separating getDataForComplex functions for each docking algorithm

src/fileIO.c

@@ -26,12 +26,12 @@ char* deblank(char* input){
 }
 
 struct docking_results* getDataForComplex_ATTRACT(){
+    const int MAXSIZE_LINE = 100000;
     FILE* condFile_stream = NULL;
-    int numberOfConf = 0, rc = 0;
-    int idConf = 0, i = 0;
+    int numberOfConf = 0;
+    int i = 0;
     int line = 1, auto_pivot = 0;
     struct docking_results* dock_res = NULL;
-    const int MAXSIZE_LINE = 100000;
     char buf[MAXSIZE_LINE] = "";
     int nr = 0;
     float pivot[2][3] = {{0,0,0},{0,0,0}};
@@ -107,6 +107,10 @@ struct docking_results* getDataForComplex_ATTRACT(){
             break;
     }
 
+    /* The pivot has been read, now we need to check if any protein is 
+     * centered
+     */
+
     int centered_R = -1, centered_L = -1;
 
     /* Check if the receptor is centered or not */
@@ -247,96 +251,276 @@ struct docking_results* getDataForComplex_ATTRACT(){
     return dock_res;
 }
 
-struct docking_results* getDataForComplex(){
+struct docking_results* getDataForComplex_ZDOCK(){
     char* buf = NULL;
     char buf2[100] = "";
     FILE* condFile_stream = NULL;
     int numberOfConf = 0, rc = 0;
-    int idConf = 0, buf4 = 0, i = 0;
+    int idConf = 0, i = 0;
     float buf3 = 0;
     size_t len = 2000;
     struct docking_results* dock_res = NULL;
 
     condFile_stream = fopen(dockingFile,"r");
 
-    if(HEX){
-        for(i=0;i<NB_HEADER_LINE_HEX;i++){
-            rc = getline(&buf,&len,condFile_stream);
-        }
-    }
-
-    if(ZDOCK){
     rc = fscanf(condFile_stream,"%d %f %d",&ZDOCK_GRID_SIZE,&ZDOCK_GRID_UNIT,&ZDOCK_PROT_FIXED);
     rc = fscanf(condFile_stream,"%f %f %f",&ZDOCK_REC_A_ROT,&ZDOCK_REC_B_ROT,&ZDOCK_REC_G_ROT);
     rc = fscanf(condFile_stream,"%f %f %f",&ZDOCK_LIG_A_ROT,&ZDOCK_LIG_B_ROT,&ZDOCK_LIG_G_ROT);
     rc = fscanf(condFile_stream,"%s %f %f %f",buf2,&ZDOCK_REC_X_TRANS,&ZDOCK_REC_Y_TRANS,&ZDOCK_REC_Z_TRANS);
     rc = fscanf(condFile_stream,"%s %f %f %f",buf2,&ZDOCK_LIG_X_TRANS,&ZDOCK_LIG_Y_TRANS,&ZDOCK_LIG_Z_TRANS);
-    }
 
     /* Get the number of conformations */
-    if(HEX){
-        rc = fscanf(condFile_stream,"%f %f",&buf3,&buf3);
-    }else{
     rc = getline(&buf,&len,condFile_stream); /* Get rid of the rest of the line */
-    }
-    if(ZDOCK){
     numberOfConf++;
-    }else if(buf3 > numberOfConf){
-        numberOfConf = (int) buf3;
-    }
 
     while(!feof(condFile_stream)){
-        if(HEX){
-            rc = fscanf(condFile_stream,"%f %f",&buf3,&buf3);
-        }else{
         rc = fscanf(condFile_stream,"%f",&buf3);
-        }
         rc = getline(&buf,&len,condFile_stream); /* Get rid of the rest of the line */
-        if(ZDOCK){
         if(feof(condFile_stream)){
             break;
         }
         numberOfConf++;
-        }else if(buf3 > numberOfConf)
         numberOfConf = (int) buf3;
     }
-    if(ZDOCK)
     numberOfConf--;
     rewind(condFile_stream);
 
