fix errors and memory leaks. Reconstruction not quite working yet though

src/INTBuilder.c

@@ -346,7 +346,7 @@ int main(int argc, char** argv){
             newPDB = rotate_ATTRACT(pdbL,newPDB,dock_res,target_conf,0);
 
             /*For the receptor */
-            newPDB_R = rotate_ATTRACT(pdbR,newPDB,dock_res,target_conf,1);
+            newPDB_R = rotate_ATTRACT(pdbR,newPDB_R,dock_res,target_conf,1);
         }else{
             newPDB = rotate_global(pdbL,pdbR,newPDB,dock_res->distCenters[target_conf],
                                 dock_res->theta[target_conf],dock_res->phi[target_conf],
@@ -366,9 +366,12 @@ int main(int argc, char** argv){
             writePDB(newPDB, ligand,target_conf);
         }
         freePDB(newPDB);
-        freePDB(newPDB_R);
         newPDB   = NULL;
-        newPDB_R = NULL;
+
+        if(newPDB_R != NULL){
+            freePDB(newPDB_R);
+            newPDB_R = NULL;
+        }
     }else{ /* For all conformations */
         for(i=1;i<=dock_res->nbConf;i++){
 
@@ -405,10 +408,10 @@ int main(int argc, char** argv){
                                     dock_res->gamma[i]);
             }else if(ATTRACT){
                 /* For the ligand */
-                newPDB = rotate_ATTRACT(pdbL,newPDB,dock_res,target_conf,0);
+                newPDB = rotate_ATTRACT(pdbL,newPDB,dock_res,i,0);
 
                 /*For the receptor */
-                newPDB_R = rotate_ATTRACT(pdbR,newPDB,dock_res,target_conf,1);
+                newPDB_R = rotate_ATTRACT(pdbR,newPDB_R,dock_res,i,1);
             }else{
                 newPDB = rotate_global(pdbL,pdbR,newPDB,dock_res->distCenters[i],
                                     dock_res->theta[i],dock_res->phi[i],
@@ -429,9 +432,12 @@ int main(int argc, char** argv){
             }
         }
         freePDB(newPDB);
-        freePDB(newPDB_R);
         newPDB   = NULL;
-        newPDB_R = NULL;
+        if(newPDB_R != NULL){
+            printf("point %p\n",newPDB_R);
+            freePDB(newPDB_R);
+            newPDB_R = NULL;
+        }
     }
 
     freePDB(pdbL);

src/allocate.c

@@ -19,6 +19,21 @@ void freeDock(struct docking_results* dock_res){
         free(dock_res->trans_X);
         free(dock_res->trans_Y);
         free(dock_res->trans_Z);
+    }else if(ATTRACT){
+        free(dock_res->phi_R);
+        free(dock_res->ssi_R);
+        free(dock_res->rot_R);
+        free(dock_res->phi_L);
+        free(dock_res->ssi_L);
+        free(dock_res->rot_L);
+
+        free(dock_res->trans_X_R);
+        free(dock_res->trans_Y_R);
+        free(dock_res->trans_Z_R);
+        free(dock_res->trans_X_L);
+        free(dock_res->trans_Y_L);
+        free(dock_res->trans_Z_L);
+
     }else{
         free(dock_res->distCenters);
         free(dock_res->theta);
@@ -46,7 +61,7 @@ struct docking_results* allocate_dockingResults(int nbConf){
     }
     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;
@@ -57,7 +72,6 @@ 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){
@@ -86,74 +100,72 @@ struct docking_results* allocate_dockingResults(int nbConf){
         exit(EXIT_FAILURE);
     }
 
-    
-    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);
-    }
+    if(ATTRACT){
+        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_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_R = malloc((2*nbConf)*sizeof(int));
+        if(dock_res->trans_Y_R == 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_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_Z_L = malloc((2*nbConf)*sizeof(int));
-    if(dock_res->trans_Z_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);
+        }
 
