biotite.structure.io.pdbx¶

This subpackage provides support for the the modern PDBx file formats. The CIFFile class provides dictionary-like access to every field in text-based mmCIF files. BinaryCIFFile provides analogous functionality for the BinaryCIF format. Additional utility functions allow reading and writing structures from/to these files.

High-level functionality¶

`get_sequence`	Get the protein and nucleotide sequences from the `entity_poly.pdbx_seq_one_letter_code_can` entry.
`get_model_count`	Get the number of models contained in a `PDBxFile`.
`get_structure`	Create an `AtomArray` or `AtomArrayStack` from the `atom_site` category in a `PDBxFile`.
`set_structure`	Set the `atom_site` category with atom information from an `AtomArray` or `AtomArrayStack`.
`get_component`	Create an `AtomArray` for a chemical component from the `chem_comp_atom` and, if available, the `chem_comp_bond` category in a `PDBxFile`.
`set_component`	Set the `chem_comp_atom` and, if bonds are available, `chem_comp_bond` category with atom information from an `AtomArray`.
`list_assemblies`	List the biological assemblies that are available for the structure in the given file.
`get_assembly`	Build the given biological assembly.

CIF format¶

`CIFFile`	This class represents a CIF file.
`CIFBlock`	This class represents a block in a `CIFFile`.
`CIFCategory`	This class represents a category in a `CIFBlock`.
`CIFColumn`	This class represents a single column in a `CIFCategory`.
`CIFData`	This class represents the data in a `CIFColumn`.

BinaryCIF format¶

`BinaryCIFFile`	This class represents a BinaryCIF file.
`BinaryCIFBlock`	This class represents a block in a `BinaryCIFFile`.
`BinaryCIFCategory`	This class represents a category in a `BinaryCIFBlock`.
`BinaryCIFColumn`	This class represents a single column in a `CIFCategory`.
`BinaryCIFData`	This class represents the data in a `BinaryCIFColumn`.

BinaryCIF encodings¶

`ByteArrayEncoding`	Encoding that encodes an array into bytes.
`FixedPointEncoding`	Lossy encoding that multiplies floating point values with a given factor and subsequently rounds them to the nearest integer.
`IntervalQuantizationEncoding`	Lossy encoding that sorts floating point values into bins.
`RunLengthEncoding`	Encoding that compresses runs of equal values into pairs of (value, run length).
`DeltaEncoding`	Encoding that encodes an array of integers into an array of consecutive differences.
`IntegerPackingEncoding`	Encoding that compresses an array of 32-bit integers into an array of smaller sized integers.
`StringArrayEncoding`	Encoding that compresses an array of strings into an array of indices that point to the unique strings in that array.
`TypeCode`	This enum type represents integers that represent data types in BinaryCIF.

Miscellaneous¶

`DeserializationError`
`MaskValue`	This enum type represents the possible values of a mask array.
`PDBxFile`	This class represents the legacy interface to CIF files.
`SerializationError`