 "fparams.h"
#include "memhandler.h"

Go to the source code of this file.

Defines
#define	M_NSPIRAL   100
#define	M_PADDING   1.0
#define	M_PROBE_SIZE   1.4
#define	M_PROBE_SIZE2   2.2
#define	PI   3.1415926535897931
Functions
int	atom_not_in_list (s_atm *a, s_atm **atoms, int natoms)
void	set_ASA (s_desc *desc, s_pdb *pdb, s_vvertice **tvert, int nvert)
int *	get_unique_atoms (s_vvertice **tvert, int nvert, int *n_ua, s_atm **p, int na)
float *	get_points_on_sphere (int nop)
int *	get_surrounding_atoms_idx (s_vvertice **tvert, int nvert, s_pdb *pdb, int *n_sa)

---

Define Documentation

#define M_NSPIRAL   100

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/>.

Definition at line 61 of file asa.h.

Referenced by set_ASA().

#define M_PADDING   1.0

Definition at line 62 of file asa.h.

Referenced by get_surrounding_atoms_idx().

#define M_PROBE_SIZE   1.4

Definition at line 63 of file asa.h.

Referenced by set_ASA().

#define M_PROBE_SIZE2   2.2

Definition at line 64 of file asa.h.

Referenced by set_ASA().

#define PI   3.1415926535897931

Definition at line 65 of file asa.h.

Referenced by get_points_on_sphere(), and set_ASA().

---

Function Documentation

int atom_not_in_list	(	s_atm *	a,
		s_atm **	atoms,
		int	natoms
	)

float* get_points_on_sphere

(

int

nop

)

## FUNCTION: get_points_on_sphere

## SPECIFICATION: This function takes an integer as argument and returns a unit sphere with distributed points on its surface according to the Golden Section Spiral Distribution

## PARAMETRES: @ int nop : number of points to create on the unit sphere (resolution of the surface)

## RETURN: float* : list of points on the unit sphere

Definition at line 443 of file asa.c.

References PI.

Referenced by set_ASA().

                                     {
    float *pts =NULL;
    pts=(float *) malloc(sizeof (float) * nop * 3);
    float inc = PI * (3.0 - sqrt(5.0));
    float off = 2.0 / (float) nop;
    float y, r, phi;
    int k;
    for (k = 0; k < nop; k++) {
        y = ((float) k) * off - 1.0 + (off / 2.0);
        r = sqrt(1.0 - y * y);
        phi = k * inc;
        pts[3 * k] = cos(phi) * r;
        pts[3 * k + 1] = y;
        pts[3 * k + 2] = sin(phi) * r;
    }
    return pts;
}

int* get_surrounding_atoms_idx	(	s_vvertice **	tvert,
		int	nvert,
		s_pdb *	pdb,
		int *	n_sa
	)

## FUNCTION: get_surrounding_atoms_idx

## SPECIFICATION: Get atom ids around a given set of voronoi vertices

## PARAMETRES: @ s_vvertices **tvert : List of pointers to voronoi vertices, @ int nvert : Number of Voronoi vertices @ s_pdb *pdb : Structure of the protein @ int *n_sa : Pointer to int holding the number of surrounding atoms

## RETURN: int * : atom ids of surrounding atoms

Definition at line 107 of file asa.c.

References ddist(), in_tab(), s_pdb::latoms_p, M_PADDING, s_pdb::natoms, s_vvertice::ray, s_atm::symbol, s_vvertice::x, s_atm::x, s_vvertice::y, s_atm::y, s_vvertice::z, and s_atm::z.

Referenced by set_ASA(), and write_pocket_pdb_DB().

                                                                                  {
    s_atm *a=NULL;
    int *sa=NULL;
    int i,z,flag=0;
    *n_sa=0;
    for(i=0;i<pdb->natoms;i++){
        a=pdb->latoms_p[i];
        //consider only heavy atoms for vdw incr.
        if(strncmp(a->symbol,"H",1)){
            flag=0;
            for(z=0;z<nvert && !flag;z++){
                //flag=atom_not_in_list(a,sa,*n_sa);
                flag=in_tab(sa,*n_sa,i);
                if(!flag && ddist(a->x,a->y,a->z,tvert[z]->x,tvert[z]->y,tvert[z]->z)<(tvert[z]->ray+M_PADDING)*(tvert[z]->ray+M_PADDING)){
                    *n_sa=*n_sa+1;
                    if(sa==NULL){
                        sa=(int *)malloc(sizeof(int));
                        sa[*n_sa-1]=i;
                    }
                    else {
                        sa=(int *)realloc(sa,sizeof(int)*(*n_sa));
                        sa[*n_sa-1]=i;
                    }
                }
            }
        }
    }
    return sa;
}

int* get_unique_atoms	(	s_vvertice **	tvert,
		int	nvert,
		int *	n_ua,
		s_atm **	atoms,
		int	na
	)

## FUNCTION: get_unique_atoms

## SPECIFICATION: Get a list of unique atom ids near the pocket

## PARAMETRES: @ s_vvertices **tvert : List of pointers to voronoi vertices, @ int nvert : Number of Voronoi vertices @ int *n_sa : Pointer to int holding the number of surrounding atoms @ s_atm **atoms : List of pointers to atoms @ int na : Number of atoms in atoms

## RETURN: int * : atom ids of unique atoms

Definition at line 157 of file asa.c.

