bugfix

In principle we have three types of structures in the scorer (terrible I know).
1) the actual strucures that are only molcked 2) the structures as they are used
in the chain mapper (complete backbone) 3) same as 1) but stereochecked.
The alignments required at this position are of category 3 but they were 2.

modules/mol/alg/pymod/scoring.py

@@ -952,19 +952,24 @@ class Scorer:
         # lDDT requires a flat mapping with mdl_ch as key and trg_ch as value
         flat_mapping = self.mapping.GetFlatMapping(mdl_as_key=True)
 
-        lddt_alns = dict()
+        # make alignments accessible by mdl seq name
+        stereochecked_alns = dict()
         for aln in self.stereochecked_aln:
             mdl_seq = aln.GetSequence(1)
-            lddt_alns[mdl_seq.name] = aln
+            stereochecked_alns[mdl_seq.name] = aln
+        alns = dict()
+        for aln in self.aln:
+            mdl_seq = aln.GetSequence(1)
+            alns[mdl_seq.name] = aln
 
         lddt_chain_mapping = dict()
         for mdl_ch, trg_ch in flat_mapping.items():
-            if mdl_ch in lddt_alns:
+            if mdl_ch in stereochecked_alns:
                 lddt_chain_mapping[mdl_ch] = trg_ch
 
         lddt_score = self.lddt_scorer.lDDT(self.stereochecked_model,
                                            chain_mapping = lddt_chain_mapping,
-                                           residue_mapping = lddt_alns,
+                                           residue_mapping = stereochecked_alns,
                                            check_resnames=False,
                                            local_lddt_prop="lddt")[0]
         local_lddt = dict()
@@ -990,8 +995,7 @@ class Scorer:
                     # fetch trg residue from non-stereochecked aln
                     trg_r = None
                     if cname in flat_mapping:
-                        aln = self.mapping.alns[(flat_mapping[cname], cname)]
-                        for col in aln:
+                        for col in alns[cname]:
                             if col[0] != '-' and col[1] != '-':
                                 if col.GetResidue(1).number == r.number:
                                     trg_r = col.GetResidue(0)