     /* This is with the first MAXDo format */
-    if(MAXDo){
-        rc = getline(&buf,&len,condFile_stream); /* Get rid of the first line */
-    }else if(ZDOCK){
     for(i=0;i<NB_HEADER_LINE_ZDOCK;i++)
         rc = getline(&buf,&len,condFile_stream);
-    }else if(HEX){
+
+    /* Now that we know how many conformations we are dealing with
+     * allocate a structure large enough
+     */
+    dock_res = allocate_dockingResults(numberOfConf);
+
+    while(!feof(condFile_stream)){
+        idConf++;
+
+        /* We confirm that this conformation exists in the MAXDo file */
+        dock_res->t_conf[idConf] = 1;
+
+        /* This happens when we arrive on the last line */
+        if(feof(condFile_stream)){
+            break;
+        }
+
+        rc = fscanf(condFile_stream,"%f %f %f %f %f %f",&dock_res->alpha[idConf],&dock_res->beta[idConf],&dock_res->gamma[idConf],&dock_res->trans_X[idConf],&dock_res->trans_Y[idConf],&dock_res->trans_Z[idConf]);
+        rc = getline(&buf,&len,condFile_stream); /* Get rid of the rest of the line */
+
+
+        /* theta and phi angles are written in Radian already
+         * However that is not the case for alpha, beta and gamma angles
+         */
+
+        /* This happens when we arrive on the last line */
+        if(feof(condFile_stream)){
+            break;
+        }
+    }
+
+    dock_res->nbConf = numberOfConf;
+
+    fclose(condFile_stream);
+    free(buf);
+    return dock_res;
+}
+
+struct docking_results* getDataForComplex_HEX(){
+    char* buf = NULL;
+    FILE* condFile_stream = NULL;
+    int numberOfConf = 0, rc = 0;
+    int idConf = 0, buf4 = 0, i = 0;
+    float buf3 = 0;
+    size_t len = 2000;
+    struct docking_results* dock_res = NULL;
+
+    condFile_stream = fopen(dockingFile,"r");
+
+    if(HEX){
         for(i=0;i<NB_HEADER_LINE_HEX;i++){
             rc = getline(&buf,&len,condFile_stream);
         }
     }
 
+    /* Get the number of conformations */
+    rc = fscanf(condFile_stream,"%f %f",&buf3,&buf3);
+
+    if(buf3 > numberOfConf){
+        numberOfConf = (int) buf3;
+    }
+
+    while(!feof(condFile_stream)){
+        rc = fscanf(condFile_stream,"%f %f",&buf3,&buf3);
+        rc = getline(&buf,&len,condFile_stream); /* Get rid of the rest of the line */
+
+        if(buf3 > numberOfConf)
+            numberOfConf = (int) buf3;
+    }
+    rewind(condFile_stream);
+
+    /* This is with the first MAXDo format */
+    for(i=0;i<NB_HEADER_LINE_HEX;i++){
+        rc = getline(&buf,&len,condFile_stream);
+    }
+
     /* Now that we know how many conformations we are dealing with
      * allocate a structure large enough
      */
     dock_res = allocate_dockingResults(numberOfConf);
 
