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Fix for tox unit test
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@yokochi47
yokochi47 committed Mar 28, 2024
1 parent d5d6c82 commit 1b74793
Showing 1 changed file with 60 additions and 63 deletions.
123 changes: 60 additions & 63 deletions wwpdb/utils/nmr/NmrDpUtility.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17510,7 +17510,7 @@ def __extractNonStandardResidue__(self, file_name, sf_framecode, lp_category, in

# DAOTHER-9065
else:
warn = f"Residue ({s['chain_id']}:{seq_id}:{comp_id}) was not specified. "\
warn = f"Residue ({ps['chain_id']}:{seq_id}:{comp_id}) was not specified. "\
"Please update the sequence in the Macromolecules page."

self.report.warning.appendDescription('sequence_mismatch',
Expand Down Expand Up @@ -28326,7 +28326,7 @@ def __testResidueVariant(self):
cif_input_source = self.report.input_sources[src_id]
cif_input_source_dic = cif_input_source.get()

has_poly_seq = has_key_value(input_source_dic, 'polymer_sequence')
has_poly_seq = has_key_value(cif_input_source_dic, 'polymer_sequence')

if not has_poly_seq:
return False
Expand Down Expand Up @@ -28793,10 +28793,10 @@ def __validateStrMr(self):
if src_id < 0:
return False

input_source = self.report.input_sources[src_id]
input_source_dic = input_source.get()
cif_input_source = self.report.input_sources[src_id]
cif_input_source_dic = cif_input_source.get()

has_poly_seq = has_key_value(input_source_dic, 'polymer_sequence')
has_poly_seq = has_key_value(cif_input_source_dic, 'polymer_sequence')

if not has_poly_seq:
return False
Expand Down Expand Up @@ -30852,9 +30852,6 @@ def __mergeStrPk(self):
if src_id < 0:
return False

input_source = self.report.input_sources[src_id]
input_source_dic = input_source.get()

if self.__pk_sf_holder is None:
self.__pk_sf_holder = []

Expand Down Expand Up @@ -31131,10 +31128,10 @@ def __validateLegacyMr(self):
if src_id < 0:
return False

input_source = self.report.input_sources[src_id]
input_source_dic = input_source.get()
cif_input_source = self.report.input_sources[src_id]
cif_input_source_dic = cif_input_source.get()

has_poly_seq = has_key_value(input_source_dic, 'polymer_sequence')
has_poly_seq = has_key_value(cif_input_source_dic, 'polymer_sequence')

if not has_poly_seq:
return False
Expand Down Expand Up @@ -33972,10 +33969,10 @@ def __validateStrPk(self):
if src_id < 0:
return False

input_source = self.report.input_sources[src_id]
input_source_dic = input_source.get()
cif_input_source = self.report.input_sources[src_id]
cif_input_source_dic = cif_input_source.get()

has_poly_seq = has_key_value(input_source_dic, 'polymer_sequence')
has_poly_seq = has_key_value(cif_input_source_dic, 'polymer_sequence')

if not has_poly_seq:
return False
Expand Down Expand Up @@ -41005,14 +41002,14 @@ def __detectCoordContentSubType(self):
if src_id < 0:
return False

input_source = self.report.input_sources[src_id]
input_source_dic = input_source.get()
cif_input_source = self.report.input_sources[src_id]
cif_input_source_dic = cif_input_source.get()

if has_key_value(input_source_dic, 'content_subtype'):
if has_key_value(cif_input_source_dic, 'content_subtype'):
return False

# file_name = input_source_dic['file_name']
file_type = input_source_dic['file_type']
# file_name = cif_input_source_dic['file_name']
file_type = cif_input_source_dic['file_type']

# initialize loop counter
lp_counts = {t: 0 for t in self.cif_content_subtypes}
Expand Down Expand Up @@ -41046,7 +41043,7 @@ def __detectCoordContentSubType(self):

content_subtypes = {k: lp_counts[k] for k in lp_counts if lp_counts[k] > 0}

input_source.setItemValue('content_subtype', content_subtypes)
cif_input_source.setItemValue('content_subtype', content_subtypes)

return True

Expand All @@ -41059,21 +41056,21 @@ def __extractCoordPolymerSequence(self):
if src_id < 0:
return False

input_source = self.report.input_sources[src_id]
input_source_dic = input_source.get()
cif_input_source = self.report.input_sources[src_id]
cif_input_source_dic = cif_input_source.get()

