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Resolve case where there is no valid restraint, but only insufficient…
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…_atom_selection errors due to arbitrary shift of sequence number that does not match with any coordinate sequence schemes (2lzs)
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@yokochi47
yokochi47 committed Jul 19, 2024
1 parent 5c17f36 commit d561011
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Showing 5 changed files with 416 additions and 8 deletions.
18 changes: 10 additions & 8 deletions wwpdb/utils/nmr/AlignUtil.py
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Original file line number Diff line number Diff line change
Expand Up @@ -779,10 +779,11 @@ def sortPolySeqRst(polySeqRst, nonPolyRemap=None):
idx = 0
for seqId in ps['seq_id']:
if seqId is not None and seqId in _seqIds:
_compIds[_seqIds.index(seqId)] = ps['comp_id'][idx]
_authCompIds[_seqIds.index(seqId)] = ps['auth_comp_id'][idx]
if ps['auth_comp_id'][idx] in emptyValue:
_authCompIds[_seqIds.index(seqId)] = ps['comp_id'][idx]
_idx = _seqIds.index(seqId)
_compIds[_idx] = ps['comp_id'][idx]
_authCompIds[_idx] = ps['auth_comp_id'][idx] if 'auth_comp_id' in ps else _compIds[_idx]
if _authCompIds[_idx] in emptyValue:
_authCompIds[_idx] = _compIds[_idx]
idx += 1

ps['seq_id'] = _seqIds
Expand Down Expand Up @@ -815,10 +816,11 @@ def sortPolySeqRst(polySeqRst, nonPolyRemap=None):

for idx, seqId in enumerate(ps['seq_id']):
if minSeqId <= seqId <= maxSeqId:
_compIds[_seqIds.index(seqId)] = ps['comp_id'][idx]
_authCompIds[_seqIds.index(seqId)] = ps['auth_comp_id'][idx]
if ps['auth_comp_id'][idx] in emptyValue:
_authCompIds[_seqIds.index(seqId)] = ps['comp_id'][idx]
_idx = _seqIds.index(seqId)
_compIds[_idx] = ps['comp_id'][idx]
_authCompIds[_idx] = ps['auth_comp_id'][idx] if 'auth_comp_id' in ps else _compIds[_idx]
if _authCompIds[_idx] in emptyValue:
_authCompIds[_idx] = _compIds[_idx]

_endSeqIds = []
_endCompIds = []
Expand Down
133 changes: 133 additions & 0 deletions wwpdb/utils/nmr/mr/CharmmMRParserListener.py
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Original file line number Diff line number Diff line change
Expand Up @@ -787,6 +787,138 @@ def exitCharmm_mr(self, ctx: CharmmMRParser.Charmm_mrContext): # pylint: disabl
else:
self.reasonsForReParsing['np_seq_id_remap'] = seqIdRemap

# attempt to resolve case where there is no valid restraint, but only insufficient atom selection errors
# due to arbitrary shift of sequence number that does not match with any coordinate sequence schemes (2lzs)
if self.__reasons is None and len(self.__polySeqRst) == 0 and len(self.__polySeqRstFailed) > 0\
and any(f for f in self.__f if '[Insufficient atom selection]' in f):
if len(self.__polySeqRstFailedAmbig) > 0:
mergePolySeqRstAmbig(self.__polySeqRstFailed, self.__polySeqRstFailedAmbig)
sortPolySeqRst(self.__polySeqRstFailed)

seqAlignFailed, _ = alignPolymerSequence(self.__pA, self.__polySeq, self.__polySeqRstFailed)

for sa in seqAlignFailed:
if sa['conflict'] == 0:
chainId = sa['test_chain_id']
_ps = next((_ps for _ps in self.__polySeqRstFailedAmbig if _ps['chain_id'] == chainId), None)
if _ps is None:
continue
for seqId, compIds in zip(_ps['seq_id'], _ps['comp_ids']):
for compId in list(compIds):
_polySeqRstFailed = copy.deepcopy(self.__polySeqRstFailed)
updatePolySeqRst(_polySeqRstFailed, chainId, seqId, compId)
sortPolySeqRst(_polySeqRstFailed)
_seqAlignFailed, _ = alignPolymerSequence(self.__pA, self.__polySeq, _polySeqRstFailed)
_sa = next((_sa for _sa in _seqAlignFailed if _sa['test_chain_id'] == chainId), None)
if _sa is None or _sa['conflict'] > 0:
continue
updatePolySeqRst(self.__polySeqRstFailed, chainId, seqId, compId)
sortPolySeqRst(self.__polySeqRstFailed)

seqAlignFailed, _ = alignPolymerSequence(self.__pA, self.__polySeq, self.__polySeqRstFailed)
chainAssignFailed, _ = assignPolymerSequence(self.__pA, self.__ccU, self.__file_type,
self.__polySeq, self.__polySeqRstFailed, seqAlignFailed)

if chainAssignFailed is not None:

seqIdRemap = []

cyclicPolymer = {}

for ca in chainAssignFailed:
ref_chain_id = ca['ref_chain_id']
test_chain_id = ca['test_chain_id']

sa = next(sa for sa in seqAlignFailed
if sa['ref_chain_id'] == ref_chain_id
and sa['test_chain_id'] == test_chain_id)

