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avoid leaving open file handles #70

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Merged
clami66 merged 1 commit into from
Aug 8, 2025
Merged

avoid leaving open file handles #70

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8 changes: 5 additions & 3 deletions src/DockQ/parsers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ class MMCIFParser(Bio.PDB.MMCIFParser):
def get_structure(
self,
structure_id,
filename,
file,
chains=[],
parse_hetatms=False,
auth_chains=True,
Expand All @@ -24,15 +24,15 @@ def get_structure(

Arguments:
- structure_id - string, the id that will be used for the structure
- filename - name of mmCIF file, OR an open text mode file handle
- file - name of mmCIF file, OR an open text mode file handle

"""
self.auth_chains = auth_chains
self.auth_residues = True
with warnings.catch_warnings():
if self.QUIET:
warnings.filterwarnings("ignore", category=PDBConstructionWarning)
self._mmcif_dict = MMCIF2Dict(filename)
self._mmcif_dict = MMCIF2Dict(file)
sequences, is_het = self._build_structure(
structure_id, chains, parse_hetatms=parse_hetatms
)
Expand All @@ -43,6 +43,7 @@ def get_structure(
for chain in model:
chain.sequence = sequences[chain.id]
chain.is_het = is_het[chain.id]
file.close()
return model

def _build_structure(self, structure_id, chains, parse_hetatms):
Expand Down Expand Up @@ -295,6 +296,7 @@ def get_structure(self, id, file, chains, parse_hetatms, model_number=0):
for chain in model:
chain.sequence = sequences[chain.id]
chain.is_het = is_het[chain.id]
file.close()
return model

def _parse(self, header_coords_trailer, chains, parse_hetatms):
Expand Down