file_name = input_source_dic['file_name']
file_type = input_source_dic['file_type']
file_name = cif_input_source_dic['file_name']
file_type = cif_input_source_dic['file_type']

if input_source_dic['content_subtype'] is None:
if cif_input_source_dic['content_subtype'] is None:
return False

content_subtype = 'poly_seq'

if content_subtype not in input_source_dic['content_subtype']:
if content_subtype not in cif_input_source_dic['content_subtype']:
return False

if has_key_value(input_source_dic, 'polymer_sequence'):
if has_key_value(cif_input_source_dic, 'polymer_sequence'):
return False

alias = False
Expand Down Expand Up @@ -41147,7 +41144,7 @@ def __extractCoordPolymerSequence(self):
if len(poly_seq) > 0 and poly_seq_cache_path is not None:
write_as_pickle(poly_seq, poly_seq_cache_path)

input_source.setItemValue('polymer_sequence', poly_seq)
cif_input_source.setItemValue('polymer_sequence', poly_seq)

not_superimposed_ensemble = {}
exactly_overlaid_ensemble = {}
Expand Down Expand Up @@ -41400,14 +41397,14 @@ def __extractCoordAtomSite(self):
if self.__coord_atom_site is not None:
return True

input_source = self.report.input_sources[src_id]
input_source_dic = input_source.get()
cif_input_source = self.report.input_sources[src_id]
cif_input_source_dic = cif_input_source.get()

file_name = input_source_dic['file_name']
file_name = cif_input_source_dic['file_name']

has_poly_seq = has_key_value(input_source_dic, 'polymer_sequence')
has_poly_seq = has_key_value(cif_input_source_dic, 'polymer_sequence')

polymer_sequence = input_source_dic['polymer_sequence'] if has_poly_seq else []
polymer_sequence = cif_input_source_dic['polymer_sequence'] if has_poly_seq else []

if has_poly_seq and any('auth_chain_id' not in ps for ps in polymer_sequence):
has_poly_seq = False
Expand Down Expand Up @@ -41610,17 +41607,17 @@ def __extractCoordPolymerSequenceInLoop(self):

__errors = self.report.getTotalErrors()

input_source = self.report.input_sources[src_id]
input_source_dic = input_source.get()
cif_input_source = self.report.input_sources[src_id]
cif_input_source_dic = cif_input_source.get()

file_name = input_source_dic['file_name']
file_type = input_source_dic['file_type']
file_name = cif_input_source_dic['file_name']
file_type = cif_input_source_dic['file_type']

poly_seq_list_set = {}

for content_subtype in self.cif_content_subtypes:

if content_subtype in ('entry_info', 'poly_seq', 'branched', 'non_poly') or (not has_key_value(input_source_dic['content_subtype'], content_subtype)):
if content_subtype in ('entry_info', 'poly_seq', 'branched', 'non_poly') or (not has_key_value(cif_input_source_dic['content_subtype'], content_subtype)):
continue

poly_seq_list_set[content_subtype] = []
Expand Down Expand Up @@ -41717,7 +41714,7 @@ def __extractCoordPolymerSequenceInLoop(self):
return False

if len(poly_seq_list_set) > 0:
input_source.setItemValue('polymer_sequence_in_loop', poly_seq_list_set)
cif_input_source.setItemValue('polymer_sequence_in_loop', poly_seq_list_set)

return True

Expand All @@ -41735,17 +41732,17 @@ def __extractCoordCommonPolymerSequence(self):
if src_id < 0:
return False

input_source = self.report.input_sources[src_id]
input_source_dic = input_source.get()
cif_input_source = self.report.input_sources[src_id]
cif_input_source_dic = cif_input_source.get()

has_poly_seq = has_key_value(input_source_dic, 'polymer_sequence')
has_poly_seq_in_loop = has_key_value(input_source_dic, 'polymer_sequence_in_loop')
has_poly_seq = has_key_value(cif_input_source_dic, 'polymer_sequence')
has_poly_seq_in_loop = has_key_value(cif_input_source_dic, 'polymer_sequence_in_loop')

# pass if poly_seq exists
if has_poly_seq or (not has_poly_seq_in_loop):
return False

polymer_sequence_in_loop = input_source_dic['polymer_sequence_in_loop']
polymer_sequence_in_loop = cif_input_source_dic['polymer_sequence_in_loop']

chain_ids = set()

