diff --git a/actions/ost-compare-ligand-structures b/actions/ost-compare-ligand-structures
index 2801c7319a75ee86e612b683b4ef43bfd3b3a9f5..cb5527b9e781ee6297c935f4cd1d52bfc358fb26 100644
--- a/actions/ost-compare-ligand-structures
+++ b/actions/ost-compare-ligand-structures
@@ -68,10 +68,10 @@ keys:
in chain mapping. That is 1) pass the same size threshold as for chem_groups
2) can be aligned to any of the chem groups with a sequence identity
threshold that can be controlled by --chem-map-seqid-thresh.
- * "unmapped_mdl_chains": Model chains that could be considered in chain mapping,
- i.e. are long enough, but could not be mapped to any chem group.
- Depends on --chem-map-seqid-thresh. A mapping for each model chain can be
- enforced by setting it to 0.
+ * "mdl_chains_without_chem_mapping": Model chains that could be considered in
+ chain mapping, i.e. are long enough, but could not be mapped to any chem
+ group. Depends on --chem-map-seqid-thresh. A mapping for each model chain can
+ be enforced by setting it to 0.
* "status": SUCCESS if everything ran through. In case of failure, the only
content of the JSON output will be \"status\" set to FAILURE and an
additional key: "traceback".
@@ -903,7 +903,7 @@ def _Process(model, model_ligands, reference, reference_ligands, args):
# add info relevant for chain mapping and cleanup
out["chem_groups"] = scorer._chain_mapper.chem_groups
out["chem_mapping"] = scorer._chem_mapping
- out["unmapped_mdl_chains"] = scorer._unmapped_mdl_chains
+ out["mdl_chains_without_chem_mapping"] = scorer._mdl_chains_without_chem_mapping
out["model_cleanup_log"] = scorer.model_cleanup_log
out["reference_cleanup_log"] = scorer.target_cleanup_log
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 025a3737f27ca9030080c7492ebc8a8e56a62c24..ec843dba9c75eb81f2c568efe90e13d14d7cf05c 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -33,14 +33,14 @@ comparison:
in chain mapping. That is 1) pass the same size threshold as fo chem_groups
2) can be aligned to any of the chem groups with a sequence identity
threshold that can be controlled by --chem-map-seqid-thresh.
- * "unmapped_mdl_chains": Model chains that could be considered in chain mapping,
- i.e. are long enough, but could not be mapped to any chem group.
- Depends on --chem-map-seqid-thresh. A mapping for each model chain can be
- enforced by setting it to 0.
+ * "mdl_chains_without_chem_mapping": Model chains that could be considered in
+ chain mapping, i.e. are long enough, but could not be mapped to any chem
+ group. Depends on --chem-map-seqid-thresh. A mapping for each model chain can
+ be enforced by setting it to 0.
* "chain_mapping": A dictionary with reference chain names as keys and the
mapped model chain names as values. Missing chains are either not mapped
(but present in "chem_groups", "chem_mapping"), were not mapped to any chem
- group (present in "unmapped_mdl_chains") or were not considered in
+ group (present in "mdl_chains_without_chem_mapping") or were not considered in
chain mapping (short peptides etc.)
* "aln": Pairwise sequence alignment for each pair of mapped chains in fasta
format.
@@ -994,7 +994,8 @@ def _Process(model, reference, args, model_format, reference_format):
out["model_chains"] = [ch.GetName() for ch in scorer.model.chains]
out["chem_groups"] = scorer.chain_mapper.chem_groups
out["chem_mapping"] = scorer.mapping.chem_mapping
- out["unmapped_mdl_chains"] = scorer.mapping.unmapped_mdl_chains
+ out["mdl_chains_without_chem_mapping"] = \
+ scorer.mapping.mdl_chains_without_chem_mapping
out["chain_mapping"] = scorer.mapping.GetFlatMapping()
out["aln"] = [_AlnToFastaStr(aln) for aln in scorer.aln]
out["inconsistent_residues"] = ir
diff --git a/modules/doc/actions.rst b/modules/doc/actions.rst
index 09913c44a5b41f5f8094363e72d47dd0c36ddcdd..1610738437c33a857d52025858714e840e4a67bb 100644
--- a/modules/doc/actions.rst
+++ b/modules/doc/actions.rst
@@ -92,14 +92,14 @@ Details on the usage (output of ``ost compare-structures --help``):
in chain mapping. That is 1) pass the same size threshold as fo chem_groups
2) can be aligned to any of the chem groups with a sequence identity
threshold that can be controlled by --chem-map-seqid-thresh.
