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PEP8 cleanup
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@yokochi47
yokochi47 committed Sep 9, 2024
1 parent a4321b9 commit 6c342ab
Showing 1 changed file with 26 additions and 25 deletions.
51 changes: 26 additions & 25 deletions wwpdb/utils/nmr/NEFTranslator/NEFTranslator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2688,15 +2688,15 @@ def refresh_entity_assembly(_loop, _alt_chain_id_list):
sync_seq = False
resolve_entity_assembly(_loop, _alt_chain_id_list, sync_seq) # pylint: disable=cell-var-from-loop

def sync_entity_assembly_with_entity(_loop):
if len(chain_id_set) == 0 and 'Entity_ID' in _loop.tags:
def sync_entity_assembly_with_entity(_loop, _chain_id_set, _alt_chain_id_set):
if len(_chain_id_set) == 0 and 'Entity_ID' in _loop.tags:
_pre_tag = ['Entity_ID']
_pre_chain_data = get_lp_tag(_loop, _pre_tag)
entity_id_set = set()
for _row in _pre_chain_data:
if _row not in emptyValue:
entity_id_set.add(_row)
if len(entity_id_set) > 0 and len(entity_id_set) == len(alt_chain_id_set): # 2rqz
if len(entity_id_set) > 0 and len(entity_id_set) == len(_alt_chain_id_set):
chain_id_col = _loop.tags.index('Entity_assembly_ID')
entity_id_col = _loop.tags.index('Entity_ID')
for r in _loop.data:
Expand All @@ -2709,7 +2709,7 @@ def sync_entity_assembly_with_entity(_loop):
resolve_entity_assembly(loop, list(alt_chain_id_set), True)

else: # 2lpk, 2lnh
if not sync_entity_assembly_with_entity(loop): # 2rqz
if not sync_entity_assembly_with_entity(loop, chain_id_set, alt_chain_id_set): # 2rqz
chain_id_col = loop.tags.index('Entity_assembly_ID')
alt_chain_id_col = loop.tags.index('Auth_asym_ID')
for r in loop.data:
Expand All @@ -2718,7 +2718,7 @@ def sync_entity_assembly_with_entity(_loop):
if len(chain_id_set) <= len(alt_chain_id_set):
refresh_entity_assembly(loop, list(alt_chain_id_set))

elif not sync_entity_assembly_with_entity(loop): # 2kxc
elif not sync_entity_assembly_with_entity(loop, chain_id_set, alt_chain_id_set): # 2kxc
if (len(alt_chain_id_set) == 1 and len(chain_id_set) == 1)\
or (len(alt_chain_id_set) > len(chain_id_set)): # 5xv8, 2n7k
refresh_entity_assembly(loop, list(alt_chain_id_set))
Expand Down Expand Up @@ -2755,26 +2755,27 @@ def sync_entity_assembly_with_entity(_loop):
alt_chain_id_col = loop.tags.index('Auth_asym_ID')
auth_seq_id_col = loop.tags.index('Auth_seq_ID')
auth_comp_id_col = loop.tags.index('Auth_comp_ID')
chain_id_col = loop.tags.index('Entity_assembly_ID') if 'Entity_assembly_ID' in loop.tags else -1
seq_id_col = loop.tags.index('Comp_index_ID') if 'Comp_index_ID' in loop.tags else -1
alt_seq_id_col = loop.tags.index('Seq_ID') if 'Seq_ID' in loop.tags else -1
entity_id_col = loop.tags.index('Entity_ID') if 'Entity_ID' in loop.tags else -1

def fill_ligand(idx, np):
def fill_ligand(_loop, idx, np):
try:
seq_key = (np['auth_chain_id'], np['auth_seq_id'][0], np['comp_id'][0])
if seq_key in coord_assembly_checker['auth_to_star_seq']:
chain_id_col = _loop.tags.index('Entity_assembly_ID') if 'Entity_assembly_ID' in _loop.tags else -1
seq_id_col = _loop.tags.index('Comp_index_ID') if 'Comp_index_ID' in _loop.tags else -1
alt_seq_id_col = _loop.tags.index('Seq_ID') if 'Seq_ID' in _loop.tags else -1
entity_id_col = _loop.tags.index('Entity_ID') if 'Entity_ID' in _loop.tags else -1

_entity_assembly_id, _seq_id, _entity_id, _ = coord_assembly_checker['auth_to_star_seq'][seq_key]
row = loop.data[idx] # pylint: disable=cell-var-from-loop
if chain_id_col != -1: # pylint: disable=cell-var-from-loop
row[chain_id_col] = str(_entity_assembly_id) # pylint: disable=cell-var-from-loop
if seq_id_col != -1: # pylint: disable=cell-var-from-loop
row[seq_id_col] = str(_seq_id) # pylint: disable=cell-var-from-loop
if alt_seq_id_col != -1: # pylint: disable=cell-var-from-loop
row[alt_seq_id_col] = str(_seq_id) # pylint: disable=cell-var-from-loop
if entity_id_col != -1: # pylint: disable=cell-var-from-loop
row[entity_id_col] = str(_entity_id) # pylint: disable=cell-var-from-loop
row[alt_chain_id_col], row[auth_seq_id_col], row[comp_id_col], row[auth_comp_id_col] =\
_row = _loop.data[idx]
if chain_id_col != -1:
_row[chain_id_col] = str(_entity_assembly_id)
if seq_id_col != -1:
_row[seq_id_col] = str(_seq_id)
if alt_seq_id_col != -1:
_row[alt_seq_id_col] = str(_seq_id)
if entity_id_col != -1:
_row[entity_id_col] = str(_entity_id)
_row[alt_chain_id_col], _row[auth_seq_id_col], _row[comp_id_col], _row[auth_comp_id_col] =\
seq_key[0], str(seq_key[1]), seq_key[2], seq_key[2] # pylint: disable=cell-var-from-loop
except (KeyError, TypeError):
pass
Expand Down Expand Up @@ -2814,19 +2815,19 @@ def fill_ligand(idx, np):
if np is not None:
if auth_comp_id in np['comp_id']:
ligands = 1
fill_ligand(idx, np)
fill_ligand(loop, idx, np)
if ligands == 0:
for np in cif_np:
ligands += np['comp_id'].count(auth_comp_id)
if ligands == 1:
for np in cif_np:
if auth_comp_id in np['comp_id']:
fill_ligand(idx, np)
fill_ligand(loop, idx, np)
break
elif ligands > 1:
for np in cif_np:
if auth_comp_id in np['comp_id'] and auth_seq_id in np['auth_seq_id']:
fill_ligand(idx, np)
fill_ligand(loop, idx, np)
break
if ligands == 0:
for np in cif_np:
Expand All @@ -2835,12 +2836,12 @@ def fill_ligand(idx, np):
if ligands == 1:
for np in cif_np:
if 'alt_comp_id' in np and auth_comp_id in np['alt_comp_id']:
fill_ligand(idx, np)
fill_ligand(loop, idx, np)
break
elif ligands > 1:
for np in cif_np:
if 'alt_comp_id' in np and auth_comp_id in np['alt_comp_id'] and auth_seq_id in np['auth_seq_id']:
fill_ligand(idx, np)
fill_ligand(loop, idx, np)
break

seq_data = get_lp_tag(loop, tags)
Expand Down

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