Expand Down Expand Up @@ -41807,7 +41804,7 @@ def __extractCoordCommonPolymerSequence(self):
asm.append({'chain_id': chain_id, 'seq_id': seq_id_list, 'comp_id': comp_id_list})

if len(asm) > 0:
input_source.setItemValue('polymer_sequence', asm)
cif_input_source.setItemValue('polymer_sequence', asm)

return True

Expand All @@ -41820,18 +41817,18 @@ def __extractCoordNonStandardResidue(self):
if src_id < 0:
return False

input_source = self.report.input_sources[src_id]
input_source_dic = input_source.get()
cif_input_source = self.report.input_sources[src_id]
cif_input_source_dic = cif_input_source.get()

# file_name = input_source_dic['file_name']
# file_type = input_source_dic['file_type']
# file_name = cif_input_source_dic['file_name']
# file_type = cif_input_source_dic['file_type']

has_poly_seq = has_key_value(input_source_dic, 'polymer_sequence')
has_poly_seq = has_key_value(cif_input_source_dic, 'polymer_sequence')

if not has_poly_seq:
return False

polymer_sequence = input_source_dic['polymer_sequence']
polymer_sequence = cif_input_source_dic['polymer_sequence']

asm = []

Expand Down Expand Up @@ -41866,7 +41863,7 @@ def __extractCoordNonStandardResidue(self):
asm.append(ent)

if len(asm) > 0:
input_source.setItemValue('non_standard_residue', asm)
cif_input_source.setItemValue('non_standard_residue', asm)

return True

Expand All @@ -41881,20 +41878,20 @@ def __appendCoordPolymerSequenceAlignment(self):

# sequence alignment inside coordinate file

input_source = self.report.input_sources[src_id]
input_source_dic = input_source.get()
cif_input_source = self.report.input_sources[src_id]
cif_input_source_dic = cif_input_source.get()

has_poly_seq = has_key_value(input_source_dic, 'polymer_sequence')
has_poly_seq_in_loop = has_key_value(input_source_dic, 'polymer_sequence_in_loop')
has_poly_seq = has_key_value(cif_input_source_dic, 'polymer_sequence')
has_poly_seq_in_loop = has_key_value(cif_input_source_dic, 'polymer_sequence_in_loop')

if not has_poly_seq:
return False

polymer_sequence = input_source_dic['polymer_sequence']
polymer_sequence = cif_input_source_dic['polymer_sequence']

if has_poly_seq_in_loop:

polymer_sequence_in_loop = input_source_dic['polymer_sequence_in_loop']
polymer_sequence_in_loop = cif_input_source_dic['polymer_sequence_in_loop']

for content_subtype in polymer_sequence_in_loop.keys():

Expand Down Expand Up @@ -46912,7 +46909,7 @@ def __testTautomerOfHistidinePerModel(self):
cif_input_source = self.report.input_sources[src_id]
cif_input_source_dic = cif_input_source.get()

has_poly_seq = has_key_value(input_source_dic, 'polymer_sequence')
has_poly_seq = has_key_value(cif_input_source_dic, 'polymer_sequence')

if not has_poly_seq:
return False
Expand Down Expand Up @@ -47486,7 +47483,7 @@ def __extractCoordDisulfideBond(self):
if src_id < 0:
return False

input_source = self.report.input_sources[src_id]
cif_input_source = self.report.input_sources[src_id]

chain_assign_dic = self.report.chain_assignment.get()

Expand Down Expand Up @@ -47555,7 +47552,7 @@ def __extractCoordDisulfideBond(self):
asm.append(disulf)

if len(asm) > 0:
input_source.setItemValue('disulfide_bond', asm)
cif_input_source.setItemValue('disulfide_bond', asm)

self.report.setDisulfideBond(True)

Expand Down Expand Up @@ -47876,7 +47873,7 @@ def __extractCoordOtherBond(self):
if src_id < 0:
return False

input_source = self.report.input_sources[src_id]
cif_input_source = self.report.input_sources[src_id]

chain_assign_dic = self.report.chain_assignment.get()

Expand Down Expand Up @@ -47945,7 +47942,7 @@ def __extractCoordOtherBond(self):
asm.append(other)

if len(asm) > 0:
input_source.setItemValue('other_bond', asm)
cif_input_source.setItemValue('other_bond', asm)

self.report.setOtherBond(True)

Expand Down

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