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DAOTHER-9520: (1) Fix KeyError exception of the previous commit, (2) …
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…Refresh _Ambiguous_atom_chem_shift loop, and (3) Make sure to be NEF complient (Reveme _nef_chemical_shift_list.Data_file_name and _nef_chemical_shift_list.ID)
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@yokochi47
yokochi47 committed Jun 28, 2024
1 parent a2f38a4 commit 5077bde
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Showing 12 changed files with 435 additions and 308 deletions.
28 changes: 20 additions & 8 deletions wwpdb/utils/nmr/NEFTranslator/NEFTranslator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -94,7 +94,7 @@
# 13-Sep-2023 M. Yokochi - fix/improve NEF atom nomenclature mapping (v3.5.0, DAOTHER-8817)
# 02-Oct-2023 M. Yokochi - do not reorganize _Gen_dist_constraint.ID (v3.5.1, DAOTHER-8855)
# 11-Jun-2024 M. Yokochi - add support for ligand remapping in annotation process (v3.6.0, DAOTHER-9286)
# 27-Jun-2024 M. Yokochi - do not evaluate value in case of ValueError exception (v3.6.1, DAOTHER-9520)
# 28-Jun-2024 M. Yokochi - do not evaluate value in case of ValueError exception (v3.6.1, DAOTHER-9520)
##
""" Bi-directional translator between NEF and NMR-STAR
@author: Kumaran Baskaran, Masashi Yokochi
Expand Down Expand Up @@ -3648,7 +3648,6 @@ def skip_empty_value_error(lp, idx):
else:
raise ValueError(get_idx_msg(idx_tag_ids, tags, ent)
+ f"{name} {val!r} must be {self.readableItemType[type]}.")
continue

if (type == 'index-int' and ent[name] <= 0)\
or (type == 'positive-int' and (ent[name] < 0 or (ent[name] == 0 and 'enforce-non-zero' in k and k['enforce-non-zero']))):
Expand All @@ -3665,6 +3664,7 @@ def skip_empty_value_error(lp, idx):
f"as defined by {self.readableItemType[type]}.")
if type == 'positive-int-as-str':
row[j] = ent[name] = str(ent[name])

elif type == 'pointer-index':
try:
ent[name] = int(val)
Expand Down Expand Up @@ -3692,7 +3692,6 @@ def skip_empty_value_error(lp, idx):
else:
raise ValueError(get_idx_msg(idx_tag_ids, tags, ent)
+ f"{name} {val!r} must be {self.readableItemType[type]}.")
continue

if ent[name] <= 0:
raise ValueError(get_idx_msg(idx_tag_ids, tags, ent)
Expand Down Expand Up @@ -3752,6 +3751,7 @@ def skip_empty_value_error(lp, idx):
f.append(f"[Zero value error] {get_idx_msg(idx_tag_ids, tags, ent)}"
f"{name} {val!r} should not be zero, "
f"as defined by {self.readableItemType[type]}.")

elif type == 'range-float':
try:
_range = k['range']
Expand Down Expand Up @@ -3852,6 +3852,7 @@ def skip_empty_value_error(lp, idx):
ent[name] = val
except KeyError:
raise ValueError(f"Enumeration of key item {name} is not defined")

elif type == 'enum-int':
try:
enum = k['enum']
Expand Down Expand Up @@ -3894,11 +3895,11 @@ def skip_empty_value_error(lp, idx):
val = indexToLetter(letterToDigit(val, 1) - 1)
elif 'default' in k:
val = k['default']
elif skip_empty_value_error(loop, idx):
continue
else:
elif excl_missing_data:
missing_mandatory_data = True
continue
elif skip_empty_value_error(loop, idx):
continue
if 'uppercase' in k and k['uppercase']:
val = val.upper()
row[j] = ent[name] = val
Expand Down Expand Up @@ -3981,6 +3982,7 @@ def skip_empty_value_error(lp, idx):
else:
raise ValueError(get_idx_msg(idx_tag_ids, tags, ent)
+ f"{name} {val!r} must be {self.readableItemType[type]}.")

