Adding parameters : --force or -f will allow the user to choose weither or not…

Adding parameters : --force or -f will allow the user to choose weither or not clashes should be taken into account. Conformations with too many clashes will be skipped

src/INTBuilder.c

@@ -95,7 +95,7 @@ void getCandidatesForP1(struct pdb_values* pdb2, struct residue** t_candid1, str
     }
 }
 
-void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL){
+void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL, int confID){
     /* This function will output the docking interface between pdbR and pdbL
      * To compute the docking interface, we considered that any residue of P1 at or closer than 10A
      * of a residue of P2 will represent a contact
@@ -122,6 +122,10 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL){
     struct residue** t_candidateR = NULL;
     int nbCandR = pdbR->nbRes, nbCandL = pdbL->nbRes;
 
+    /** Here we reset the number of clashes as this is a new interface computation **/
+    clash = 0;
+
+
     t_candidateL = malloc((2*pdbL->nbRes)*sizeof(struct residue*));
     if(t_candidateL == NULL){
         perror("malloc");
@@ -192,7 +196,7 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL){
             /* For each candidate residue of the ligand */
             for(k=0;k<nbCandL;k++){
                 /* If both the residues we are looking at are already selected */
-                if(t_candidateL[k]->isCandidate && t_candidateR[i]->isCandidate){
+                if(force && t_candidateL[k]->isCandidate && t_candidateR[i]->isCandidate){
                     continue;
                 }
                 for(l=0;l<t_candidateL[k]->nbAtom;l++){
@@ -201,20 +205,46 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL){
                     z2 = t_candidateL[k]->z[l];
 
                     dist = sqrt((x1-x2)*(x1-x2) + (y1-y2)*(y1-y2) + (z1-z2)*(z1-z2));
+                    if(dist < DIST_FOR_CLASH){
+                        clash++;
+                        if(clash >= TOO_MUCH_CLASHES){
+                            break;
+                        }
+                        continue;
+                    }
                     if(dist <= DIST_FOR_CONTACT){
                         t_candidateR[i]->isCandidate = 1;
                         t_candidateL[k]->isCandidate = 1;
                         break;
                     }
                 }
+                if(clash >= TOO_MUCH_CLASHES){
+                    break;
+                }
+            }
+            if(clash >= TOO_MUCH_CLASHES){
+                break;
+            }
         }
+        if(clash >= TOO_MUCH_CLASHES){
+            break;
         }
     }
     
+    printf("number of clashes : %d \n",clash);
+    
+    /* If the amount of clashes is still ok */
+    if(clash < TOO_MUCH_CLASHES){
         /* Output the ligand's interface */
+        fprintf(outputFile_lig,"%d ",confID);
         write_candidate(t_candidateL,nbCandL,outputFile_lig);
+        fprintf(outputFile_lig,"\n");
+
         /* Output the receptor's interface */
+        fprintf(outputFile_rec,"%d ",confID);
         write_candidate(t_candidateR,nbCandR,outputFile_rec);
+        fprintf(outputFile_rec,"\n");
+    }
 
     free(t_candidateL);
     free(t_candidateR);
@@ -252,11 +282,7 @@ int main(int argc, char** argv){
 
     if(complexPDB){    /* If we are building for a given complex, no rotation */
         /* Write the number of the conformation and get the interface */
-        fprintf(outputFile_lig,"%d ",i);
-        fprintf(outputFile_rec,"%d ",i);
-        getInterface(pdbR,pdbL);
-        fprintf(outputFile_lig,"\n");
-        fprintf(outputFile_rec,"\n");
+        getInterface(pdbR,pdbL,0);
 
         if(constructPDB){
             writePDB(newPDB, ligand,target_conf);
@@ -274,11 +300,7 @@ int main(int argc, char** argv){
 
