Fix issue with mutations when chain appears in multiple places in PDB file…

Fix issue with mutations when chain appears in multiple places in PDB file separated by other chains.

pdbfixer/pdbfixer.py

@@ -739,15 +739,16 @@ class PDBFixer(object):
         """
 
         # First find residues based on our table of standard substitutions.
-
         index_to_old_name = dict((r.index, r.name) for r in self.topology.residues())
         index_to_new_residues = {}
 
-        chain_id_to_chain_number = dict((c.id, k) for k, c in enumerate(self.topology.chains()))
-        chain_number = chain_id_to_chain_number[chain_id]
-        chain = list(self.topology.chains())[chain_number]
-
-        resSeq_to_index = dict((int(r.id), k) for k, r in enumerate(chain.residues()))
+        chain_numbers = list()
+        resSeq_to_index = dict()
+        for (chain_number, chain) in enumerate(self.topology.chains()):
+            if chain.id == chain_id:
+                chain_numbers.append(chain_id)
+                for (residue_number, residue) in enumerate(chain.residues()):
+                    resSeq_to_index[int(residue.id)] = residue_number
 
         for mut_str in mutations:
             old_name, resSeq, new_name = mut_str.split("-")

pdbfixer/tests/test_mutate.py

@@ -47,8 +47,6 @@ def test_mutate_2():
     desired_atom_names = set(["C", "N", "CA", "CB", "CG", "CD1", "CD2", "O", "H", "HA", "HB2", "HB3", "HD11", "HD12", "HD13", "HD21", "HD22", "HD23", "HG"])
     assert atom_names == desired_atom_names, "Atom Names did not match for LEU 57"
 
-
-
 @raises(ValueError)
 def test_mutate_3_fails():
     fixer = pdbfixer.PDBFixer(pdbid='1VII')
@@ -65,3 +63,7 @@ def test_mutate_5_fails():
     fixer = pdbfixer.PDBFixer(pdbid='1VII')
     fixer.applyMutations(["ALA-1000-GLY", "SER-56-ALA"], "A")
 
+def test_mutate_multiple_copies_of_chain_A():
+    fixer = pdbfixer.PDBFixer(pdbid='1OL5')
+    fixer.applyMutations(['TPO-287-THR','TPO-288-THR'], "A")
+