Added 'list' (.dat) file reader, fixed setting sequence in segmentmodel_from_lists_

mrdna/readers/__init__.py

@@ -26,5 +26,20 @@ def read_vhelix(maya_file, **model_parameters):
     model.set_sequence(m13seq*10)
     return model
 
+def read_list(infile,**model_parameters):
+    import numpy as np
+    try:
+        data = np.loadtxt(infile)
+    except:
+        data = np.loadtxt(infile,skiprows=1) # strip header
+    coords = data[:,:3]*10
+    bp = data[:,3]
+    stack = data[:,4]
+    three_prime = data[:,5]
+
+    from .segmentmodel_from_lists import model_from_basepair_stack_3prime
+    return model_from_basepair_stack_3prime(coords, bp, stack, three_prime)
+
+
 def read_atomic_pdb(pdb_file, **model_parameters):
     return SegmentModelFromPdb(pdb_file)

mrdna/readers/segmentmodel_from_lists.py

@@ -250,6 +250,7 @@ def model_from_basepair_stack_3prime(coordinates, basepair, stack, three_prime,
 
 
     if sequence is None:
-        model.randomize_unset_sequence()
+        for s in model.segments:
+            s.randomize_unset_sequence()
 
     return model