adaptation to HCMD2 format. Modif of writePDB function (takes the num of the conformation)

src/INTBuilder.c

@@ -93,7 +93,7 @@ void getCandidatesForP1(struct pdb_values* pdb2, struct residue** t_candid1, str
     }
 }
 
-void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL, int numConf){
+void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL){
     int i = 0, j = 0, k = 0, l = 0;
     int oldCandL = -1, oldCandR = -1;
     float x1 = 0, y1 = 0, z1 = 0;
@@ -129,7 +129,18 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL, int numConf)
         oldCandL = nbCandL;
         oldCandR = nbCandR;
         getCandidatesForP1(pdbR,t_candidateL,t_candidateR,&nbCandL,&nbCandR);
+        if(nbCandL == 0 || nbCandR == 0){
+            nbCandL = 0;
+            nbCandR = 0;
+            break;
+        }
+
         getCandidatesForP1(pdbL,t_candidateR,t_candidateL,&nbCandR,&nbCandL);
+        if(nbCandL == 0 || nbCandR == 0){
+            nbCandL = 0;
+            nbCandR = 0;
+            break;
+        }
     }
     //printf("NB_ITER %d\n",k);
 
@@ -186,6 +197,79 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL, int numConf)
 }
 
 
+struct docking_results* getDataForComplex_HCMD2(){
+    char* buf = NULL;
+    char buf2[5];
+    FILE* condFile_stream = NULL;
+    int numberOfConf = 0, rc;
+    size_t len = 2000;
+    struct docking_results* dock_res = NULL;
+
+
+    strncpy(buf2,receptor,4);
+    buf2[4] = '\0';
+    //sprintf(totalFilePath,"%s/%s/Cond.%s.%s.UB.global.dat",dockingFile,buf2,receptor,ligand);
+
+    if(access(dockingFile,F_OK) == -1){
+        /* File does not exists, 4 file in this case
+         * Return NULL, which should be treated accordingly
+         */
+        fprintf(stderr,"No such file : %s\n",dockingFile);
+        exit(EXIT_FAILURE);
+    }
+
+    condFile_stream = fopen(dockingFile,"r");
+
+    /* Get the number of conformations */
+    float buf3 = 0;
+    rc = fscanf(condFile_stream,"%f",&buf3);
+    rc = getline(&buf,&len,condFile_stream); /* Get rid of the rest of the line */
+    if(buf3 > numberOfConf)
+        numberOfConf = (int) buf3;
+
+    while(!feof(condFile_stream)){
+        rc = fscanf(condFile_stream,"%f",&buf3);
+        rc = getline(&buf,&len,condFile_stream); /* Get rid of the rest of the line */
+        if(buf3 > numberOfConf)
+            numberOfConf = (int) buf3;
+    }
+    numberOfConf++;
+    rewind(condFile_stream);
+    rc = getline(&buf,&len,condFile_stream); /* Get rid of the first line */
+
+    dock_res = allocate_dockingResults(numberOfConf);
+
+
+    int idConf = 0, buf4, prevID = -1;
+
+    while(!feof(condFile_stream)){
+        /* We take the first value as it is the ID of the conformation */
+        rc = fscanf(condFile_stream,"%d %d %d %d",&idConf,&buf4, &buf4, &buf4);
+        if(prevID == idConf){
+            break;
+        }else{
+            prevID = 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]);
+        /* printf("%d %f %f %f %f %f %f\n",idConf,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 */
+
+
+        //dock_res->theta[idConf] = dock_res->theta[idConf]*cdr;
+        //dock_res->phi[idConf]  = dock_res->phi[idConf]*cdr;
+
+        dock_res->alpha[idConf] = dock_res->alpha[idConf]*CDR;
+        dock_res->beta[idConf]  = dock_res->beta[idConf]*CDR;
+        dock_res->gamma[idConf] = dock_res->gamma[idConf]*CDR;
+    }
+
+    dock_res->nbConf = numberOfConf;
+
+    fclose(condFile_stream);
+    free(buf);
+    return dock_res;
+}
 
 struct docking_results* getDataForComplex(){
     char* buf = NULL;
@@ -418,21 +502,20 @@ void removeSpace(char* string){
     }
 }
 
-void writePDB(struct pdb_values* pdb, char* protName){
+void writePDB(struct pdb_values* pdb, char* protName, int nConf){
     int i = 0, j = 0;
     char buf[500];
     FILE* fw = NULL;
 
