diff --git a/modules/bindings/pymod/dockq.py b/modules/bindings/pymod/dockq.py
index ff920f627e7f6332986f0a0d093e5a2face5641d..f096b868ed77251334fd25d4728a2d70b0270bde 100644
--- a/modules/bindings/pymod/dockq.py
+++ b/modules/bindings/pymod/dockq.py
@@ -91,10 +91,6 @@ def _Setup(mdl, ref, mdl_ch1, mdl_ch2, ref_ch1, ref_ch2):
# Interface with more chains...
raise NotImplementedError("DockQ computations beyond two interacting "
"chains has not been properly tested...")
- #mdl_chain_names = mdl_ch1 + mdl_ch2
- #ref_chain_names = ref_ch1 + ref_ch2
- #mdl_to_dump = mdl_to_dump.Select(f"cname={','.join(mdl_chain_names)}")
- #ref_to_dump = ref_to_dump.Select(f"cname={','.join(ref_chain_names)}")
# first write structures to string, only create a tmpdir and the actual
# files if this succeeds
diff --git a/modules/mol/alg/pymod/contact_score.py b/modules/mol/alg/pymod/contact_score.py
index b5ddeb10b7d3d3b7072e2a9bbbac28b9a78d9c4b..5dd7e48a8f5ba71dd3d4624af06688650783e275 100644
--- a/modules/mol/alg/pymod/contact_score.py
+++ b/modules/mol/alg/pymod/contact_score.py
@@ -200,9 +200,9 @@ class ContactEntity:
for cname in self.chain_names:
# q1 selects stuff in current chain that is close to any other chain
- q1 = f"cname={cname} and {self.contact_d} <> [cname!={cname}]"
+ q1 = f"cname={mol.QueryQuoteName(cname)} and {self.contact_d} <> [cname!={mol.QueryQuoteName(cname)}]"
# q2 selects stuff in other chains that is close to current chain
- q2 = f"cname!={cname} and {self.contact_d} <> [cname={cname}]"
+ q2 = f"cname!={mol.QueryQuoteName(cname)} and {self.contact_d} <> [cname={mol.QueryQuoteName(cname)}]"
v1 = self.view.Select(q1)
v2 = self.view.Select(q2)
v1_p = [geom.Vec3List([a.pos for a in r.atoms]) for r in v1.residues]
diff --git a/modules/mol/alg/pymod/dockq.py b/modules/mol/alg/pymod/dockq.py
index d3695c1de54ea43bda7cb9a61af332b4dca9023f..2db14d1f6aeafed2bb182ed7760aa4388c8c9ef7 100644
--- a/modules/mol/alg/pymod/dockq.py
+++ b/modules/mol/alg/pymod/dockq.py
@@ -44,11 +44,11 @@ def _PreprocessStructures(mdl, ref, mdl_ch1, mdl_ch2, ref_ch1, ref_ch2,
tmp = ch1_aln.GetSequence(0)
ref_s1 = seq.CreateSequence(tmp.GetName(), str(tmp))
ref_s1.SetOffset(tmp.GetOffset())
- ref_s1.AttachView(ref.Select(f"cname={ref_ch1}"))
+ ref_s1.AttachView(ref.Select(f"cname={mol.QueryQuoteName(ref_ch1)}"))
tmp = ch1_aln.GetSequence(1)
mdl_s1 = seq.CreateSequence(tmp.GetName(), str(tmp))
mdl_s1.SetOffset(tmp.GetOffset())
- mdl_s1.AttachView(mdl.Select(f"cname={mdl_ch1}"))
+ mdl_s1.AttachView(mdl.Select(f"cname={mol.QueryQuoteName(mdl_ch1)}"))
new_ch1_aln = seq.CreateAlignment(ref_s1, mdl_s1)
for col in new_ch1_aln:
if col[0] != '-' and col[1] != '-':
