adding the possibility to compute the interface between two PDBs already docked

src/INTBuilder.c

@@ -543,6 +543,18 @@ int main(int argc, char** argv){
             writePDB(newPDB, ligand,target_conf);
         }
         freePDB(newPDB);
+    }else 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");
+
+        if(constructPDB){
+            writePDB(newPDB, ligand,target_conf);
+        }
     }else{ /* For all conformations */
         for(i=1;i<dock_res->nbConf;i++){
 

src/param.c

@@ -23,6 +23,9 @@ void print_usage() {
     "                   If nothing is specified, the current directory is used\n"
     "<-pose>            Desired conformation. Default will compute all conformations\n"
     "<-HCMD2>           Means that the docking file is in the HCMD2 MAXDo format\n"
+    "<-complex>         This option means that we look at two PDBs instead of looking\n"
+    "                   at the dockingFile. Both PBDs for '-rec' and '-lig' must be in\n"
+    "                   '-pdbDir'\n"
     );
 }
 
@@ -42,6 +45,7 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
     constructPDB    = 0;
     target_conf     = -1;
     HCMD2           = 0;
+    complexPDB      = 0;
     outputDir       = NULL;
     outputPDB       = NULL;
     verbose_file    = NULL;
@@ -104,6 +108,8 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
             }
         }else if(strcmp(argv[i],"-HCMD2") == 0){
             HCMD2 = 1;
+        }else if(strcmp(argv[i],"-complex") == 0){
+            complexPDB = 1;
         }else if(strcmp(argv[i],"-h") == 0 ||
                 strcmp(argv[i],"--help") == 0){
             print_help = 1;
@@ -114,7 +120,7 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
         }
     }
 
-    if(dockingFile == NULL){
+    if(dockingFile == NULL && !complexPDB){
         fprintf(stderr,"The docking file has to be provided\n\n");
         if(!print_help)
             print_usage();
@@ -175,6 +181,21 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
             exit(EXIT_FAILURE);
         }
         outputFile_lig = fopen(buf,"w");
+    }else if(complexPDB){
+        sprintf(buf,"%s/%s-%s_rec_0_dockinter.txt",outputDir,receptor,ligand);
+        outputFile_rec = fopen(buf,"w");
+        if(outputFile_rec == NULL){
+            perror("fopen");
+            exit(EXIT_FAILURE);
+        }
+
+        sprintf(buf,"%s/%s-%s_lig_0_dockinter.txt",outputDir,receptor,ligand);
+        outputFile_lig = fopen(buf,"w");
+        if(outputFile_lig == NULL){
+            perror("fopen");
+            exit(EXIT_FAILURE);
+        }
+        outputFile_lig = fopen(buf,"w");
     }else{
         sprintf(buf,"%s/%s-%s_rec_dockinter.txt",outputDir,receptor,ligand);
         outputFile_rec = fopen(buf,"w");

src/struct.h

@@ -21,6 +21,7 @@ int     verbose;            /* 1 if we are in verbose mode */
 int     constructPDB;       /* 1 if we should build the PDB */
 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 */
 FILE*   verbose_file;       /* If verbose mode, the output file */
 char*   pdbDir;             /* Directory containing the PDBs */
 char*   receptor;           /* Name of the receptor */