asa.c File Reference

#include "../headers/asa.h"

Go to the source code of this file.

Functions

int atom_in_list (s_atm *a, s_atm **atoms, int natoms)
int * get_surrounding_atoms_idx (s_vvertice **tvert, int nvert, s_pdb *pdb, int *n_sa)
int * get_unique_atoms (s_vvertice **tvert, int nvert, int *n_ua, s_atm **atoms, int na)
s_atm ** get_unique_atoms_DEPRECATED (s_vvertice **tvert, int nvert, int *n_ua)
void set_ASA (s_desc *desc, s_pdb *pdb, s_vvertice **tvert, int nvert)
float * get_points_on_sphere (int nop)

Function Documentation

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

## FUNCTION: atom_not_in_list

## SPECIFICATION: This function checks if the atom a is in the list of atoms "atoms"

## PARAMETRES: @ s_atm *a : The query atom, @ s_atm **atoms : The set of atoms to test @ int natoms : number of atoms in the set of atoms

## RETURN: 1 if a is in atoms, 0 if not

Definition at line 74 of file asa.c.

References s_atm::id.

Referenced by get_unique_atoms_DEPRECATED().

00074                                                      {
00075     int i;
00076     if(atoms){
00077         for(i = 0 ; i < natoms ; i++){
00078             if(atoms[i]==a) {
00079                 if(atoms[i]->id != a->id) {
00080                     fprintf(stdout,"WARNING asa.c: atom in the list but with different ID!") ;
00081                 }
00082                 return 1;
00083             }
00084         }
00085     }
00086     return 0;
00087 }

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().

00443                                      {
00444     float *pts =NULL;
00445     pts=(float *) malloc(sizeof (float) * nop * 3);
00446     float inc = PI * (3.0 - sqrt(5.0));
00447     float off = 2.0 / (float) nop;
00448     float y, r, phi;
00449     int k;
00450     for (k = 0; k < nop; k++) {
00451         y = ((float) k) * off - 1.0 + (off / 2.0);
00452         r = sqrt(1.0 - y * y);
00453         phi = k * inc;
00454         pts[3 * k] = cos(phi) * r;
00455         pts[3 * k + 1] = y;
00456         pts[3 * k + 2] = sin(phi) * r;
00457     }
00458     return pts;
00459 }

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().

00107                                                                                   {
00108     s_atm *a=NULL;
00109     int *sa=NULL;
00110     int i,z,flag=0;
00111     *n_sa=0;
00112     for(i=0;i<pdb->natoms;i++){
00113         a=pdb->latoms_p[i];
00114         //consider only heavy atoms for vdw incr.
00115         if(strncmp(a->symbol,"H",1)){
00116             flag=0;
00117             for(z=0;z<nvert && !flag;z++){
00118                 //flag=atom_not_in_list(a,sa,*n_sa);
00119                 flag=in_tab(sa,*n_sa,i);
00120                 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)){
00121                     *n_sa=*n_sa+1;
00122                     if(sa==NULL){
00123                         sa=(int *)malloc(sizeof(int));
00124                         sa[*n_sa-1]=i;
00125                     }
00126                     else {
00127                         sa=(int *)realloc(sa,sizeof(int)*(*n_sa));
00128                         sa[*n_sa-1]=i;
00129                     }
00130                 }
00131             }
00132         }
00133     }
00134     return sa;
00135 }

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.

00157                                                                                     {
00158     s_atm *a=NULL;
00159     int *ua=NULL;
00160     int z,j;
00161     int ca_idx;
00162     *n_ua=0;
00163     int flag=0;
00164 
00165     s_vvertice *vcur = NULL ;
00166     s_atm **neighs = NULL ;
00167 /*
00168     fprintf(stdout, "\nIn get unique atom\n") ;
00169 */
00170     for(z=0;z<nvert;z++){
00171         vcur = tvert[z] ;
00172         neighs = tvert[z]->neigh ;
00173         for(j=0;j<4;j++){
00174             a=neighs[j];
00175             flag=in_tab(ua,*n_ua,a->id);
00176             if(!flag) {
00177                 *n_ua=*n_ua+1;
00178                 if(ua==NULL) ua=(int *)malloc(sizeof(int));
00179                 else ua=(int *)realloc(ua,sizeof(int)*(*n_ua));
00180                 
00181                 if(a->id-1 < na && a==atoms[a->id-1]) {
00182                     ua[*n_ua-1]=a->id-1;
00183                /*     if(a->id >= 1631) {
00184                         fprintf(stdout, "\nSetting bad id! %d", a->id ) ;
00185                     }*/
00186                 }
00187                 else {
00188                     for(ca_idx=0;ca_idx<na;ca_idx++){
00189                         if(a==atoms[ca_idx]) {
00190                             ua[*n_ua-1]=ca_idx;
00191 
00192                  /*           if(ca_idx >= 1631) {
00193 
00194                                 fprintf(stdout, "\nSetting bad id! %d", ca_idx ) ;
00195                             }*/
00196                             break;
00197                         }
00198                     }
00199                 }
00200             }
00201         }
00202     }
00203 
00204     return ua;
00205 }

s_atm** get_unique_atoms_DEPRECATED ( s_vvertice **  tvert,
int  nvert,
int *  n_ua 
)

Definition at line 208 of file asa.c.

