Overview

pdbsearch is a Python library for searching for PDB structures using the RCSB web services.

Basic Search

The default search will return PDB entry IDs, with no filtering:

>>> import pdbsearch
>>> results = pdbsearch.search()
>>> print(results)
{'query_id': '9a0c3543-0e29-462c-8357-f286293d9896', 'result_type': 'entry',
 'total_count': 247417, 'result_set': [{'identifier': '100D', 'score': 1.0},
 {'identifier': '101D', 'score': 1.0}, {'identifier': '101M', 'score': 1.0},
 {'identifier': '102D', 'score': 1.0}, {'identifier': '102L', 'score': 1.0},
 {'identifier': '102M', 'score': 1.0}, {'identifier': '103D', 'score': 1.0},
 {'identifier': '103L', 'score': 1.0}, {'identifier': '103M', 'score': 1.0},
 {'identifier': '104D', 'score': 1.0}]}

The JSON returned is the direct output from the RCSB search API. By default, it returns 10 results at a time.

Services

RCSB defines a number of services which search in different ways. For example, the full text search service will search the entire PDB database for the given term, and you can access this with the term keyword argument:

>>> results = pdbsearch.search(term="thymidine kinase")

You can search for entries with other services, using the correct keyword arguments:

>>> # Sequence service
>>> results = pdbsearch.search(protein="MALWMRLLPLLALLALWGPDPAAA")
>>> results = pdbsearch.search(dna="ATGCATGCATGC", identity=0.95, evalue=1e-10)
>>> results = pdbsearch.search(rna="AUGCAUGCAUGC")
>>>
>>> # Sequence motif service
>>> results = pdbsearch.search(protein="C-X-C-X(2)-[LIVMYFWC]", pattern_type="prosite")
>>> results = pdbsearch.search(dna="GTXXCA", pattern_type="simple")
>>> results = pdbsearch.search(rna="AUG{2}C", pattern_type="regex")
>>>
>>> # Structure service (requires the ID of a specific assembly to look for)
>>> results = pdbsearch.search(structure="4HHB-1", operator="relaxed_shape_match")
>>>
>>> # Structure motif service (requires a residue pattern in some entry)
>>> results = pdbsearch.search(entry="4HHB", residues=(("A", 10), ("A", 20)))
>>>
>>> # Chemical service
>>> results = pdbsearch.search(smiles="CC(C)C", match_type="graph-relaxed-stereo")
>>> results = pdbsearch.search(inchi="InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2")

The most useful service however, is the text service. The documentation for the RCSB search API lists a number of attributes that you can search on, and which can be viewed here. For example, pdbx_entity_nonpoly.name or rcsb_nonpolymer_entity.pdbx_number_of_molecules. You pass these as keyword arguments to the pdbsearch.search() function, with the prefix __ in place of the dot.

>>> results = pdbsearch.search(pdbx_entity_nonpoly__name="glucose")
>>> results = pdbsearch.search(rcsb_nonpolymer_entity__pdbx_number_of_molecules=0)

As the RCSB documentation indicates, you can use a variety of operators to modify how you search, and these are encoded as suffixes to the keyword arguments:

• __gt: greater

• __lt: less

• __gte: greater_or_equal

• __lte: less_or_equal

• __in: in

• __exists: exists

• __range: range (use tuple for exclusive range, list for inclusive range)

• __contains: contains_phrase

• __contains_phrase: contains_phrase

• __contains_words: contains_words

• __not: not

You can also use the __not suffix to negate the search.

>>> results = pdbsearch.search(pdbx_entity_nonpoly__name__not="glucose")
>>> results = pdbsearch.search(rcsb_nonpolymer_entity__pdbx_number_of_molecules__not=0)

There is a very similar search service called the text_chem service, which has a different set of attributes (in practice a subset of the structure attributes) but which works the same way. It searches properties of chemical compounds, such as formula weight. The search function will default to using this service if you are searching for small molecules.

>>> results = pdbsearch.search(return_type="mol_definition", chem_comp__formula_weight__lt=1000)

Return Types

The above examples all search for entries (i.e. PDB files) but the RCSB API also lets you search for other types of objects, such as polymer entities, non-polymer entities, and chemical compounds.

The type of object you search for is determined by the return_type parameter. The possible values are: entry, assembly, polymer_entity, non_polymer_entity, polymer_instance, mol_definition. Where the term you are searching for does not correspond to the type of object you are searching for (i.e. doing a sequence search but asking for non-polymer entities), the API will use entries as a base (i.e finding all entries with a polymer entity matching your sequence, and then returning all non-polymer entities in those entries).

Alternatively, there are specific functions for searching for each of these types of objects - pdbsearch.search_entries, pdbsearch.search_assemblies, etc.

Multiple Queries

You can combine any of the above parameters to search multiple services at once. These will be combined with an and operator.