@@ -69,11 +69,11 @@ def _PreprocessStructures(mdl, ref, mdl_ch1, mdl_ch2, ref_ch1, ref_ch2,
tmp = ch2_aln.GetSequence(0)
ref_s2 = seq.CreateSequence(tmp.GetName(), str(tmp))
ref_s2.SetOffset(tmp.GetOffset())
- ref_s2.AttachView(ref.Select(f"cname={ref_ch2}"))
+ ref_s2.AttachView(ref.Select(f"cname={mol.QueryQuoteName(ref_ch2)}"))
tmp = ch2_aln.GetSequence(1)
mdl_s2 = seq.CreateSequence(tmp.GetName(), str(tmp))
mdl_s2.SetOffset(tmp.GetOffset())
- mdl_s2.AttachView(mdl.Select(f"cname={mdl_ch2}"))
+ mdl_s2.AttachView(mdl.Select(f"cname={mol.QueryQuoteName(mdl_ch2)}"))
new_ch2_aln = seq.CreateAlignment(ref_s2, mdl_s2)
for col in new_ch2_aln:
if col[0] != '-' and col[1] != '-':
@@ -92,7 +92,7 @@ def _PreprocessStructures(mdl, ref, mdl_ch1, mdl_ch2, ref_ch1, ref_ch2,
dockq_idx += 1
else:
# go by residue numbers
- for mdl_r in mdl.Select(f"cname={mdl_ch1}").residues:
+ for mdl_r in mdl.Select(f"cname={mol.QueryQuoteName(mdl_ch1)}").residues:
ref_r = ref.FindResidue(ref_ch1, mdl_r.GetNumber())
if ref_r.IsValid():
ref_r.SetIntProp("dockq_idx", dockq_idx)
@@ -100,7 +100,7 @@ def _PreprocessStructures(mdl, ref, mdl_ch1, mdl_ch2, ref_ch1, ref_ch2,
ref_r.SetIntProp("dockq_mapped", 1)
mdl_r.SetIntProp("dockq_mapped", 1)
dockq_idx += 1
- for mdl_r in mdl.Select(f"cname={mdl_ch2}").residues:
+ for mdl_r in mdl.Select(f"cname={mol.QueryQuoteName(mdl_ch2)}").residues:
ref_r = ref.FindResidue(ref_ch2, mdl_r.GetNumber())
if ref_r.IsValid():
ref_r.SetIntProp("dockq_idx", dockq_idx)
@@ -124,8 +124,8 @@ def _PreprocessStructures(mdl, ref, mdl_ch1, mdl_ch2, ref_ch1, ref_ch2,
dockq_idx += 1
def _GetContacts(ent, ch1, ch2, dist_thresh):
- int1 = ent.Select(f"cname={ch1} and {dist_thresh} <> [cname={ch2}]")
- int2 = ent.Select(f"cname={ch2} and {dist_thresh} <> [cname={ch1}]")
+ int1 = ent.Select(f"cname={mol.QueryQuoteName(ch1)} and {dist_thresh} <> [cname={mol.QueryQuoteName(ch2)}]")
+ int2 = ent.Select(f"cname={mol.QueryQuoteName(ch2)} and {dist_thresh} <> [cname={mol.QueryQuoteName(ch1)}]")
contacts = set()
int1_p = [geom.Vec3List([a.pos for a in r.atoms]) for r in int1.residues]
int2_p = [geom.Vec3List([a.pos for a in r.atoms]) for r in int2.residues]
@@ -160,8 +160,8 @@ def _RMSDScores(mdl, ref, mdl_ch1, mdl_ch2, ref_ch1, ref_ch2, dist_thresh=10.0):
sup_atoms = ['CA','C','N','O']
# make mapped residues accessible by the dockq_idx property
- mapped_mdl = mdl.Select(f"cname={mdl_ch1},{mdl_ch2} and grdockq_mapped=1")
- mapped_ref = ref.Select(f"cname={ref_ch1},{ref_ch2} and grdockq_mapped=1")
+ mapped_mdl = mdl.Select(f"cname={mol.QueryQuoteName(mdl_ch1)},{mol.QueryQuoteName(mdl_ch2)} and grdockq_mapped=1")
+ mapped_ref = ref.Select(f"cname={mol.QueryQuoteName(ref_ch1)},{mol.QueryQuoteName(ref_ch2)} and grdockq_mapped=1")
