Merge branch 'release-1.0.0'

eltetrado

@@ -19,7 +19,7 @@ from Bio.PDB import PDBParser, MMCIFParser, Structure, Residue, Atom
 from Bio.PDB.Atom import DisorderedAtom
 from Bio.PDB.StructureBuilder import StructureBuilder
 
-__version__ = '0.0.2-rc4'
+__version__ = '1.0.0'
 
 LW_SCORE = {
     'cWW': 1, 'tWW': 2, 'cWH': 3, 'tWH': 4, 'cWS': 5, 'tWS': 6,
@@ -529,7 +529,7 @@ class Analysis:
                 classification = list(self.__get_classification())
                 score = (
                     sum(scores[c] for c in classification),
-                    self.__sum_squares_chain_distances(chain_groups, permutation))
+                    self.__sum_squares_chain_distances(permutation))
                 # print('Checking reorder:', ', '.join(permutation), ''.join(classification))
                 if score < best_score:
                     best_score = score
@@ -577,9 +577,10 @@ class Analysis:
                     break
         return chains.values()
 
-    def __sum_squares_chain_distances(self, chain_groups: Iterable[set], chain_order: Tuple) -> int:
+    def __sum_squares_chain_distances(self, chain_order: Tuple) -> int:
         chain_pairs = set(
-            (frozenset((p.pair[0].chain, p.pair[1].chain)) for h in self.helices for t in h.tetrads for p in t.pairs))
+            (frozenset((p.pair[0].chain, p.pair[1].chain)) for h in self.helices for t in h.tetrads for p in t.pairs
+             if p.pair[0].chain != p.pair[1].chain))
         index = {chain: chain_order.index(chain) for chain in chain_order}
         sum_sq = 0
         for c1, c2 in chain_pairs:

has_tetrad

@@ -10,7 +10,7 @@ import tempfile
 
 from collections import defaultdict
 
-__version__ = '0.0.2-rc4'
+__version__ = '1.0.0'
 
 
 class Pair: