diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index f5e10d58c80624c56635169228f69cf557309919..932e00332bfd3956f806acd0a7be026def4e2b37 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -19,6 +19,14 @@ from ost import geom
from ost.mol.alg import lddt
from ost.mol.alg import qsscore
+def _CSel(ent, cnames):
+ """ Returns view with specified chains
+
+ Ensures that quotation marks are around chain names to not confuse
+ OST query language with weird special characters.
+ """
+ query = "cname=" + ','.join([mol.QueryQuoteName(cname) for cname in cnames])
+ return ent.Select(query)
class MappingResult:
""" Result object for the chain mapping functions in :class:`ChainMapper`
@@ -383,7 +391,9 @@ class ReprResult:
chain_rnums[chname].append(str(rnum))
chain_queries = list()
for k,v in chain_rnums.items():
- chain_queries.append(f"(cname={k} and rnum={','.join(v)})")
+ q = f"(cname={mol.QueryQuoteName(k)} and "
+ q += f"rnum={','.join(v)})"
+ chain_queries.append(q)
self._ost_query = " or ".join(chain_queries)
return self._ost_query
@@ -840,8 +850,8 @@ class ChainMapper:
for ref_ch, mdl_ch in zip(ref_group, mdl_group):
if ref_ch is not None and mdl_ch is not None:
aln = ref_mdl_alns[(ref_ch, mdl_ch)]
- aln.AttachView(0, self.target.Select(f"cname={ref_ch}"))
- aln.AttachView(1, mdl.Select(f"cname={mdl_ch}"))
+ aln.AttachView(0, _CSel(self.target, [ref_ch]))
+ aln.AttachView(1, _CSel(mdl, [mdl_ch]))
alns[(ref_ch, mdl_ch)] = aln
return MappingResult(self.target, mdl, self.chem_groups, one_to_one,
alns)
@@ -876,8 +886,8 @@ class ChainMapper:
for ref_ch, mdl_ch in zip(ref_group, mdl_group):
if ref_ch is not None and mdl_ch is not None:
aln = ref_mdl_alns[(ref_ch, mdl_ch)]
- aln.AttachView(0, self.target.Select(f"cname={ref_ch}"))
- aln.AttachView(1, mdl.Select(f"cname={mdl_ch}"))
+ aln.AttachView(0, _CSel(self.target, [ref_ch]))
+ aln.AttachView(1, _CSel(mdl, [mdl_ch]))
alns[(ref_ch, mdl_ch)] = aln
return MappingResult(self.target, mdl, self.chem_groups, mapping,
@@ -957,8 +967,8 @@ class ChainMapper:
for ref_ch, mdl_ch in zip(ref_group, mdl_group):
if ref_ch is not None and mdl_ch is not None:
aln = ref_mdl_alns[(ref_ch, mdl_ch)]
- aln.AttachView(0, self.target.Select(f"cname={ref_ch}"))
- aln.AttachView(1, mdl.Select(f"cname={mdl_ch}"))
+ aln.AttachView(0, _CSel(self.target, [ref_ch]))
+ aln.AttachView(1, _CSel(mdl, [mdl_ch]))
alns[(ref_ch, mdl_ch)] = aln
return MappingResult(self.target, mdl, self.chem_groups, one_to_one,
alns)
@@ -993,8 +1003,8 @@ class ChainMapper:
for ref_ch, mdl_ch in zip(ref_group, mdl_group):
if ref_ch is not None and mdl_ch is not None:
aln = ref_mdl_alns[(ref_ch, mdl_ch)]
- aln.AttachView(0, self.target.Select(f"cname={ref_ch}"))
- aln.AttachView(1, mdl.Select(f"cname={mdl_ch}"))
+ aln.AttachView(0, _CSel(self.target, [ref_ch]))
+ aln.AttachView(1, _CSel(mdl, [mdl_ch]))
alns[(ref_ch, mdl_ch)] = aln
return MappingResult(self.target, mdl, self.chem_groups, mapping,
@@ -1095,8 +1105,8 @@ class ChainMapper:
for ref_ch, mdl_ch in zip(ref_group, mdl_group):
if ref_ch is not None and mdl_ch is not None:
aln = ref_mdl_alns[(ref_ch, mdl_ch)]
