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DAOTHER-9065: Fix extended sequence handling when depositors upload N…
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…MR-STAR file associated with existing BMRB entry (D_1300044764, BMRB 51791)
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@yokochi47
yokochi47 committed Jan 31, 2024
1 parent b581eed commit 1b34d32
Showing 1 changed file with 122 additions and 0 deletions.
122 changes: 122 additions & 0 deletions wwpdb/utils/nmr/NmrDpUtility.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23871,6 +23871,55 @@ def get_auth_seq_scheme(chain_id, seq_id):

return auth_asym_id, auth_seq_id

def get_label_seq_scheme(chain_id, seq_id):
auth_asym_id = auth_seq_id = label_seq_id = None

if seq_id is not None:

if chain_assign is not None:
auth_asym_id = next((ca['ref_chain_id'] for ca in chain_assign if ca['test_chain_id'] == chain_id), None)
if auth_asym_id is not None:
sa = next((sa for sa in seq_align
if sa['ref_chain_id'] == auth_asym_id and sa['test_chain_id'] == chain_id
and seq_id in sa['ref_auth_seq_id' if 'ref_auth_seq_id' in sa else 'ref_seq_id']
and sa['sequence_coverage'] >= LOW_SEQ_COVERAGE), None)
if sa is not None:
_ref_seq_id_name = 'ref_auth_seq_id' if 'ref_auth_seq_id' in sa else 'ref_seq_id'
auth_seq_id, label_seq_id = next(((ref_seq_id, test_seq_id)
for ref_seq_id, test_seq_id
in zip(sa[_ref_seq_id_name], sa['test_seq_id'])
if ref_seq_id == seq_id), (None, None))

if (auth_asym_id is None or auth_seq_id is None) and br_seq_align is not None:
auth_asym_id = next((ca['ref_chain_id'] for ca in br_chain_assign if ca['test_chain_id'] == chain_id), None)
if auth_asym_id is not None:
sa = next((sa for sa in br_seq_align
if sa['ref_chain_id'] == auth_asym_id and sa['test_chain_id'] == chain_id
and seq_id in sa['ref_auth_seq_id' if 'ref_auth_seq_id' in sa else 'ref_seq_id']
and sa['sequence_coverage'] >= LOW_SEQ_COVERAGE), None)
if sa is not None:
_ref_seq_id_name = 'ref_auth_seq_id' if 'ref_auth_seq_id' in sa else 'ref_seq_id'
auth_seq_id, label_seq_id = next(((ref_seq_id, test_seq_id)
for ref_seq_id, test_seq_id
in zip(sa[_ref_seq_id_name], sa['test_seq_id'])
if ref_seq_id == seq_id), (None, None))

if (auth_asym_id is None or auth_seq_id is None) and np_seq_align is not None:
auth_asym_id = next((ca['ref_chain_id'] for ca in np_chain_assign if ca['test_chain_id'] == chain_id), None)
if auth_asym_id is not None:
sa = next((sa for sa in np_seq_align
if sa['ref_chain_id'] == auth_asym_id and sa['test_chain_id'] == chain_id
and seq_id in sa['ref_auth_seq_id' if 'ref_auth_seq_id' in sa else 'ref_seq_id']
and sa['sequence_coverage'] >= LOW_SEQ_COVERAGE), None)
if sa is not None:
_ref_seq_id_name = 'ref_auth_seq_id' if 'ref_auth_seq_id' in sa else 'ref_seq_id'
auth_seq_id, label_seq_id = next(((ref_seq_id, test_seq_id)
for ref_seq_id, test_seq_id
in zip(sa[_ref_seq_id_name], sa['test_seq_id'])
if ref_seq_id == seq_id), (None, None))

return auth_asym_id, auth_seq_id, label_seq_id

def fill_cs_row(lp, index, _row, prefer_auth_atom_name, coord_atom_site, _seq_key, comp_id, atom_id, src_lp, src_idx):
fill_auth_atom_id = self.__annotation_mode or (_row[19] in emptyValue and _row[18] not in emptyValue)
fill_orig_atom_id = _row[23] not in emptyValue
Expand Down Expand Up @@ -24539,6 +24588,7 @@ def fill_cs_row(lp, index, _row, prefer_auth_atom_name, coord_atom_site, _seq_ke

can_auth_asym_id_mapping = {} # DAOTHER-8751
seq_id_offset_for_unmapped = {} # DAOTHER-9065
label_seq_id_offset_for_extended = {} # D_1300044764

trial = 0

Expand Down Expand Up @@ -25288,6 +25338,78 @@ def test_seq_id_offset(lp, index, row, _row, _idx, chain_id, seq_id, comp_id, of
index, _row = _index, __row
break

if not resolved and seq_id is not None and has_coordinate:

def test_seq_id_offset(lp, index, row, _row, _idx, chain_id, seq_id, comp_id, offset):
_resolved = False
_index = index

auth_asym_id, auth_seq_id, label_seq_id = get_label_seq_scheme(chain_id, seq_id + offset)
if auth_asym_id is not None and auth_seq_id is not None:
_resolved = True

item = next((item for item in entity_assembly if item['auth_asym_id'] == auth_asym_id), None)

if item is not None and ps is not None and any(_ps for _ps in ps_common
if _ps['chain_id'] == chain_id
and label_seq_id in _ps['seq_id']):
entity_assembly_id = item['entity_assembly_id']
entity_id = item['entity_id']

seq_key = next((k for k, v in auth_to_star_seq.items()
if k[0] == auth_asym_id and k[1] == auth_seq_id
and v[0] == entity_assembly_id and v[2] == entity_id), None)

if seq_key is not None:
_, _label_seq_id, _, _ = auth_to_star_seq[seq_key]

if entity_id not in label_seq_id_offset_for_extended or _label_seq_id - label_seq_id == label_seq_id_offset_for_extended[entity_id]:
seq_id += (label_seq_id - auth_seq_id)
seq_id += (_label_seq_id - label_seq_id)

if entity_id not in label_seq_id_offset_for_extended:
label_seq_id_offset_for_extended[entity_id] = _label_seq_id - label_seq_id

_row[1], _row[2], _row[3], _row[4] =\
entity_assembly_id, entity_id, seq_id, seq_id

_row[16] = _row[20] = auth_asym_id
if _row[21] in emptyValue:
_row[21] = _row[17]
if _row[22] in emptyValue:
_row[22] = _row[18]
if _row[23] in emptyValue:
_row[23] = _row[19]

_index, _row = fill_cs_row(lp, index, _row, prefer_auth_atom_name,
coord_atom_site, None,
comp_id, atom_id, loop, _idx)

else:
_resolved = False

else:
_resolved = False

else:
_resolved = False

return _resolved, _index, _row

found = False
for offset in range(1, 1000):
resolved, _index, __row = test_seq_id_offset(lp, index, row, _row, idx, chain_id, seq_id, comp_id, offset)

if resolved:
index, _row = _index, __row
break

resolved, _index, __row = test_seq_id_offset(lp, index, row, _row, idx, chain_id, seq_id, comp_id, -offset)

if resolved:
index, _row = _index, __row
break

if not resolved and chain_id in can_auth_asym_id_mapping: # DAOTHER-8751, 8755
mapping = can_auth_asym_id_mapping[chain_id]

Expand Down

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