ch = mapped_mdl.FindChain(mdl_ch1)
mdl_ch1_residues = {r.GetIntProp("dockq_idx"): r for r in ch.residues}
ch = mapped_mdl.FindChain(mdl_ch2)
@@ -173,8 +173,8 @@ def _RMSDScores(mdl, ref, mdl_ch1, mdl_ch2, ref_ch1, ref_ch2, dist_thresh=10.0):
# iRMSD
#######
- int1 = ref.Select(f"cname={ref_ch1} and {dist_thresh} <> [cname={ref_ch2}]")
- int2 = ref.Select(f"cname={ref_ch2} and {dist_thresh} <> [cname={ref_ch1}]")
+ int1 = ref.Select(f"cname={mol.QueryQuoteName(ref_ch1)} and {dist_thresh} <> [cname={mol.QueryQuoteName(ref_ch2)}]")
+ int2 = ref.Select(f"cname={mol.QueryQuoteName(ref_ch2)} and {dist_thresh} <> [cname={mol.QueryQuoteName(ref_ch1)}]")
ref_pos = geom.Vec3List()
mdl_pos = geom.Vec3List()
for r in int1.residues:
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index b56e2dbe61f98cc0b5b10393c4ed3938198b5cdd..f94e1740edbc4bf6a455276d569a54f79a19b2e8 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -1537,8 +1537,8 @@ class LigandScorer:
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)]
- trg_view = chain_mapper.target.Select(f"cname={ref_ch}")
- mdl_view = mdl.Select(f"cname={mdl_ch}")
+ trg_view = chain_mapper.target.Select(f"cname={mol.QueryQuoteName(ref_ch)}")
+ mdl_view = mdl.Select(f"cname={mol.QueryQuoteName(mdl_ch)}")
aln.AttachView(0, trg_view)
aln.AttachView(1, mdl_view)
alns[(ref_ch, mdl_ch)] = aln
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index 0f8e3ee560849f6fb60d60c8a07f663e8a8fe822..d0d3cf84de72cdcbda735b59362374968dcd6bd3 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -1368,14 +1368,14 @@ class Scorer:
cname = ch.GetName()
s = ''.join([r.one_letter_code for r in ch.residues])
s = seq.CreateSequence(ch.GetName(), s)
- s.AttachView(target.Select(f"cname='{cname}'"))
+ s.AttachView(target.Select(f"cname={mol.QueryQuoteName(cname)}"))
trg_seqs[ch.GetName()] = s
mdl_seqs = dict()
for ch in model.chains:
cname = ch.GetName()
s = ''.join([r.one_letter_code for r in ch.residues])
s = seq.CreateSequence(cname, s)
- s.AttachView(model.Select(f"cname='{cname}'"))
+ s.AttachView(model.Select(f"cname={mol.QueryQuoteName(cname)}"))
mdl_seqs[ch.GetName()] = s
alns = list()
@@ -1767,7 +1767,7 @@ class Scorer:
result = {ch.GetName(): list() for ch in ent.chains}
for ch in ent.chains:
cname = ch.GetName()
- sel = repr_ent.Select(f"(cname='{cname}' and 8 <> [cname!='{cname}'])")
+ sel = repr_ent.Select(f"(cname={mol.QueryQuoteName(cname)} and 8 <> [cname!={mol.QueryQuoteName(cname)}])")
result[cname] = [r.GetNumber() for r in sel.residues]
return result
@@ -1834,9 +1834,9 @@ class Scorer:
# => all residues within 8A of r and within 12A of any other chain
# q1 selects for everything in same chain and within 8A of r_pos
- q1 = f"(cname='{mdl_ch}' and 8 <> {{{r_pos[0]},{r_pos[1]},{r_pos[2]}}})"
