fix reconstruction using ATTRACT

LICENCE

@@ -3,15 +3,10 @@
 # chloe.dequeker@upmc.fr, elodie.laine@upmc.fr, alessandra.carbone@lip6.fr 
 # UMR 7238 Biologie Computationnelle et Quantitative
 # 
-# Used library or packages:
-# Eigen library, under GNU Free Documentation License 1.2
-# Numpy package under the BSD license
-# MDtraj python package under the Lesser GNU General Public License (LGPL v2.1+)
+# This software is a computer program whose purpose is to compute the interface of 
+# two PDB. Both PDB are therefore required. Moreover, this software has the advantage 
+# of parsing the output format of docking software.
 #
-# This software is a computer program whose purpose is to dissect proteins 
-# dynamical architectures. It requires as input the MD trajectorie(s) of the  
-# studied protein and a PDB file of the same protein.
-# 
 # This software is governed by the CeCILL license under French law and abiding
 # by the rules of distribution of free software. You can use, modify and/or
 # redistribute the software under the terms of the CeCILL license as circulated

src/INTBuilder.c

@@ -434,7 +434,6 @@ int main(int argc, char** argv){
         freePDB(newPDB);
         newPDB   = NULL;
         if(newPDB_R != NULL){
-            printf("point %p\n",newPDB_R);
             freePDB(newPDB_R);
             newPDB_R = NULL;
         }

src/fileIO.c

@@ -114,9 +114,9 @@ struct docking_results* getDataForComplex_ATTRACT(){
 
     /* 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)
+        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)
+        if (strlen(buf) >= 25 && strncmp(buf, "#centered receptor: false", 25) == 0)
             centered_R = 0;
     }
     /* No valid value */
@@ -128,14 +128,14 @@ struct docking_results* getDataForComplex_ATTRACT(){
 
     /* 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)
+        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)
+        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)
+        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)
+        if (strlen(buf) >= 23 && strncmp(buf, "#centered ligand: false", 23) == 0)
             centered_L = 0;
     }
     /* No valid value */

src/rotation.c

@@ -119,6 +119,10 @@ struct pdb_values* rotate_ATTRACT(struct pdb_values* pdb, struct pdb_values* new
             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{
+            trans_X = dock_res->trans_X_R[target_conf];
+            trans_Y = dock_res->trans_Y_R[target_conf];
+            trans_Z = dock_res->trans_Z_R[target_conf];
         }
     }else{
         cp = cos(dock_res->phi_L[target_conf]);
@@ -145,6 +149,10 @@ struct pdb_values* rotate_ATTRACT(struct pdb_values* pdb, struct pdb_values* new
             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;
+        }else{
+            trans_X = dock_res->trans_X_L[target_conf];
+            trans_Y = dock_res->trans_Y_L[target_conf];
+            trans_Z = dock_res->trans_Z_L[target_conf];
         }
     }
 
@@ -167,9 +175,9 @@ struct pdb_values* rotate_ATTRACT(struct pdb_values* pdb, struct pdb_values* new
 
     for(i=0;i<newPDB->nbRes;i++){
         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];
+            xx = newPDB->residues[i].x[j] - pivot_X;
+            yy = newPDB->residues[i].y[j] - pivot_Y;
+            zz = newPDB->residues[i].z[j] - pivot_Z;
 
             newPDB->residues[i].x[j] = xx * rot_mat[0] + yy * rot_mat[1] + zz * rot_mat[2];
             newPDB->residues[i].y[j] = xx * rot_mat[3] + yy * rot_mat[4] + zz * rot_mat[5];