fix some bugs

mrdna/readers/segmentmodel_from_oxdna_pinyi.py

@@ -140,7 +140,7 @@ def mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc=None,get_nt_p
         basepair_pos = r + base_dir*10.0
         normal_dir = -conf_data[:,6:9]
         perp_dir = np.cross(base_dir, normal_dir)
-        orientation = np.array([np.array(o).T.dot(_yrot) for o in zip(perp_dir,-base_dir,-normal_dir)]).T
+        orientation = np.array([np.array(o).T.dot(_yrot) for o in zip(perp_dir,-base_dir,-normal_dir)])
         seq=nt_prop["seq"]
         bp=nt_prop["bp"]
         stack=nt_prop["stack"]
@@ -148,6 +148,8 @@ def mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc=None,get_nt_p
         nt_prop["orientation"]=orientation
         nt_prop["r"]=list(r)
     except:
+        if virt2nuc is not None:
+            logger.info("warning: virt2nuc not read. guessing structure...")
         ## Reverse direction so indices run 5'-to-3'
         top_data = [a[::-1] for a in top_data]
         conf_data = conf_data[::-1,:]