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Reimplement supporting for ligand split during annotation (D_13000430…
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…61, DAOTHER-8817)
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@yokochi47
yokochi47 committed Mar 15, 2024
1 parent ad6a6a7 commit 3f24913
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Showing 2 changed files with 113 additions and 67 deletions.
93 changes: 66 additions & 27 deletions wwpdb/utils/nmr/NmrDpUtility.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24798,15 +24798,24 @@ def fill_cs_row(lp, index, _row, prefer_auth_atom_name, coord_atom_site, _seq_ke
_row[1], _row[2], _row[3], _row[4] = entity_assembly_id, entity_id, seq_id, seq_id

if prefer_auth_atom_name:
if has_orig_seq:
orig_atom_id = _row[23]
_atom_id = atom_id
if comp_id in auth_atom_name_to_id and _atom_id in auth_atom_name_to_id[comp_id]:
_row[19] = atom_id = auth_atom_name_to_id[comp_id][_atom_id]
if _seq_key in coord_atom_site:
_coord_atom_site = coord_atom_site[_seq_key]
if comp_id in auth_atom_name_to_id and comp_id == _coord_atom_site['comp_id']:
if _atom_id in auth_atom_name_to_id[comp_id]:
if auth_atom_name_to_id[comp_id][_atom_id] in _coord_atom_site['atom_id']:
_row[19] = atom_id = auth_atom_name_to_id[comp_id][_atom_id]
elif 'split_comp_id' not in _coord_atom_site and has_orig_seq and orig_atom_id in auth_atom_name_to_id[comp_id]:
_row[19] = atom_id = auth_atom_name_to_id[comp_id][orig_atom_id]
if 'alt_atom_id' in _coord_atom_site and _atom_id in _coord_atom_site['alt_atom_id']\
and comp_id == _coord_atom_site['comp_id']:
_row[19] = atom_id = _coord_atom_site['atom_id'][_coord_atom_site['alt_atom_id'].index(_atom_id)]
# DAOTHER-8751, 8817 (D_1300043061)
if 'alt_comp_id' in _coord_atom_site and 'alt_atom_id' in _coord_atom_site\
and _atom_id in _coord_atom_site['alt_atom_id']:
comp_id = _coord_atom_site['alt_comp_id'][_coord_atom_site['alt_atom_id'].index(_atom_id)]
elif 'alt_comp_id' in _coord_atom_site and 'alt_atom_id' in _coord_atom_site\
and _atom_id in _coord_atom_site['alt_atom_id']\
and comp_id == _coord_atom_site['alt_comp_id'][_coord_atom_site['alt_atom_id'].index(_atom_id)]:
_row[18] = comp_id
# 'Entity_assembly_ID', 'Entity_ID', 'Comp_index_ID', 'Seq_ID', 'Comp_ID', 'Auth_asym_ID', 'Auth_seq_ID'
cca_row = next((cca_row for cca_row in self.__cca_dat
Expand All @@ -24816,14 +24825,16 @@ def fill_cs_row(lp, index, _row, prefer_auth_atom_name, coord_atom_site, _seq_ke
if comp_id in auth_atom_name_to_id_ext and _atom_id in auth_atom_name_to_id_ext[comp_id]\
and len(set(_coord_atom_site['alt_comp_id'])) > 1:
_row[19] = atom_id = auth_atom_name_to_id_ext[comp_id][_atom_id]
else:
_row[19] = atom_id = _coord_atom_site['atom_id'][_coord_atom_site['alt_atom_id'].index(_atom_id)]
elif 'split_comp_id' in _coord_atom_site:
for _comp_id in _coord_atom_site['split_comp_id']:
