PDBxFile¶
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class
simtk.openmm.app.pdbxfile.
PDBxFile
(file)¶ PDBxFile parses a PDBx/mmCIF file and constructs a Topology and a set of atom positions from it.
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__init__
(file)¶ Load a PDBx/mmCIF file.
The atom positions and Topology can be retrieved by calling getPositions() and getTopology().
- Parameters
file (string) – the name of the file to load. Alternatively you can pass an open file object.
Methods
__init__
(file)Load a PDBx/mmCIF file.
Get the number of frames stored in the file.
getPositions
([asNumpy, frame])Get the atomic positions.
Get the Topology of the model.
writeFile
(topology, positions[, file, …])Write a PDBx/mmCIF file containing a single model.
writeHeader
(topology[, file, entry, keepIds])Write out the header for a PDBx/mmCIF file.
writeModel
(topology, positions[, file, …])Write out a model to a PDBx/mmCIF file.
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getTopology
()¶ Get the Topology of the model.
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getNumFrames
()¶ Get the number of frames stored in the file.
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getPositions
(asNumpy=False, frame=0)¶ Get the atomic positions.
- Parameters
asNumpy (bool=False) – if true, the values are returned as a numpy array instead of a list of Vec3s
frame (int=0) – the index of the frame for which to get positions
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static
writeFile
(topology, positions, file=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>, keepIds=False, entry=None)¶ Write a PDBx/mmCIF file containing a single model.
- Parameters
topology (Topology) – The Topology defining the model to write
positions (list) – The list of atomic positions to write
file (file=stdout) – A file to write to
keepIds (bool=False) – If True, keep the residue and chain IDs specified in the Topology rather than generating new ones. Warning: It is up to the caller to make sure these are valid IDs that satisfy the requirements of the PDBx/mmCIF format. Otherwise, the output file will be invalid.
entry (str=None) – The entry ID to assign to the CIF file
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static
writeHeader
(topology, file=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>, entry=None, keepIds=False)¶ Write out the header for a PDBx/mmCIF file.
- Parameters
topology (Topology) – The Topology defining the molecular system being written
file (file=stdout) – A file to write the file to
entry (str=None) – The entry ID to assign to the CIF file
keepIds (bool=False) – If True, keep the residue and chain IDs specified in the Topology rather than generating new ones. Warning: It is up to the caller to make sure these are valid IDs that satisfy the requirements of the PDBx/mmCIF format. Otherwise, the output file will be invalid.
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static
writeModel
(topology, positions, file=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>, modelIndex=1, keepIds=False)¶ Write out a model to a PDBx/mmCIF file.
- Parameters
topology (Topology) – The Topology defining the model to write
positions (list) – The list of atomic positions to write
file (file=stdout) – A file to write the model to
modelIndex (int=1) – The model number of this frame
keepIds (bool=False) – If True, keep the residue and chain IDs specified in the Topology rather than generating new ones. Warning: It is up to the caller to make sure these are valid IDs that satisfy the requirements of the PDBx/mmCIF format. Otherwise, the output file will be invalid.
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