Automatically write atomic ENM in multiresolution_simulation; fixed error in...

Automatically write atomic ENM in multiresolution_simulation; fixed error in ENM causing failure for square lattice

mrdna/readers/segmentmodel_from_pdb.py

@@ -255,6 +255,6 @@ if __name__ == "__main__":
 
     model._clear_beads()
     model._generate_atomic_model(scale=1.0)
-    model._write_atomic_ENM( 'test-from-pdb', lattice_type="honeycomb" )
+    model.write_atomic_ENM( 'test-from-pdb' )
 
     model.atomic_simulate( outputPrefix = 'test-from-pdb' )

mrdna/segmentmodel.py

@@ -2376,10 +2376,13 @@ class SegmentModel(ArbdModel):
         for s in self.strands:
             s.update_atomic_orientations(orientation)
 
-    def _write_atomic_ENM(self, prefix, lattice_type=None):
+    def write_atomic_ENM(self, prefix, lattice_type=None):
         ## TODO: ensure atomic model was generated already
         if lattice_type is None:
-            lattice_type = self.lattice_type
+            try:
+                lattice_type = self.lattice_type
+            except:
+                lattice_type = "square"
 
         if lattice_type == "square":
             enmTemplate = enmTemplateSQ
@@ -2429,9 +2432,9 @@ class SegmentModel(ArbdModel):
                                 if lattice_type == 'honeycomb':
                                     correctionKey = ','.join((key,n1,n2))
                                     assert(correctionKey in enmCorrectionsHC)
-                                dk,dr = enmCorrectionsHC[correctionKey]
-                                k  = float(dk)
-                                d += float(dr)
+                                    dk,dr = enmCorrectionsHC[correctionKey]
+                                    k  = float(dk)
+                                    d += float(dr)
 
                                 i = nt1._get_atomic_index(name=n1)
                                 j = nt2._get_atomic_index(name=n2)

mrdna/simulate.py

@@ -97,6 +97,7 @@ def multiresolution_simulation( model, output_name,
         model.update_splines(coordinates)
         model._clear_beads()
         model._generate_atomic_model(scale=backbone_scale)
+        model.write_atomic_ENM( output_prefix )
         model.atomic_simulate( outputPrefix = output_prefix )
 
         ret = directory