From 78e9d6c4e12880305c895066bd54669a5da5c4ef Mon Sep 17 00:00:00 2001 From: yokochi47 Date: Sat, 6 Apr 2024 00:45:46 +0900 Subject: [PATCH] Minor code refactoring --- wwpdb/utils/nmr/NmrDpUtility.py | 43 ++++++++------------------------- 1 file changed, 10 insertions(+), 33 deletions(-) diff --git a/wwpdb/utils/nmr/NmrDpUtility.py b/wwpdb/utils/nmr/NmrDpUtility.py index 26055fb0f..0f119eb53 100644 --- a/wwpdb/utils/nmr/NmrDpUtility.py +++ b/wwpdb/utils/nmr/NmrDpUtility.py @@ -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 @@ -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 @@ -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 @@ -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] @@ -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] @@ -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 @@ -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 @@ -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 @@ -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: @@ -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 @@ -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: @@ -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