pyms-nist-search

======================== PyMassSpec NIST Search

.. start short_desc

PyMassSpec extension for searching mass spectra using NIST's Mass Spectrum Search Engine.

.. end short_desc

.. image:: https://img.shields.io/appveyor/build/domdfcoding/pyms-nist-search/master?logo=appveyor :target: https://ci.appveyor.com/project/domdfcoding/pyms-nist-search/branch/master :alt: AppVeyor Windows Build Status

.. start shields

.. list-table:: :stub-columns: 1 :widths: 10 90

* - Docs
  - |docs| |docs_check|
* - Tests
  - |actions_linux| |actions_windows| |coveralls|
* - PyPI
  - |pypi-version| |supported-versions| |supported-implementations| |wheel|
* - Activity
  - |commits-latest| |commits-since| |maintained| |pypi-downloads|
* - QA
  - |codefactor| |actions_flake8| |actions_mypy|
* - Other
  - |license| |language| |requires|

.. |docs| image:: https://img.shields.io/readthedocs/pynist/latest?logo=read-the-docs :target: https://pynist.readthedocs.io/en/latest :alt: Documentation Build Status

.. |docs_check| image:: https://github.com/domdfcoding/pynist/workflows/Docs%20Check/badge.svg :target: https://github.com/domdfcoding/pynist/actions?query=workflow%3A%22Docs+Check%22 :alt: Docs Check Status

.. |actions_linux| image:: https://github.com/domdfcoding/pynist/workflows/Linux/badge.svg :target: https://github.com/domdfcoding/pynist/actions?query=workflow%3A%22Linux%22 :alt: Linux Test Status

.. |actions_windows| image:: https://github.com/domdfcoding/pynist/workflows/Windows/badge.svg :target: https://github.com/domdfcoding/pynist/actions?query=workflow%3A%22Windows%22 :alt: Windows Test Status

.. |actions_flake8| image:: https://github.com/domdfcoding/pynist/workflows/Flake8/badge.svg :target: https://github.com/domdfcoding/pynist/actions?query=workflow%3A%22Flake8%22 :alt: Flake8 Status

.. |actions_mypy| image:: https://github.com/domdfcoding/pynist/workflows/mypy/badge.svg :target: https://github.com/domdfcoding/pynist/actions?query=workflow%3A%22mypy%22 :alt: mypy status

.. |requires| image:: https://dependency-dash.repo-helper.uk/github/domdfcoding/pynist/badge.svg :target: https://dependency-dash.repo-helper.uk/github/domdfcoding/pynist/ :alt: Requirements Status

.. |coveralls| image:: https://img.shields.io/coveralls/github/domdfcoding/pynist/master?logo=coveralls :target: https://coveralls.io/github/domdfcoding/pynist?branch=master :alt: Coverage

.. |codefactor| image:: https://img.shields.io/codefactor/grade/github/domdfcoding/pynist?logo=codefactor :target: https://www.codefactor.io/repository/github/domdfcoding/pynist :alt: CodeFactor Grade

.. |pypi-version| image:: https://img.shields.io/pypi/v/pyms-nist-search :target: https://pypi.org/project/pyms-nist-search/ :alt: PyPI - Package Version

.. |supported-versions| image:: https://img.shields.io/pypi/pyversions/pyms-nist-search?logo=python&logoColor=white :target: https://pypi.org/project/pyms-nist-search/ :alt: PyPI - Supported Python Versions

.. |supported-implementations| image:: https://img.shields.io/pypi/implementation/pyms-nist-search :target: https://pypi.org/project/pyms-nist-search/ :alt: PyPI - Supported Implementations

.. |wheel| image:: https://img.shields.io/pypi/wheel/pyms-nist-search :target: https://pypi.org/project/pyms-nist-search/ :alt: PyPI - Wheel

.. |license| image:: https://img.shields.io/github/license/domdfcoding/pynist :target: https://github.com/domdfcoding/pynist/blob/master/LICENSE :alt: License

.. |language| image:: https://img.shields.io/github/languages/top/domdfcoding/pynist :alt: GitHub top language

.. |commits-since| image:: https://img.shields.io/github/commits-since/domdfcoding/pynist/v0.7.2 :target: https://github.com/domdfcoding/pynist/pulse :alt: GitHub commits since tagged version

.. |commits-latest| image:: https://img.shields.io/github/last-commit/domdfcoding/pynist :target: https://github.com/domdfcoding/pynist/commit/master :alt: GitHub last commit

.. |maintained| image:: https://img.shields.io/maintenance/yes/2024 :alt: Maintenance

.. |pypi-downloads| image:: https://img.shields.io/pypi/dm/pyms-nist-search :target: https://pypi.org/project/pyms-nist-search/ :alt: PyPI - Downloads

.. end shields

PyMassSpec extension for searching mass spectra using NIST's Spectrum Search Engine

PyMassSpec NIST Search is Free Software licensed under the GNU Lesser General Public License Version 3 <https://www.gnu.org/licenses/lgpl-3.0.en.html>_

A copy of the MassBank of North America database, in JSON, MSP and NIST Library formats, is included for the purposes of these tests. This library was created on 22 April 2020 using the "parse_mona_json.py" script and Lib2Nist. Licensed under the CC BY 4.0 License. For a list of contributors, see the file MoNA_GCMS_Library/AUTHORS

.. TODO: add links.

Installation

.. begin installation .. end installation

Usage

You will need to supply your own copy of the NIST Mass Spectral library to use this software.

The main class in this library is the Engine class. This class performs the actual searching. Start by initialising the search engine as follows:

.. code-block:: python

search = pyms_nist_search.Engine(
		FULL_PATH_TO_MAIN_LIBRARY,
		pyms_nist_search.NISTMS_MAIN_LIB,
		FULL_PATH_TO_WORK_DIR,
		)

Where FULL_PATH_TO_MAIN_LIBRARY is the path to the location of your mass spectral library, and FULL_PATH_TO_WORK_DIR is the path to the working directory to be used by the search engine.

A MassSpectrum object can then be searched as follows:

.. code-block:: python

search.full_search_with_ref_data(mass_spec)

This will return a list of tuples consisting of SearchResult and ReferenceData objects for the possible identities of the mass spectrum.

A list of just the SearchResult objects can be obtained with this method:

.. code-block:: python

hit_list = search.full_search(mass_spec)

For each of these hits, the reference data can be obtained as follows:

.. code-block:: python

for hit in hit_list:
	ref_data = search.get_reference_data(hit.spec_loc)

TODO

1. Write comprehensive tests using pytest