References s_atm::id, in_tab(), and s_vvertice::neigh.

                                                                                    {
    s_atm *a=NULL;
    int *ua=NULL;
    int z,j;
    int ca_idx;
    *n_ua=0;
    int flag=0;

    s_vvertice *vcur = NULL ;
    s_atm **neighs = NULL ;
/*
    fprintf(stdout, "\nIn get unique atom\n") ;
*/
    for(z=0;z<nvert;z++){
        vcur = tvert[z] ;
        neighs = tvert[z]->neigh ;
        for(j=0;j<4;j++){
            a=neighs[j];
            flag=in_tab(ua,*n_ua,a->id);
            if(!flag) {
                *n_ua=*n_ua+1;
                if(ua==NULL) ua=(int *)malloc(sizeof(int));
                else ua=(int *)realloc(ua,sizeof(int)*(*n_ua));
                
                if(a->id-1 < na && a==atoms[a->id-1]) {
                    ua[*n_ua-1]=a->id-1;
               /*     if(a->id >= 1631) {
                        fprintf(stdout, "\nSetting bad id! %d", a->id ) ;
                    }*/
                }
                else {
                    for(ca_idx=0;ca_idx<na;ca_idx++){
                        if(a==atoms[ca_idx]) {
                            ua[*n_ua-1]=ca_idx;

                 /*           if(ca_idx >= 1631) {

                                fprintf(stdout, "\nSetting bad id! %d", ca_idx ) ;
                            }*/
                            break;
                        }
                    }
                }
            }
        }
    }

    return ua;
}

void set_ASA	(	s_desc *	desc,
		s_pdb *	pdb,
		s_vvertice **	tvert,
		int	nvert
	)

## FUNCTION: set_ASA

## SPECIFICATION: The actual ASA calculation, resulst are written to the descriptor structure

## PARAMETRES: @ s_desc *desc : Structure of descriptors @ s_pdb *pdb : Structure containing the protein @ s_vvertices **tvert : List of pointers to Voronoi vertices @ int nvert : Number of vertices

## RETURN: void

Definition at line 267 of file asa.c.

References ddist(), s_atm::electroneg, get_points_on_sphere(), get_surrounding_atoms_idx(), get_unique_atoms_DEPRECATED(), s_pdb::latoms_p, M_NSPIRAL, M_PROBE_SIZE, M_PROBE_SIZE2, my_malloc(), s_desc::n_abpa, PI, s_atm::radius, s_vvertice::ray, s_desc::surf_apol_vdw14, s_desc::surf_apol_vdw22, s_desc::surf_pol_vdw14, s_desc::surf_pol_vdw22, s_desc::surf_vdw14, s_desc::surf_vdw22, s_atm::x, s_atm::y, and s_atm::z.

Referenced by set_descriptors().

{
    desc->surf_pol_vdw14=0.0;
    desc->surf_apol_vdw14=0.0;
    desc->surf_vdw14=0.0;
    desc->surf_vdw22=0.0;
    desc->surf_pol_vdw22=0.0;
    desc->surf_apol_vdw22=0.0;
    desc->n_abpa=0;
    int *sa=NULL;    /*surrounding atoms container*/
    /*int *ua=NULL;    /*unique atoms contacting vvertices*/
    s_atm ** ua = NULL ;
    
    int n_sa = 0;
    int n_ua = 0;
    int i;
    sa=get_surrounding_atoms_idx(tvert,nvert,pdb, &n_sa);
    /*ua=get_unique_atoms_DEPRECATED(tvert,nvert, &n_ua,pdb->latoms_p,pdb->natoms);*/

    ua=get_unique_atoms_DEPRECATED(tvert,nvert, &n_ua);
    float *abpatmp=NULL;
    abpatmp=(float *)my_malloc(sizeof(float)*n_ua);
/*
    for(i = 0 ; i < pdb->natoms ; i++) {
        if(pdb->latoms_p[i]->id > 1631) {
            fprintf(stdout, "\nWTF at %d %d", i,pdb->latoms_p[i]->id) ;
        }
    }
    for( i = 0 ; i < n_ua ; i++) {
        if(ua[i] > 1631)
            fprintf(stdout, "Atom %d: %d\n", i, ua[i]) ;

