From be69cfb5fb4ad0efed9a2c93be4c091a265513b2 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Fri, 25 May 2018 20:06:53 +0200
Subject: [PATCH] Deal with chain names with spaces or only space.
---
modules/mol/alg/pymod/qsscoring.py | 60 +++++++++++++++++++++---------
1 file changed, 42 insertions(+), 18 deletions(-)
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index 919b5a72f..0f4edcc53 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -1240,6 +1240,28 @@ 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
+ and putting quotation marks where needed.
+ :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)
+
# QS entity
def _CleanInputEntity(ent):
@@ -1263,13 +1285,7 @@ def _CleanInputEntity(ent):
# remove them from *ent*
if removed_chains:
- chain_set = set()
- for ch_name in removed_chains:
- if ch_name in ['-', '_', ' ']:
- chain_set.add('"%c"' % ch_name)
- else:
- chain_set.add(ch_name)
- view = ent.Select('cname!=%s' % ','.join(chain_set))
+ view = ent.Select('cname!=%s' % _FixSelectChainNames(removed_chains))
ent_new = mol.CreateEntityFromView(view, True)
ent_new.SetName(ent.GetName())
else:
@@ -1476,6 +1492,13 @@ def _GetAlignedResidues(qs_ent_1, qs_ent_2, chem_mapping, max_ca_per_chain,
:param chem_mapping: See :attr:`QSscorer.chem_mapping`
:param max_ca_per_chain: See :attr:`QSscorer.max_ca_per_chain_for_cm`
"""
+ # make sure name doesn't contain spaces and is unique
+ def _FixName(seq_name, seq_names):
+ # get rid of spaces and make it unique
+ seq_name = seq_name.replace(' ', '-')
+ while seq_name in seq_names:
+ seq_name += '-'
+ return seq_name
# resulting views into CA entities using CA chain sequences
ent_view_1 = qs_ent_1.ca_entity.CreateEmptyView()
ent_view_2 = qs_ent_2.ca_entity.CreateEmptyView()
@@ -1489,12 +1512,12 @@ def _GetAlignedResidues(qs_ent_1, qs_ent_2, chem_mapping, max_ca_per_chain,
seq_to_empty_view = dict()
for ch in group_1:
sequence = ca_chains_1[ch].Copy()
- sequence.name = qs_ent_1.GetName() + '.' + ch
+ sequence.name = _FixName(qs_ent_1.GetName() + '.' + ch, seq_to_empty_view)
seq_to_empty_view[sequence.name] = ent_view_1
seq_list.AddSequence(sequence)
for ch in group_2:
sequence = ca_chains_2[ch].Copy()
- sequence.name = qs_ent_2.GetName() + '.' + ch
+ sequence.name = _FixName(qs_ent_2.GetName() + '.' + ch, seq_to_empty_view)
seq_to_empty_view[sequence.name] = ent_view_2
seq_list.AddSequence(sequence)
alnc = ClustalW(seq_list, clustalw=clustalw_bin)
@@ -1564,8 +1587,8 @@ def _FindSymmetry(qs_ent_1, qs_ent_2, ent_to_cm_1, ent_to_cm_2, chem_mapping):
for _, symm_1, symm_2 in sorted(best_symm):
s1 = symm_1[0]
s2 = symm_2[0]
- group_1 = ent_to_cm_1.Select('cname=%s' % ','.join(s1))
- group_2 = ent_to_cm_2.Select('cname=%s' % ','.join(s2))
+ group_1 = ent_to_cm_1.Select('cname=%s' % _FixSelectChainNames(s1))
+ group_2 = ent_to_cm_2.Select('cname=%s' % _FixSelectChainNames(s2))
# check if by superposing a pair of chains within the symmetry group to
# superpose all chains within the symmetry group
# -> if successful, the symmetry groups are compatible
@@ -1944,7 +1967,8 @@ def _GetClosestChainInterface(ent, ref_chain, chains):
# inaccurate. Also it could be extracted from QSscoreEntity.contacts.
closest = []
for ch in chains:
- iface_view = ent.Select('cname=%s and 10 <> [cname=%s]' % (ref_chain, ch))
+ iface_view = ent.Select('cname="%s" and 10 <> [cname="%s"]' \
+ % (ref_chain, ch))
nr_res = iface_view.residue_count
closest.append((nr_res, ch))
closest_chain = max(closest)[1]
@@ -2156,8 +2180,8 @@ def _CheckClosedSymmetry(ent_1, ent_2, symm_1, symm_2, chem_mapping,
# to superpose the full oligomer (e.g. if some chains are open/closed)
for c1, c2 in itertools.product(g1, g2):
# get superposition transformation
- chain_1 = ent_1.Select('cname=%s' % c1)
- chain_2 = ent_2.Select('cname=%s' % c2)
+ chain_1 = ent_1.Select('cname="%s"' % c1)
+ chain_2 = ent_2.Select('cname="%s"' % c2)
res = mol.alg.SuperposeSVD(chain_1, chain_2, apply_transform=False)
# look for overlaps
mapping = _GetSuperpositionMapping(ent_1, ent_2, chem_mapping,
@@ -2261,8 +2285,8 @@ def _GetMappedRMSD(ent_1, ent_2, chain_mapping, transformation):
atoms = []
for c1, c2 in chain_mapping.iteritems():
# get views and atom counts
- chain_1 = ent_1.Select('cname=%s' % c1)
- chain_2 = ent_2.Select('cname=%s' % c2)
+ chain_1 = ent_1.Select('cname="%s"' % c1)
+ chain_2 = ent_2.Select('cname="%s"' % c2)
atom_count = chain_1.atom_count
if atom_count != chain_2.atom_count:
raise RuntimeError('Chains in _GetMappedRMSD must be perfectly aligned!')
@@ -2294,13 +2318,13 @@ class _CachedRMSD:
def GetChainView1(self, cname):
"""Get cached view on chain *cname* for :attr:`ent_1`."""
if cname not in self._chain_views_1:
- self._chain_views_1[cname] = self.ent_1.Select('cname=%s' % cname)
+ self._chain_views_1[cname] = self.ent_1.Select('cname="%s"' % cname)
return self._chain_views_1[cname]
def GetChainView2(self, cname):
"""Get cached view on chain *cname* for :attr:`ent_2`."""
if cname not in self._chain_views_2:
- self._chain_views_2[cname] = self.ent_2.Select('cname=%s' % cname)
+ self._chain_views_2[cname] = self.ent_2.Select('cname="%s"' % cname)
return self._chain_views_2[cname]
def GetSuperposition(self, c1, c2):
--
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