- * "unmapped_mdl_chains": Model chains that could be considered in chain mapping,
+ * "mdl_chains_without_chem_mapping": Model chains that could be considered in chain mapping,
i.e. are long enough, but could not be mapped to any chem group.
Depends on --chem-map-seqid-thresh. A mapping for each model chain can be
enforced by setting it to 0.
* "chain_mapping": A dictionary with reference chain names as keys and the
mapped model chain names as values. Missing chains are either not mapped
(but present in "chem_groups", "chem_mapping"), were not mapped to any chem
- group (present in "unmapped_mdl_chains") or were not considered in
+ group (present in "mdl_chains_without_chem_mapping") or were not considered in
chain mapping (short peptides etc.)
* "aln": Pairwise sequence alignment for each pair of mapped chains in fasta
format.
@@ -613,7 +613,7 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
in chain mapping. That is 1) pass the same size threshold as for chem_groups
2) can be aligned to any of the chem groups with a sequence identity
threshold that can be controlled by --chem-map-seqid-thresh.
- * "unmapped_mdl_chains": Model chains that could be considered in chain mapping,
+ * "mdl_chains_without_chem_mapping": Model chains that could be considered in chain mapping,
i.e. are long enough, but could not be mapped to any chem group.
Depends on --chem-map-seqid-thresh. A mapping for each model chain can be
enforced by setting it to 0.
diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index 16691471e1a230762b484a385e83ed6cd5a4d079..dec705c52aa752150c5bd08aff373f39f03d8e74 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -37,12 +37,12 @@ class MappingResult:
such objects yourself.
"""
def __init__(self, target, model, chem_groups, chem_mapping,
- unmapped_mdl_chains, mapping, alns, opt_score=None):
+ mdl_chains_without_chem_mapping, mapping, alns, opt_score=None):
self._target = target
self._model = model
self._chem_groups = chem_groups
self._chem_mapping = chem_mapping
- self._unmapped_mdl_chains = unmapped_mdl_chains
+ self._mdl_chains_without_chem_mapping = mdl_chains_without_chem_mapping
self._mapping = mapping
self._alns = alns
self._opt_score = opt_score
@@ -85,14 +85,14 @@ class MappingResult:
return self._chem_mapping
@property
- def unmapped_mdl_chains(self):
+ def mdl_chains_without_chem_mapping(self):
""" Model chains that cannot be mapped to :attr:`chem_groups`
Depends on parameterization of :class:`ChainMapper`
:class:`list` of class:`str` (chain names)
"""
- return self._unmapped_mdl_chains
+ return self._mdl_chains_without_chem_mapping
@property
def mapping(self):
@@ -776,7 +776,7 @@ class ChainMapper:
"""
mdl, mdl_pep_seqs, mdl_nuc_seqs = self.ProcessStructure(model)
mapping = [list() for x in self.chem_groups]
- unmapped_mdl_chains = list()
+ mdl_chains_without_chem_mapping = list()
alns = [seq.AlignmentList() for x in self.chem_groups]
for s in mdl_pep_seqs:
@@ -786,7 +786,7 @@ class ChainMapper:
seq_id_thr = self.mdl_map_pep_seqid_thr,
min_aln_length = self.min_pep_length)
if idx is None:
- unmapped_mdl_chains.append(s.GetName())
+ mdl_chains_without_chem_mapping.append(s.GetName())
else:
mapping[idx].append(s.GetName())
alns[idx].append(aln)
@@ -798,12 +798,12 @@ class ChainMapper:
