mrdna/RELEASE-VERSION

-1.0a.dev178
+1.0a.dev180

mrdna/readers/segmentmodel_from_pdb.py

@@ -95,7 +95,7 @@ def residues_within( cutoff, coords1, coords2, sel1, sel2 ):
 
     return arr_idx1, arr_idx2, distance_matrix
 
-def find_base_position_orientation( u, selection_text='all' ):
+def find_base_position_orientation( u, selection_text='nucleic' ):
     ## Find orientation and center of each nucleotide
     transforms,centers = [[],[]]
     for r in u.select_atoms(selection_text).residues:
@@ -126,7 +126,7 @@ def find_base_position_orientation( u, selection_text='all' ):
     transforms = np.array(transforms)
     return centers,transforms
 
-def find_basepairs( u, centers, transforms, selection_text='all' ):
+def find_basepairs( u, centers, transforms, selection_text='nucleic' ):
     bonds = { b:"resname {} and name {}".format(resnames[b],bp_bond_atoms[b])
               for b in bases }
 
@@ -193,7 +193,7 @@ def find_basepairs( u, centers, transforms, selection_text='all' ):
     #     ...
     return basepairs
 
-def find_stacks_mdanalysis( u, centers, transforms, selection_text='all' ):
+def find_stacks_mdanalysis( u, centers, transforms, selection_text='nucleic' ):
 
     ## Find orientation and center of each nucleotide
     expected_stack_positions = []
@@ -281,7 +281,7 @@ def break_into_contiguous_groups(sequence):
 
 def get_lists_from_pdb(*args, **kwargs):
     u = mda.Universe(*args,**kwargs)
-    for a in u.select_atoms("resname DT* and name C7").atoms:
+    for a in u.select_atoms("resname DT* THY and name C7").atoms:
         a.name = "C5M"
 
     ter = read_ter_from_pdb(*args)

mrdna/segmentmodel.py

@@ -2045,7 +2045,8 @@ class SegmentModel(ArbdModel):
         assert( d > 0.2 )
         if key not in self._bonded_potential:
             kT = self.configuration.temperature * 0.0019872065 # kcal/mol
-            self._bonded_potential[key] = WLCSKBond( d, lp, kT, range_=(0,1200) )
+            _pot = WLCSKBond( d, lp, kT, range_=(0,1200) )
+            self._bonded_potential[key] = _pot
         return self._bonded_potential[key]
 
     def _get_wlc_sk_angle_potential(self, d):
@@ -2765,31 +2766,19 @@ class SegmentModel(ArbdModel):
                 bead.type_ = beadtype_s[key]
             else:
                 t0 = bead.type_
-                t = ParticleType(t0.name)
-                t.__dict__ = deepcopy(t0.__dict__)
+                newname = f'{char}{beadtype_count[char]:03d}'
+                kwargs = {k:v for k,v in bead.type_.__dict__.items() if k not in ParticleType.excludedAttributes}
+                t = ParticleType( name=newname, **kwargs )
                 t.__dict__["nts"] = bead.num_nt*2 if char in ("D","O") else bead.num_nt
-                # t.name = t.name + "%03d" % (t.nts*10**decimals)
-                t.name = char + "%03d" % (beadtype_count[char])
                 t.mass = t.nts * 150
                 t.diffusivity = 120 if t.nts == 0 else min( 50 / np.sqrt(t.nts/5), 120)
                 beadtype_count[char] += 1
                 #print( "{} --> {} ({})".format(num_nt0, bead.num_nt, t.name) )
                 bead.type_ = t
                 beadtype_s[key]=t
-            """
-                t = deepcopy(bead.type_)
-                t.__dict__["nts"] = bead.num_nt*2 if char in ("D","O") else bead.num_nt
-                # t.name = t.name + "%03d" % (t.nts*10**decimals)
-                t.name = char + "%03d" % (beadtype_count[char])
-                t.mass = t.nts * 150
-                t.diffusivity = 120 if t.nts == 0 else min( 50 / np.sqrt(t.nts/5), 120)
-                beadtype_count[char] += 1
-                # if self.DEBUG: print( "{} --> {} ({})".format(num_nt0, bead.num_nt, t.name) )
                 beadtype_s[key] = bead.type_ = t
-            """
         # (cluster_size[c-1])
 
-
         import scipy.cluster.hierarchy as hcluster
         beads = [b for s in segments for b in s if b.type_.name[0].upper() in ("D","O")]
         data = np.array([b.num_nt for b in beads])[:,np.newaxis]