- aln.AttachView(0, self.target.Select(f"cname={ref_ch}"))
- aln.AttachView(1, mdl.Select(f"cname={mdl_ch}"))
+ aln.AttachView(0, _CSel(self.target, [ref_ch]))
+ aln.AttachView(1, _CSel(mdl, [mdl_ch]))
alns[(ref_ch, mdl_ch)] = aln
return MappingResult(self.target, mdl, self.chem_groups, one_to_one,
alns)
@@ -1174,8 +1184,8 @@ class ChainMapper:
for ref_ch, mdl_ch in zip(ref_group, mdl_group):
if ref_ch is not None and mdl_ch is not None:
aln = ref_mdl_alns[(ref_ch, mdl_ch)]
- aln.AttachView(0, self.target.Select(f"cname={ref_ch}"))
- aln.AttachView(1, mdl.Select(f"cname={mdl_ch}"))
+ aln.AttachView(0, _CSel(self.target, [ref_ch]))
+ aln.AttachView(1, _CSel(mdl, [mdl_ch]))
alns[(ref_ch, mdl_ch)] = aln
return MappingResult(self.target, mdl, self.chem_groups, final_mapping,
@@ -1301,7 +1311,7 @@ class ChainMapper:
substructure_ref_mdl_alns = dict()
mdl_views = dict()
for ch in mdl.chains:
- mdl_views[ch.GetName()] = mdl.Select(f"cname={ch.GetName()}")
+ mdl_views[ch.GetName()] = _CSel(mdl, [ch.GetName()])
for chem_group, mapping in zip(substructure_chem_groups,
substructure_chem_mapping):
for ref_ch in chem_group:
@@ -1316,7 +1326,7 @@ class ChainMapper:
idx_in_seq = ref_seq.GetPos(idx)
tmp[idx_in_seq] = ref_seq[idx_in_seq]
ref_seq = seq.CreateSequence(ref_ch, ''.join(tmp))
- ref_seq.AttachView(substructure.Select(f"cname={ref_ch}"))
+ ref_seq.AttachView(_CSel(substructure, [ref_ch]))
mdl_seq = full_aln.GetSequence(1)
mdl_seq = seq.CreateSequence(mdl_seq.GetName(),
mdl_seq.GetString())
@@ -1491,7 +1501,7 @@ class ChainMapper:
s = ''.join([r.one_letter_code for r in ch.residues])
s = seq.CreateSequence(ch.GetName(), s)
- s.AttachView(view.Select(f"cname={ch.GetName()}"))
+ s.AttachView(_CSel(view, [ch.GetName()]))
if n_pep == n_res:
polypep_seqs.AddSequence(s)
elif n_nuc == n_res:
@@ -1509,7 +1519,7 @@ class ChainMapper:
# select for chains for which we actually extracted the sequence
chain_names = [s.GetAttachedView().chains[0].name for s in polypep_seqs]
chain_names += [s.GetAttachedView().chains[0].name for s in polynuc_seqs]
- view = view.Select(f"cname={','.join(chain_names)}")
+ view = _CSel(view, chain_names)
return (view, polypep_seqs, polynuc_seqs)
@@ -1976,14 +1986,15 @@ class _lDDTDecomposer:
def _SetupScorer(self):
for ch in self.ref.chains:
# Select everything close to that chain
- query = f"{self.inclusion_radius} <> [cname={ch.GetName()}] "
- query += f"and cname!={ch.GetName()}"
+ query = f"{self.inclusion_radius} <> "
+ query += f"[cname={mol.QueryQuoteName(ch.GetName())}] "
+ query += f"and cname!={mol.QueryQuoteName(ch.GetName())}"
for close_ch in self.ref.Select(query).chains:
k1 = (ch.GetName(), close_ch.GetName())
k2 = (close_ch.GetName(), ch.GetName())
if k1 not in self.interface_scorer and \
k2 not in self.interface_scorer:
- dimer_ref = self.ref.Select(f"cname={k1[0]},{k1[1]}")
+ dimer_ref = _CSel(self.ref, [k1[0], k1[1]])
s = lddt.lDDTScorer(dimer_ref, bb_only=True)
self.interface_scorer[k1] = s
self.interface_scorer[k2] = s
@@ -2005,7 +2016,7 @@ class _lDDTDecomposer:
# add any missing single chain scorer
for ch in self.ref.chains:
if ch.GetName() not in self.single_chain_scorer:
