end rotation ATTRACT

src/rotation.c

@@ -68,19 +68,86 @@ void sphericToxyz(float *x, float *y, float *z, float x0, float y0, float z0, fl
     *z = z0 + R * cos(theta);
 }
 
-struct pdb_values* rotate_R_ATTRACT(struct pdb_values* pdb, struct pdb_values* newPDB, struct docking_results* dock_res, int target_conf){
+/* This function aims at rotating a protein using the ATTRACT output format (DOF file). 
+ * The rotation will only consider a docking using two proteins, and will not consider the 
+ * normal modes that could have been included for a conformation
+ *
+ * A parameter 'isRec' is set, as to know if we are considering the receptor or the ligand in the
+ * 'pdb' parameter. Different rotations and translations may apply.
+ */
+struct pdb_values* rotate_ATTRACT(struct pdb_values* pdb, struct pdb_values* newPDB, struct docking_results* dock_res, int target_conf, int isRec){
     int i = 0, j = 0;
     float rot_mat[9];
 
     float xx = 0, yy = 0, zz = 0;
+    float cp = 0, cs = 0, cr = 0, sp = 0, ss = 0, sr = 0;
+    float pivot_X = 0, pivot_Y = 0, pivot_Z = 0;
+    float trans_X = 0, trans_Y = 0, trans_Z = 0;
+
+    /* Copy the pdb into newPDB (which will be returned */
+    if(newPDB == NULL){
+        newPDB = allocate_pdb(pdb->nbRes);
+        newPDB->nbAtom = pdb->nbAtom;
+    }
+    memcpy(newPDB->residues,pdb->residues,pdb->nbRes*sizeof(struct residue));
+
+    /* Now set the different values depending if we are considering
+     * the receptor or the ligand
+     */
+    if(isRec){
+        cp = cos(dock_res->phi_R[target_conf]);
+        cs = cos(dock_res->ssi_R[target_conf]);
+        cr = cos(dock_res->rot_R[target_conf]);
+        sp = sin(dock_res->phi_R[target_conf]);
+        ss = sin(dock_res->ssi_R[target_conf]);
+        sr = sin(dock_res->rot_R[target_conf]);
+
+        /* If the receptor is centered, we need to substract the 
+         * pivot from all of its atoms
+         */
+        if(dock_res->auto_pivot){
+            pivot_X = newPDB->centerX;
+            pivot_Y = newPDB->centerY;
+            pivot_Z = newPDB->centerZ;
+        }else{
+            pivot_X = dock_res->pivot_X_R;
+            pivot_Y = dock_res->pivot_Y_R;
+            pivot_Z = dock_res->pivot_Z_R;
+        }
+
+        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;
+        }
+    }else{
+        cp = cos(dock_res->phi_L[target_conf]);
+        cs = cos(dock_res->ssi_L[target_conf]);
+        cr = cos(dock_res->rot_L[target_conf]);
+        sp = sin(dock_res->phi_L[target_conf]);
+        ss = sin(dock_res->ssi_L[target_conf]);
+        sr = sin(dock_res->rot_L[target_conf]);
+
+        /* If the ligand is centered, we need to substract the 
+         * pivot 
+         */
+        if(dock_res->auto_pivot){
+            pivot_X = newPDB->centerX;
+            pivot_Y = newPDB->centerY;
+            pivot_Z = newPDB->centerZ;
+        }else{
+            pivot_X = dock_res->pivot_X_L;
+            pivot_Y = dock_res->pivot_Y_L;
+            pivot_Z = dock_res->pivot_Z_L;
+        }
+
+        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;
+        }
+    }
 
