diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py index 4cfcc614da4fa81dba62c2ba10343fe7beaa06c5..42acf8554120d20cce4b7288fdca821dacd04c42 100644 --- a/modules/mol/alg/pymod/scoring.py +++ b/modules/mol/alg/pymod/scoring.py @@ -1339,14 +1339,14 @@ 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='{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='{cname}'")) mdl_seqs[ch.GetName()] = s alns = list() @@ -1738,7 +1738,7 @@ 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='{cname}' and 8 <> [cname!='{cname}'])") result[cname] = [r.GetNumber() for r in sel.residues] return result @@ -1805,7 +1805,7 @@ 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='{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}])" mdl_patch_one = self.model.CreateEmptyView() @@ -1818,7 +1818,7 @@ 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!='{mdl_ch}')") close_stuff = sel.FindWithin(r_pos, 8) min_pos = None min_dist = 42.0 @@ -1829,9 +1829,9 @@ 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!='{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='{mdl_ch}'])" mdl_patch_two = self.model.CreateEmptyView() sel = repr_mdl.Select(" and ".join([q1, q2])) for r in sel.residues: @@ -2082,8 +2082,8 @@ 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='{ref_ch}'") + mdl_view = mdl.Select(f"cname='{mdl_ch}'") aln.AttachView(0, trg_view) aln.AttachView(1, mdl_view) alns[(ref_ch, mdl_ch)] = aln