- single_chain_ref = self.ref.Select(f"cname={ch.GetName()}")
+ single_chain_ref = _CSel(self.ref, [ch.GetName()])
self.single_chain_scorer[ch.GetName()] = \
lddt.lDDTScorer(single_chain_ref, bb_only = True)
self.n += self.single_chain_scorer[ch.GetName()].n_distances
@@ -2044,7 +2055,7 @@ class _lDDTDecomposer:
if not (ref_ch, mdl_ch) in self.single_chain_cache:
alns = dict()
alns[mdl_ch] = self.ref_mdl_alns[(ref_ch, mdl_ch)]
- mdl_sel = self.mdl.Select(f"cname={mdl_ch}")
+ mdl_sel = _CSel(self.mdl, [mdl_ch])
s = self.single_chain_scorer[ref_ch]
_,_,_,conserved,_,_,_ = s.lDDT(mdl_sel,
residue_mapping=alns,
@@ -2062,7 +2073,7 @@ class _lDDTDecomposer:
alns = dict()
alns[mdl_ch1] = self.ref_mdl_alns[(ref_ch1, mdl_ch1)]
alns[mdl_ch2] = self.ref_mdl_alns[(ref_ch2, mdl_ch2)]
- mdl_sel = self.mdl.Select(f"cname={mdl_ch1},{mdl_ch2}")
+ mdl_sel = _CSel(self.mdl, [mdl_ch1, mdl_ch2])
s = self.interface_scorer[(ref_ch1, ref_ch2)]
_,_,_,conserved,_,_,_ = s.lDDT(mdl_sel,
residue_mapping=alns,
@@ -2110,7 +2121,8 @@ class _lDDTGreedySearcher(_lDDTDecomposer):
for ch in self.mdl.chains:
ch_name = ch.GetName()
self.mdl_neighbors[ch_name] = set()
- query = f"{d} <> [cname={ch_name}] and cname !={ch_name}"
+ query = f"{d} <> [cname={mol.QueryQuoteName(ch_name)}]"
+ query += f" and cname !={mol.QueryQuoteName(ch_name)}"
for close_ch in self.mdl.Select(query).chains:
self.mdl_neighbors[ch_name].add(close_ch.GetName())
@@ -2531,7 +2543,7 @@ class _QSScoreGreedySearcher(qsscore.QSScorer):
self.single_chain_scorer = dict()
self.single_chain_cache = dict()
for ch in self.ref.chains:
- single_chain_ref = self.ref.Select(f"cname={ch.GetName()}")
+ single_chain_ref = _CSel(self.ref, [ch.GetName()])
self.single_chain_scorer[ch.GetName()] = \
lddt.lDDTScorer(single_chain_ref, bb_only = True)
@@ -2539,7 +2551,7 @@ class _QSScoreGreedySearcher(qsscore.QSScorer):
if not (ref_ch, mdl_ch) in self.single_chain_cache:
alns = dict()
alns[mdl_ch] = self.ref_mdl_alns[(ref_ch, mdl_ch)]
- mdl_sel = self.mdl.Select(f"cname={mdl_ch}")
+ mdl_sel = _CSel(self.mdl, [mdl_ch])
s = self.single_chain_scorer[ref_ch]
_,_,_,conserved,_,_,_ = s.lDDT(mdl_sel,
residue_mapping=alns,
@@ -3309,7 +3321,7 @@ def _ExtractMSAPos(msa, s_idx, indices, view):
Indices refers to column indices in msa!
"""
s = msa.GetSequence(s_idx)
- s_v = view.Select(f"cname={s.GetName()}")
+ s_v = _CSel(view, [s.GetName()])
# sanity check
assert(len(s.GetGaplessString()) == len(s_v.residues))
diff --git a/modules/mol/alg/pymod/lddt.py b/modules/mol/alg/pymod/lddt.py
index 92f41ec4cc97e79bf69df6b63131b1ba913edd6d..0f464d02bd28a330473191472c44275df9cc0263 100644
--- a/modules/mol/alg/pymod/lddt.py
+++ b/modules/mol/alg/pymod/lddt.py
@@ -682,8 +682,8 @@ class lDDTScorer:
ch_name = chain.GetName()
if ch_name not in chain_mapping:
sm = self.symmetry_settings
- dummy_scorer = lDDTScorer(model.Select("cname="+ch_name),
- self.compound_lib,
+ mdl_sel = model.Select(f"cname={mol.QueryQuoteName(ch_name)}")
+ dummy_scorer = lDDTScorer(mdl_sel, self.compound_lib,
symmetry_settings = sm,
inclusion_radius = self.inclusion_radius,
bb_only = self.bb_only)