Modif makefile to put exec in current directory

Makefile

@@ -9,7 +9,7 @@ BINARY=INTBuilder
 all: $(BINARY)
 
 $(BINARY): $(SRC_DIR)/$(OBJECTS)
-	cd $(SRC_DIR) && $(CC)  $(OBJECTS) -o $@ $(LDFLAGS)
+	cd $(SRC_DIR) && $(CC)  $(OBJECTS) -o ../$@ $(LDFLAGS)
 
 %.o: $(SRC_DIR)/%.c
 	$(CC) $(CFLAGS) $< -o $(SRC_DIR)/$@

src/INTBuilder.c

@@ -454,11 +454,9 @@ int main(int argc, char** argv){
 
     pdbR = readPDB(receptor);
     pdbL = readPDB(ligand);
-
-    if(target_conf > 0){
     getAnglesFromCA1andCA5_sophie(pdbL,&alpha,&beta,&gamma);
 
-        
+    if(target_conf > 0){
         dalpha = dock_res->alpha[target_conf] - alpha;
         dbeta  = dock_res->beta[target_conf]  - beta;
         dgamma = dock_res->gamma[target_conf] - gamma;
@@ -476,8 +474,6 @@ int main(int argc, char** argv){
     }else{
         for(i=0;i<dock_res->nbConf;i++){
             // For all conformations
-            getAnglesFromCA1andCA5_sophie(pdbL,&alpha,&beta,&gamma);
-
             dalpha = dock_res->alpha[i] - alpha;
             dbeta  = dock_res->beta[i]  - beta;
             dgamma = dock_res->gamma[i] - gamma;

src/rotation.c

@@ -32,8 +32,8 @@ struct pdb_values* rotate_sophie(struct pdb_values* pdb, struct pdb_values* pdbR
     if(newPDB == NULL){
         newPDB = allocate_pdb(pdb->nbRes);
         newPDB->nbAtom = pdb->nbAtom;
-        memcpy(newPDB->residues,pdb->residues,pdb->nbRes*sizeof(struct residue));
     }
+    memcpy(newPDB->residues,pdb->residues,pdb->nbRes*sizeof(struct residue));
     
 
     float newX = pdbR->centerX + R*sin(theta)*cos(phi);
@@ -80,6 +80,10 @@ struct pdb_values* rotate_sophie(struct pdb_values* pdb, struct pdb_values* pdbR
            newPDB->yCA1 = (newPDB->yCA1 - pdb->centerY) + newY;
            newPDB->zCA1 = (newPDB->zCA1 - pdb->centerZ) + newZ;
 
+           newPDB->xCA5 = (newPDB->xCA5 - pdb->centerX) + newX;
+           newPDB->yCA5 = (newPDB->yCA5 - pdb->centerY) + newY;
+           newPDB->zCA5 = (newPDB->zCA5 - pdb->centerZ) + newZ;
+
            newPDB->centerX = newX;
            newPDB->centerY = newY;
            newPDB->centerZ = newZ;