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

src/INTBuilder.c

@@ -16,7 +16,7 @@ void getCandidatesForP1(struct pdb_values* pdb2, struct residue** t_candid1, str
      * of P1. At the end of the function, the first *nbCand1 residues in t_candid1 will
      * correspond to P1 candidates
      */
-    
+
     float x = 0, y = 0, z = 0;
     float centerX = 0, centerY = 0, centerZ = 0;
     float dist = 0, minDist = -1, maxDist = -1, threshold_dist = 0;
@@ -64,7 +64,7 @@ void getCandidatesForP1(struct pdb_values* pdb2, struct residue** t_candid1, str
             }
         }
     }
-    
+
     /* We remove every residue on pdb1 that is closer than treshold_dist from the center
      * of mass
      */
@@ -74,10 +74,10 @@ void getCandidatesForP1(struct pdb_values* pdb2, struct residue** t_candid1, str
     }
 
     *nbCand1 = 0;
-    
+
     for(i=0;i<nbCandInit1;i++){
         for(j=0;j<t_candid1[i]->nbAtom;j++){
-            
+
             x = t_candid1[i]->x[j];
             y = t_candid1[i]->y[j];
             z = t_candid1[i]->z[j];
@@ -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;
@@ -129,10 +129,21 @@ 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);
-   
+
     for(i=0;i<nbCandR;i++){
         t_candidateR[i]->isCandidate = 0;
     }
@@ -140,7 +151,7 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL, int numConf)
         t_candidateL[i]->isCandidate = 0;
     }
 
-    /* Don't worry for that, this is only O(n^2) over the remaining 
+    /* Don't worry for that, this is only O(n^2) over the remaining
      * candidate residues for each protein
      * for each receptor resdiue candidate, we look at each of its atoms
      * for each ligand residue candidate, we llok at each of its atoms
@@ -180,12 +191,85 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL, int numConf)
             fprintf(outputFile_rec,"'%s' '%c' ",strtok(t_candidateR[i]->idRes," "),t_candidateR[i]->chain);
     }
 
-    
+
     free(t_candidateL);
     free(t_candidateR);
 }
 
 
+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;
@@ -201,13 +285,13 @@ struct docking_results* getDataForComplex(){
     //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 
+        /* 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");
     rc = getline(&buf,&len,condFile_stream); /* Get rid of first line */
 
@@ -232,7 +316,7 @@ struct docking_results* getDataForComplex(){
 
 
     int idConf = 0, buf4, prevID = -1;
-    
+
     while(!feof(condFile_stream)){
         rc = fscanf(condFile_stream,"%d %d",&idConf,&buf4);
         if(prevID == idConf){
@@ -243,7 +327,7 @@ struct docking_results* getDataForComplex(){
 
         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 */
-            
+
 
         //dock_res->theta[idConf] = dock_res->theta[idConf]*cdr;
         //dock_res->phi[idConf]  = dock_res->phi[idConf]*cdr;
@@ -252,7 +336,7 @@ struct docking_results* getDataForComplex(){
         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);
@@ -267,32 +351,32 @@ struct pdb_values* readPDB(char* protein) {
     size_t len = 2000;
     char totalFilePath[200];
     char buf2[15];
-    char buf3[50]; 
+    char buf3[50];
     char bufID[10] = "\0";
 
     char* buf = NULL;
     FILE* pdbFile_stream = NULL;
     struct pdb_values* pdb_prot = NULL;
 
-    
+
     sprintf(totalFilePath,"%s/%s.pdb",pdbDir,protein);
     if(access(totalFilePath,F_OK) == -1){
-        /* File does not exists, 4 file in this case 
-         * Return NULL, which should be treated accordingly 
+        /* File does not exists, 4 file in this case
+         * Return NULL, which should be treated accordingly
          */
         fprintf(stderr,"No such file : %s\n",totalFilePath);
         exit(1);
     }
-    
+
     pdbFile_stream = fopen(totalFilePath,"r");
     if(pdbFile_stream == NULL){
         perror("fopen");
         exit(EXIT_FAILURE);
     }
-    
+
     strcpy(buf3,"\0");
     while(!feof(pdbFile_stream)){
-        rc = getline(&buf,&len,pdbFile_stream); 
+        rc = getline(&buf,&len,pdbFile_stream);
         strncpy(buf2,buf,4);
         buf2[4] = '\0';
         if(strcmp("ATOM",buf2) == 0){
@@ -397,7 +481,7 @@ struct pdb_values* readPDB(char* protein) {
     pdb_prot->centerX /= pdb_prot->nbAtom;
     pdb_prot->centerY /= pdb_prot->nbAtom;
     pdb_prot->centerZ /= pdb_prot->nbAtom;
-    
+
     free(buf);
     fclose(pdbFile_stream);
     return pdb_prot;
@@ -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]);
         }
@@ -450,14 +533,18 @@ int main(int argc, char** argv){
     struct pdb_values* pdbL = NULL;
     struct pdb_values* pdbR = NULL;
     struct pdb_values* newPDB = NULL;
-    struct docking_results* dock_res = NULL; 
+    struct docking_results* dock_res = NULL;
     float dalpha = 0, dbeta = 0, dgamma = 0;
 
     parseLineOfArgument(argc,argv);
     printf("Computing %s and %s ...",receptor,ligand);
     fflush(stdout);
 
-    dock_res = getDataForComplex();
+    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

-#ifndef  INTB_HEADER
+#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"
 
 /*************************************************/