pdbsearch.search

pdbsearch.search.search(return_type='entry', **kwargs)[source]

Searches the RCSB API with multiple nodes, based on the parameters given. Any nodes created will be combined using an “and” operator.

Parameters:

  • term (str) – the search term for full text search.

  • protein (str) – a protein sequence or pattern.

  • dna (str) – a DNA sequence or pattern.

  • rna (str) – an RNA sequence or pattern.

  • identity (float) – the identity cutoff for sequence search.

  • evalue (float) – the evalue cutoff for sequence search.

  • pattern_type (str) – the type of pattern for sequence motif search.

  • structure (str) – a structure identifier for structure search.

  • operator (str) – the operator for structure search.

  • entry (str) – a PDB entry identifier for structure motif search.

  • residues (tuple) – a tuple of residue numbers for structure motif search.

  • rmsd (float) – the RMSD cutoff for structure motif search.

  • exchanges (dict) – a dictionary of residue exchanges for structure motif search.

  • smiles (str) – a SMILES string for chemical search.

  • inchi (str) – an InChI string for chemical search.

  • match_type (str) – the type of match for chemical search.

  • return_type (str) – the type of data to return.

  • return_all (bool) – whether to return all results, unpaginated.

  • start (int) – the start index of the results.

  • rows (int) – the number of results to return.

  • sort (str or list[str]) – the attribute or attributes to sort by.

  • counts_only (bool) – whether to return only the count of results.

  • content_types (list[str]) – the PDB types (experimental/computational).

  • facets (list[str]) – RCSB aggregation terms.

Return type:

dict

pdbsearch.search.search_assemblies(**kwargs)[source]

Searches the RCSB API for assemblies, based on the parameters given.

Parameters:

  • return_all (bool) – whether to return all results, unpaginated.

  • start (int) – the start index of the results.

  • rows (int) – the number of results to return.

  • sort (str or list[str]) – the attribute or attributes to sort by.

  • counts_only (bool) – whether to return only the count of results.

  • content_types (list[str]) – the PDB types (experimental/computational).

  • facets (list[str]) – RCSB aggregation terms.

Return type:

dict

pdbsearch.search.search_entries(**kwargs)[source]

Searches the RCSB API for entries, based on the parameters given.

Parameters:

  • return_all (bool) – whether to return all results, unpaginated.

  • start (int) – the start index of the results.

  • rows (int) – the number of results to return.

  • sort (str or list[str]) – the attribute or attributes to sort by.

  • counts_only (bool) – whether to return only the count of results.

  • content_types (list[str]) – the PDB types (experimental/computational).

  • facets (list[str]) – RCSB aggregation terms.

Return type:

dict

pdbsearch.search.search_mols(**kwargs)[source]

Searches the RCSB API for chemical structures, based on the parameters given.

Parameters:

  • return_all (bool) – whether to return all results, unpaginated.

  • start (int) – the start index of the results.

  • rows (int) – the number of results to return.

  • sort (str or list[str]) – the attribute or attributes to sort by.

  • counts_only (bool) – whether to return only the count of results.

  • content_types (list[str]) – the PDB types (experimental/computational).

  • facets (list[str]) – RCSB aggregation terms.

Return type:

dict

pdbsearch.search.search_non_polymer_entities(**kwargs)[source]

Searches the RCSB API for non-polymer entities, based on the parameters given.

Parameters:

  • return_all (bool) – whether to return all results, unpaginated.

  • start (int) – the start index of the results.

  • rows (int) – the number of results to return.

  • sort (str or list[str]) – the attribute or attributes to sort by.

  • counts_only (bool) – whether to return only the count of results.

  • content_types (list[str]) – the PDB types (experimental/computational).

  • facets (list[str]) – RCSB aggregation terms.

Return type:

dict

pdbsearch.search.search_polymer_entities(**kwargs)[source]

Searches the RCSB API for polymer entities, based on the parameters given.

Parameters:

  • return_all (bool) – whether to return all results, unpaginated.

  • start (int) – the start index of the results.

  • rows (int) – the number of results to return.

  • sort (str or list[str]) – the attribute or attributes to sort by.

  • counts_only (bool) – whether to return only the count of results.

  • content_types (list[str]) – the PDB types (experimental/computational).

  • facets (list[str]) – RCSB aggregation terms.

Return type:

dict

pdbsearch.search.search_polymers(**kwargs)[source]

Searches the RCSB API for polymer instances, based on the parameters given.

Parameters:

  • return_all (bool) – whether to return all results, unpaginated.

  • start (int) – the start index of the results.

  • rows (int) – the number of results to return.

  • sort (str or list[str]) – the attribute or attributes to sort by.

  • counts_only (bool) – whether to return only the count of results.

  • content_types (list[str]) – the PDB types (experimental/computational).

  • facets (list[str]) – RCSB aggregation terms.

Return type:

dict