if _comp_id == comp_id:
continue
__seq_key = (_seq_key[0], _seq_key[1], _comp_id)
if __seq_key not in coord_atom_site:
continue
__coord_atom_site = coord_atom_site[__seq_key]
if __coord_atom_site is None:
continue
if 'alt_comp_id' in __coord_atom_site and 'alt_atom_id' in __coord_atom_site\
and _atom_id in __coord_atom_site['alt_atom_id']:
comp_id = _comp_id
Expand Down Expand Up @@ -34447,15 +34458,20 @@ def get_auth_seq_scheme(chain_id, seq_id):

if prefer_auth_atom_name:
_atom_id = atom_id
if comp_id in auth_atom_name_to_id and _atom_id in auth_atom_name_to_id[comp_id]:
atom_id = auth_atom_name_to_id[comp_id][_atom_id]
_seq_key = (seq_key[0], seq_key[1])
if _seq_key in coord_atom_site:
_coord_atom_site = coord_atom_site[_seq_key]
if comp_id in auth_atom_name_to_id and comp_id == _coord_atom_site['comp_id']\
and _atom_id in auth_atom_name_to_id[comp_id]:
if auth_atom_name_to_id[comp_id][_atom_id] in _coord_atom_site['atom_id']:
atom_id = auth_atom_name_to_id[comp_id][_atom_id]
if 'alt_atom_id' in _coord_atom_site and _atom_id in _coord_atom_site['alt_atom_id']\
and comp_id == _coord_atom_site['comp_id']:
atom_id = _coord_atom_site['atom_id'][_coord_atom_site['alt_atom_id'].index(_atom_id)]
# DAOTHER-8751, 8817 (D_1300043061)
if 'alt_comp_id' in _coord_atom_site and 'alt_atom_id' in _coord_atom_site\
and _atom_id in _coord_atom_site['alt_atom_id']:
comp_id = _coord_atom_site['alt_comp_id'][_coord_atom_site['alt_atom_id'].index(_atom_id)]
elif 'alt_comp_id' in _coord_atom_site and 'alt_atom_id' in _coord_atom_site\
and _atom_id in _coord_atom_site['alt_atom_id']\
and comp_id == _coord_atom_site['alt_comp_id'][_coord_atom_site['alt_atom_id'].index(_atom_id)]:
# 'Entity_assembly_ID', 'Entity_ID', 'Comp_index_ID', 'Seq_ID', 'Comp_ID', 'Auth_asym_ID', 'Auth_seq_ID'
cca_row = next((cca_row for cca_row in self.__cca_dat
if cca_row[4] == comp_id and cca_row[5] == _seq_key[0] and cca_row[6] == _seq_key[1]), None)
Expand All @@ -34464,6 +34480,8 @@ def get_auth_seq_scheme(chain_id, seq_id):
if comp_id in auth_atom_name_to_id_ext and _atom_id in auth_atom_name_to_id_ext[comp_id]\
and len(set(_coord_atom_site['alt_comp_id'])) > 1:
atom_id = auth_atom_name_to_id_ext[comp_id][_atom_id]
else:
atom_id = _coord_atom_site['atom_id'][_coord_atom_site['alt_atom_id'].index(_atom_id)]
elif 'split_comp_id' in _coord_atom_site:
for _comp_id in _coord_atom_site['split_comp_id']:
if _comp_id == comp_id:
Expand Down Expand Up @@ -34545,15 +34563,20 @@ def get_auth_seq_scheme(chain_id, seq_id):

if prefer_auth_atom_name:
_atom_id = atom_id
if comp_id in auth_atom_name_to_id and _atom_id in auth_atom_name_to_id[comp_id]:
atom_id = auth_atom_name_to_id[comp_id][_atom_id]
_seq_key = (seq_key[0], seq_key[1])
if _seq_key in coord_atom_site:
_coord_atom_site = coord_atom_site[_seq_key]
if comp_id in auth_atom_name_to_id and comp_id == _coord_atom_site['comp_id']\
