biotite.database.rcsb

A subpackage for downloading files from the RCSB PDB.

Queries

Query

A representation of a JSON query for the RCSB search API.

SingleQuery

A terminal query node for the RCSB search API.

CompositeQuery

A group query node for the RCSB search API.

BasicQuery

A text query for searching for a given term across all available fields.

FieldQuery

A text query for searching for values in a given field using the given operator.

SequenceQuery

A query for protein/DNA/RNA molecules with a sequence similar to a given input sequence using MMseqs2.

MotifQuery

A query for protein/DNA/RNA molecules containing the given sequence motif.

StructureQuery

A query for protein/DNA/RNA molecules with structural similarity to the query structure.

Sorting and grouping

Sorting

Grouping

A representation of the JSON grouping options of the RCSB search API.

DepositGrouping

This class groups PDB entries if they were deposited as a collection.

IdentityGrouping

This class groups protein chains with a given sequence identity with each other.

UniprotGrouping

This class groups protein chains that point to the same Uniprot accession ID.

Search and fetch

count

Count PDB entries that meet the given query requirements, via the RCSB search API.

search

Get all PDB IDs that meet the given query requirements, via the RCSB search API.

fetch

Download structure files (or sequence files) from the RCSB PDB in various formats.