         /* Write the number of the conformation and get the interface */
         if(!doNotOutputINT){
-            fprintf(outputFile_lig,"%d ",i);
-            fprintf(outputFile_rec,"%d ",i);
-            getInterface(pdbR,newPDB);
-            fprintf(outputFile_lig,"\n");
-            fprintf(outputFile_rec,"\n");
+            getInterface(pdbR,newPDB,target_conf);
         }
 
         if(constructPDB){
@@ -312,11 +334,7 @@ int main(int argc, char** argv){
 
             /* Write the number of the conformation and get the interface */
             if(!doNotOutputINT){
-                fprintf(outputFile_lig,"%d ",i);
-                fprintf(outputFile_rec,"%d ",i);
-                getInterface(pdbR,newPDB);
-                fprintf(outputFile_lig,"\n");
-                fprintf(outputFile_rec,"\n");
+                getInterface(pdbR,newPDB,i);
             }
 
             if(constructPDB){

src/INTBuilder.h

@@ -4,7 +4,7 @@
 #define INTB_HEADER
 
 void getCandidatesForP1(struct pdb_values* pdb2, struct residue** t_candid1, struct residue** t_candid2, int* nbCand1, int* nbCand2);
-void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL);
+void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL, int confID);
 void removeSpace(char* string);
 int main(int argc, char** argv);
 

src/fileIO.c

@@ -61,10 +61,15 @@ struct docking_results* getDataForComplex(){
         if(feof(condFile_stream)){
             break;
         }
+        /* printf("curConf : %d\n",idConf); */
+
 
         rc = fscanf(condFile_stream,"%f %f %f %f %f %f",&dock_res->distCenters[idConf],&dock_res->theta[idConf],&dock_res->phi[idConf],&dock_res->alpha[idConf],&dock_res->beta[idConf],&dock_res->gamma[idConf]);
         rc = getline(&buf,&len,condFile_stream); /* Get rid of the rest of the line */
 
+        if(idConf == 137)
+        printf("\n%f %f %f %f %f %f\n",dock_res->distCenters[idConf],dock_res->theta[idConf],dock_res->phi[idConf],dock_res->alpha[idConf],dock_res->beta[idConf],dock_res->gamma[idConf]);
+
         /* theta and phi angles are written in Radian already
          * However that is not the case for alpha, beta and gamma angles
          */

src/param.c

@@ -30,6 +30,8 @@ void print_usage() {
     "<-HCMD2>           Means that the docking file is in the HCMD2 MAXDo format\n"
     "<-noOutput>        Will prevent the program to output the docking interface\n"
     "                   Useful if you only want to use the '-outputPDB' option\n"
+    "<--force/-f>       Will force the computation of the pause even in case of\n"
+    "                   huge number of clashes (threshold defined in struct.h)\n"
     );
 }
 
@@ -51,6 +53,8 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
     HCMD2           = 0;
     complexPDB      = 0;
     doNotOutputINT  = 0;
+    clash           = 0;
+    force           = 0;
     outputDir       = NULL;
     outputPDB       = NULL;
     verbose_file    = NULL;
@@ -120,6 +124,9 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
         }else if(strcmp(argv[i],"-h") == 0 ||
                 strcmp(argv[i],"--help") == 0){
             print_help = 1;
+        }else if(strcmp(argv[i],"-f") == 0 ||
+                strcmp(argv[i],"--force") == 0){
+            force = 1;
         }else if(strcmp(argv[i],"-v") == 0 ||
                 strcmp(argv[i],"--verbose") == 0){
             verbose = 1;

src/struct.h

@@ -11,8 +11,12 @@
 
 #define COEF_DEGREE_TO_RADIAN 0.017453293   /* Coefficient to convert degrees to radians */
 #define NB_MAX_ATOM_PER_RES 100              /* No residue has more atoms than that */
+#define TOO_MUCH_CLASHES 20                /* If not forcing, program will skip conformation after 
+                                            * this number of clashes */
 #define DIST_FOR_CONTACT 6                 /* Distance under which we consider 
                                              * two residues are in contact */
+#define DIST_FOR_CLASH 2           /* Distance in Angstrom under which we consider 
+                                    * the contact is a clash */
 
 /* This is the format of a line in a PDB file */
 #define FORMAT_LINE_PDB "ATOM  %5d  %3s %3s %c%5s   %8.3f%8.3f%8.3f\n" 
@@ -23,6 +27,8 @@ int     target_conf;        /* 1 if we are specific to one conformation */
 int     HCMD2;              /* 1 if this is HCMD2 format */
 int     complexPDB;         /* 1 if we are computing the interface of a given complex */
 int     doNotOutputINT;     /* 1 if we don't want to output the interface */
+int     clash;              /* Maybe be incremented in case of clashes */
+int     force;              /* Will output even if clash, may increase computation time */
 FILE*   verbose_file;       /* If verbose mode, the output file */
 char*   pdbDir;             /* Directory containing the PDBs */
 char*   receptor;           /* Name of the receptor */