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, common trajectory formats can be loaded as well.
Content#
This file class represents a trajectory file interfacing a trajectory file class from biotraj. |
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Load an |
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Save an |
Subpackages#
The MOL format is used to depict atom positions and bonds for small molecules. |
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This subpackage is used for reading and writing trajectories in the compressed Gromacs XTC format. |
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This subpackage is used for reading and writing trajectories in the AMBER NetCDF format. |
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This subpackage is used for reading and writing trajectories in the CDC format used by software like CHARMM, OpenMM and NAMD. |
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This subpackage is used for reading and writing an |
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This subpackage is used for reading and writing an |
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This subpackage is used for reading and writing trajectories in the uncompressed Gromacs TRR format. |
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This subpackage is used for reading and writing an |
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This subpackage provides support for the the modern PDBx file formats. |