poly_seq_model = next(ps for ps in self.__polySeq
if ps['auth_chain_id'] == ref_chain_id)
poly_seq_rst = next(ps for ps in self.__polySeqRstFailed
if ps['chain_id'] == test_chain_id)

seq_id_mapping = {}
for ref_seq_id, mid_code, test_seq_id in zip(sa['ref_seq_id'], sa['mid_code'], sa['test_seq_id']):
if mid_code == '|' and test_seq_id is not None:
try:
seq_id_mapping[test_seq_id] = next(auth_seq_id for auth_seq_id, seq_id
in zip(poly_seq_model['auth_seq_id'], poly_seq_model['seq_id'])
if seq_id == ref_seq_id and isinstance(auth_seq_id, int))
except StopIteration:
pass

if ref_chain_id not in cyclicPolymer:
cyclicPolymer[ref_chain_id] =\
isCyclicPolymer(self.__cR, self.__polySeq, ref_chain_id,
self.__representativeModelId, self.__representativeAltId, self.__modelNumName)

if cyclicPolymer[ref_chain_id]:

poly_seq_model = next(ps for ps in self.__polySeq
if ps['auth_chain_id'] == ref_chain_id)

offset = None
for seq_id, comp_id in zip(poly_seq_rst['seq_id'], poly_seq_rst['comp_id']):
if seq_id is not None and seq_id not in seq_id_mapping:
_seq_id = next((_seq_id for _seq_id, _comp_id in zip(poly_seq_model['seq_id'], poly_seq_model['comp_id'])
if _seq_id not in seq_id_mapping.values() and _comp_id == comp_id), None)
if _seq_id is not None:
offset = seq_id - _seq_id
break

if offset is not None:
for seq_id in poly_seq_rst['seq_id']:
if seq_id is not None and seq_id not in seq_id_mapping:
seq_id_mapping[seq_id] = seq_id - offset

if any(k for k, v in seq_id_mapping.items() if k != v)\
and not any(k for k, v in seq_id_mapping.items()
if v in poly_seq_model['seq_id']
and k == poly_seq_model['auth_seq_id'][poly_seq_model['seq_id'].index(v)]):
seqIdRemap.append({'chain_id': test_chain_id, 'seq_id_dict': seq_id_mapping})

if len(seqIdRemap) > 0:
if 'seq_id_remap' not in self.reasonsForReParsing:
self.reasonsForReParsing['seq_id_remap'] = seqIdRemap

if any(ps for ps in self.__polySeq if 'identical_chain_id' in ps):
polySeqRst, chainIdMapping = splitPolySeqRstForMultimers(self.__pA, self.__polySeq, self.__polySeqRstFailed, chainAssignFailed)

if polySeqRst is not None and (not self.__hasNonPoly or len(self.__polySeq) // len(self.__nonPoly) in (1, 2)):
self.__polySeqRst = polySeqRst
if 'chain_id_remap' not in self.reasonsForReParsing:
self.reasonsForReParsing['chain_id_remap'] = chainIdMapping

if len(self.__polySeq) == 1 and len(self.__polySeqRstFailed) == 1:
polySeqRst, chainIdMapping, modelChainIdExt =\
splitPolySeqRstForExactNoes(self.__pA, self.__polySeq, self.__polySeqRstFailed, chainAssignFailed)

if polySeqRst is not None:
self.__polySeqRst = polySeqRst
if 'chain_id_clone' not in self.reasonsForReParsing:
self.reasonsForReParsing['chain_id_clone'] = chainIdMapping
if 'model_chain_id_ext' not in self.reasonsForReParsing:
self.reasonsForReParsing['model_chain_id_ext'] = modelChainIdExt

if self.__hasNonPoly:
polySeqRst, nonPolyMapping = splitPolySeqRstForNonPoly(self.__ccU, self.__nonPoly, self.__polySeqRstFailed,
seqAlignFailed, chainAssignFailed)

if polySeqRst is not None:
self.__polySeqRst = polySeqRst
if 'non_poly_remap' not in self.reasonsForReParsing:
self.reasonsForReParsing['non_poly_remap'] = nonPolyMapping

if self.__hasBranched:
polySeqRst, branchedMapping = splitPolySeqRstForBranched(self.__pA, self.__polySeq, self.__branched, self.__polySeqRstFailed,
chainAssignFailed)

if polySeqRst is not None:
self.__polySeqRst = polySeqRst
if 'branched_remap' not in self.reasonsForReParsing:
self.reasonsForReParsing['branched_remap'] = branchedMapping

# """
# if 'label_seq_scheme' in self.reasonsForReParsing and self.reasonsForReParsing['label_seq_scheme']:
# if 'non_poly_remap' in self.reasonsForReParsing:
Expand Down Expand Up @@ -3175,6 +3307,7 @@ def update_np_seq_id_remap_request(np, ligands):
except ValueError:
pass

if len(_factor['seq_id']) == 1:
if len(_factor['atom_id']) == 1 and 'comp_id' not in _factor:
compIds = guessCompIdFromAtomId(_factor['atom_id'], self.__polySeq, self.__nefT)
if compIds is not None:
Expand Down
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