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Use common vocabulary for _Spectral_dim.Spectral_region
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@yokochi47
yokochi47 committed Dec 11, 2024
1 parent 698b830 commit 035b498
Showing 1 changed file with 62 additions and 46 deletions.
108 changes: 62 additions & 46 deletions wwpdb/utils/nmr/pk/BasePKParserListener.py
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Original file line number Diff line number Diff line change
Expand Up @@ -792,35 +792,43 @@ def fillPkAuxLoops(self, spectrum_names: Optional[dict]):
if 125 < center < 130:
__v['atom_type'] = 'C'
__v['atom_isotope_number'] = 13
__v['axis_code'] = 'C_aro'
__v['axis_code'] = 'C-aromatic'
elif 115 < center < 125:
__v['atom_type'] = 'N'
__v['atom_isotope_number'] = 15
__v['axis_code'] = 'N_ami'
__v['axis_code'] = 'N'
elif 170 < center < 180:
__v['atom_type'] = 'C'
__v['atom_isotope_number'] = 13
__v['axis_code'] = 'CO'
elif 6 < center < 9:
__v['atom_type'] = 'H'
__v['atom_isotope_number'] = 1
__v['axis_code'] = 'H_ami_or_aro'
__v['axis_code'] = 'HN/H-aromatic'
elif 4 < center < 6:
__v['atom_type'] = 'H'
__v['atom_isotope_number'] = 1
__v['axis_code'] = 'H'
__v['axis_code'] = 'H' # all
elif 2 < center < 4:
__v['atom_type'] = 'H'
__v['atom_isotope_number'] = 1
__v['axis_code'] = 'H_ali'
__v['axis_code'] = 'H-aliphatic'
elif 0 < center < 2:
__v['atom_type'] = 'H'
__v['atom_isotope_number'] = 1
__v['axis_code'] = 'H-methyl'
elif 60 < center < 90:
__v['atom_type'] = 'C'
__v['atom_isotope_number'] = 13
__v['axis_code'] = 'C'
__v['axis_code'] = 'C' # all
elif 30 < center < 50:
__v['atom_type'] = 'C'
__v['atom_isotope_number'] = 13
__v['axis_code'] = 'C_ali'
__v['axis_code'] = 'C-aliphatic'
elif 10 < center < 30:
__v['atom_type'] = 'C'
__v['atom_isotope_number'] = 13
__v['axis_code'] = 'C-methyl'

isotope_number = __v['atom_isotope_number']

Expand All @@ -836,21 +844,25 @@ def fillPkAuxLoops(self, spectrum_names: Optional[dict]):
if __v['spectral_region'] is None and __v['freq_hint'].size > 0:
atom_type = __v['atom_type']
if 125 < center < 130 and atom_type == 'C':
__v['spectral_region'] = 'C_aro'
__v['spectral_region'] = 'C-aromatic'
elif 115 < center < 125 and atom_type == 'N':
__v['spectral_region'] = 'N_ami'
__v['spectral_region'] = 'N'
elif 170 < center < 180 and atom_type == 'C':
__v['spectral_region'] = 'CO'
elif 6 < center < 9 and atom_type == 'H':
__v['spectral_region'] = 'H_ami_or_aro'
__v['spectral_region'] = 'HN/H-aromatic'
elif 4 < center < 6 and atom_type == 'H':
__v['spectral_region'] = 'H_all'
__v['spectral_region'] = 'H' # all
elif 2 < center < 4 and atom_type == 'H':
__v['spectral_region'] = 'H_ali'
__v['spectral_region'] = 'H-aliphatic'
elif 0 < center < 2 and atom_type == 'H':
__v['spectral_region'] = 'H-methyl'
elif 60 < center < 90 and atom_type == 'C':
__v['spectral_region'] = 'C_all'
__v['spectral_region'] = 'C' # all
elif 30 < center < 50 and atom_type == 'C':
__v['spectral_region'] = 'C_ali'
__v['spectral_region'] = 'C-aliphatic'
elif 10 < center < 20 and atom_type == 'C':
__v['spectral_region'] = 'C-methyl'