and _atom_id in auth_atom_name_to_id[comp_id]:
if auth_atom_name_to_id[comp_id][_atom_id] in _coord_atom_site['atom_id']:
atom_id = auth_atom_name_to_id[comp_id][_atom_id]
if 'alt_atom_id' in _coord_atom_site and _atom_id in _coord_atom_site['alt_atom_id']\
and comp_id == _coord_atom_site['comp_id']:
atom_id = _coord_atom_site['atom_id'][_coord_atom_site['alt_atom_id'].index(_atom_id)]
# DAOTHER-8751, 8817 (D_1300043061)
if 'alt_comp_id' in _coord_atom_site and 'alt_atom_id' in _coord_atom_site\
and _atom_id in _coord_atom_site['alt_atom_id']:
comp_id = _coord_atom_site['alt_comp_id'][_coord_atom_site['alt_atom_id'].index(_atom_id)]
elif 'alt_comp_id' in _coord_atom_site and 'alt_atom_id' in _coord_atom_site\
and _atom_id in _coord_atom_site['alt_atom_id']\
and comp_id == _coord_atom_site['alt_comp_id'][_coord_atom_site['alt_atom_id'].index(_atom_id)]:
# 'Entity_assembly_ID', 'Entity_ID', 'Comp_index_ID', 'Seq_ID', 'Comp_ID', 'Auth_asym_ID', 'Auth_seq_ID'
cca_row = next((cca_row for cca_row in self.__cca_dat
if cca_row[4] == comp_id and cca_row[5] == _seq_key[0] and cca_row[6] == _seq_key[1]), None)
Expand All @@ -34562,6 +34585,8 @@ def get_auth_seq_scheme(chain_id, seq_id):
if comp_id in auth_atom_name_to_id_ext and _atom_id in auth_atom_name_to_id_ext[comp_id]\
and len(set(_coord_atom_site['alt_comp_id'])) > 1:
atom_id = auth_atom_name_to_id_ext[comp_id][_atom_id]
else:
atom_id = _coord_atom_site['atom_id'][_coord_atom_site['alt_atom_id'].index(_atom_id)]
elif 'split_comp_id' in _coord_atom_site:
for _comp_id in _coord_atom_site['split_comp_id']:
if _comp_id == comp_id:
Expand Down Expand Up @@ -34662,15 +34687,20 @@ def get_auth_seq_scheme(chain_id, seq_id):

if prefer_auth_atom_name:
_atom_id = atom_id
if comp_id in auth_atom_name_to_id and _atom_id in auth_atom_name_to_id[comp_id]:
atom_id = auth_atom_name_to_id[comp_id][_atom_id]
_seq_key = (seq_key[0], seq_key[1])
if _seq_key in coord_atom_site:
_coord_atom_site = coord_atom_site[_seq_key]
if comp_id in auth_atom_name_to_id and comp_id == _coord_atom_site['comp_id']\
and _atom_id in auth_atom_name_to_id[comp_id]:
if auth_atom_name_to_id[comp_id][_atom_id] in _coord_atom_site['atom_id']:
atom_id = auth_atom_name_to_id[comp_id][_atom_id]
if 'alt_atom_id' in _coord_atom_site and _atom_id in _coord_atom_site['alt_atom_id']\
and comp_id == _coord_atom_site['comp_id']:
atom_id = _coord_atom_site['atom_id'][_coord_atom_site['alt_atom_id'].index(_atom_id)]
# DAOTHER-8751, 8817 (D_1300043061)
if 'alt_comp_id' in _coord_atom_site and 'alt_atom_id' in _coord_atom_site\
and _atom_id in _coord_atom_site['alt_atom_id']:
comp_id = _coord_atom_site['alt_comp_id'][_coord_atom_site['alt_atom_id'].index(_atom_id)]
elif 'alt_comp_id' in _coord_atom_site and 'alt_atom_id' in _coord_atom_site\
and _atom_id in _coord_atom_site['alt_atom_id']\
and comp_id == _coord_atom_site['alt_comp_id'][_coord_atom_site['alt_atom_id'].index(_atom_id)]:
