adding getdataComplex for ATTRACT

src/allocate.c

@@ -44,8 +44,9 @@ struct docking_results* allocate_dockingResults(int nbConf){
         perror("malloc");
         exit(EXIT_FAILURE);
     }
+    memset(dock_res,0,sizeof(struct docking_results));
     dock_res->nbConf      = nbConf;
-    dock_res->listEner    = NULL;
+    /* dock_res->listEner    = NULL;
     dock_res->distCenters = NULL;
     dock_res->theta       = NULL;
     dock_res->phi         = NULL;
@@ -56,6 +57,7 @@ struct docking_results* allocate_dockingResults(int nbConf){
     dock_res->trans_X     = NULL;
     dock_res->trans_Y     = NULL;
     dock_res->trans_Z     = NULL;
+    */
 
     dock_res->listEner = malloc((2*nbConf)*sizeof(float));
     if(dock_res->listEner == NULL){
@@ -84,7 +86,73 @@ struct docking_results* allocate_dockingResults(int nbConf){
         exit(EXIT_FAILURE);
     }
 
-    /* Only HEX uses translation values */
+    
+    dock_res->phi_R = malloc((2*nbConf)*sizeof(float));
+    if(dock_res->phi_R == NULL){
+        perror("malloc");
+        exit(EXIT_FAILURE);
+    }
+    dock_res->ssi_R = malloc((2*nbConf)*sizeof(float));
+    if(dock_res->ssi_R == NULL){
+        perror("malloc");
+        exit(EXIT_FAILURE);
+    }
+    dock_res->rot_R = malloc((2*nbConf)*sizeof(float));
+    if(dock_res->rot_R == NULL){
+        perror("malloc");
+        exit(EXIT_FAILURE);
+    }
+    dock_res->phi_L = malloc((2*nbConf)*sizeof(float));
+    if(dock_res->phi_L == NULL){
+        perror("malloc");
+        exit(EXIT_FAILURE);
+    }
+    dock_res->ssi_L = malloc((2*nbConf)*sizeof(float));
+    if(dock_res->ssi_L == NULL){
+        perror("malloc");
+        exit(EXIT_FAILURE);
+    }
+    dock_res->rot_L = malloc((2*nbConf)*sizeof(float));
+    if(dock_res->rot_L == NULL){
+        perror("malloc");
+        exit(EXIT_FAILURE);
+    }
+    dock_res->trans_X_R = malloc((2*nbConf)*sizeof(int));
+    if(dock_res->trans_X_R == NULL){
+        perror("malloc");
+        exit(EXIT_FAILURE);
+    }
+
+    dock_res->trans_Y_R = malloc((2*nbConf)*sizeof(int));
+    if(dock_res->trans_Y_R == NULL){
+        perror("malloc");
+        exit(EXIT_FAILURE);
+    }
+
+    dock_res->trans_Z_R = malloc((2*nbConf)*sizeof(int));
+    if(dock_res->trans_Z_R == NULL){
+        perror("malloc");
+        exit(EXIT_FAILURE);
+    }
+    dock_res->trans_X_L = malloc((2*nbConf)*sizeof(int));
+    if(dock_res->trans_X_L == NULL){
+        perror("malloc");
+        exit(EXIT_FAILURE);
+    }
+
+    dock_res->trans_Y_L = malloc((2*nbConf)*sizeof(int));
+    if(dock_res->trans_Y_L == NULL){
+        perror("malloc");
+        exit(EXIT_FAILURE);
+    }
+
+    dock_res->trans_Z_L = malloc((2*nbConf)*sizeof(int));
+    if(dock_res->trans_Z_L == NULL){
+        perror("malloc");
+        exit(EXIT_FAILURE);
+    }
+
+    /* Only HEX and ZDOCK use translation values */
     if(HEX || ZDOCK){
         dock_res->trans_X = malloc((2*nbConf)*sizeof(int));
         if(dock_res->trans_X == NULL){
@@ -121,7 +189,7 @@ struct docking_results* allocate_dockingResults(int nbConf){
         }
     }
 
