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make unite_chains True in parseMMCIFStream
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jamesmkrieger committed Oct 12, 2023
1 parent 39feb39 commit 709014a
Showing 1 changed file with 5 additions and 8 deletions.
13 changes: 5 additions & 8 deletions prody/proteins/ciffile.py
Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,10 @@ class MMCIFParseError(Exception):
alternate locations will be parsed and each will be appended as a
distinct coordinate set, default is ``"A"``
:type altloc: str
:arg unite_chains: unite chains with the same segment name
Default is *False*
:type unite_chains: bool
"""

_PDBSubsets = {'ca': 'ca', 'calpha': 'ca', 'bb': 'bb', 'backbone': 'bb'}
Expand All @@ -71,13 +75,6 @@ def parseMMCIF(pdb, **kwargs):
:arg pdb: a PDB identifier or a filename
If needed, mmCIF files are downloaded using :func:`.fetchPDB()` function.
:type pdb: str
:arg chain: comma separated string or list-like of chain IDs
:type chain: str, tuple, list, :class:`~numpy.ndarray`
:arg unite_chains: unite chains with the same segment name
Default is *False*
:type unite_chains: bool
"""
chain = kwargs.pop('chain', None)
segment = kwargs.pop('segment', None)
Expand Down Expand Up @@ -163,7 +160,7 @@ def parseMMCIFStream(stream, **kwargs):
subset = kwargs.get('subset')
chain = kwargs.get('chain')
segment = kwargs.get('segment')
unite_chains = kwargs.get('unite_chains')
unite_chains = kwargs.get('unite_chains', True)
altloc = kwargs.get('altloc', 'A')
header = kwargs.get('header', False)
assert isinstance(header, bool), 'header must be a boolean'
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