if __v['freq_hint'].size > 0 and d > 2 and __d >= 2\
and self.exptlMethod != 'SOLID-STATE NMR' and __v['atom_isotope_number'] == 13:
Expand All @@ -875,12 +887,12 @@ def fillPkAuxLoops(self, spectrum_names: Optional[dict]):
__v['sweep_width_units'] = 'Hz'

for __v in _v.values():
if __v['axis_code'] == 'H_ami_or_aro':
has_a = any(___v['spectral_region'] == 'C_aro' for ___v in _v.values())
__v['axis_code'] = 'H_aro' if has_a else 'H_ami'
if __v['spectral_region'] == 'H_ami_or_aro':
has_a = any(___v['spectral_region'] == 'C_aro' for ___v in _v.values())
__v['spectral_region'] = 'H_aro' if has_a else 'H_ami'
if __v['axis_code'] == 'HN/H-aromatic':
has_a = any(___v['spectral_region'] == 'C-aromatic' for ___v in _v.values())
__v['axis_code'] = 'H-aromatic' if has_a else 'HN'
if __v['spectral_region'] == 'HN/H-aromatic':
has_a = any(___v['spectral_region'] == 'C-aromatic' for ___v in _v.values())
__v['spectral_region'] = 'H-aromatic' if has_a else 'HN'

for d, v in self.spectral_dim.items():
for _id, cur_spectral_dim in v.items():
Expand All @@ -895,14 +907,15 @@ def fillPkAuxLoops(self, spectrum_names: Optional[dict]):
# onebond: 'Any transfer that connects only directly bonded atoms in this experiment'
for _dim_id1, _dict1 in cur_spectral_dim.items():
_region1 = _dict1['spectral_region']
if _region1 in ('H_ami', 'H_ali', 'H_aro'):
if _region1 in ('HN', 'H-aliphatic', 'H-aromatic', 'H-methyl'):
cases = 0
max_corr_eff = 0.0
for _dim_id2, _dict2 in cur_spectral_dim.items():
_region2 = _dict2['spectral_region']
if (_region1 == 'H_ami' and _region2 == 'N_ami')\
or (_region1 == 'H_ali' and _region2 == 'C_ali')\
or (_region1 == 'H_aro' and _region2 == 'C_aro'):
if (_region1 == 'HN' and _region2 == 'N')\
or (_region1 == 'H-aliphatic' and _region2 == 'C-aliphatic')\
or (_region1 == 'H-aromatic' and _region2 == 'C-aromatic')\
or (_region1 == 'H-methyl' and _region2 == 'C-methyl'):
if 'yes' in (_dict1['acquisition'], _dict2['acquisition']):
if not any(_transfer for _transfer in cur_spectral_dim_transfer
if _transfer['type'] == 'onebond'
Expand All @@ -914,9 +927,10 @@ def fillPkAuxLoops(self, spectrum_names: Optional[dict]):
if cases == 1:
for _dim_id2, _dict2 in cur_spectral_dim.items():
_region2 = _dict2['spectral_region']
if (_region1 == 'H_ami' and _region2 == 'N_ami')\
or (_region1 == 'H_ali' and _region2 == 'C_ali')\
or (_region1 == 'H_aro' and _region2 == 'C_aro'):
if (_region1 == 'HN' and _region2 == 'N')\
or (_region1 == 'H-aliphatic' and _region2 == 'C-aliphatic')\
or (_region1 == 'H-aromatic' and _region2 == 'C-aromatic')\
or (_region1 == 'H-methyl' and _region2 == 'C-methyl'):
if 'yes' in (_dict1['acquisition'], _dict2['acquisition']):
if not any(_transfer for _transfer in cur_spectral_dim_transfer
if _transfer['type'] == 'onebond'
Expand All @@ -931,9 +945,10 @@ def fillPkAuxLoops(self, spectrum_names: Optional[dict]):
elif cases > 1:
for _dim_id2, _dict2 in cur_spectral_dim.items():
_region2 = _dict2['spectral_region']
if (_region1 == 'H_ami' and _region2 == 'N_ami')\
or (_region1 == 'H_ali' and _region2 == 'C_ali')\
or (_region1 == 'H_aro' and _region2 == 'C_aro'):
if (_region1 == 'HN' and _region2 == 'N')\
or (_region1 == 'H-aliphatic' and _region2 == 'C-aliphatic')\
or (_region1 == 'H-aromatic' and _region2 == 'C-aromatic')\
or (_region1 == 'H-methyl' and _region2 == 'C-methyl'):
if 'yes' in (_dict1['acquisition'], _dict2['acquisition']):
if not any(_transfer for _transfer in cur_spectral_dim_transfer
if _transfer['type'] == 'onebond'
Expand All @@ -949,12 +964,13 @@ def fillPkAuxLoops(self, spectrum_names: Optional[dict]):

