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Minor code refactoring
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@yokochi47
yokochi47 committed Apr 5, 2024
1 parent a373e44 commit 78e9d6c
Showing 1 changed file with 10 additions and 33 deletions.
43 changes: 10 additions & 33 deletions wwpdb/utils/nmr/NmrDpUtility.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24730,8 +24730,7 @@ def fill_cs_row(lp, index, _row, prefer_auth_atom_name, coord_atom_site, _seq_ke
auth_to_star_seq_ann[seq_key] # pylint: disable=pointless-statement
_seq_key = (seq_key[0], seq_key[1])
if _seq_key in coord_atom_site: # DAOTHER-8817
_coord_atom_site = coord_atom_site[_seq_key]
auth_comp_id = _coord_atom_site['comp_id']
auth_comp_id = coord_atom_site[_seq_key]['comp_id']
except KeyError:
continue

Expand Down Expand Up @@ -29335,8 +29334,7 @@ def get_auth_seq_scheme(chain_id, seq_id):
auth_to_star_seq_ann[seq_key] # pylint: disable=pointless-statement
_seq_key = (seq_key[0], seq_key[1])
if _seq_key in coord_atom_site: # DAOTHER-8817
_coord_atom_site = coord_atom_site[_seq_key]
comp_id = _coord_atom_site['comp_id']
comp_id = coord_atom_site[_seq_key]['comp_id']
except KeyError:
continue

Expand All @@ -29361,14 +29359,6 @@ def get_auth_seq_scheme(chain_id, seq_id):

try:
auth_to_star_seq[seq_key] # pylint: disable=pointless-statement
"""
_seq_key = (seq_key[0], seq_key[1])
if _seq_key in coord_atom_site: # DAOTHER-8817
_coord_atom_site = coord_atom_site[_seq_key]
if 'chain_id' in _coord_atom_site:
chain_id = auth_chain_id = _coord_atom_site['chain_id']
comp_id = _coord_atom_site['comp_id']
"""
except KeyError:
if self.__annotation_mode or self.__native_combined:
chain_id = next((_auth_asym_id for _auth_asym_id, _auth_seq_id, _auth_comp_id in auth_to_star_seq
Expand Down Expand Up @@ -29660,7 +29650,7 @@ def get_auth_seq_scheme(chain_id, seq_id):
for row_ in dat:

for d in range(atom_dim_num):
chain_id = auth_chain_id = row_[d]
chain_id = row_[d]
seq_id = int(row_[atom_dim_num + d])
comp_id = row_[atom_dim_num * 2 + d]
atom_id = row_[atom_dim_num * 3 + d]
Expand Down Expand Up @@ -29698,7 +29688,7 @@ def get_auth_seq_scheme(chain_id, seq_id):
for row_ in dat:

for d in range(atom_dim_num):
chain_id = auth_chain_id = row_[d]
chain_id = row_[d]
seq_id = int(row_[atom_dim_num + d])
comp_id = row_[atom_dim_num * 2 + d]
atom_id = row_[atom_dim_num * 3 + d]
Expand All @@ -29709,8 +29699,7 @@ def get_auth_seq_scheme(chain_id, seq_id):
auth_to_star_seq_ann[seq_key] # pylint: disable=pointless-statement
_seq_key = (seq_key[0], seq_key[1])
if _seq_key in coord_atom_site: # DAOTHER-8817
_coord_atom_site = coord_atom_site[_seq_key]
comp_id = _coord_atom_site['comp_id']
comp_id = coord_atom_site[_seq_key]['comp_id']
except KeyError:
continue

Expand All @@ -29735,14 +29724,6 @@ def get_auth_seq_scheme(chain_id, seq_id):

try:
auth_to_star_seq[seq_key] # pylint: disable=pointless-statement
"""
_seq_key = (seq_key[0], seq_key[1])
if _seq_key in coord_atom_site: # DAOTHER-8817
_coord_atom_site = coord_atom_site[_seq_key]
if 'chain_id' in _coord_atom_site:
chain_id = auth_chain_id = _coord_atom_site['chain_id']
comp_id = _coord_atom_site['comp_id']
"""
except KeyError:
if self.__annotation_mode or self.__native_combined:
chain_id = next((_auth_asym_id for _auth_asym_id, _auth_seq_id, _auth_comp_id in auth_to_star_seq
Expand Down Expand Up @@ -34610,8 +34591,7 @@ def get_auth_seq_scheme(chain_id, seq_id):
else:
_seq_key = (seq_key[0], seq_key[1])
if _seq_key in coord_atom_site: # DAOTHER-8817
_coord_atom_site = coord_atom_site[_seq_key]
comp_id = _coord_atom_site['comp_id']
comp_id = coord_atom_site[_seq_key]['comp_id']
except (ValueError, TypeError):
has_auth_seq = valid_auth_seq = False

Expand Down Expand Up @@ -34660,8 +34640,7 @@ def get_auth_seq_scheme(chain_id, seq_id):
if seq_key in auth_to_star_seq_ann:
_seq_key = (seq_key[0], seq_key[1])
if _seq_key in coord_atom_site: # DAOTHER-8817
_coord_atom_site = coord_atom_site[_seq_key]
comp_id = _coord_atom_site['comp_id']
comp_id = coord_atom_site[_seq_key]['comp_id']

if atom_id not in emptyValue:

Expand Down Expand Up @@ -34690,8 +34669,7 @@ def get_auth_seq_scheme(chain_id, seq_id):
else:
_seq_key = (seq_key[0], seq_key[1])
if _seq_key in coord_atom_site: # DAOTHER-8817
_coord_atom_site = coord_atom_site[_seq_key]
comp_id = _coord_atom_site['comp_id']
comp_id = coord_atom_site[_seq_key]['comp_id']
except (ValueError, TypeError):
has_auth_seq = valid_auth_seq = False

Expand Down Expand Up @@ -34733,8 +34711,7 @@ def get_auth_seq_scheme(chain_id, seq_id):
if seq_key in auth_to_star_seq_ann:
_seq_key = (seq_key[0], seq_key[1])
if _seq_key in coord_atom_site: # DAOTHER-8817
_coord_atom_site = coord_atom_site[_seq_key]
comp_id = _coord_atom_site['comp_id']
comp_id = coord_atom_site[_seq_key]['comp_id']

if atom_id not in emptyValue:

Expand Down Expand Up @@ -42531,7 +42508,7 @@ def __appendCoordPolymerSequenceAlignment(self):
if length == unmapped + conflict:
continue

self.__native_combined = True # DAOTHER-881
self.__native_combined = True # DAOTHER-8817

else:
continue
Expand Down

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