a

mrdna/readers/segmentmodel_from_cadnano.py

@@ -60,29 +60,6 @@ def get_lattice(part):
             print("WARNING: unable to determine cadnano part lattice type")
     return lattice_type
         
-def get_helix_angle(cadnanopart,helix_id, indices):
-        """ Get "start_orientation" for helix """
-        # import ipdb
-        # ipdb.set_trace()
-        """ FROM CADNANO2.5
-        + angle is CCW
-        - angle is CW
-        Right handed DNA rotates clockwise from 5' to 3'
-        we use the convention the 5' end starts at 0 degrees
-        and it's pair is minor_groove_angle degrees away
-        direction, hence the minus signs.  eulerZ
-        """
-
-        hp, bpr, tpr, eulerZ, mgroove = cadnanopart.vh_properties.loc[helix_id,
-                                                                    ['helical_pitch',
-                                                                     'bases_per_repeat',
-                                                                     'turns_per_repeat',
-                                                                     'eulerZ',
-                                                                     'minor_groove_angle']]
-        twist_per_base = tpr*360./bpr
-        # angle = eulerZ - twist_per_base*indices + 0.5*mgroove + 180
-        angle = eulerZ + twist_per_base*indices - 0.5*mgroove
-        return angle
             
 def mrdna_model_from_cadnano(json_data,**model_parameters):
         part,vslist=decode_cadnano_part(json_data)
@@ -97,6 +74,6 @@ def mrdna_model_from_cadnano(json_data,**model_parameters):
             except:
                 origins = {hid:part.getVirtualHelixOrigin(hid)[:2] for hid in part.getidNums()}
         cad_bps=part.getIndices(0)
-        
+
 
     model = model_from_basepair_stack_3prime( r, bp, stack, three_prime, seq, orientation, **model_parameters )