Metadata-Version: 1.2
Name: pyms_nist_search
Version: 0.4.14
Summary: PyMassSpec extension for searching mass spectra using NIST's Mass Spectrum Search Engine
Home-page: https://github.com/domdfcoding/pyms_nist_search
Author: Dominic Davis-Foster
Author-email: dominic@davis-foster.co.uk
License: LGPLv3
Description: ************************
        PyMassSpec NIST Search
        ************************
        
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        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.
        
        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. Build a user library for use in tests
        2. Allow user libraries to be used. IIRC they can't be currently.
        3. Write comprehensive tests using pytest
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: Microsoft :: Windows :: Windows 10
Classifier: Operating System :: Microsoft :: Windows :: Windows 7
Classifier: Operating System :: Microsoft :: Windows :: Windows 8.1
Classifier: Operating System :: POSIX :: Linux
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)
Classifier: Programming Language :: C
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=3.6
