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DAOTHER-9644: Reconciled fix for 2kny
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@yokochi47
yokochi47 committed Aug 22, 2024
1 parent 2108b19 commit 52d0fed
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Showing 2 changed files with 75 additions and 19 deletions.
81 changes: 62 additions & 19 deletions wwpdb/utils/nmr/io/CifReader.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -927,12 +927,25 @@ def getPolymerSequence(self, catName, keyItems, withStructConf=False, withRmsd=F
BEG_ATOM = "O3'"
END_ATOM = "P"

has_ins_code = False

for p in range(len(authSeqDict[c]) - 1):
s_p = authSeqDict[c][p]
s_q = authSeqDict[c][p + 1]

if s_p is None or s_q is None:
continue

if s_p == s_q:
has_ins_code = True
continue

if s_p + 1 != s_q:

if has_ins_code:
has_ins_code = False
continue

auth_seq_id_1 = s_p
auth_seq_id_2 = s_q

Expand Down Expand Up @@ -982,7 +995,7 @@ def getPolymerSequence(self, catName, keyItems, withStructConf=False, withRmsd=F
ent['seq_id'] = seqDict[c]
ent['comp_id'] = compDict[c]
if c in insCodeDict:
if any(i for i in insCodeDict[c] if i not in self.emptyValue):
if any(ic for ic in insCodeDict[c] if ic not in self.emptyValue):
ent['ins_code'] = insCodeDict[c]
if any(s for s in labelSeqDict[c] if s not in self.emptyValue):
if c in labelSeqDict and all(isinstance(s, int) for s in labelSeqDict[c]):
Expand All @@ -1005,19 +1018,34 @@ def getPolymerSequence(self, catName, keyItems, withStructConf=False, withRmsd=F
if auth_comp_id_col != -1:
ent['auth_comp_id'] = []
if auth_scheme:
for s in authSeqDict[c]:
row = next((row for row in rowList if row[chain_id_col] == c and int(row[auth_seq_id_col]) == s), None)
if row is not None:
comp_id = row[auth_comp_id_col]
if comp_id not in self.emptyValue:
ent['auth_comp_id'].append(comp_id)
if ins_code_col != -1:
for s, ic in zip(authSeqDict[c], insCodeDict[c]):
row = next((row for row in rowList if row[chain_id_col] == c
and int(row[auth_seq_id_col]) == s and row[ins_code_col] == ic), None)
if row is not None:
comp_id = row[auth_comp_id_col]
if comp_id not in self.emptyValue:
ent['auth_comp_id'].append(comp_id)
else:
ent['auth_comp_id'].append('.')
else:
ent['auth_comp_id'].append('.')
else:
for s in authSeqDict[c]:
row = next((row for row in rowList if row[chain_id_col] == c
and int(row[auth_seq_id_col]) == s), None)
if row is not None:
comp_id = row[auth_comp_id_col]
if comp_id not in self.emptyValue:
ent['auth_comp_id'].append(comp_id)
else:
ent['auth_comp_id'].append('.')
else:
ent['auth_comp_id'].append('.')
else:
ent['auth_comp_id'].append('.')
else:
for s in seqDict[c]:
row = next((row for row in rowList if row[chain_id_col] == c and int(row[seq_id_col]) == s), None)
row = next((row for row in rowList if row[chain_id_col] == c
and int(row[seq_id_col]) == s), None)
if row is not None:
comp_id = row[auth_comp_id_col]
if comp_id not in self.emptyValue:
Expand All @@ -1032,19 +1060,34 @@ def getPolymerSequence(self, catName, keyItems, withStructConf=False, withRmsd=F
if alt_comp_id_col != -1:
ent['alt_comp_id'] = []
if auth_scheme:
for s in authSeqDict[c]:
row = next((row for row in rowList if row[chain_id_col] == c and int(row[auth_seq_id_col]) == s), None)
if row is not None:
comp_id = row[alt_comp_id_col]
if comp_id not in self.emptyValue:
ent['alt_comp_id'].append(comp_id)
if ins_code_col != -1:
for s, ic in zip(authSeqDict[c], insCodeDict[c]):
row = next((row for row in rowList if row[chain_id_col] == c
and int(row[auth_seq_id_col]) == s and row[ins_code_col] == ic), None)
if row is not None:
comp_id = row[alt_comp_id_col]
if comp_id not in self.emptyValue:
ent['alt_comp_id'].append(comp_id)
else:
ent['alt_comp_id'].append('.')
else:
ent['alt_comp_id'].append('.')
else:
for s in authSeqDict[c]:
row = next((row for row in rowList if row[chain_id_col] == c
and int(row[auth_seq_id_col]) == s), None)
if row is not None:
comp_id = row[alt_comp_id_col]
if comp_id not in self.emptyValue:
ent['alt_comp_id'].append(comp_id)
else:
ent['alt_comp_id'].append('.')
else:
ent['alt_comp_id'].append('.')
else:
ent['alt_comp_id'].append('.')
else:
for s in seqDict[c]:
row = next((row for row in rowList if row[chain_id_col] == c and int(row[seq_id_col]) == s), None)
row = next((row for row in rowList if row[chain_id_col] == c
and int(row[seq_id_col]) == s), None)
if row is not None:
comp_id = row[alt_comp_id_col]
if comp_id not in self.emptyValue:
Expand Down
13 changes: 13 additions & 0 deletions wwpdb/utils/nmr/mr/ParserListenerUtil.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3583,12 +3583,25 @@ def to_np_array(a):
BEG_ATOM = "O3'"
END_ATOM = "P"

has_ins_code = False

for p in range(len(ps['auth_seq_id']) - 1):
s_p = ps['auth_seq_id'][p]
s_q = ps['auth_seq_id'][p + 1]

if s_p is None or s_q is None:
continue

if s_p == s_q:
has_ins_code = True
continue

if s_p + 1 != s_q:

if has_ins_code:
has_ins_code = False
continue

auth_seq_id_1 = s_p
auth_seq_id_2 = s_q

Expand Down

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