Adding the atom resolution for detecting interfaces

src/INTBuilder.c

@@ -183,7 +183,7 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL, int confID){
     /* 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
+     * for each ligand residue candidate, we look at each of its atoms
      */
 
     /* For each candidate residue of the receptor */
@@ -216,6 +216,11 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL, int confID){
                     if(dist <= DIST_FOR_CONTACT){
                         t_candidateR[i]->isCandidate = 1;
                         t_candidateL[k]->isCandidate = 1;
+
+                        /* We keep the values updated for atoms in any case */
+                        t_candidateR[i]->isAtomCandidate[j] = 1;
+                        t_candidateL[k]->isAtomCandidate[l] = 1;
+
                         break;
                     }
                 }
@@ -232,7 +237,6 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL, int confID){
         }
     }
     
-    printf("number of clashes : %d \n",clash);
     
     /* If the amount of clashes is still ok */
     if(clash < TOO_MUCH_CLASHES){

src/fileIO.c

@@ -275,21 +275,52 @@ void write_candidate(struct residue** t_candid, int sizeCand, FILE* output_strea
     /* Output the residues selected as being part of the interface in the array
      * t_candid
      */
-    int i = 0, j = 0, k= 0, len = 0;
-    char buf[15];
-
-    for(i=0;i<sizeCand;i++){
-        if(t_candid[i]->isCandidate){
-            len = strlen(t_candid[i]->idRes);
-            k = 0;
-            for(j=0;j<len;j++){
-                if(t_candid[i]->idRes[j] != ' '){
-                    buf[k] = t_candid[i]->idRes[j];
-                    k++;
-            }            }
-            buf[k] = '\0';
-            fprintf(output_stream,"'%s' '%c' ",buf,t_candid[i]->chain);
-            fflush(output_stream);
+    int i = 0, j = 0, k= 0, l = 0, len = 0;
+    char buf[15] = "", buf2[15] = "";
+
+    if(atom_res){
+        for(i=0;i<sizeCand;i++){
+            for(j=0;j<t_candid[i]->nbAtom;j++){
+                if(t_candid[i]->isAtomCandidate[j]){
+
+                    /* Getting the residue name */
+                    len = strlen(t_candid[i]->idRes);
+                    k = 0;
+                    for(l=0;l<len;l++){
+                        if(t_candid[i]->idRes[l] != ' '){
+                            buf[k] = t_candid[i]->idRes[l];
+                            k++;
+                        }
+                    }
+
+                    /* Now, getting the atom name */
+                    len = strlen(t_candid[i]->atomType[j]);
+                    k = 0;
+                    for(l=0;l<len;l++){
+                        if(t_candid[i]->atomType[j][l] != ' '){
+                            buf2[k] = t_candid[i]->atomType[j][l];
+                            k++;
+                    }            }
+                    buf2[k] = '\0';
+                    fprintf(output_stream,"'%s' '%c' '%s' ",buf,t_candid[i]->chain, buf2);
+                    fflush(output_stream);
+                }
+            }
+        }
+    }else{
+        for(i=0;i<sizeCand;i++){
+            if(t_candid[i]->isCandidate){
+                len = strlen(t_candid[i]->idRes);
+                k = 0;
+                for(j=0;j<len;j++){
+                    if(t_candid[i]->idRes[j] != ' '){
+                        buf[k] = t_candid[i]->idRes[j];
+                        k++;
+                }            }
+                buf[k] = '\0';
+                fprintf(output_stream,"'%s' '%c' ",buf,t_candid[i]->chain);
+                fflush(output_stream);
+            }
         }
     }
 }

src/param.c

@@ -22,15 +22,16 @@ void print_usage() {
     "<-lig>             name of the ligand\n"
     "OPTIONAL\n"
     "=========\n\n"
-    "<-outputPDB>       Output directory for the constructed PDB (ligand)\n"
+    "<-outputPDB>.......Output directory for the constructed PDB (ligand)\n"
     "                   If nothing is specified, there will be no PDB output\n"
-    "<-o>               Output directory for the docking interface\n"
+    "<-o>...............Output directory for the docking interface\n"
     "                   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"
-    "<-noOutput>        Will prevent the program to output the docking interface\n"
+    "<-pose>............Desired conformation. Default will compute all conformations\n"
+    "<--atom-res>.......If specified, will computed the interface at atom level\n"
+    "<-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"
+    "<--force/-f>.......Will force the computation of the pause even in case of\n"
     "                   huge number of clashes (threshold defined in struct.h)\n"
     );
 }
@@ -55,6 +56,7 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
     doNotOutputINT  = 0;
     clash           = 0;
     force           = 0;
+    atom_res        = 0;
     outputDir       = NULL;
     outputPDB       = NULL;
     verbose_file    = NULL;
@@ -117,6 +119,8 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
             }
         }else if(strcmp(argv[i],"-HCMD2") == 0){
             HCMD2 = 1;
+        }else if(strcmp(argv[i],"--atom-res") == 0){
+            atom_res = 1;
         }else if(strcmp(argv[i],"-noOutput") == 0){
             doNotOutputINT = 1;
         }else if(strcmp(argv[i],"-complex") == 0){

src/struct.h

@@ -27,6 +27,7 @@ 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     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 */
 FILE*   verbose_file;       /* If verbose mode, the output file */
@@ -58,16 +59,17 @@ struct pdb_values {
 
 /* Structure that contains all the informations we need for a residue */
 struct residue {
-    char    idRes[10];                          /* ID of the residue */
-    char    chain;                              /* Chain to which the residue belongs */
-    char    resName[10];                        /* Name of the residue */
-    float   x[NB_MAX_ATOM_PER_RES];             /* Array containing the x for each of its atom */
-    float   y[NB_MAX_ATOM_PER_RES];             /* Array containing the y for each of its atom */
-    float   z[NB_MAX_ATOM_PER_RES];             /* Array containing the z for each of its atom */
-    char    atomType[NB_MAX_ATOM_PER_RES][10];  /* Array containing the type of atom */
-    int     idAtom[NB_MAX_ATOM_PER_RES];        /* ID of the atom */
-    int     nbAtom;                             /* Number of atom for this residue */
-    int     isCandidate;                        /* 1 if this residue belongs to the docking interface */
+    char    idRes[10];                            /* ID of the residue */
+    char    chain;                                /* Chain to which the residue belongs */
+    char    resName[10];                          /* Name of the residue */
+    float   x[NB_MAX_ATOM_PER_RES];               /* Array containing the x for each of its atom */
+    float   y[NB_MAX_ATOM_PER_RES];               /* Array containing the y for each of its atom */
+    float   z[NB_MAX_ATOM_PER_RES];               /* Array containing the z for each of its atom */
+    char    atomType[NB_MAX_ATOM_PER_RES][10];    /* Array containing the type of atom */
+    int     idAtom[NB_MAX_ATOM_PER_RES];          /* ID of the atom */
+    int     nbAtom;                               /* Number of atom for this residue */
+    int     isCandidate;                          /* 1 if this residue belongs to the docking interface */
+    int     isAtomCandidate[NB_MAX_ATOM_PER_RES]; /* 1 if the atom belongs to the docking interface */
 };
 
 struct docking_results {