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Append _Spectral_dim and _Spectral_dim_transfer loops
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@yokochi47
yokochi47 committed Dec 6, 2024
1 parent 6d2c570 commit cd212c0
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Showing 3 changed files with 146 additions and 13 deletions.
2 changes: 1 addition & 1 deletion wwpdb/utils/nmr/NmrDpUtility.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32240,7 +32240,7 @@ def __mergeAnyPkAsIs(self):
sf = master_entry.get_saveframe_by_name(sf_framecode)
text_data = get_first_sf_tag(sf, 'Text_data')

if any(loop for loop in sf.loops if loop.category in ('_Peak_raw_format', '_Peak'))\
if any(loop for loop in sf.loops if loop.category in ('_Peak_row_format', '_Peak'))\
or text_data not in emptyValue:

list_id += 1
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114 changes: 106 additions & 8 deletions wwpdb/utils/nmr/mr/ParserListenerUtil.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2020,13 +2020,23 @@
{'name': 'Entry_ID', 'type': 'str', 'mandatory': True}
])

NMR_STAR_AUX_LP_CATEGORIES = {'dist_restraint': ['_Gen_dist_constraint_software_param']
NMR_STAR_AUX_LP_CATEGORIES = {'dist_restraint': ['_Gen_dist_constraint_software_param'
],
'spectral_peak': ['_Spectral_dim', 'Spectral_dim_transfer'
]
}

NMR_STAR_AUX_LP_KEY_ITEMS = {'dist_restraint': {'_Gen_dist_constraint_software_param': [
{'name': 'Software_ID', 'type': 'int', 'mandatory': True},
{'name': 'Type', 'type': 'str', 'mandatory': True}]
}
{'name': 'Software_ID', 'type': 'int'},
{'name': 'Type', 'type': 'str'}]
},
'spectral_peak': {'_Spectral_dim': [
{'name': 'ID', 'type': 'positive-int', 'auto-increment': True}
],
'_Spectral_dim_transfer': [
{'name': 'Spectral_dim_ID_1', 'type': 'positive-int'},
{'name': 'Spectral_dim_ID_2', 'type': 'positive-int'}]
}
}

NMR_STAR_AUX_LP_DATA_ITEMS = {'dist_restraint': {'_Gen_dist_constraint_software_param': [
Expand All @@ -2035,7 +2045,39 @@
{'name': 'Gen_dist_constraint_list_ID', 'type': 'pointer-index', 'mandatory': True,
'default': '1', 'default-from': 'parent'},
{'name': 'Entry_ID', 'type': 'str', 'mandatory': True}]
}
},
'spectral_peak': {'_Spectral_dim': [
{'name': 'Atom_type', 'type': 'enum', 'mandatory': True,
'enum': set(ISOTOPE_NUMBERS_OF_NMR_OBS_NUCS.keys()),
'enforce-enum': True},
{'name': 'Atom_isotope_number', 'type': 'enum-int', 'mandatory': True,
'enum': set(ALLOWED_ISOTOPE_NUMBERS),
'enforce-enum': True},
{'name': 'Axis_code', 'type': 'str'},
{'name': 'Spectrometer_frequency', 'type': 'positive-float', 'mandatory': False,
'enforce-non-zero': True},
{'name': 'Spectral_region', 'type': 'str', 'mandatory': True},
{'name': 'Sweep_width', 'type': 'positive-float', 'mandatory': False,
'enforce-non-zero': True},
{'name': 'Sweep_width_units', 'type': 'enum', 'mandatory': True,
'enum': ('ppm', 'Hz'),
'enforce-enum': True},
{'name': 'Value_first_point', 'type': 'float', 'mandatory': False},
{'name': 'Absolute_peak_positions', 'type': 'bool', 'mandatory': False},
{'name': 'Acquisition', 'type': 'bool', 'mandatory': False},
{'name': 'Center_frequency_offset', 'type': 'float', 'mandatory': False},
{'name': 'Spectral_peak_list_ID', 'type': 'pointer-index', 'mandatory': True,
'default': '1', 'default-from': 'parent'},
{'name': 'Entry_ID', 'type': 'str', 'mandatory': True}],
'Spectral_dim_transfer': [
{'name': 'Type', 'type': 'enum', 'mandatory': True,
'enum': ('onebond', 'jcoupling', 'jmultibond', 'relayed', 'relayed-alternate', 'through-space'),
'enforce-enum': True},
{'name': 'Indirect', 'type': 'bool', 'mandatory': False},
{'name': 'Spectral_peak_list_ID', 'type': 'pointer-index', 'mandatory': True,
'default': '1', 'default-from': 'parent'},
{'name': 'Entry_ID', 'type': 'str', 'mandatory': True}]
}
}

CARTN_DATA_ITEMS = [{'name': 'Cartn_x', 'type': 'float', 'alt_name': 'x'},
Expand Down Expand Up @@ -2075,15 +2117,15 @@
'atom_type': None,
'atom_isotope_number': None,
'spectral_region': None,
'magnetization_linkage_id': None,
# 'magnetization_linkage_id': None, not required for _Peak_row_format loop
'sweep_width': None,
'sweep_width_unit': None,
'value_first_point': None,
'absolute_peak_positions': None,
'acquisition': None,
'center_frequency_offset': None,
'encoding_code': None,
'encoded_reduced_dimension_id': None
# 'encoding_code': None, not required for _Peak_row_format loop
# 'encoded_reduced_dimension_id': None not required for _Peak_row_format loop
}