-    for(i=0;i<nbConf;i++){
+    for(i=0;i<1+nbConf;i++){
         dock_res->listEner[i]    = 0;
 
         dock_res->alpha[i]       = 0;

src/fileIO.c

@@ -26,19 +26,224 @@ char* deblank(char* input){
 }
 
 struct docking_results* getDataForComplex_ATTRACT(){
-    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;
+    int idConf = 0, 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}};
 
     condFile_stream = fopen(dockingFile,"r");
+
+    /* Read the header */
+    /*******************/
+    int done = 0, ok = 1;
+    while(!done){
+        done = 1;
+
+        /* If we are not able to read the line */
+        if(!fgets(buf, MAXSIZE_LINE, condFile_stream)){
+            ok = 0;
+        }
+
+        /* These are the lines before the pivot */
+        else if(strlen(buf) < 8 || strncmp(buf, "#pivot ", 7)){
+            if (strlen(buf) < 2 || buf[0] != '#' || buf[1] != '#') ok = 0;
+            else done = 0;
+        }
+
+        if(!ok){
+            fprintf(stderr, "Reading error in %s, line %d: expected pivot point or '#pivot auto'\n", dockingFile, line);
+            fclose(condFile_stream);
+            exit(EXIT_FAILURE);
+        }
+
+        if(!done)
+            continue;
+
+        /* Checking pivot */
+
+        /* If this is auto */
+        if(!(strncmp(buf+7,"auto", 4))){
+            auto_pivot = 1;
+        }else{
+            auto_pivot = 0;
+            ok = 1;
+            
+            /* We only consider two structures docking */
+            for(i=0;i<2;i++){
+                if(ok){
+                    /* This is not a pivot line */
+                    if(strncmp(buf, "#pivot ", 7) != 0) 
+                        ok = 0;
+                    /* Could not properly read the pivot line */
+                    else if(sscanf(buf+7, "%d %f %f %f", &nr, &pivot[i][0], &pivot[i][1], &pivot[i][2]) < 4)
+                        ok = 0;
+                    /* Error in the pivot ID */
+                    else if (nr != i+1)
+                        ok = 0;    
+                }
+
+                /* If some error occured */
+                if(!ok){
+                    fprintf(stderr, "Reading error in %s, line %d: expected pivot point\n", dockingFile, line);
+                    fclose(condFile_stream);
+                    exit(EXIT_FAILURE);
+                }
+
+                if(i < 1){ /* get to next pivot line */
+                    /* If we couldn't read properly */
+                    if(!fgets(buf,MAXSIZE_LINE,condFile_stream))
+                        ok = 0;
+                    line++;
+                }
+            }
+        }
+
+        if(done)
+            break;
+    }
+
+    int centered_R = -1, centered_L = -1;
+
+    /* Check if the receptor is centered or not */
+    if(fgets(buf,MAXSIZE_LINE,condFile_stream)){
+        if (strlen(buf) >= 24 && strncmp(buf, "#centered receptor: true", 24) != 0)
+            centered_R = 1;
+        if (strlen(buf) >= 25 && strncmp(buf, "#centered receptor: false", 25) != 0)
+            centered_R = 0;
+    }
+    /* No valid value */
+    if(centered_R < 0){
+        fprintf(stderr, "Reading error in %s, line %d: expected '#centered receptor: true' or '#centered receptor: false'\n", dockingFile, line);
+        fclose(condFile_stream);
+        exit(EXIT_FAILURE);
+    }
+
+    /* Check if the ligand is centered or not */
+    if(fgets(buf,MAXSIZE_LINE,condFile_stream)){
+        if (strlen(buf) >= 23 && strncmp(buf, "#centered ligands: true", 23) != 0)
+            centered_L = 1;
+        if (strlen(buf) >= 24 && strncmp(buf, "#centered ligands: false", 24) != 0)
+            centered_L = 0;
+
+        if (strlen(buf) >= 22 && strncmp(buf, "#centered ligand: true", 22) != 0)
+            centered_L = 1;
+        if (strlen(buf) >= 23 && strncmp(buf, "#centered ligand: false", 23) != 0)
+            centered_L = 0;
+    }
+    /* No valid value */
+    if(centered_L < 0){
+        fprintf(stderr, "Reading error in %s, line %d: expected '#centered ligand: true' or '#centered ligand: false'\n", dockingFile, line);
+        fclose(condFile_stream);
+        exit(EXIT_FAILURE);
+    }
+
     
+    /* Now that we have read the header, we need to get the number of 
+     * conformations
+     */
+    long file_pos = ftell(condFile_stream);
+    while(!feof(condFile_stream)){
+        fgets(buf,MAXSIZE_LINE,condFile_stream);
+
+        /* This is not the line with the ID of the structure */
+        if(buf[0] != '#' || buf[1] == '#'){
+            continue;
+        }
+        
+        /* Now, we know the line begins with only one '#' */
+        numberOfConf++;
+    }
 
