PDBxFile¶

class openmm.app.pdbxfile.PDBxFile(file)¶

PDBxFile parses a PDBx/mmCIF file and constructs a Topology and a set of atom positions from it.

__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.
`getNumFrames`()	Get the number of frames stored in the file.
`getPositions`([asNumpy, frame])	Get the atomic positions.
`getTopology`()	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.

getTopology()¶: Get the Topology of the model.

getNumFrames()¶: Get the number of frames stored in the file.

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

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 (string or file) – the name of the file to write. Alternatively you can pass an open file object.
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

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.

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.