-    sprintf(buf,"%s/%s.pdb",outputPDB,protName);
+    sprintf(buf,"%s/%s_%d.pdb",outputPDB,protName,nConf);
     fw = fopen(buf,"w");
     if(fw == NULL){
         perror("fopen");
         exit(EXIT_FAILURE);
     }
-
     for(i=0;i<pdb->nbRes;i++){
         for(j=0;j<pdb->residues[i].nbAtom;j++){
-            fprintf(fw,"ATOM  %5d  %3s %3s %c%5s   %8.3f%8.3f%8.3f\n",pdb->residues[i].idAtom[j],
+            fprintf(fw,FORMAT_LINE_PDB,pdb->residues[i].idAtom[j],
             pdb->residues[i].atomType[j],pdb->residues[i].resName,pdb->residues[i].chain,
             pdb->residues[i].idRes,pdb->residues[i].x[j],pdb->residues[i].y[j],pdb->residues[i].z[j]);
         }
@@ -457,7 +540,11 @@ int main(int argc, char** argv){
     printf("Computing %s and %s ...",receptor,ligand);
     fflush(stdout);
 
+    if(HCMD2){
+        dock_res = getDataForComplex_HCMD2();
+    }else{
         dock_res = getDataForComplex();
+    }
 
     pdbR = readPDB(receptor);
     pdbL = readPDB(ligand);
@@ -472,10 +559,10 @@ int main(int argc, char** argv){
                             dock_res->theta[target_conf],dock_res->phi[target_conf],
                             dalpha,dbeta,dgamma,dock_res,target_conf);
 
-        getInterface(pdbR,newPDB,target_conf);
+        getInterface(pdbR,newPDB);
 
         if(constructPDB){
-            writePDB(newPDB, ligand);
+            writePDB(newPDB, ligand,target_conf);
         }
         freePDB(newPDB);
     }else{
@@ -491,12 +578,12 @@ int main(int argc, char** argv){
 
             fprintf(outputFile_lig,"%d ",i);
             fprintf(outputFile_rec,"%d ",i);
-            getInterface(pdbR,newPDB,i);
+            getInterface(pdbR,newPDB);
             fprintf(outputFile_lig,"\n");
             fprintf(outputFile_rec,"\n");
 
             if(constructPDB){
-                writePDB(newPDB, ligand);
+                writePDB(newPDB, ligand,i);
             }
             freePDB(newPDB);
         }

src/INTBuilder.h

+#include "struct.h"
+
 #ifndef INTB_HEADER
 #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, int numConf);
+void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL);
 struct docking_results* getDataForComplex();
+struct docking_results* getDataForComplex_HCMD2();
 struct pdb_values* readPDB(char* protein) ;
 void removeSpace(char* string);
-void writePDB(struct pdb_values* pdb, char* protName);
+void writePDB(struct pdb_values* pdb, char* protName, int nbConf);
 int main(int argc, char** argv);
 
 #endif

src/param.c

@@ -35,6 +35,7 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
     verbose         = 0;
     constructPDB    = 0;
     target_conf     = -1;
+    HCMD2           = 0;
     outputDir       = NULL;
     outputPDB       = NULL;
     verbose_file    = NULL;
@@ -99,6 +100,8 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
                 fprintf(stderr,"Specific conformation not valid\n");
                 exit(EXIT_SUCCESS);
             }
+        }else if(strcmp(argv[i],"-HCMD2") == 0){
+            HCMD2 = 1;
         }else if(strcmp(argv[i],"-h") == 0 ||
                 strcmp(argv[i],"--help") == 0){
             print_help = 1;

src/struct.h

@@ -13,6 +13,7 @@ int     nbThreads;
 int     verbose;
 int     constructPDB;
 int     target_conf;
+int     HCMD2;
 FILE*   verbose_file;
 char*   pdbDir;
 char*   receptor;
@@ -25,6 +26,7 @@ FILE*   outputFile_lig;
 #define CDR 0.017453293
 #define NB_MAX_ATOM_PER_RES 20
 #define DIST_FOR_CONTACT 10
+#define FORMAT_LINE_PDB "ATOM  %5d  %3s %3s %c%5s   %8.3f%8.3f%8.3f\n"
 
 /*************************************************/