Fixed polygon_mesh reader so that it works with user-generated .ma files, not...

Fixed polygon_mesh reader so that it works with user-generated .ma files, not just autogenerated ones

mrdna/readers/__init__.py

@@ -8,15 +8,11 @@ def read_cadnano(json_file, **model_parameters):
     return model_from_cadnano_json(data, **model_parameters)
 
 def read_vhelix(maya_file, **model_parameters):
-    from .polygon_mesh import parse_maya_file, convert_maya_to_segments
+    from .polygon_mesh import parse_maya_file, convert_maya_bases_to_segment_model
     from ..model.dna_sequence import m13 as m13seq
-    from ..segmentmodel import SegmentModel
 
-    data = parse_maya_file(maya_file)
-    segments, dsSegmentDict = convert_maya_to_segments( data )
-    if 'dimensions' not in model_parameters:
-        model_parameters['dimensions']=(5000,5000,5000)
-    model = SegmentModel( segments,**model_parameters )
+    maya_bases = parse_maya_file(maya_file)
+    model = convert_maya_bases_to_segment_model( maya_bases, **model_parameters )
     model.set_sequence(m13seq*10)
     return model