add cite for tacoxdna

mrdna/readers/segmentmodel_from_oxdna_pinyi.py

@@ -90,6 +90,7 @@ def mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc=None,get_nt_p
         return L
     def get_virt2nuc(virt2nuc,top_data):
         sys.modules["libs"]=libs
+        logger.info("""You are using a feature that depends on the tacoxdna library: A. Suma et al., 2019, "TacoxDNA: A user‐friendly web server for simulations of complex DNA structures, from single strands to origami", J. Comput. Chem. 40, 2586""")
         virt_pickle=open(virt2nuc,"rb")
         vh_vb,pattern=pickle.load(virt_pickle)
         L1=_find_vh_vb_table(vh_vb._scaf,1)
@@ -131,13 +132,14 @@ def mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc=None,get_nt_p
         return nt_prop
     try:
         nt_prop=get_virt2nuc(virt2nuc,top_data)
+
         r=conf_data[:,:3] * 8.518
         base_dir = conf_data[:,3:6]
         # basepair_pos = r + base_dir*6.0
         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)])
+        orientation = np.array([np.array(o).T.dot(_yrot) for o in zip(perp_dir,-base_dir,-normal_dir)]).T
         seq=nt_prop["seq"]
         bp=nt_prop["bp"]
         stack=nt_prop["stack"]