PDBxFile

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.

__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.
__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__
__setattr__

x.__setattr__(‘name’, value) <==> x.name = value

__sizeof__() → int

size of object in memory, in bytes

__str__
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
getTopology()

Get the Topology of the model.

static writeFile(topology, positions, file=<open file '<stdout>', mode 'w'>, 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
static writeHeader(topology, file=<open file '<stdout>', mode 'w'>, 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=<open file '<stdout>', mode 'w'>, 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.