+ q1 = f"(cname={mol.QueryQuoteName(mdl_ch)} and 8 <> {{{r_pos[0]},{r_pos[1]},{r_pos[2]}}})"
# q2 selects for everything within 12A of any other chain
- q2 = f"(12 <> [cname!={mdl_ch}])"
+ q2 = f"(12 <> [cname!={mol.QueryQuoteName(mdl_ch)}])"
mdl_patch_one = self.model.CreateEmptyView()
sel = repr_mdl.Select(" and ".join([q1, q2]))
for r in sel.residues:
@@ -1847,7 +1847,7 @@ class Scorer:
# the closest residue to r is identified in any other chain, and the
# patch is filled with residues that are within 8A of that residue and
# within 12A of chain from r
- sel = repr_mdl.Select(f"(cname!='{mdl_ch}')")
+ sel = repr_mdl.Select(f"(cname!={mol.QueryQuoteName(mdl_ch)})")
close_stuff = sel.FindWithin(r_pos, 8)
min_pos = None
min_dist = 42.0
@@ -1858,9 +1858,9 @@ class Scorer:
min_dist = dist
# q1 selects for everything not in mdl_ch but within 8A of min_pos
- q1 = f"(cname!='{mdl_ch}' and 8 <> {{{min_pos[0]},{min_pos[1]},{min_pos[2]}}})"
+ q1 = f"(cname!={mol.QueryQuoteName(mdl_ch)} and 8 <> {{{min_pos[0]},{min_pos[1]},{min_pos[2]}}})"
# q2 selects for everything within 12A of mdl_ch
- q2 = f"(12 <> [cname='{mdl_ch}'])"
+ q2 = f"(12 <> [cname={mol.QueryQuoteName(mdl_ch)}])"
mdl_patch_two = self.model.CreateEmptyView()
sel = repr_mdl.Select(" and ".join([q1, q2]))
for r in sel.residues:
@@ -2111,8 +2111,8 @@ class Scorer:
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)]
- trg_view = chain_mapper.target.Select(f"cname='{ref_ch}'")
- mdl_view = mdl.Select(f"cname='{mdl_ch}'")
+ trg_view = chain_mapper.target.Select(f"cname={mol.QueryQuoteName(ref_ch)}")
+ mdl_view = mdl.Select(f"cname={mol.QueryQuoteName(mdl_ch)}")
aln.AttachView(0, trg_view)
aln.AttachView(1, mdl_view)
alns[(ref_ch, mdl_ch)] = aln
diff --git a/modules/mol/alg/src/biounit.cc b/modules/mol/alg/src/biounit.cc
index 72e2cc97034f2fa48a78e980797bc78e3bc51aa2..e21f0a58bc5cb6a2855e6f1f37af198f36196b22 100644
--- a/modules/mol/alg/src/biounit.cc
+++ b/modules/mol/alg/src/biounit.cc
@@ -255,9 +255,9 @@ ost::mol::EntityHandle CreateBU(const ost::mol::EntityHandle& asu,
// derive all bonds related to that chain_intvl
// potentially also interchain bonds
std::stringstream query_ss;
- query_ss << "cname=" << au_chains[chain_intvl][0];
+ query_ss << "cname=" << mol::QueryQuoteName(au_chains[chain_intvl][0]);
for(uint i = 1; i < au_chains[chain_intvl].size(); ++i) {
- query_ss << ',' << au_chains[chain_intvl][i];
+ query_ss << ',' << mol::QueryQuoteName(au_chains[chain_intvl][i]);
}
ost::mol::EntityView asu_view = asu.Select(query_ss.str());
const ost::mol::BondHandleList& bond_list = asu_view.GetBondList();