# 'Entity_assembly_ID', 'Entity_ID', 'Comp_index_ID', 'Seq_ID', 'Comp_ID', 'Auth_asym_ID', 'Auth_seq_ID'
cca_row = next((cca_row for cca_row in self.__cca_dat
if cca_row[4] == comp_id and cca_row[5] == _seq_key[0] and cca_row[6] == _seq_key[1]), None)
Expand All @@ -34679,6 +34709,8 @@ def get_auth_seq_scheme(chain_id, seq_id):
if comp_id in auth_atom_name_to_id_ext and _atom_id in auth_atom_name_to_id_ext[comp_id]\
and len(set(_coord_atom_site['alt_comp_id'])) > 1:
atom_id = auth_atom_name_to_id_ext[comp_id][_atom_id]
else:
atom_id = _coord_atom_site['atom_id'][_coord_atom_site['alt_atom_id'].index(_atom_id)]
elif 'split_comp_id' in _coord_atom_site:
for _comp_id in _coord_atom_site['split_comp_id']:
if _comp_id == comp_id:
Expand Down Expand Up @@ -34752,15 +34784,20 @@ def get_auth_seq_scheme(chain_id, seq_id):

if prefer_auth_atom_name:
_atom_id = atom_id
if comp_id in auth_atom_name_to_id and _atom_id in auth_atom_name_to_id[comp_id]:
atom_id = auth_atom_name_to_id[comp_id][_atom_id]
_seq_key = (seq_key[0], seq_key[1])
if _seq_key in coord_atom_site:
_coord_atom_site = coord_atom_site[_seq_key]
if comp_id in auth_atom_name_to_id and comp_id == _coord_atom_site['comp_id']\
and _atom_id in auth_atom_name_to_id[comp_id]:
if auth_atom_name_to_id[comp_id][_atom_id] in _coord_atom_site['atom_id']:
atom_id = auth_atom_name_to_id[comp_id][_atom_id]
if 'alt_atom_id' in _coord_atom_site and _atom_id in _coord_atom_site['alt_atom_id']\
and comp_id == _coord_atom_site['comp_id']:
atom_id = _coord_atom_site['atom_id'][_coord_atom_site['alt_atom_id'].index(_atom_id)]
# DAOTHER-8751, 8817 (D_1300043061)
if 'alt_comp_id' in _coord_atom_site and 'alt_atom_id' in _coord_atom_site\
and _atom_id in _coord_atom_site['alt_atom_id']:
comp_id = _coord_atom_site['alt_comp_id'][_coord_atom_site['alt_atom_id'].index(_atom_id)]
elif 'alt_comp_id' in _coord_atom_site and 'alt_atom_id' in _coord_atom_site\
and _atom_id in _coord_atom_site['alt_atom_id']\
and comp_id == _coord_atom_site['alt_comp_id'][_coord_atom_site['alt_atom_id'].index(_atom_id)]:
# 'Entity_assembly_ID', 'Entity_ID', 'Comp_index_ID', 'Seq_ID', 'Comp_ID', 'Auth_asym_ID', 'Auth_seq_ID'
cca_row = next((cca_row for cca_row in self.__cca_dat
if cca_row[4] == comp_id and cca_row[5] == _seq_key[0] and cca_row[6] == _seq_key[1]), None)
Expand All @@ -34769,6 +34806,8 @@ def get_auth_seq_scheme(chain_id, seq_id):
if comp_id in auth_atom_name_to_id_ext and _atom_id in auth_atom_name_to_id_ext[comp_id]\
and len(set(_coord_atom_site['alt_comp_id'])) > 1:
atom_id = auth_atom_name_to_id_ext[comp_id][_atom_id]
else:
atom_id = _coord_atom_site['atom_id'][_coord_atom_site['alt_atom_id'].index(_atom_id)]
elif 'split_comp_id' in _coord_atom_site:
for _comp_id in _coord_atom_site['split_comp_id']:
if _comp_id == comp_id:
Expand Down
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