mdtraj.formats.PDBTrajectoryFile¶
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class
mdtraj.formats.
PDBTrajectoryFile
(filename, mode='r', force_overwrite=True, standard_names=True)¶ Interface for reading and writing Protein Data Bank (PDB) files
Parameters: filename : str
The filename to open. A path to a file on disk.
mode : {‘r’, ‘w’}
The mode in which to open the file, either ‘r’ for read or ‘w’ for write.
force_overwrite : bool
If opened in write mode, and a file by the name of filename already exists on disk, should we overwrite it?
standard_names : bool, default=True
If True, non-standard atomnames and residuenames are standardized to conform with the current PDB format version. If set to false, this step is skipped.
See also
mdtraj.load_pdb
- High-level wrapper that returns a
md.Trajectory
Notes
When writing pdb files, mdtraj follows the PDB3.0 standard as closely as possible. During reading however, we try to be more lenient. For instance, we will parse common nonstandard atom names during reading, and convert them into the standard names. The replacement table used by mdtraj is at {mdtraj_source}/formats/pdb/data/pdbNames.xml.
Attributes
positions
The cartesian coordinates of all of the atoms in each frame. topology
The topology from this PDB file. closed
Whether the file is closed Methods
close
()Close the PDB file set_chain_names
(values)Set the cycle of chain names used when writing PDB files write
(positions, topology[, modelIndex, …])Write a PDB file to disk -
__init__
(filename, mode='r', force_overwrite=True, standard_names=True)¶
Methods
__init__
(filename[, mode, force_overwrite, …])close
()Close the PDB file set_chain_names
(values)Set the cycle of chain names used when writing PDB files write
(positions, topology[, modelIndex, …])Write a PDB file to disk -
close
()¶ Close the PDB file
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closed
¶ Whether the file is closed
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positions
¶ The cartesian coordinates of all of the atoms in each frame. Available when a file is opened in mode=’r’
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classmethod
set_chain_names
(values)¶ Set the cycle of chain names used when writing PDB files
When writing PDB files, PDBTrajectoryFile translates each chain’s index into a name – the name is what’s written in the file. By default, chains are named with the letters A-Z.
Parameters: values : list
A list of chacters (strings of length 1) that the PDB writer will cycle through to choose chain names.
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topology
¶ The topology from this PDB file. Available when a file is opened in mode=’r’
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unitcell_angles
¶ The unitcell angles (3-tuple) in this PDB file. May be None
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unitcell_lengths
¶ The unitcell lengths (3-tuple) in this PDB file. May be None
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write
(positions, topology, modelIndex=None, unitcell_lengths=None, unitcell_angles=None, bfactors=None)¶ Write a PDB file to disk
Parameters: positions : array_like
The list of atomic positions to write.
topology : mdtraj.Topology
The Topology defining the model to write.
modelIndex : {int, None}
If not None, the model will be surrounded by MODEL/ENDMDL records with this index
unitcell_lengths : {tuple, None}
Lengths of the three unit cell vectors, or None for a non-periodic system
unitcell_angles : {tuple, None}
Angles between the three unit cell vectors, or None for a non-periodic system
bfactors : array_like, default=None, shape=(n_atoms,)
Save bfactors with pdb file. Should contain a single number for each atom in the topology