References atom_in_list(), and s_vvertice::neigh.

Referenced by set_ASA().

00209 {
00210     s_vvertice *vcur = NULL ;
00211     s_atm **neighs = NULL ;
00212 
00213     s_atm *a=NULL;
00214     s_atm **ua=(s_atm **) malloc(sizeof(s_atm*)*10);
00215 
00216     int tab_size = 10 ;
00217     int nb_ua = 0;
00218     int z = 0, j = 0;
00219 
00220     /* Loop over each vertice */
00221     for(z = 0 ; z < nvert ; z++){
00222         vcur = tvert[z] ;
00223         neighs = tvert[z]->neigh ;
00224 
00225         /* Loop over each vertice neighbors */
00226         for(j = 0 ; j < 4 ; j++) {
00227             a = neighs[j];
00228             if(atom_in_list(a, ua, nb_ua) == 0) {
00229                 ua[nb_ua] = a;
00230 
00231                 nb_ua = nb_ua + 1;
00232                 if(nb_ua >= tab_size){
00233                     ua = (s_atm **) realloc(ua,sizeof(s_atm*)*(nb_ua+10));
00234                     tab_size += 10 ;
00235                 }
00236             }
00237         }
00238     }
00239 
00240     *n_ua = nb_ua ;
00241 
00242     return ua;
00243 }

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().