-    float pivot_X_R, pivot_Y_R, pivot_Z_R;
-    float cp = cos(dock_res->phi_R[target_conf]);
-    float cs = cos(dock_res->ssi_R[target_conf]);
-    float cr = cos(dock_res->rot_R[target_conf]);
-    float sp = sin(dock_res->phi_R[target_conf]);
-    float ss = sin(dock_res->ssi_R[target_conf]);
-    float sr = sin(dock_res->rot_R[target_conf]);
     float cscp = cs * cp;
     float cssp = cs * sp;
     float sscp = ss * cp;
@@ -98,25 +165,6 @@ struct pdb_values* rotate_R_ATTRACT(struct pdb_values* pdb, struct pdb_values* n
     rot_mat[7] = -sr * ss;
     rot_mat[8] = cs;
 
-    /* If the receptor is centered, we need to substract the 
-     * pivot from all of its atoms
-     */
-    if(dock_res->auto_pivot){
-        pivot_X_R = newPDB->centerX;
-        pivot_Y_R = newPDB->centerY;
-        pivot_Z_R = newPDB->centerZ;
-    }else{
-        pivot_X_R = dock_res->pivot_X_R;
-        pivot_Y_R = dock_res->pivot_Y_R;
-        pivot_Z_R = dock_res->pivot_Z_R;
-    }
-
-    if(dock_res->centered_R){
-        dock_res->trans_X_R[i] -= pivot_X_R;
-        dock_res->trans_Y_R[i] -= pivot_Y_R;
-        dock_res->trans_Z_R[i] -= pivot_Z_R;
-    }
-
     for(i=0;i<newPDB->nbRes;i++){
         for(j=0;i<newPDB->residues[i].nbAtom;j++){
             xx = newPDB->residues[i].x[j];
@@ -127,54 +175,15 @@ struct pdb_values* rotate_R_ATTRACT(struct pdb_values* pdb, struct pdb_values* n
             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_R;
-            newPDB->residues[i].y[j] = newPDB->residues[i].y[j] + dock_res->trans_Y_R[target_conf] + pivot_Y_R;
-            newPDB->residues[i].z[j] = newPDB->residues[i].z[j] + dock_res->trans_Z_R[target_conf] + pivot_Z_R;
+            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;
         }
     }
 
     return newPDB;
 }
 
-struct pdb_values* rotate_ATTRACT(struct pdb_values* pdb, struct pdb_values* newPDB, struct docking_results* dock_res, int target_conf, int isRec){
-    int i = 0, j = 0;
-
-    /* Copy the pdb into newPDB (which will be returned */
-    if(newPDB == NULL){
-        newPDB = allocate_pdb(pdb->nbRes);
-        newPDB->nbAtom = pdb->nbAtom;
-    }
-    memcpy(newPDB->residues,pdb->residues,pdb->nbRes*sizeof(struct residue));
-    
-    if(isRec){
-        /* If the receptor is centered, we need to substract the 
-         * pivot from all of its atoms
-         */
-        if(dock_res->centered_R){
-            for(i=0;i<newPDB->nbRes;i++){
-                for(j=0;j<newPDB->residues[i].nbAtom;j++){
-                    newPDB->residues[i].x[j] -= dock_res->pivot_X_R;
-                    newPDB->residues[i].y[j] -= dock_res->pivot_Y_R;
-                    newPDB->residues[i].z[j] -= dock_res->pivot_Z_R;
-                }
-            }
-        }
-    }else{
-        /* Same thing for the ligand */
-        if(dock_res->centered_L){
-            for(i=0;i<newPDB->nbRes;i++){
-                for(j=0;j<newPDB->residues[i].nbAtom;j++){
-                    newPDB->residues[i].x[j] -= dock_res->pivot_X_R;
-                    newPDB->residues[i].y[j] -= dock_res->pivot_Y_R;
-                    newPDB->residues[i].z[j] -= dock_res->pivot_Z_R;
-                }
-            }
-        }
-    }
-    
-    return newPDB;
-}
-
 
 struct pdb_values* rotate_ZDOCK(struct pdb_values* pdb, struct pdb_values* newPDB, float trans_X, float trans_Y, float trans_Z, float alpha, float beta, float gamma){
     /* This function aims at rotating the pdb parameter and gets its new coordinates