Expand Down Expand Up @@ -8056,6 +8098,62 @@ def getPkRow(pkSubtype: str, id: int, indexId: int,
return row


def getSpectralDimRow(id: int, listId: int, entryId: str, meta: dict) -> List[Any]:
""" Return row data for a _Spectral_dim loop.
@return: data array
"""

content_subtype = 'spectral_peak'
lp_category = '_Spectral_dim'

key_size = len(NMR_STAR_AUX_LP_KEY_ITEMS[content_subtype][lp_category])
data_items = NMR_STAR_AUX_LP_DATA_ITEMS[content_subtype][lp_category]

row = [None] * (key_size + len(data_items))

row[0] = id

for idx, data_item in enumerate(data_items, start=key_size):
data_name = data_item['name'].lower()
if data_name in meta:
row[idx] = meta[data_name]

row[-2] = listId
row[-1] = entryId

return row


def getSpectralDimTransferRow(listId: int, entryId: str, meta: dict) -> List[Any]:
""" Return row data for a _Spectral_dim_transfer loop.
@return: data array
"""

content_subtype = 'spectral_peak'
lp_category = '_Spectral_dim_transfer'

key_items = NMR_STAR_AUX_LP_KEY_ITEMS[content_subtype][lp_category]
data_items = NMR_STAR_AUX_LP_DATA_ITEMS[content_subtype][lp_category]

key_size = len(key_items)

row = [None] * (key_size + len(data_items))

for idx, key_item in enumerate(key_items):
key_name = key_item['name'].lower()
row[idx] = meta[key_name]

for idx, data_item in enumerate(data_items, start=key_size):
data_name = data_item['name'].lower()
if data_name in meta:
row[idx] = meta[data_name]

row[-2] = listId
row[-1] = entryId

return row


def getMaxEffDigits(vals: List[str]) -> int:
""" Return maximum effective precision of float strings.
"""
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43 changes: 39 additions & 4 deletions wwpdb/utils/nmr/pk/BasePKParserListener.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,9 @@
decListIdCounter,
getSaveframe,
getPkLoop,
getAuxLoops,
getSpectralDimRow,
getSpectralDimTransferRow,
getMaxEffDigits,
roundString,
ISOTOPE_NUMBERS_OF_NMR_OBS_NUCS,
Expand Down Expand Up @@ -91,6 +94,9 @@
decListIdCounter,
getSaveframe,
getPkLoop,
getAuxLoops,
getSpectralDimRow,
getSpectralDimTransferRow,
getMaxEffDigits,
roundString,
ISOTOPE_NUMBERS_OF_NMR_OBS_NUCS,
Expand Down Expand Up @@ -423,7 +429,7 @@ def enter(self):

def exit(self, spectrum_names: Optional[dict] = None):

self.fillSpectralDimTransfer(spectrum_names)
self.fillPkAuxLoops(spectrum_names)

try:

Expand Down Expand Up @@ -760,7 +766,7 @@ def fillAtomTypeInCase(self, _dim_id: int, atom_type: str) -> bool:
return True
return False

def fillSpectralDimTransfer(self, spectrum_names: Optional[dict]):
def fillPkAuxLoops(self, spectrum_names: Optional[dict]):
if len(self.spectral_dim) > 0:
for d, v in self.spectral_dim.items():
for _id, _v in v.items():
Expand Down Expand Up @@ -1140,7 +1146,7 @@ def fillSpectralDimTransfer(self, spectrum_names: Optional[dict]):
if 'yes' in (_dict1['acquisition'], _dict2['acquisition']):
transfer = {'spectral_dim_id_1': min([_dim_id1, _dim_id2]),
'spectral_dim_id_2': max([_dim_id1, _dim_id2]),
'type': 'through-space?',
'type': 'through-space', # optimistic inferencing?
'indirect': 'yes'}
cur_spectral_dim_transfer.append(transfer)

Expand All @@ -1156,7 +1162,7 @@ def fillSpectralDimTransfer(self, spectrum_names: Optional[dict]):
if 'yes' in (_dict1['acquisition'], _dict2['acquisition']):
transfer = {'spectral_dim_id_1': min([_dim_id1, _dim_id2]),
'spectral_dim_id_2': max([_dim_id1, _dim_id2]),
'type': 'through-space?',
'type': 'through-space', # optimistic inferencing?
'indirect': 'yes'}
cur_spectral_dim_transfer.append(transfer)

Expand All @@ -1173,6 +1179,35 @@ def fillSpectralDimTransfer(self, spectrum_names: Optional[dict]):
for transfer in cur_spectral_dim_transfer:
print(transfer)

if self.createSfDict__:
self.cur_subtype = f'peak{d}d'
self.cur_list_id = _id

sf = self.getSf()

list_id = sf['list_id']
sf['aux_loops'] = getAuxLoops('spectral_peak')

aux_lp = next((aux_lp for aux_lp in sf['aux_loops'] if aux_lp.category == '_Spectral_dim'), None)

if aux_lp is None:
continue

for _dim_id, _dict in cur_spectral_dim.items():
aux_lp.add_data(getSpectralDimRow(_dim_id, list_id, self.entryId, _dict))

sf['saveframe'].add_loop(aux_lp)

aux_lp = next((aux_lp for aux_lp in sf['aux_loops'] if aux_lp.category == '_Spectral_dim_transfer'), None)

if aux_lp is None:
continue

for _dict in cur_spectral_dim_transfer:
aux_lp.add_data(getSpectralDimTransferRow(list_id, self.entryId, _dict))

sf['saveframe'].add_loop(aux_lp)

def validatePeak2D(self, index: int, pos_1: float, pos_2: float,
pos_unc_1: Optional[float], pos_unc_2: Optional[float],
lw_1: Optional[float], lw_2: Optional[float],
Expand Down

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