>>> results = pdbsearch.search(
    return_type="polymer_entity",
    term="thymidine kinase",
    chem_comp__formula_weight__lt=1000,
    pdbx_struct_assembly__details__not__contains="good",
    protein="MALWMRLLPLLALLALWGPDPAAA",
    dna="ATGCATGCATGC",
    rna="AUGCAUGCAUGC",
    identity=0.95,
    evalue=1e-10,
    structure="4HHB-1",
    operator="relaxed_shape_match",
    entry="4HHB",
    residues=(("A", 10), ("A", 20)),
    rmsd=0.5,
    exchanges={("A", 10): ["ASP"], ("A", 20): ["HIS"]},
    smiles="CC(C)C",
    inchi="InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2",
    match_type="graph-relaxed-stereo",
)

Request Options

You can control how the search is performed and returned with various request option parameters:

>>> # Return all results in one response
>>> results = pdbsearch.search(term="thymidine kinase", return_all=True)
>>>
>>> # Return only the count of results
>>> results = pdbsearch.search(term="thymidine kinase", counts_only=True)
>>>
>>> # Return results starting from the 10th result
>>> results = pdbsearch.search(term="thymidine kinase", start=10)
>>>
>>> # Return 20 results at a time
>>> results = pdbsearch.search(term="thymidine kinase", rows=20)
>>>
>>> # Sort results by the deposit date (descending)
>>> results = pdbsearch.search(term="thymidine kinase", sort="-rcsb_accession_info.deposit_date")
>>>
>>> # Sort results by the polymer entity count (ascending)
>>> results = pdbsearch.search(term="thymidine kinase", sort="rcsb_assembly_info.polymer_entity_count")
>>>
>>> # Sort results by multiple attributes
>>> results = pdbsearch.search(term="thymidine kinase", sort=["-rcsb_accession_info.deposit_date", "rcsb_assembly_info.polymer_entity_count"])
>>>
>>> # Return results with computational content type only
>>> results = pdbsearch.search(term="thymidine kinase", content_types=["computational"])
>>>
>>> # Use the API's facets functionality (see their documentation for more details)
>>> results = pdbsearch.search(term="thymidine kinase", facets=[...])

Nodes and Queries

The pdbsearch.search() function is useful for simple queries, but it has some limitations.

1. If using multiple queries, they will always be combined with an and operator.

2. You can only provide one value per argument - if you have multiple protein sequences, you can’t search for them all at once.

It can sometimes be useful to access the underlying node system that pdbsearch.search() is built on for more complex queries. This solves both of the above limitations.

Nodes

Each of the search services has a function for creating a single search node.

>>> # Full text search node
>>> node = pdbsearch.full_text_node(term="thymidine kinase")
>>>
>>> # Text search node
>>> node = pdbsearch.text_node(pdbx_struct_assembly__details__not__contains="good")
>>>
>>> # Text chem search node
>>> node = pdbsearch.text_chem_node(chem_comp__formula_weight__lt=1000)
>>>
>>> # Sequence search nodes
>>> node = pdbsearch.sequence_node(protein="MALWMRLLPLLALLALWGPDPAAA", identity=0.95, evalue=1e-10)
>>> node = pdbsearch.sequence_node(dna="ATGCATGCATGC", identity=0.95, evalue=1e-10)
>>> node = pdbsearch.sequence_node(rna="AUGCAUGCAUGC", identity=0.95, evalue=1e-10)
>>>
>>> # Sequence motif search node
>>> node = pdbsearch.seqmotif_node(protein="C-X-C-X(2)-[LIVMYFWC]", pattern_type="prosite")
>>>
>>> # Structure search node
>>> node = pdbsearch.structure_node("4HHB-1", operator="relaxed_shape_match")
>>>
>>> # Structure motif search node
>>> node = pdbsearch.strucmotif_node("4HHB", residues=(("A", 10), ("A", 20)), rmsd=0.5, exchanges={("A", 10): ["ASP"], ("A", 20): ["HIS"]})
>>>
>>> # Chemical search nodes
>>> node = pdbsearch.chemical_node(smiles="CC(C)C", match_type="graph-relaxed-stereo")
>>> node = pdbsearch.chemical_node(inchi="InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2", match_type="graph-relaxed-stereo")

You can execute any of these nodes individually using their pdbsearch.query() method. These can take a return_type parameter, and all of the request option parameters.

>>> results = node.query("entry", return_all=True, sort="-rcsb_accession_info.deposit_date")

Combining Nodes

All node objects have an and_ and or_ method, which can be used to combine them with other nodes.

>>> node1 = pdbsearch.full_text_node(term="thymidine kinase")
>>> node2 = pdbsearch.text_node(pdbx_struct_assembly__details__not__contains="good")
>>> node3 = pdbsearch.sequence_node(protein="MALWMRLLPLLALLALWGPDPAAA", identity=0.95, evalue=1e-10)
>>> node4 = pdbsearch.sequence_node(dna="ATGCATGCATGC", identity=0.95, evalue=1e-10)
>>> node5 = pdbsearch.sequence_node(rna="AUGCAUGCAUGC", identity=0.95, evalue=1e-10)
>>> node = node1.and_(node2).or_(node3.and_(node4.or_(node5)))
>>> results = node.query("entry", return_all=True, sort="-rcsb_accession_info.deposit_date")

Schemas

The text and text_chem services have a schema that defines the attributes you can search on. These can be read here and here respectively.

They are also available as JSON schema objects, here and here respectively. This is important as pdbsearch needs to know type information about the attributes in order to know which operator to use sometimes, and it needs to know which parameter names correspond to this service when parsing a pdbsearch.search() function call.

For this reason, a simplified form of the schema (all attributes, but only the information about them pdbsearch needs) is hardcoded into the library. To ensure the library always uses the most up to date information, it will try to update its own local copy of the schema from the RCSB API when the library is imported.

This can be disabled by setting the PDBSEARCH_NO_UPDATE environment variable.

You can also download the full schema using a CLI command:

pdbsearch schema > schema.json
pdbsearch schema --chemical --indent 4 > chemical_schema.json

The downloaded schema information will be cached locally, so that it doesn’t fetch the schema every time pdbsearch runs - to delete this local cache, you can run:

pdbsearch clearschema