00268 {
00269     desc->surf_pol_vdw14=0.0;
00270     desc->surf_apol_vdw14=0.0;
00271     desc->surf_vdw14=0.0;
00272     desc->surf_vdw22=0.0;
00273     desc->surf_pol_vdw22=0.0;
00274     desc->surf_apol_vdw22=0.0;
00275     desc->n_abpa=0;
00276     int *sa=NULL;    /*surrounding atoms container*/
00277     /*int *ua=NULL;    /*unique atoms contacting vvertices*/
00278     s_atm ** ua = NULL ;
00279     
00280     int n_sa = 0;
00281     int n_ua = 0;
00282     int i;
00283     sa=get_surrounding_atoms_idx(tvert,nvert,pdb, &n_sa);
00284     /*ua=get_unique_atoms_DEPRECATED(tvert,nvert, &n_ua,pdb->latoms_p,pdb->natoms);*/
00285 
00286     ua=get_unique_atoms_DEPRECATED(tvert,nvert, &n_ua);
00287     float *abpatmp=NULL;
00288     abpatmp=(float *)my_malloc(sizeof(float)*n_ua);
00289 /*
00290     for(i = 0 ; i < pdb->natoms ; i++) {
00291         if(pdb->latoms_p[i]->id > 1631) {
00292             fprintf(stdout, "\nWTF at %d %d", i,pdb->latoms_p[i]->id) ;
00293         }
00294     }
00295     for( i = 0 ; i < n_ua ; i++) {
00296         if(ua[i] > 1631)
00297             fprintf(stdout, "Atom %d: %d\n", i, ua[i]) ;
00298 
00299     }
00300 */
00301 
00302     s_atm *a,*cura;
00303     float *curpts=NULL,tz,tx,ty,dsq,area;
00304     int j=0,iv,k,burried,nnburried,vidx,vrefburried;
00305     curpts=get_points_on_sphere(M_NSPIRAL);
00306     for(i=0;i<n_ua;i++){
00307         abpatmp[i]=0.0;
00308 /*
00309         fprintf(stdout, "\nUA %d (%d): %d (%d)", i, pdb->natoms, ua [i], n_ua);
00310 */
00311 /*
00312         if(ua [i] >= pdb->natoms) {
00313             fprintf(stdout, "\nWOOPS at %d! %d \n", i, ua[i]) ;//exit(0) ;
00314         }
00315 */
00316 /*
00317         cura=pdb->latoms_p[ua[i]];
00318 */
00319         cura = ua[i] ;
00320         nnburried=0;
00321         
00322         for(k=0;k<M_NSPIRAL;k++){
00323             burried=0;
00324             j=0;
00325             tx=cura->x+curpts[3*k]*(cura->radius+M_PROBE_SIZE);
00326             ty=cura->y+curpts[3*k+1]*(cura->radius+M_PROBE_SIZE);
00327             tz=cura->z+curpts[3*k+2]*(cura->radius+M_PROBE_SIZE);
00328             vrefburried=1;
00329             for(iv=0;iv<nvert;iv++){
00330                 for(vidx=0;vidx<4;vidx++){
00331                     if(cura==tvert[iv]->neigh[vidx]){
00332                         if(ddist(tx,ty,tz,tvert[iv]->x,tvert[iv]->y,tvert[iv]->z)<=tvert[iv]->ray*tvert[iv]->ray) vrefburried=0;
00333                     }
00334                 }
00335             }
00336             while(!burried && j< n_sa && !vrefburried){
00337                 a=pdb->latoms_p[sa[j]];
00338                 if(a!=cura){
00339                     dsq=ddist(tx,ty,tz,a->x,a->y,a->z);
00340                     if(dsq<(a->radius+M_PROBE_SIZE)*(a->radius+M_PROBE_SIZE)) burried=1;
00341                 }
00342                 j++;
00343             }
00344             if(!burried && !vrefburried) {
00345                 nnburried++;
00346             }
00347         }
00348         area=(4*PI*(cura->radius+M_PROBE_SIZE)*(cura->radius+M_PROBE_SIZE)/(float)M_NSPIRAL)*nnburried;
00349         abpatmp[i]=area;
00350         if(cura->electroneg<2.8) desc->surf_apol_vdw14=desc->surf_apol_vdw14+area;
00351         else desc->surf_pol_vdw14=desc->surf_pol_vdw14+area;
00352         desc->surf_vdw14=desc->surf_vdw14+area;
00353         
00354     }
00355     
00356 
00357     /*now test with vdw +2.2*/
00358     for(i=0;i<n_ua;i++){
00359 /*
00360         fprintf(stdout, "\nUA %d (%d): %d (%d)", i, pdb->natoms, ua [i], n_ua);
00361 */
00362 /*
00363         if(ua [i] >= pdb->natoms) {
00364             fprintf(stdout, "\nWOOPS at %d! %d \n", i, ua[i]) ;//exit(0) ;
00365         }
00366 */
00367 /*
00368         cura=pdb->latoms_p[ua[i]];
00369 */
00370         cura = ua[i] ;
00371         nnburried=0;
00372 
00373         for(k=0;k<M_NSPIRAL;k++){
00374             burried=0;
00375             j=0;
00376             tx=cura->x+curpts[3*k]*(cura->radius+M_PROBE_SIZE2);
00377             ty=cura->y+curpts[3*k+1]*(cura->radius+M_PROBE_SIZE2);
00378             tz=cura->z+curpts[3*k+2]*(cura->radius+M_PROBE_SIZE2);
00379             vrefburried=1;
00380             for(iv=0;iv<nvert;iv++){
00381                 for(vidx=0;vidx<4;vidx++){
00382                     if(cura==tvert[iv]->neigh[vidx]){
00383                         if(ddist(tx,ty,tz,tvert[iv]->x,tvert[iv]->y,tvert[iv]->z)<=tvert[iv]->ray*tvert[iv]->ray) vrefburried=0;
00384                     }
00385                 }
00386             }
00387             while(!burried && j< n_sa && !vrefburried){
00388                 a=pdb->latoms_p[sa[j]];
00389                 if(a!=cura){
00390                     dsq=ddist(tx,ty,tz,a->x,a->y,a->z);
00391                     if(dsq<(a->radius+M_PROBE_SIZE2)*(a->radius+M_PROBE_SIZE2)) burried=1;
00392                 }
00393                 j++;
00394             }
00395             if(!burried && !vrefburried) {
00396                 nnburried++;
00397             }
00398         }
00399         area=(4*PI*(cura->radius+M_PROBE_SIZE2)*(cura->radius+M_PROBE_SIZE2)/(float)M_NSPIRAL)*nnburried;
00400         if(cura->electroneg<2.8) {
00401             if(area<=abpatmp[i] && abpatmp[i] <=10.0 && area > 0.0){
00402                 desc->n_abpa+=1;
00403             }
00404             desc->surf_apol_vdw22=desc->surf_apol_vdw22+area;
00405         }
00406         else desc->surf_pol_vdw22=desc->surf_pol_vdw22+area;
00407         desc->surf_vdw22=desc->surf_vdw22+area;
00408 
00409     }
00410     free(curpts);
00411 
00412 
00413 
00414     curpts=NULL;
00415    /* for(i=0;i<n_ua-1;i++){
00416         free(ua[i]);
00417     }*/
00418     
00419     free(ua);
00420     free(sa);
00421 
00422     sa=NULL;
00423     ua=NULL;
00424 }

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