seq_id_thr = self.mdl_map_nuc_seqid_thr,
min_aln_length = self.min_nuc_length)
if idx is None:
- unmapped_mdl_chains.append(s.GetName())
+ mdl_chains_without_chem_mapping.append(s.GetName())
else:
mapping[idx].append(s.GetName())
alns[idx].append(aln)
- return (mapping, alns, unmapped_mdl_chains, mdl)
+ return (mapping, alns, mdl_chains_without_chem_mapping, mdl)
def GetlDDTMapping(self, model, inclusion_radius=15.0,
@@ -893,10 +893,10 @@ class ChainMapper:
raise RuntimeError(f"Strategy must be in {strategies}")
if chem_mapping_result is None:
- chem_mapping, chem_group_alns, unmapped_mdl_chains, mdl = \
+ chem_mapping, chem_group_alns, mdl_chains_without_chem_mapping, mdl = \
self.GetChemMapping(model)
else:
- chem_mapping, chem_group_alns, unmapped_mdl_chains, mdl = \
+ chem_mapping, chem_group_alns, mdl_chains_without_chem_mapping, mdl = \
chem_mapping_result
ref_mdl_alns = _GetRefMdlAlns(self.chem_groups,
@@ -914,7 +914,7 @@ class ChainMapper:
aln = ref_mdl_alns[(ref_ch, mdl_ch)]
alns[(ref_ch, mdl_ch)] = aln
return MappingResult(self.target, mdl, self.chem_groups, chem_mapping,
- unmapped_mdl_chains, one_to_one, alns)
+ mdl_chains_without_chem_mapping, one_to_one, alns)
if strategy == "heuristic":
if _NMappingsWithin(self.chem_groups, chem_mapping,
@@ -956,7 +956,7 @@ class ChainMapper:
alns[(ref_ch, mdl_ch)] = aln
return MappingResult(self.target, mdl, self.chem_groups, chem_mapping,
- unmapped_mdl_chains, mapping, alns,
+ mdl_chains_without_chem_mapping, mapping, alns,
opt_score = opt_lddt)
@@ -1031,10 +1031,10 @@ class ChainMapper:
raise RuntimeError(f"strategy must be {strategies}")
if chem_mapping_result is None:
- chem_mapping, chem_group_alns, unmapped_mdl_chains, mdl = \
+ chem_mapping, chem_group_alns, mdl_chains_without_chem_mapping, mdl = \
self.GetChemMapping(model)
else:
- chem_mapping, chem_group_alns, unmapped_mdl_chains, mdl = \
+ chem_mapping, chem_group_alns, mdl_chains_without_chem_mapping, mdl = \
chem_mapping_result
ref_mdl_alns = _GetRefMdlAlns(self.chem_groups,
self.chem_group_alignments,
@@ -1050,7 +1050,7 @@ class ChainMapper:
aln = ref_mdl_alns[(ref_ch, mdl_ch)]
alns[(ref_ch, mdl_ch)] = aln
return MappingResult(self.target, mdl, self.chem_groups, chem_mapping,
- unmapped_mdl_chains, one_to_one, alns)
+ mdl_chains_without_chem_mapping, one_to_one, alns)
if strategy == "heuristic":
if _NMappingsWithin(self.chem_groups, chem_mapping,
@@ -1093,7 +1093,7 @@ class ChainMapper:
alns[(ref_ch, mdl_ch)] = aln
return MappingResult(self.target, mdl, self.chem_groups, chem_mapping,
- unmapped_mdl_chains, mapping, alns,
+ mdl_chains_without_chem_mapping, mapping, alns,
opt_score = opt_qsscore)
def GetRMSDMapping(self, model, strategy = "heuristic", subsampling=50,
@@ -1146,10 +1146,10 @@ class ChainMapper:
raise RuntimeError(f"strategy must be {strategies}")
if chem_mapping_result is None:
- chem_mapping, chem_group_alns, unmapped_mdl_chains, mdl = \
+ chem_mapping, chem_group_alns, mdl_chains_without_chem_mapping, mdl = \
self.GetChemMapping(model)
else:
- chem_mapping, chem_group_alns, unmapped_mdl_chains, mdl = \
+ chem_mapping, chem_group_alns, mdl_chains_without_chem_mapping, mdl = \
chem_mapping_result
ref_mdl_alns = _GetRefMdlAlns(self.chem_groups,
self.chem_group_alignments,
@@ -1166,7 +1166,7 @@ class ChainMapper:
aln = ref_mdl_alns[(ref_ch, mdl_ch)]
alns[(ref_ch, mdl_ch)] = aln
return MappingResult(self.target, mdl, self.chem_groups, chem_mapping,
- unmapped_mdl_chains, one_to_one, alns)
+ mdl_chains_without_chem_mapping, one_to_one, alns)
trg_group_pos, mdl_group_pos = _GetRefPos(self.target, mdl,
self.chem_group_alignments,
@@ -1237,7 +1237,7 @@ class ChainMapper:
alns[(ref_ch, mdl_ch)] = aln
return MappingResult(self.target, mdl, self.chem_groups, chem_mapping,
- unmapped_mdl_chains, final_mapping, alns)
+ mdl_chains_without_chem_mapping, final_mapping, alns)
def GetMapping(self, model, n_max_naive = 40320):
""" Convenience function to get mapping with currently preferred method
@@ -1365,10 +1365,10 @@ class ChainMapper:
# perform mapping and alignments on full structures
if chem_mapping_result is None:
- chem_mapping, chem_group_alns, unmapped_mdl_chains, mdl = \
+ chem_mapping, chem_group_alns, mdl_chains_without_chem_mapping, mdl = \
self.GetChemMapping(model)
else:
- chem_mapping, chem_group_alns, unmapped_mdl_chains, mdl = \
+ chem_mapping, chem_group_alns, mdl_chains_without_chem_mapping, mdl = \
chem_mapping_result
ref_mdl_alns = _GetRefMdlAlns(self.chem_groups,
self.chem_group_alignments,
@@ -1529,7 +1529,7 @@ class ChainMapper:
:attr:`chem_groups`
:type model: :class:`ost.mol.EntityView`/:class:`ost.mol.EntityHandle`
"""
- chem_mapping, chem_group_alns, unmapped_mdl_chains, mdl = \
+ chem_mapping, chem_group_alns, mdl_chains_without_chem_mapping, mdl = \
self.GetChemMapping(model)
return _NMappings(self.chem_groups, chem_mapping)
diff --git a/modules/mol/alg/pymod/ligand_scoring_base.py b/modules/mol/alg/pymod/ligand_scoring_base.py
index f676463bdd3761e8579f9ebe50f48cd750a6417b..cf0a73f498dae5e42381fd1372983333f4a29cd1 100644
--- a/modules/mol/alg/pymod/ligand_scoring_base.py
+++ b/modules/mol/alg/pymod/ligand_scoring_base.py
@@ -502,7 +502,7 @@ class LigandScorer:
self.__chem_mapping = None
self.__chem_group_alns = None
self.__ref_mdl_alns = None
- self.__unmapped_mdl_chains = None
+ self.__mdl_chains_without_chem_mapping = None
self.__chain_mapping_mdl = None
# keep track of states
@@ -1165,7 +1165,7 @@ class LigandScorer:
def _chem_mapping(self):
if self.__chem_mapping is None:
self.__chem_mapping, self.__chem_group_alns, \
- self.__unmapped_mdl_chains, self.__chain_mapping_mdl = \
+ self.__mdl_chains_without_chem_mapping, self.__chain_mapping_mdl = \
self._chain_mapper.GetChemMapping(self.model)
return self.__chem_mapping
@@ -1173,7 +1173,7 @@ class LigandScorer:
def _chem_group_alns(self):
if self.__chem_group_alns is None:
self.__chem_mapping, self.__chem_group_alns, \
- self.__unmapped_mdl_chains, self.__chain_mapping_mdl = \
+ self.__mdl_chains_without_chem_mapping, self.__chain_mapping_mdl = \
self._chain_mapper.GetChemMapping(self.model)
return self.__chem_group_alns
@@ -1192,17 +1192,17 @@ class LigandScorer:
if self.__chain_mapping_mdl is None:
with _SinkVerbosityLevel():
self.__chem_mapping, self.__chem_group_alns, \
- self.__unmapped_mdl_chains, self.__chain_mapping_mdl = \
+ self.__mdl_chains_without_chem_mapping, self.__chain_mapping_mdl = \
self._chain_mapper.GetChemMapping(self.model)
return self.__chain_mapping_mdl
@property
- def _unmapped_mdl_chains(self):
- if self.__unmapped_mdl_chains is None:
+ def _mdl_chains_without_chem_mapping(self):
