From c57f05a517ce39ede69a48ba49dbbdcc84b06b65 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Wed, 26 Jul 2017 16:23:11 +0200
Subject: [PATCH] SCHWED-2440: better error handling when aligning non-peptide
chains.
---
modules/mol/alg/pymod/superpose.py | 23 +++++++++++++++--------
1 file changed, 15 insertions(+), 8 deletions(-)
diff --git a/modules/mol/alg/pymod/superpose.py b/modules/mol/alg/pymod/superpose.py
index c748ae6e3..20298737a 100644
--- a/modules/mol/alg/pymod/superpose.py
+++ b/modules/mol/alg/pymod/superpose.py
@@ -190,19 +190,26 @@ def _MatchResidueByAln(ent_a, ent_b, atoms, alnmethod):
atmset = ParseAtomNames(atoms)
## iterate chains
for i in range(0, n_chains):
+ ## fetch chains (peptide-linking residues only)
chain_a = ent_a.chains[i]
chain_b = ent_b.chains[i]
+ chain_view_a = chain_a.Select('protein=true')
+ chain_view_b = chain_b.Select('protein=true')
+ if chain_view_a.chain_count == 0 or chain_view_b.chain_count == 0:
+ # skip empty chains
+ continue
## fetch residues
- s_a = ''.join([r.one_letter_code
- for r in chain_a.Select('protein=True').residues])
- s_b = ''.join([r.one_letter_code
- for r in chain_b.Select('protein=True').residues])
+ s_a = ''.join([r.one_letter_code for r in chain_view_a.residues])
+ s_b = ''.join([r.one_letter_code for r in chain_view_b.residues])
## create sequence from residue lists & alignment
seq_a = ost.seq.CreateSequence(chain_a.name, s_a)
seq_b = ost.seq.CreateSequence(chain_b.name, s_b)
aln_a_b = alnmethod(seq_a, seq_b, ost.seq.alg.BLOSUM62)
+ if not aln_a_b:
+ # skip failed alignments
+ continue
## evaluate alignment
- max_aln_res = 0
+ max_aln_res = -1
for a in range(0, len(aln_a_b)):
aln = aln_a_b[a]
aln_res_len = 0
@@ -218,13 +225,13 @@ def _MatchResidueByAln(ent_a, ent_b, atoms, alnmethod):
aln = aln_a_b[max_aln_idx]
## bind chain to alignment
- aln.AttachView(0, chain_a.Select('protein=True'))
- aln.AttachView(1, chain_b.Select('protein=True'))
+ aln.AttachView(0, chain_view_a)
+ aln.AttachView(1, chain_view_b)
## select residues (only replacement edges)
for i in max_matches:
r_a = aln.GetResidue(0,i)
r_b = aln.GetResidue(1,i)
- result_a,result_b=_fetch_atoms(r_a, r_b, result_a, result_b, atmset)
+ result_a, result_b = _fetch_atoms(r_a, r_b, result_a, result_b, atmset)
result_a.AddAllInclusiveBonds()
result_b.AddAllInclusiveBonds()
return result_a, result_b
--
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