mdtraj.formats.PDBTrajectoryFile

class mdtraj.formats.PDBTrajectoryFile(filename, mode='r', force_overwrite=True, standard_names=True, top=None, bond_orders=False)[source]

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

Parameters:

filename (path-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_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.
top (mdtraj.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
bond_orders (bool, default=False) – If False (default), the parser ignores any additional duplicate bonds in the CONECT section. If True, the reader will respect and infer bond order/type based on the CONECT section, where consecutive listing of bonds are treated as having a higher bond order. If the bond is listed multiple times in the CONECT section, the highest listed bond order prevails.

positions

Type:: np.ndarray, shape=(n_frames, n_atoms, 3)

topology

Type:: mdtraj.Topology

closed

Type:: bool

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.

See also

mdtraj.load_pdb: High-level wrapper that returns a md.Trajectory

Attributes:

closed: Whether the file is closed
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.

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, bond_orders=False)[source]

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

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.