    }
*/

    s_atm *a,*cura;
    float *curpts=NULL,tz,tx,ty,dsq,area;
    int j=0,iv,k,burried,nnburried,vidx,vrefburried;
    curpts=get_points_on_sphere(M_NSPIRAL);
    for(i=0;i<n_ua;i++){
        abpatmp[i]=0.0;
/*
        fprintf(stdout, "\nUA %d (%d): %d (%d)", i, pdb->natoms, ua [i], n_ua);
*/
/*
        if(ua [i] >= pdb->natoms) {
            fprintf(stdout, "\nWOOPS at %d! %d \n", i, ua[i]) ;//exit(0) ;
        }
*/
/*
        cura=pdb->latoms_p[ua[i]];
*/
        cura = ua[i] ;
        nnburried=0;
        
        for(k=0;k<M_NSPIRAL;k++){
            burried=0;
            j=0;
            tx=cura->x+curpts[3*k]*(cura->radius+M_PROBE_SIZE);
            ty=cura->y+curpts[3*k+1]*(cura->radius+M_PROBE_SIZE);
            tz=cura->z+curpts[3*k+2]*(cura->radius+M_PROBE_SIZE);
            vrefburried=1;
            for(iv=0;iv<nvert;iv++){
                for(vidx=0;vidx<4;vidx++){
                    if(cura==tvert[iv]->neigh[vidx]){
                        if(ddist(tx,ty,tz,tvert[iv]->x,tvert[iv]->y,tvert[iv]->z)<=tvert[iv]->ray*tvert[iv]->ray) vrefburried=0;
                    }
                }
            }
            while(!burried && j< n_sa && !vrefburried){
                a=pdb->latoms_p[sa[j]];
                if(a!=cura){
                    dsq=ddist(tx,ty,tz,a->x,a->y,a->z);
                    if(dsq<(a->radius+M_PROBE_SIZE)*(a->radius+M_PROBE_SIZE)) burried=1;
                }
                j++;
            }
            if(!burried && !vrefburried) {
                nnburried++;
            }
        }
        area=(4*PI*(cura->radius+M_PROBE_SIZE)*(cura->radius+M_PROBE_SIZE)/(float)M_NSPIRAL)*nnburried;
        abpatmp[i]=area;
        if(cura->electroneg<2.8) desc->surf_apol_vdw14=desc->surf_apol_vdw14+area;
        else desc->surf_pol_vdw14=desc->surf_pol_vdw14+area;
        desc->surf_vdw14=desc->surf_vdw14+area;
        
    }
    

    /*now test with vdw +2.2*/
    for(i=0;i<n_ua;i++){
/*
        fprintf(stdout, "\nUA %d (%d): %d (%d)", i, pdb->natoms, ua [i], n_ua);
*/
/*
        if(ua [i] >= pdb->natoms) {
            fprintf(stdout, "\nWOOPS at %d! %d \n", i, ua[i]) ;//exit(0) ;
        }
*/
/*
        cura=pdb->latoms_p[ua[i]];
*/
        cura = ua[i] ;
        nnburried=0;

        for(k=0;k<M_NSPIRAL;k++){
            burried=0;
            j=0;
            tx=cura->x+curpts[3*k]*(cura->radius+M_PROBE_SIZE2);
            ty=cura->y+curpts[3*k+1]*(cura->radius+M_PROBE_SIZE2);
            tz=cura->z+curpts[3*k+2]*(cura->radius+M_PROBE_SIZE2);
            vrefburried=1;
            for(iv=0;iv<nvert;iv++){
                for(vidx=0;vidx<4;vidx++){
                    if(cura==tvert[iv]->neigh[vidx]){
                        if(ddist(tx,ty,tz,tvert[iv]->x,tvert[iv]->y,tvert[iv]->z)<=tvert[iv]->ray*tvert[iv]->ray) vrefburried=0;
                    }
                }
            }
            while(!burried && j< n_sa && !vrefburried){
                a=pdb->latoms_p[sa[j]];
                if(a!=cura){
                    dsq=ddist(tx,ty,tz,a->x,a->y,a->z);
                    if(dsq<(a->radius+M_PROBE_SIZE2)*(a->radius+M_PROBE_SIZE2)) burried=1;
                }
                j++;
            }
            if(!burried && !vrefburried) {
                nnburried++;
            }
        }
        area=(4*PI*(cura->radius+M_PROBE_SIZE2)*(cura->radius+M_PROBE_SIZE2)/(float)M_NSPIRAL)*nnburried;
        if(cura->electroneg<2.8) {
            if(area<=abpatmp[i] && abpatmp[i] <=10.0 && area > 0.0){
                desc->n_abpa+=1;
            }
            desc->surf_apol_vdw22=desc->surf_apol_vdw22+area;
        }
        else desc->surf_pol_vdw22=desc->surf_pol_vdw22+area;
        desc->surf_vdw22=desc->surf_vdw22+area;

    }
    free(curpts);



    curpts=NULL;
   /* for(i=0;i<n_ua-1;i++){
        free(ua[i]);
    }*/
    
    free(ua);
    free(sa);

    sa=NULL;
    ua=NULL;
}