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

MaskValue

This enum type represents the possible values of a mask array.

PDBxFile

This class represents the legacy interface to CIF files.