-    /* Only HEX and ZDOCK use translation values */
-    if(HEX || ZDOCK){
+        dock_res->trans_Z_L = malloc((2*nbConf)*sizeof(int));
+        if(dock_res->trans_Z_L == NULL){
+            perror("malloc");
+            exit(EXIT_FAILURE);
+        }
+    }else if(HEX || ZDOCK){
         dock_res->trans_X = malloc((2*nbConf)*sizeof(int));
         if(dock_res->trans_X == NULL){
             perror("malloc");
@@ -189,9 +201,8 @@ struct docking_results* allocate_dockingResults(int nbConf){
         }
     }
 
-    for(i=0;i<1+nbConf;i++){
+    for(i=0;i<nbConf+1;i++){
         dock_res->listEner[i]    = 0;
-
         dock_res->alpha[i]       = 0;
         dock_res->beta[i]        = 0;
         dock_res->gamma[i]       = 0;
@@ -200,6 +211,20 @@ struct docking_results* allocate_dockingResults(int nbConf){
             dock_res->trans_X[i]    = 0;
             dock_res->trans_Y[i]    = 0;
             dock_res->trans_Z[i]    = 0;
+        }else if(ATTRACT){
+            dock_res->phi_R[i] = 0;
+            dock_res->ssi_R[i] = 0;
+            dock_res->rot_R[i] = 0;
+            dock_res->phi_L[i] = 0;
+            dock_res->ssi_L[i] = 0;
+            dock_res->rot_L[i] = 0;
+
+            dock_res->trans_X_R[i] = 0;
+            dock_res->trans_Y_R[i] = 0;
+            dock_res->trans_Z_R[i] = 0;
+            dock_res->trans_X_L[i] = 0;
+            dock_res->trans_Y_L[i] = 0;
+            dock_res->trans_Z_L[i] = 0;
         }else{
             dock_res->distCenters[i] = 0;
             dock_res->theta[i]       = 0;

src/fileIO.c

@@ -26,13 +26,12 @@ char* deblank(char* input){
 }
 
 struct docking_results* getDataForComplex_ATTRACT(){
-    const int MAXSIZE_LINE = 100000;
     FILE* condFile_stream = NULL;
     int numberOfConf = 0;
     int i = 0;
     int line = 1, auto_pivot = 0;
     struct docking_results* dock_res = NULL;
-    char buf[MAXSIZE_LINE] = "";
+    char buf[MAXSIZE_LINE];
     int nr = 0;
     float pivot[2][3] = {{0,0,0},{0,0,0}};
 
@@ -151,8 +150,9 @@ struct docking_results* getDataForComplex_ATTRACT(){
      * conformations
      */
     long file_pos = ftell(condFile_stream);
-    while(!feof(condFile_stream)){
-        fgets(buf,MAXSIZE_LINE,condFile_stream);
+    while(fgets(buf,MAXSIZE_LINE,condFile_stream)){
+        if(feof(condFile_stream))
+            break;
 
         /* This is not the line with the ID of the structure */
         if(buf[0] != '#' || buf[1] == '#'){
@@ -220,6 +220,10 @@ struct docking_results* getDataForComplex_ATTRACT(){
                     fclose(condFile_stream);
                     exit(EXIT_FAILURE);
                 }
+
+                /* We confirm that this conformation exists */
+                dock_res->t_conf[curConf] = 1;
+
                 mode = 1;
                 continue;
             }
@@ -404,10 +408,9 @@ struct docking_results* getDataForComplex_HEX(){
 
 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;
+    int idConf = 0, buf4 = 0;
     float buf3 = 0;
     size_t len = 2000;
     struct docking_results* dock_res = NULL;
@@ -483,10 +486,9 @@ struct docking_results* getDataForComplex_MAXDO(){
 
 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;
+    int idConf = 0;
     float buf3 = 0;
     size_t len = 2000;
     struct docking_results* dock_res = NULL;
@@ -563,10 +565,9 @@ struct docking_results* getDataForComplex_HCMD2(){
 
