refine.c File Reference

#include "../headers/refine.h"

Go to the source code of this file.

Functions
void	refinePockets (c_lst_pockets *pockets, s_fparams *params)
void	dropSmallNpolarPockets (c_lst_pockets *pockets, s_fparams *params)
void	drop_tiny (c_lst_pockets *pockets)
void	reIndexPockets (c_lst_pockets *pockets)

---

Function Documentation

void drop_tiny

(

c_lst_pockets *

pockets

)

## FUNCTION: drop_tiny -- ## SPECIFICATION: Drop really tiny pockets (< 5 alpha spheres)

## PARAMETRES: @ c_lst_pockets *pockets : The list of pockets.

## RETURN: void

Definition at line 176 of file refine.c.

References dropPocket(), c_lst_pockets::first, c_lst_pockets::n_pockets, c_lst_vertices::n_vertices, node_pocket::next, node_pocket::pocket, and s_pocket::v_lst.

{
        node_pocket *npcur = pockets->first,
                                *npnext = NULL ;
        while(npcur) {
                npnext = npcur->next ;

                if(npcur->pocket->v_lst->n_vertices < 2){
                /* If the pocket is really small, drop it */
                        dropPocket(pockets, npcur);
                }

                if(pockets->n_pockets <= 0) fprintf(stderr, "! No Pockets Found while refining\n");
                npcur = npnext ;
        }
}

void dropSmallNpolarPockets	(	c_lst_pockets *	pockets,
		s_fparams *	params
	)

## FUNCTION: dropSmallNpolarPockets -- ## SPECIFICATION: Refine algorithm: will remove small pockets (depends on the corresponding parameters in params), pockets containing less than NB apolar alpha spheres (given in params)..

## PARAMETRES: @ c_lst_pockets *pockets : The list of pockets. @ s_fparams *params : Parameters

## RETURN: void

Definition at line 130 of file refine.c.

References dropPocket(), c_lst_pockets::first, s_fparams::min_pock_nb_asph, c_lst_pockets::n_pockets, c_lst_vertices::n_vertices, s_pocket::nAlphaApol, node_pocket::next, node_pocket::pocket, s_fparams::refine_min_apolar_asphere_prop, and s_pocket::v_lst.

Referenced by search_pocket().

{
        double pasph = 0.0 ;
        node_pocket *npcur = NULL,
                                *nextPocket1 = NULL;
        s_pocket *pcur = NULL ;
        
        if(pockets) {
                npcur = pockets->first ;
                while(npcur) {
                        pcur = npcur->pocket ;
                        nextPocket1 = npcur->next ;
                        pasph = (float)((float)pcur->nAlphaApol/(float)pcur->v_lst->n_vertices) ;


                        if(pcur->v_lst->n_vertices < (size_t) params->min_pock_nb_asph 
                                ||  pasph <  (params->refine_min_apolar_asphere_prop)){
                        /* If the pocket is too small or has not enough apolar alpha
                         * spheres, drop it */
                                dropPocket(pockets, npcur);             
                        }

                        if(pockets->n_pockets <= 0) fprintf(stderr, "! No Pockets Found while refining\n");
                        npcur = nextPocket1 ;
                }
        }
        else {
                fprintf(stderr, "! No pockets to drop from (argument NULL: %p).\n", pockets) ;
        }

}

void refinePockets	(	c_lst_pockets *	pockets,
		s_fparams *	params
	)

## FUNCTION: refinePockets

## SPECIFICATION: Refine algorithm: will merge two pockets whose barycenters are close together (distance criteria given in params).

## PARAMETRES: @ c_lst_pockets *pockets : The list of pockets. @ s_fparams *params : Parameters

## RETURN: void

Definition at line 78 of file refine.c.

References s_pocket::bary, dist(), c_lst_pockets::first, mergePockets(), node_pocket::next, and node_pocket::pocket.

Referenced by search_pocket().

{
        node_pocket *nextPocket;
        node_pocket *curMobilePocket;

        node_pocket *pcur = NULL ;

        float *pbary = NULL, 
                  *mpbary = NULL, dst ;

        if(pockets) {
                pcur = pockets->first ;
                while(pcur) {
                        pbary = pcur->pocket->bary ;
                        curMobilePocket = pcur->next ;

                        while(curMobilePocket) {
                                mpbary = curMobilePocket->pocket->bary ;
                                nextPocket = curMobilePocket->next ;
                                dst = dist(pbary[0], pbary[1], pbary[2], mpbary[0], mpbary[1], mpbary[2]) ;
                                if(dst < params->refine_clust_dist) {
                                // Merge pockets if barycentres are close to each other
                                        mergePockets(pcur, curMobilePocket, pockets);           
                                }
                                curMobilePocket = nextPocket ;
                        }

                        pcur = pcur->next ;
                }
        }
        else {
                fprintf(stderr, "! No pocket to refine! (argument NULL: %p).\n", pockets) ;
        }
}

void reIndexPockets

(

c_lst_pockets *

pockets

)

## FUNCTION: reIndexPockets

## SPECIFICATION: Reindex pockets, after dropping and merging operations on pockets and recalculate barycentres in the same loop

## PARAMETRES: @ c_lst_pockets *pockets: The list of pockets.

## RETURN: void

Definition at line 208 of file refine.c.

References s_pocket::bary, c_lst_vertices::first, c_lst_pockets::first, c_lst_pockets::n_pockets, node_pocket::next, node_vertice::next, node_pocket::pocket, s_vvertice::resid, s_pocket::v_lst, node_vertice::vertice, s_vvertice::x, s_vvertice::y, and s_vvertice::z.

Referenced by search_pocket().

{
        node_vertice *vcur = NULL ;
        node_pocket *pcur = NULL ;
        s_pocket *pock_cur = NULL ;

        int curPocket = 0,
                n_vert ;

        float posSum[3];

        if(pockets && pockets->n_pockets > 0) {
                pcur = pockets->first ;
                while(pcur) {
                        curPocket++ ;                                           //new index counter
                        n_vert = 0 ;

                        pock_cur = pcur->pocket ;
                        pock_cur->bary[0]=0 ;
                        pock_cur->bary[1]=0 ;
                        pock_cur->bary[2]=0 ;
                                
                        posSum[0]=0; posSum[1]=0; posSum[2]=0;
                        if(pock_cur->v_lst){
                                vcur = pock_cur->v_lst->first;
                                
                                while(vcur){
                                        posSum[0] += vcur->vertice->x;
                                        posSum[1] += vcur->vertice->y;
                                        posSum[2] += vcur->vertice->z;
                                        n_vert++;
        
                                        vcur->vertice->resid = curPocket;       //set new index
                                        vcur = vcur->next ;
                                }
                        }
                        else {
                                fprintf(stderr, "! Empty Pocket...something might be wrong over here ;).\n") ; 
                        }
                        //set new barycentre
                        pock_cur->bary[0] = posSum[0]/(float)n_vert;
                        pock_cur->bary[1] = posSum[1]/(float)n_vert;
                        pock_cur->bary[2] = posSum[2]/(float)n_vert;
                        pcur = pcur->next ;
                }
        }
        else {
                fprintf(stderr, "! No pocket to reindex.\n") ;
        }
}