for _dim_id1, _dict1 in cur_spectral_dim.items():
_region1 = _dict1['spectral_region']
if _region1 in ('H_ami', 'H_ali', 'H_aro'):
if _region1 in ('HN', 'H-aliphatic', 'H-aromatic', 'H-methyl'):
for _dim_id2, _dict2 in cur_spectral_dim.items():
_region2 = _dict2['spectral_region']
if (_region1 == 'H_ami' and _region2 == 'N_ami')\
or (_region1 == 'H_ali' and _region2 == 'C_ali')\
or (_region1 == 'H_aro' and _region2 == 'C_aro'):
if (_region1 == 'HN' and _region2 == 'N')\
or (_region1 == 'H-aliphatic' and _region2 == 'C-aliphatic')\
or (_region1 == 'H-aromatic' and _region2 == 'C-aromatic')\
or (_region1 == 'H-methyl' and _region2 == 'C-methyl'):
if _dict1['acquisition'] == 'no' and _dict2['acquisition'] == 'no':
if not any(_transfer for _transfer in cur_spectral_dim_transfer
if _transfer['type'] == 'onebond'
Expand Down Expand Up @@ -985,7 +1001,7 @@ def fillPkAuxLoops(self, spectrum_names: Optional[dict]):
elif d == 3:
for _dim_id1, _dict1 in cur_spectral_dim.items():
_region1 = _dict1['spectral_region']
if _region1 == 'H_ami':
if _region1 == 'HN':
for _dim_id2, _dict2 in cur_spectral_dim.items():
if _dim_id1 == _dim_id2 or _dict2['atom_isotope_number'] not in (1, 13):
continue
Expand All @@ -997,7 +1013,7 @@ def fillPkAuxLoops(self, spectrum_names: Optional[dict]):
cur_spectral_dim_transfer.append(transfer)
for _dim_id1, _dict1 in cur_spectral_dim.items():
_region1 = _dict1['spectral_region']
if _region1 == 'H_ali':
if _region1 == 'H-aliphatic':
for _dim_id2, _dict2 in cur_spectral_dim.items():
_isotope2 = _dict2['atom_isotope']
if _dim_id1 == _dim_id2 or _isotope2 not in (1, 13):
Expand All @@ -1016,7 +1032,7 @@ def fillPkAuxLoops(self, spectrum_names: Optional[dict]):
elif d == 4:
for _dim_id1, _dict1 in cur_spectral_dim.items():
_region1 = _dict1['spectral_region']
if _region1 == 'H_ami':
if _region1 == 'HN':
for _dim_id2, _dict2 in cur_spectral_dim.items():
if _dim_id1 == _dim_id2 or _dict2['atom_isotope_number'] != 1:
continue
Expand All @@ -1028,7 +1044,7 @@ def fillPkAuxLoops(self, spectrum_names: Optional[dict]):
cur_spectral_dim_transfer.append(transfer)
for _dim_id1, _dict1 in cur_spectral_dim.items():
_region1 = _dict1['spectral_region']
if _region1 == 'H_ali':
if _region1 == 'H-aliphatic':
for _dim_id2, _dict2 in cur_spectral_dim.items():
if _dim_id1 == _dim_id2 or _dict2['atom_isotope_number'] != 1:
continue
Expand Down Expand Up @@ -1060,7 +1076,7 @@ def fillPkAuxLoops(self, spectrum_names: Optional[dict]):
elif d == 3:
for _dim_id1, _dict1 in cur_spectral_dim.items():
_region1 = _dict1['spectral_region']
if _region1 == 'H_ami':
if _region1 == 'HN':
for _dim_id2, _dict2 in cur_spectral_dim.items():
if _dim_id1 == _dim_id2 or _dict2['atom_isotope_number'] not in (1, 13):
continue
Expand All @@ -1072,7 +1088,7 @@ def fillPkAuxLoops(self, spectrum_names: Optional[dict]):
cur_spectral_dim_transfer.append(transfer)
for _dim_id1, _dict1 in cur_spectral_dim.items():
_region1 = _dict1['spectral_region']
if _region1 == 'H_ali':
if _region1 == 'H-aliphatic':
for _dim_id2, _dict2 in cur_spectral_dim.items():
_isotope2 = _dict2['atom_isotope']
if _dim_id1 == _dim_id2 or _isotope2 not in (1, 13):
Expand All @@ -1091,7 +1107,7 @@ def fillPkAuxLoops(self, spectrum_names: Optional[dict]):
elif d == 4:
for _dim_id1, _dict1 in cur_spectral_dim.items():
_region1 = _dict1['spectral_region']
if _region1 == 'H_ami':
if _region1 == 'HN':
for _dim_id2, _dict2 in cur_spectral_dim.items():
if _dim_id1 == _dim_id2 or _dict2['atom_isotope_number'] != 1:
continue
Expand All @@ -1103,7 +1119,7 @@ def fillPkAuxLoops(self, spectrum_names: Optional[dict]):
cur_spectral_dim_transfer.append(transfer)
for _dim_id1, _dict1 in cur_spectral_dim.items():
_region1 = _dict1['spectral_region']
if _region1 == 'H_ali':
if _region1 == 'H-aliphatic':
for _dim_id2, _dict2 in cur_spectral_dim.items():
if _dim_id1 == _dim_id2 or _dict2['atom_isotope_number'] != 1:
continue
Expand All @@ -1121,7 +1137,7 @@ def fillPkAuxLoops(self, spectrum_names: Optional[dict]):
or 'noe' in alt_file_name or 'roe' in alt_file_name or 'rfdr' in alt_file_name:
for _dim_id1, _dict1 in cur_spectral_dim.items():
_region1 = _dict1['spectral_region']
if _region1 in ('H_ami', 'H_ali', 'H_aro') and d > 2:
if _region1 in ('HN', 'H-aliphatic', 'H-aromatic', 'H-methyl') and d > 2:
for _dim_id2, _dict2 in cur_spectral_dim.items():
if _dim_id1 == _dim_id2 or _dict1['atom_isotope_number'] != _dict2['atom_isotope_number']:
continue
Expand All @@ -1148,7 +1164,7 @@ def fillPkAuxLoops(self, spectrum_names: Optional[dict]):