+    while(!feof(condFile_stream)){
+        rc = fscanf(condFile_stream,"%d %d %f %f",&buf4,&idConf,&buf3,&buf3);
+
+        /* We confirm that this conformation exists in the MAXDo file */
+        dock_res->t_conf[idConf] = 1;
+
+        /* This happens when we arrive on the last line */
+        if(feof(condFile_stream)){
+            break;
+        }
+
+        rc = fscanf(condFile_stream,"%f %f %f %f %f %f",&dock_res->trans_X[idConf],&dock_res->trans_Y[idConf],&dock_res->trans_Z[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 */
+
+
+        /* theta and phi angles are written in Radian already
+         * However that is not the case for alpha, beta and gamma angles
+         */
+
+        /* This happens when we arrive on the last line */
+        if(feof(condFile_stream)){
+            break;
+        }
+    }
+
+    dock_res->nbConf = numberOfConf;
+
+    fclose(condFile_stream);
+    free(buf);
+    return dock_res;
+
+}
+
+struct docking_results* getDataForComplex_MAXDO(){
+    char* buf = NULL;
+    char buf2[100] = "";
+    FILE* condFile_stream = NULL;
+    int numberOfConf = 0, rc = 0;
+    int idConf = 0, buf4 = 0, i = 0;
+    float buf3 = 0;
+    size_t len = 2000;
+    struct docking_results* dock_res = NULL;
+
+    condFile_stream = fopen(dockingFile,"r");
+
+    /* Get the number of conformations */
+    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;
+    }
+    rewind(condFile_stream);
+
+    /* This is with the first MAXDo format */
+    rc = getline(&buf,&len,condFile_stream); /* Get rid of the first line */
 
-        if(MAXDo){ /* First MAXDo format */
+    /* Now that we know how many conformations we are dealing with
+     * allocate a structure large enough
+     */
+    dock_res = allocate_dockingResults(numberOfConf);
+
+
+    while(!feof(condFile_stream)){
         rc = fscanf(condFile_stream,"%d %d",&idConf,&buf4);
-        }else if(HEX){
-            rc = fscanf(condFile_stream,"%d %d %f %f",&buf4,&idConf,&buf3,&buf3);
-        }else if(ZDOCK){
-            idConf++;
-        }else {
-            /* Else, that means that we have a format where
+
+        /* We confirm that this conformation exists in the MAXDo file */
+        dock_res->t_conf[idConf] = 1;
+
+        /* This happens when we arrive on the last line */
+        if(feof(condFile_stream)){
+            break;
+        }
+
+        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 */
+
+
+        /* theta and phi angles are written in Radian already
+         * However that is not the case for alpha, beta and gamma angles
+         */
+
+        //dock_res->theta[idConf] = dock_res->theta[idConf]*COEF_DEGREE_TO_RADIAN;
+        //dock_res->phi[idConf]  = dock_res->phi[idConf]*COEF_DEGREE_TO_RADIAN;
+
+        /* MAXDo will output the values of alpha, beta and gamma in degrees.
+         * We need to convert those to radian for the rest of the program
+         */
+        dock_res->alpha[idConf] = dock_res->alpha[idConf] * COEF_DEGREE_TO_RADIAN;
+        dock_res->beta[idConf]  = dock_res->beta[idConf]  * COEF_DEGREE_TO_RADIAN;
+        dock_res->gamma[idConf] = dock_res->gamma[idConf] * COEF_DEGREE_TO_RADIAN;
+
+        /* This happens when we arrive on the last line */
+        if(feof(condFile_stream)){
+            break;
+        }
+    }
+
+    dock_res->nbConf = numberOfConf;
+
+    fclose(condFile_stream);
+    free(buf);
+    return dock_res;
+}
+
+struct docking_results* getDataForComplex_HCMD2(){
+    char* buf = NULL;
+    char buf2[100] = "";
+    FILE* condFile_stream = NULL;
+    int numberOfConf = 0, rc = 0;
+    int idConf = 0, buf4 = 0, i = 0;
+    float buf3 = 0;
+    size_t len = 2000;
+    struct docking_results* dock_res = NULL;
+
+    condFile_stream = fopen(dockingFile,"r");
+
+
+    /* Get the number of conformations */
+    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;
+    }
+    rewind(condFile_stream);
+
+    /* Now that we know how many conformations we are dealing with
+     * allocate a structure large enough
+     */
+    dock_res = allocate_dockingResults(numberOfConf);
+
+
+    while(!feof(condFile_stream)){
+        /* that means that we have a format where
          * values for distance between center follows directly
          * the ID of the conformation.
          */
         rc = fscanf(condFile_stream,"%d",&idConf);
-        }
 
