biotite.structure.io¶

A subpackage for reading and writing structure related data.

Macromolecular structure files (PDB, PDBx/mmCIF, BinaryCIF, etc.) and small molecule files (MOL, SDF, etc.) can be used to load an AtomArray or AtomArrayStack.

Since the data model for the AtomArray and AtomArrayStack class does not support duplicate atoms, only one altloc can be chosen for each atom. Hence, the amount of atoms may be lower in the atom array (stack) than in respective structure file.

The recommended format for reading structure files is BinaryCIF. It has by far the shortest parsing time and file size.

Besides the mentioned structure formats, Gromacs trajectory files can be loaded, if mdtraj is installed.

Content¶

`TrajectoryFile`	This file class represents a trajectory file interfacing a trajectory file class from MDtraj.
`load_structure`	Load an `AtomArray` or class`AtomArrayStack` from a structure file without the need to manually instantiate a `File` object.
`read_structure_from_ctab`	Parse a MDL connection table (Ctab) to obtain an `AtomArray`.
`save_structure`	Save an `AtomArray` or class`AtomArrayStack` to a structure file without the need to manually instantiate a `File` object.
`write_structure_to_ctab`	Convert an `AtomArray` into a MDL connection table (Ctab).

Subpackages¶

`biotite.structure.io.netcdf`	This subpackage is used for reading and writing trajectories in the AMBER NetCDF format.
`biotite.structure.io.mol`	The MOL format is used to depict atom positions and bonds for small molecules.
`biotite.structure.io.dcd`	This subpackage is used for reading and writing trajectories in the CDC format used by software like CHARMM, OpenMM and NAMD.
`biotite.structure.io.trr`	This subpackage is used for reading and writing trajectories in the uncompressed Gromacs TRR format.
`biotite.structure.io.pdbx`	This subpackage provides support for the the modern PDBx file formats.
`biotite.structure.io.pdbqt`	This subpackage is used for reading and writing an `AtomArray` or `AtomArrayStack` using the PDBQT format used by the AutoDock software series.
`biotite.structure.io.xtc`	This subpackage is used for reading and writing trajectories in the compressed Gromacs XTC format.
`biotite.structure.io.npz`	This subpackage is used for reading and writing an `AtomArray` or `AtomArrayStack` using the internal NPZ file format.
`biotite.structure.io.mmtf`	This subpackage is used for reading and writing an `AtomArray` or `AtomArrayStack` using the binary MMTF format.
`biotite.structure.io.gro`	This subpackage is used for reading and writing an `AtomArray` or `AtomArrayStack` using the Gro format used by the gromacs software package.
`biotite.structure.io.pdb`	This subpackage is used for reading and writing an `AtomArray` or `AtomArrayStack` using the popular PDB format.
`biotite.structure.io.tng`	This subpackage is used for reading and writing trajectories in the compressed Gromacs TNG format.