elif type in ('index-int', 'positive-int', 'positive-int-as-str'):
try:
ent[name] = int(val)
Expand Down Expand Up @@ -4016,7 +4018,6 @@ def skip_empty_value_error(lp, idx):
else:
raise ValueError(get_idx_msg(idx_tag_ids, tags, ent)
+ f"{name} {val!r} must be {self.readableItemType[type]}.")
continue

if (type == 'index-int' and ent[name] <= 0)\
or (type == 'positive-int' and (ent[name] < 0 or (ent[name] == 0 and 'enforce-non-zero' in d and d['enforce-non-zero']))):
Expand All @@ -4033,6 +4034,7 @@ def skip_empty_value_error(lp, idx):
f"as defined by {self.readableItemType[type]}.")
if type == 'positive-int-as-str':
row[j] = ent[name] = str(ent[name])

elif type == 'pointer-index':
try:
ent[name] = int(val)
Expand Down Expand Up @@ -4066,7 +4068,6 @@ def skip_empty_value_error(lp, idx):
else:
raise ValueError(get_idx_msg(idx_tag_ids, tags, ent)
+ f"{name} {val!r} must be {self.readableItemType[type]}.")
continue

if ent[name] <= 0:
raise ValueError(get_idx_msg(idx_tag_ids, tags, ent)
Expand All @@ -4076,6 +4077,7 @@ def skip_empty_value_error(lp, idx):
elif val != static_val[name] and _test_on_index:
raise ValueError(get_idx_msg(idx_tag_ids, tags, ent)
+ f"{name} {val} vs {static_val[name]} must be {self.readableItemType[type]}.")

elif type == 'float':
try:
ent[name] = float(val)
Expand Down Expand Up @@ -4243,6 +4245,7 @@ def skip_empty_value_error(lp, idx):
else:
f.append(f"[Range value error] {get_idx_msg(idx_tag_ids, tags, ent)}"
f"{name} {val!r} must be within range {_range}.")

elif type == 'enum':
try:
enum = d['enum']
Expand Down Expand Up @@ -4280,6 +4283,7 @@ def skip_empty_value_error(lp, idx):
ent[name] = val
except KeyError:
raise ValueError(f"Enumeration of data item {name} is not defined")

elif type == 'enum-int':
try:
enum = d['enum']
Expand Down Expand Up @@ -4318,6 +4322,7 @@ def skip_empty_value_error(lp, idx):
continue
raise ValueError(get_idx_msg(idx_tag_ids, tags, ent)
+ f"{name} {val!r} must be {self.readableItemType[type]}.")

else:
if ('remove-bad-pattern' in d and d['remove-bad-pattern']) or ('clear-bad-pattern' in d and d['clear-bad-pattern']):
if isinstance(val, str) and badPattern.match(val):
Expand Down Expand Up @@ -4825,6 +4830,7 @@ def check_sf_tag(self, star_data, file_type, category, tag_items, allowed_tags=N
ent[name] = val.lower() in trueValue
except ValueError:
raise ValueError(f"{name} {val!r} must be {self.readableItemType[type]}.")

elif type == 'int':
try:
ent[name] = int(val)
Expand All @@ -4837,6 +4843,7 @@ def check_sf_tag(self, star_data, file_type, category, tag_items, allowed_tags=N
ent[name] = int(t['default'])
else:
raise ValueError(f"{name} {val!r} must be {self.readableItemType[type]}.")

elif type in ('positive-int', 'positive-int-as-str'):
try:
ent[name] = int(val)
Expand Down Expand Up @@ -4865,11 +4872,13 @@ def check_sf_tag(self, star_data, file_type, category, tag_items, allowed_tags=N
f"as defined by {self.readableItemType[type]}.")
if type == 'positive-int-as-str':
ent[name] = str(ent[name])

elif type == 'float':
try:
ent[name] = float(val)
except ValueError:
raise ValueError(f"{name} {val!r} must be {self.readableItemType[type]}.")

elif type == 'positive-float':
try:
ent[name] = float(val)
Expand All @@ -4885,6 +4894,7 @@ def check_sf_tag(self, star_data, file_type, category, tag_items, allowed_tags=N
else:
f.append(f"[Zero value error] {name} {val!r} should not be zero, "
f"as defined by {self.readableItemType[type]}.")

elif type == 'range-float':
try:
_range = t['range']
Expand Down Expand Up @@ -4934,6 +4944,7 @@ def check_sf_tag(self, star_data, file_type, category, tag_items, allowed_tags=N
ent[name] = None
else:
f.append(f"[Range value error] {name} {val} must be within range {_range}.")

elif type == 'enum':
if val in emptyValue:
val = '?' # '.' raises internal error in NmrDpUtility
Expand Down Expand Up @@ -4965,6 +4976,7 @@ def check_sf_tag(self, star_data, file_type, category, tag_items, allowed_tags=N
ent[name] = None if val in emptyValue else val
except KeyError:
raise ValueError(f"Enumeration of tag item {name} is not defined.")

elif type == 'enum-int':
try:
enum = t['enum']
Expand Down
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