         /* We confirm that this conformation exists in the MAXDo file */
         dock_res->t_conf[idConf] = 1;
@@ -346,13 +530,7 @@ struct docking_results* getDataForComplex(){
             break;
         }
 
-        if(HEX){
-            rc = fscanf(condFile_stream,"%f %f %f %f %f %f",&dock_res->trans_X[idConf],&dock_res->trans_Y[idConf],&dock_res->trans_Z[idConf],&dock_res->alpha[idConf],&dock_res->beta[idConf],&dock_res->gamma[idConf]);
-        }else if(ZDOCK){
-            rc = fscanf(condFile_stream,"%f %f %f %f %f %f",&dock_res->alpha[idConf],&dock_res->beta[idConf],&dock_res->gamma[idConf],&dock_res->trans_X[idConf],&dock_res->trans_Y[idConf],&dock_res->trans_Z[idConf]);
-        }else{
         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 */
 
 
@@ -366,11 +544,72 @@ struct docking_results* getDataForComplex(){
         /* MAXDo will output the values of alpha, beta and gamma in degrees.
          * We need to convert those to radian for the rest of the program
          */
-        if(HCMD2 || MAXDo){
         dock_res->alpha[idConf] = dock_res->alpha[idConf] * COEF_DEGREE_TO_RADIAN;
         dock_res->beta[idConf]  = dock_res->beta[idConf]  * COEF_DEGREE_TO_RADIAN;
         dock_res->gamma[idConf] = dock_res->gamma[idConf] * COEF_DEGREE_TO_RADIAN;
+
+        /* This happens when we arrive on the last line */
+        if(feof(condFile_stream)){
+            break;
+        }
+    }
+
+    dock_res->nbConf = numberOfConf;
+
+    fclose(condFile_stream);
+    free(buf);
+    return dock_res;
+}
+
+struct docking_results* getDataForComplex_DEFAULT(){
+    char* buf = NULL;
+    char buf2[100] = "";
+    FILE* condFile_stream = NULL;
+    int numberOfConf = 0, rc = 0;
+    int idConf = 0, buf4 = 0, i = 0;
+    float buf3 = 0;
+    size_t len = 2000;
+    struct docking_results* dock_res = NULL;
+
+    condFile_stream = fopen(dockingFile,"r");
+
+    /* Get the number of conformations */
+    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;
     }
+    rewind(condFile_stream);
+
+    /* Now that we know how many conformations we are dealing with
+     * allocate a structure large enough
+     */
+    dock_res = allocate_dockingResults(numberOfConf);
+
+    while(!feof(condFile_stream)){
+        /* That means that we have a format where
+         * values for distance between center follows directly
+         * the ID of the conformation.
+         */
+        rc = fscanf(condFile_stream,"%d",&idConf);
+
+        /* We confirm that this conformation exists in the MAXDo file */
+        dock_res->t_conf[idConf] = 1;
+
+        /* This happens when we arrive on the last line */
+        if(feof(condFile_stream)){
+            break;
+        }
+
+        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 */
 
         /* This happens when we arrive on the last line */
         if(feof(condFile_stream)){
@@ -385,6 +624,22 @@ struct docking_results* getDataForComplex(){
     return dock_res;
 }
 
+struct docking_results* getDataForComplex(){
+    if(MAXDo){
+        return getDataForComplex_MAXDO();
+    }else if(HCMD2){
+        return getDataForComplex_HCMD2();
+    }else if(HEX){
+        return getDataForComplex_HEX();
+    }else if(ZDOCK){
+        return getDataForComplex_ZDOCK();
+    }else if(ATTRACT){
+        return getDataForComplex_ATTRACT();
+    }else{
+        return getDataForComplex_DEFAULT();
+    }
+}
+
 
 struct pdb_values* readPDB(char* protein) {
     /* This function reads a PDB file and fills a structure