-    return NULL;
+    if(fseek(condFile_stream,file_pos,SEEK_SET) != 0){
+        perror("fseek");
+        fclose(condFile_stream);
+        exit(EXIT_FAILURE);
+    }
+
+    /* Now that we know how many conformations we are dealing with
+     * allocate a structure large enough
+     */
+    dock_res = allocate_dockingResults(numberOfConf);
+    for(i=0;i<numberOfConf;i++){
+        dock_res->pivot_X_R  = pivot[0][0];
+        dock_res->pivot_Y_R  = pivot[0][1];
+        dock_res->pivot_Z_R  = pivot[0][2];
+        dock_res->pivot_X_L  = pivot[1][0];
+        dock_res->pivot_Y_L  = pivot[1][1];
+        dock_res->pivot_Z_L  = pivot[1][2];
+        dock_res->centered_R = centered_R;
+        dock_res->centered_L = centered_L;
+    }
+    
+    int curConf = 0;
+    int mode = 0;
+    /* modes:
+     * 0 = expecting comment
+     * 1 = expecting data
+     */
+
+    while(!feof(condFile_stream)){
+        line++; 
+
+        if(!fgets(buf,MAXSIZE_LINE,condFile_stream)){
+            if(mode == 0)
+                continue;
+            else{
+                fprintf(stderr, "Reading error in %s, line %d: expecting #\n", dockingFile, line);
+                fclose(condFile_stream);
+                exit(EXIT_FAILURE);
+            }
+        }
+
+        if(mode == 0){
+            if(buf[0] != '#'){
+                fprintf(stderr, "Reading error in %s, line %d: expecting #\n", dockingFile, line);
+                fclose(condFile_stream);
+                exit(EXIT_FAILURE);
+            }
+            if(buf[1] == '#'){
+                continue;
+            }else{ /* We can read the ID of the conformation */
+                curConf = atoi(&buf[1]);
+                if(curConf == 0){
+                    fprintf(stderr, "Reading error in %s, line %d: No valid conformation\n", dockingFile, line);
+                    fclose(condFile_stream);
+                    exit(EXIT_FAILURE);
+                }
+                mode = 1;
+                continue;
+            }
+        }
+
+        if(mode == 1){
+            if(buf[0] == '#')
+                continue;
+
+            sscanf(buf,"%f %f %f %f %f %f",&dock_res->phi_R[curConf],&dock_res->ssi_R[curConf],&dock_res->rot_R[curConf],
+                                            &dock_res->trans_X_R[curConf],&dock_res->trans_Y_R[curConf],&dock_res->trans_Z_R[curConf]);
+
+            line++;
+
+            if(!fgets(buf,MAXSIZE_LINE,condFile_stream)){
+                fprintf(stderr, "Reading error in %s, line %d\n", dockingFile, line);
+                fclose(condFile_stream);
+                exit(EXIT_FAILURE);
+            }
+
+            sscanf(buf,"%f %f %f %f %f %f",&dock_res->phi_L[curConf],&dock_res->ssi_L[curConf],&dock_res->rot_L[curConf],
+                                            &dock_res->trans_X_L[curConf],&dock_res->trans_Y_L[curConf],&dock_res->trans_Z_L[curConf]);
+
+            mode = 0;
+        }
+    }
+
+    fclose(condFile_stream);
+    return dock_res;
 }
 
 struct docking_results* getDataForComplex(){

src/struct.h

@@ -114,6 +114,27 @@ struct docking_results {
     float*              trans_Z;
     int*                t_conf;         /* 1 for a conformation position if it exists, 0 otherwise */
     int                 nbConf;         /* Number of conformations */
+
+    float               pivot_X_R;      /* Pivot for X, Y, Z for the receptor and the ligand */
+    float               pivot_Y_R;      /* when considering ATTRACT docking */
+    float               pivot_Z_R;
+    float               pivot_X_L;
+    float               pivot_Y_L;
+    float               pivot_Z_L;
+    float*              phi_R;
+    float*              ssi_R;
+    float*              rot_R;
+    float*              phi_L;
+    float*              ssi_L;
+    float*              rot_L;
+    float*              trans_X_R;
+    float*              trans_Y_R;
+    float*              trans_Z_R;
+    float*              trans_X_L;
+    float*              trans_Y_L;
+    float*              trans_Z_L;
+    int                 centered_R;
+    int                 centered_L;
 };
 
 #endif