From 4c316bf060e5f4a835c64ddfd5c96c6e4eb51dde Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Tue, 9 Jul 2019 18:25:05 +0200
Subject: [PATCH] SCHWED-4246: use quoted chain names in PDBize and qsscoring.
---
modules/io/pymod/__init__.py | 4 +++-
modules/mol/alg/pymod/qsscoring.py | 17 ++---------------
2 files changed, 5 insertions(+), 16 deletions(-)
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 70a196663..98d952269 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -381,7 +381,9 @@ def _PDBize(biounit, asu, seqres=None, min_polymer_size=10,
tmp_ops.append(tp)
trans_matrices = tmp_ops
# select chains into a view as basis for each transformation
- assu = asu.Select('cname='+','.join(chains[c_intvls[i][0]:c_intvls[i][1]]))
+ assu = asu.Select('cname='+','.join(mol.QueryQuoteName(name) \
+ for name in \
+ chains[c_intvls[i][0]:c_intvls[i][1]]))
pdbizer.Add(assu, trans_matrices, ss)
pdb_bu = pdbizer.Finish(transformation)
if transformation:
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index 565768efb..3ed23ae9e 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -1462,18 +1462,6 @@ def _AlignAtomSeqs(seq_1, seq_2):
LogWarning('%s: %s' % (seq_2.name, seq_2.string))
return aln
-def _FixSelectChainName(ch_name):
- """
- :return: String to be used with Select(cname=<RETURN>). Takes care of putting
- quotation marks where needed.
- :rtype: :class:`str`
- :param ch_name: Single chain name (:class:`str`).
- """
- if ch_name in ['-', '_', ' ']:
- return '"%c"' % ch_name
- else:
- return ch_name
-
def _FixSelectChainNames(ch_names):
"""
:return: String to be used with Select(cname=<RETURN>). Takes care of joining
@@ -1481,8 +1469,7 @@ def _FixSelectChainNames(ch_names):
:rtype: :class:`str`
:param ch_names: Some iterable list of chain names (:class:`str` items).
"""
- chain_set = set([_FixSelectChainName(ch_name) for ch_name in ch_names])
- return ','.join(chain_set)
+ return ','.join(mol.QueryQuoteName(ch_name) for ch_name in ch_names)
# QS entity
@@ -1507,7 +1494,7 @@ def _CleanInputEntity(ent):
# remove them from *ent*
if removed_chains:
- view = ent.Select('cname!=%s' % _FixSelectChainNames(removed_chains))
+ view = ent.Select('cname!=%s' % _FixSelectChainNames(set(removed_chains)))
ent_new = mol.CreateEntityFromView(view, True)
ent_new.SetName(ent.GetName())
else:
--
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