mdtraj.formats.PDBTrajectoryFile

class mdtraj.formats.PDBTrajectoryFile(filename, mode='r', force_overwrite=True, standard_names=True, top=None)

Interface for reading and writing Protein Data Bank (PDB) files

Parameters

filenamepath-like

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_overwritebool

If opened in write mode, and a file by the name of filename already exists on disk, should we overwrite it?

standard_namesbool, 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.

topmdtraj.core.Topology, default=None

if you give a topology as input the topology won’t be parsed from the pdb file it saves time if you have to parse a big number of files

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

positionsnp.ndarray, shape=(n_frames, n_atoms, 3)

The cartesian coordinates of all of the atoms in each frame.

topologymdtraj.Topology

The topology from this PDB file.

closedbool

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, top=None)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__(filename[, mode, force_overwrite, …])	Initialize self.
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

Attributes

closed	Whether the file is closed
distance_unit
positions	The cartesian coordinates of all of the atoms in each frame.
topology	The topology from this PDB file.
unitcell_angles	The unitcell angles (3-tuple) in this PDB file.
unitcell_lengths	The unitcell lengths (3-tuple) in this PDB file.