sbliven / rcsbsearch

Python interface for the RCSB search API.

rcsbsearch

Python interface for the RCSB search API.

Currently the 'text search' part of the API has been implemented. See 'Supported features' below.

This package requires python 3.7 or later.

Example

Here is a quick example of how the package is used. Two syntaxes are available for constructing queries: an "operator" API using python's comparators, and a "fluent" syntax where terms are chained together. Which to use is a matter of preference.

A runnable jupyter notebook with this example is available in notebooks/quickstart.ipynb, or can be run online using binder:

An additional example including a Covid-19 related example is in notebooks/covid.ipynb:

Operator example

Here is an example from the RCSB Search API page, using the operator syntax. This query finds symmetric dimers having a twofold rotation with the DNA-binding domain of a heat-shock transcription factor.

from rcsbsearch import TextQuery
from rcsbsearch import rcsb_attributes as attrs

# Create terminals for each query
q1 = TextQuery('"heat-shock transcription factor"')
q2 = attrs.rcsb_struct_symmetry.symbol == "C2"
q3 = attrs.rcsb_struct_symmetry.kind == "Global Symmetry"
q4 = attrs.rcsb_entry_info.polymer_entity_count_DNA >= 1

# combined using bitwise operators (&, |, ~, etc)
query = q1 & q2 & q3 & q4  # AND of all queries

# Call the query to execute it
for assemblyid in query("assembly"):
    print(assemblyid)

For a full list of attributes, please refer to the RCSB schema.

Fluent Example

Here is the same example using the fluent syntax.

from rcsbsearch import TextQuery

# Start with a Attr or TextQuery, then add terms
results = TextQuery('"heat-shock transcription factor"') \
    .and_("rcsb_struct_symmetry.symbol").exact_match("C2") \
    .and_("rcsb_struct_symmetry.kind").exact_match("Global Symmetry") \
    .and_("rcsb_entry_info.polymer_entity_count_DNA").greater_or_equal(1) \
    .exec("assembly")

# Exec produces an iterator of IDs
for assemblyid in results:
    print(assemblyid)

Supported Features

The following table lists the status of current and planned features.

• Attribute Comparison operations
• Query set operations
• Attribute contains, in_ (fluent only)
• Sequence search
• Sequence motif search
• Structural search
• Structural motif search
• Chemical search
• Rich results using the Data API

Contributions are welcome for unchecked items!

Installation

Get it from pypi:

pip install rcsbsearch

Or, download from github

Documentation

Detailed documentation is at rcsbsearch.readthedocs.io

License

Code is licensed under the BSD 3-clause license. See LICENSE for details.

Citing rcsbsearch

Please cite the rcsbsearch package by URL:

https://rcsbsearch.readthedocs.io

You should also cite the RCSB service this package utilizes:

Yana Rose, Jose M. Duarte, Robert Lowe, Joan Segura, Chunxiao Bi, Charmi Bhikadiya, Li Chen, Alexander S. Rose, Sebastian Bittrich, Stephen K. Burley, John D. Westbrook. RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive, Journal of Molecular Biology, 2020. DOI: 10.1016/j.jmb.2020.11.003

Developers

For information about building and developing rcsbsearch, see CONTRIBUTING.md