 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;
+    int idConf = 0;
     float buf3 = 0;
     size_t len = 2000;
     struct docking_results* dock_res = NULL;

src/rotation.c

@@ -116,9 +116,9 @@ struct pdb_values* rotate_ATTRACT(struct pdb_values* pdb, struct pdb_values* new
         }
 
         if(dock_res->centered_R){
-            trans_X = dock_res->trans_X_R[i] - pivot_X;
-            trans_Y = dock_res->trans_Y_R[i] - pivot_Y;
-            trans_Z = dock_res->trans_Z_R[i] - pivot_Z;
+            trans_X = dock_res->trans_X_R[target_conf] - pivot_X;
+            trans_Y = dock_res->trans_Y_R[target_conf] - pivot_Y;
+            trans_Z = dock_res->trans_Z_R[target_conf] - pivot_Z;
         }
     }else{
         cp = cos(dock_res->phi_L[target_conf]);
@@ -142,9 +142,9 @@ struct pdb_values* rotate_ATTRACT(struct pdb_values* pdb, struct pdb_values* new
         }
 
         if(dock_res->centered_L){
-            trans_X = dock_res->trans_X_L[i] - pivot_X;
-            trans_Y = dock_res->trans_Y_L[i] - pivot_Y;
-            trans_Z = dock_res->trans_Z_L[i] - pivot_Z;
+            trans_X = dock_res->trans_X_L[target_conf] - pivot_X;
+            trans_Y = dock_res->trans_Y_L[target_conf] - pivot_Y;
+            trans_Z = dock_res->trans_Z_L[target_conf] - pivot_Z;
         }
     }
 
@@ -166,7 +166,7 @@ struct pdb_values* rotate_ATTRACT(struct pdb_values* pdb, struct pdb_values* new
     rot_mat[8] = cs;
 
     for(i=0;i<newPDB->nbRes;i++){
-        for(j=0;i<newPDB->residues[i].nbAtom;j++){
+        for(j=0;j<newPDB->residues[i].nbAtom;j++){
             xx = newPDB->residues[i].x[j];
             yy = newPDB->residues[i].y[j];
             zz = newPDB->residues[i].z[j];
@@ -175,9 +175,9 @@ struct pdb_values* rotate_ATTRACT(struct pdb_values* pdb, struct pdb_values* new
             newPDB->residues[i].y[j] = xx * rot_mat[3] + yy * rot_mat[4] + zz * rot_mat[5];
             newPDB->residues[i].z[j] = xx * rot_mat[6] + yy * rot_mat[7] + zz * rot_mat[8];
 
-            newPDB->residues[i].x[j] = newPDB->residues[i].x[j] + dock_res->trans_X_R[target_conf] + pivot_X;
-            newPDB->residues[i].y[j] = newPDB->residues[i].y[j] + dock_res->trans_Y_R[target_conf] + pivot_Y;
-            newPDB->residues[i].z[j] = newPDB->residues[i].z[j] + dock_res->trans_Z_R[target_conf] + pivot_Z;
+            newPDB->residues[i].x[j] = newPDB->residues[i].x[j] + trans_X + pivot_X;
+            newPDB->residues[i].y[j] = newPDB->residues[i].y[j] + trans_Y + pivot_Y;
+            newPDB->residues[i].z[j] = newPDB->residues[i].z[j] + trans_Z + pivot_Z;
         }
     }
 

src/struct.h

@@ -17,6 +17,7 @@
                                     * the contact is a clash */
 #define NB_HEADER_LINE_HEX 12      /* Number of header lines at the top of a hex docking file */
 #define NB_HEADER_LINE_ZDOCK 5     /* Number of header lines at the top of a ZDOCK docking file */
+#define MAXSIZE_LINE 100000
 
 /* This is the format of a line in a PDB file */
 #define FORMAT_LINE_PDB_ATM "ATOM  %5d  %3s %3s %c%5s   %8.3f%8.3f%8.3f%s\n"