for _dim_id1, _dict1 in cur_spectral_dim.items():
_region1 = _dict1['spectral_region']
if _region1 in ('H_ami', 'H_ali', 'H_aro') and d > 2:
if _region1 in ('HN', 'H-aliphatic', 'H-aromatic', 'H-methyl') and d > 2:
for _dim_id2, _dict2 in cur_spectral_dim.items():
if _dim_id1 == _dim_id2 or _dict1['atom_isotope_number'] != _dict2['atom_isotope_number']:
continue
Expand All @@ -1163,7 +1179,7 @@ def fillPkAuxLoops(self, spectrum_names: Optional[dict]):

for _dim_id1, _dict1 in cur_spectral_dim.items():
_region1 = _dict1['spectral_region']
if _region1 == 'H_all' and d == 2:
if _region1 == 'H' and d == 2: # all
for _dim_id2, _dict2 in cur_spectral_dim.items():
if _dim_id1 == _dim_id2 or _dict1['spectral_region'] != _region1:
continue
Expand All @@ -1179,7 +1195,7 @@ def fillPkAuxLoops(self, spectrum_names: Optional[dict]):
if self.exptlMethod == 'SOLID-STATE NMR':
for _dim_id1, _dict1 in cur_spectral_dim.items():
_region1 = _dict1['spectral_region']
if _region1 == 'C_all' and d == 2:
if _region1 == 'C' and d == 2: # all
for _dim_id2, _dict2 in cur_spectral_dim.items():
if _dim_id1 == _dim_id2 or _dict1['spectral_region'] != _region1:
continue
Expand Down

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