dist threshold as an argument

src/INTBuilder.c

@@ -144,6 +144,8 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL, int confID){
     for(i=0;i<pdbR->nbRes;i++)
         t_candidateR[i] = &pdbR->residues[i];
 
+    int totR = pdbR->nbRes, totL = pdbL->nbRes, step = 0;
+    printf("RSTEP 0 1.0\n");printf("LSTEP 0 1.0\n");
     /* Start removing candidates */
     while(oldCandL != nbCandL && oldCandR != nbCandR){
         oldCandL = nbCandL;
@@ -165,6 +167,15 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL, int confID){
             nbCandR = 0;
             break;
         }
+        step++;
+        printf("RSTEP %d %d %d -- %f\n",step,nbCandR,totR,(float)(1-((float)(totR-nbCandR)/totR)));
+        printf("LSTEP %d %d %d -- %f\n",step,nbCandL,totL,(float)(1-((float)(totL-nbCandL)/totL)));
+
+    }
+    while(step < 15){
+        step++;
+        printf("RSTEP %d %d %d -- %f\n",step,nbCandR,totR,(float)(1-((float)(totR-nbCandR)/totR)));
+        printf("LSTEP %d %d %d -- %f\n",step,nbCandL,totL,(float)(1-((float)(totL-nbCandL)/totL)));
     }
 
     /* The first nbCandR values of t_candidateR correspond to the possible candidates

src/param.c

@@ -32,6 +32,7 @@ void print_usage() {
     "                   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"
+    "<-distTH>..........Distance for contact\n"
     "--\n"
     "Leaving this option blank means that the default format for the docking file\n"
     "will be used.\n"
@@ -55,26 +56,27 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
     struct argLine* paramVals = NULL;
 
 
-    verbose         = 0;
-    constructPDB    = 0;
-    target_conf     = -1;
-    HCMD2           = 0;
-    MAXDo           = 0;
-    HEX             = 0;
-    complexPDB      = 0;
-    doNotOutputINT  = 0;
-    clash           = 0;
-    force           = 0;
-    atom_res        = 0;
-    outputDir       = NULL;
-    outputPDB       = NULL;
-    verbose_file    = NULL;
-    dockingFile     = NULL;
-    pdbDir          = NULL;
-    receptor        = NULL;
-    ligand          = NULL;
-    outputFile_rec  = NULL;
-    outputFile_lig  = NULL;
+    verbose          = 0;
+    constructPDB     = 0;
+    HCMD2            = 0;
+    MAXDo            = 0;
+    HEX              = 0;
+    complexPDB       = 0;
+    doNotOutputINT   = 0;
+    clash            = 0;
+    force            = 0;
+    atom_res         = 0;
+    target_conf      = -1;
+    DIST_FOR_CONTACT = -1;
+    outputDir        = NULL;
+    outputPDB        = NULL;
+    verbose_file     = NULL;
+    dockingFile      = NULL;
+    pdbDir           = NULL;
+    receptor         = NULL;
+    ligand           = NULL;
+    outputFile_rec   = NULL;
+    outputFile_lig   = NULL;
 
     for(i=1; i<argc; i++){
         if(strcmp(argv[i],"-dockingFile") == 0){
@@ -123,7 +125,13 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
         }else if(strcmp(argv[i],"-pose") == 0){
             target_conf = atoi(argv[i+1]);
             if(target_conf <= 0){
-                fprintf(stderr,"Specific conformation not valid\n");
+                fprintf(stderr,"Target conformation not valid\n");
+                exit(EXIT_SUCCESS);
+            }
+        }else if(strcmp(argv[i],"-distTH") == 0){
+            DIST_FOR_CONTACT = atof(argv[i+1]);
+            if(DIST_FOR_CONTACT > 0){
+                fprintf(stderr,"The threshold distance has to be above 0.\n");
                 exit(EXIT_SUCCESS);
             }
         }else if(strcmp(argv[i],"-HCMD2") == 0){
@@ -158,6 +166,11 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
         exit(EXIT_SUCCESS);
     }
 
+    if(DIST_FOR_CONTACT == -1){
+        printf("No distance for contact specified, default distance is 5A.\n");
+        DIST_FOR_CONTACT = 5.0;
+    }
+
     if(dockingFile == NULL && !complexPDB){
         fprintf(stderr,"The docking file has to be provided\n\n");
         if(!print_help)

src/struct.h

@@ -13,8 +13,6 @@
 #define NB_MAX_ATOM_PER_RES 100              /* No residue has more atoms than that */
 #define TOO_MANY_CLASHES 20                /* If not forcing, program will skip conformation after
                                             * this number of clashes */
-#define DIST_FOR_CONTACT 5                 /* 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 */
 #define NB_HEADER_LINE_HEX 12        /* Number of header lines at the top of a hex docking file */
@@ -33,6 +31,7 @@ int     doNotOutputINT;     /* 1 if we don't want to output the interface */
 int     atom_res;           /* 1 if we want a resolution at atom's level */
 int     clash;              /* Maybe be incremented in case of clashes */
 int     force;              /* Will output even if clash, may increase computation time */
+float   DIST_FOR_CONTACT;   /* Distance under which we consider two residues are in contact */
 FILE*   verbose_file;       /* If verbose mode, the output file */
 char*   pdbDir;             /* Directory containing the PDBs */
 char*   receptor;           /* Name of the receptor */