+ if self.__mdl_chains_without_chem_mapping is None:
self.__chem_mapping, self.__chem_group_alns, \
- self.__unmapped_mdl_chains, self.__chain_mapping_mdl = \
+ self.__mdl_chains_without_chem_mapping, self.__chain_mapping_mdl = \
self._chain_mapper.GetChemMapping(self.model)
- return self.__unmapped_mdl_chains
+ return self.__mdl_chains_without_chem_mapping
def _compute_scores(self):
"""
diff --git a/modules/mol/alg/pymod/ligand_scoring_scrmsd.py b/modules/mol/alg/pymod/ligand_scoring_scrmsd.py
index b14c68b7c6174fe8999d51c749937c8477012687..699642c8ce3b16fa3074238a87e017698f897f45 100644
--- a/modules/mol/alg/pymod/ligand_scoring_scrmsd.py
+++ b/modules/mol/alg/pymod/ligand_scoring_scrmsd.py
@@ -369,7 +369,7 @@ class SCRMSDScorer(ligand_scoring_base.LigandScorer):
return (self._get_repr_input[mdl_ligand.hash_code][1],
self._chem_group_alns,
- self._unmapped_mdl_chains,
+ self._mdl_chains_without_chem_mapping,
self._get_repr_input[mdl_ligand.hash_code][0])
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index 62a0d92be481cd6d5d5b9017a5fe76a44c3ca799..9f88d18fc2db53b835d2a2e2560fff042ea55fce 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -3224,7 +3224,7 @@ class Scorer:
LogInfo("Setting custom chain mapping")
chain_mapper = self.chain_mapper
- chem_mapping, chem_group_alns, unmapped_mdl_chains, mdl = \
+ chem_mapping, chem_group_alns, mdl_chains_without_chem_mapping, mdl = \
chain_mapper.GetChemMapping(self.model)
# now that we have a chem mapping, lets do consistency checks
@@ -3308,7 +3308,7 @@ class Scorer:
return chain_mapping.MappingResult(chain_mapper.target, mdl,
chain_mapper.chem_groups,
chem_mapping,
- unmapped_mdl_chains,
+ mdl_chains_without_chem_mapping,
final_mapping, alns)
def _compute_tmscore(self):
diff --git a/modules/mol/alg/tests/test_chain_mapping.py b/modules/mol/alg/tests/test_chain_mapping.py
index 03a0bb6bc16089d53004b7c66511fab4f79dfe6b..8cca758f1de3e8fa26067c1c7b29248fde8b06c3 100644
--- a/modules/mol/alg/tests/test_chain_mapping.py
+++ b/modules/mol/alg/tests/test_chain_mapping.py
@@ -176,7 +176,7 @@ class TestChainMapper(unittest.TestCase):
mapper = ChainMapper(ref)
- chem_mapping, alns, unmapped_mdl_chains, mdl_view = mapper.GetChemMapping(mdl)
+ chem_mapping, alns, mdl_chains_without_chem_mapping, mdl_view = mapper.GetChemMapping(mdl)
self.assertEqual(len(mapper.chem_groups), 3)
self.assertEqual(len(chem_mapping), len(mapper.chem_groups))
@@ -201,12 +201,12 @@ class TestChainMapper(unittest.TestCase):
mdl = _LoadFile("mdl_different_chain_mdl.pdb")
ref = _LoadFile("mdl_different_chain_ref.pdb")
mapper = ChainMapper(ref)
- chem_mapping, alns, unmapped_mdl_chains, mdl_view = mapper.GetChemMapping(mdl)
- self.assertTrue(len(unmapped_mdl_chains)==0)
+ chem_mapping, alns, mdl_chains_without_chem_mapping, mdl_view = mapper.GetChemMapping(mdl)
+ self.assertTrue(len(mdl_chains_without_chem_mapping)==0)
mapper = ChainMapper(ref, mdl_map_pep_seqid_thr=70)
- chem_mapping, alns, unmapped_mdl_chains, mdl_view = mapper.GetChemMapping(mdl)
- self.assertEqual(unmapped_mdl_chains, ["A"])
+ chem_mapping, alns, mdl_chains_without_chem_mapping, mdl_view = mapper.GetChemMapping(mdl)
+ self.assertEqual(mdl_chains_without_chem_mapping, ["A"])
def test_chain_mapping(self):
ref = _LoadFile("3l1p.1.pdb")