PyMassSpec NIST Search¶

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

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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.

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.

Installation¶

python3 -m pip install pyms-nist-search --user

python3 -m pip install git+https://github.com/domdfcoding/pynist@master --user

Contents¶

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:

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 pyms.Spectrum.MassSpectrum object can then be searched as follows:

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:

hit_list = search.full_search(mass_spec)

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

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

API Reference¶

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

`base`¶

Base class for other PyMassSpec NIST Search classes.

class NISTBase(name='', cas='---')[source]¶

Bases: object

Base class for other PyMassSpec NIST Search classes.

Parameters

name (str) – The name of the compound. Default ''.
cas (Union[str, int]) – The CAS number of the compound. Default '---'.

Methods:

`__eq__`(other)	Return `self == other`.
`__str__`()	Return `str(self)`.
`from_dict`(dictionary)	Construct an object from a dictionary.
`from_json`(json_data)	Construct an object from json data.
`from_pynist`(pynist_dict)	Create an object from the raw data returned by the C extension.
`to_dict`()	Convert the object to a dictionary.
`to_json`()	Convert the object to json.

Attributes:

`cas`	The CAS number of the compound.
`name`	The name of the compound.

__eq__(other)[source]¶

Return self == other.

Return type: bool

__str__()[source]¶

Return str(self).

Return type: str

property cas¶

The CAS number of the compound.

Return type: str

classmethod from_dict(dictionary)[source]¶

Construct an object from a dictionary.

Parameters: dictionary (Dict[str, Any])

classmethod from_json(json_data)[source]¶

Construct an object from json data.

Parameters: json_data (str)

classmethod from_pynist(pynist_dict)[source]¶

Create an object from the raw data returned by the C extension.

Parameters: pynist_dict (Dict[str, Any])

property name¶

The name of the compound.

Return type: str

to_dict()[source]¶

Convert the object to a dictionary.

New in version 0.6.0.

Return type: Dict[str, Any]

to_json()[source]¶

Convert the object to json.

Return type: str

`docker_engine`¶

Search engine for Linux and other platforms supporting Docker.

Classes:

Engine(lib_path[, lib_type, work_dir, debug])

Search engine for Linux and other platforms supporting Docker.

Functions:

`hit_list_from_json`(json_data)	Parse json data into a list of SearchResult objects.
`hit_list_with_ref_data_from_json`(json_data)	Parse json data into a list of (SearchResult, ReferenceData) tuples.
`require_init`(func)	Decorator to ensure that functions do not run after the class has been uninitialised.

class Engine(lib_path, lib_type=1, work_dir=None, debug=False)[source]¶

Bases: object

Search engine for Linux and other platforms supporting Docker.

The first time the engine is initialized it will download the latest version of the docker image automatically. This can also be performed manually, such as to upgrade to the latest version, with the following command:

docker pull domdfcoding/pywine-pyms-nist

The engine must be uninitialized when no longer required to shut down the underlying docker container. This is achieved with the uninit() method. Alternatively, this class can be used as a contextmanager to automatically uninitialize the engine upon leaving the with block:

with pyms_nist_search.Engine(
        FULL_PATH_TO_MAIN_LIBRARY,
        pyms_nist_search.NISTMS_MAIN_LIB,
        FULL_PATH_TO_WORK_DIR,
        ) as search:
    search.full_spectrum_search(ms, n_hits=5)

Changed in version 0.6.0: Added context manager support.

Methods:

`full_search_with_ref_data`(mass_spec[, n_hits])	Perform a Full Spectrum Search of the mass spectral library, including reference data.
`full_spectrum_search`(mass_spec[, n_hits])	Perform a Full Spectrum Search of the mass spectral library.
`get_reference_data`(spec_loc)	Get reference data from the library for the compound at the given location.
`spectrum_search`(mass_spec[, n_hits])	Perform a Quick Spectrum Search of the mass spectral library.
`uninit`()	Uninitialize the Search Engine.

full_search_with_ref_data(mass_spec, n_hits=5)[source]¶

Perform a Full Spectrum Search of the mass spectral library, including reference data.

Parameters

mass_spec (MassSpectrum) – The mass spectrum to search against the library.
n_hits (int) – The number of hits to return. Default 5.

Return type

List[Tuple[SearchResult, ReferenceData]]

Returns

List of tuples containing possible identities for the mass spectrum, and the reference data.

full_spectrum_search(mass_spec, n_hits=5)[source]¶

Perform a Full Spectrum Search of the mass spectral library.

Parameters

mass_spec (MassSpectrum) – The mass spectrum to search against the library.
n_hits (int) – The number of hits to return. Default 5.

Return type

List[SearchResult]

Returns

List of possible identities for the mass spectrum.

get_reference_data(spec_loc)[source]¶

Get reference data from the library for the compound at the given location.

Parameters: spec_loc (int)
Return type: ReferenceData

spectrum_search(mass_spec, n_hits=5)[source]¶

Perform a Quick Spectrum Search of the mass spectral library.

Parameters

mass_spec (MassSpectrum) – The mass spectrum to search against the library.
n_hits (int) – The number of hits to return. Default 5.

Return type

List[SearchResult]

Returns

List of possible identities for the mass spectrum.

uninit()[source]¶: Uninitialize the Search Engine.

hit_list_from_json(json_data)[source]¶

Parse json data into a list of SearchResult objects.

Parameters: json_data (str) – str
Return type: List[SearchResult]

hit_list_with_ref_data_from_json(json_data)[source]¶

Parse json data into a list of (SearchResult, ReferenceData) tuples.

Parameters: json_data (str) – str
Return type: List[Tuple[SearchResult, ReferenceData]]

require_init(func)[source]¶

Decorator to ensure that functions do not run after the class has been uninitialised.

Parameters: func (Callable) – The function or method to wrap.
Return type: Callable

`reference_data`¶

Class to store reference data from NIST MS Search.

class ReferenceData(name='', cas='---', nist_no=0, id='', mw=0.0, formula='', contributor='', mass_spec=None, synonyms=None, exact_mass=None)[source]¶

Bases: NISTBase

Class to store reference data from NIST MS Search.

Parameters

name (str) – The name of the compound. Default ''.
cas (Union[str, int]) – The CAS number of the compound. Default '---'.
nist_no (Union[int, str]) – Default 0.
id (Union[str, int]) – Default ''.
mw (Union[float, str]) – Default 0.0.
formula (str) – The formula of the compound. Default ''.
contributor (str) – The contributor to the library. Default ''.
mass_spec (Optional[MassSpectrum]) – The reference mass spectrum. Default None.
synonyms (Optional[Sequence[str]]) – List of synonyms for the compound. Default None.

Methods:

`__repr__`()	Return a string representation of the `ReferenceData`.
`from_jcamp`(file_name[, ignore_warnings])	Create a ReferenceData object from a JCAMP-DX file.
`from_json`(json_data)	Construct an object from JSON data.
`from_mona_dict`(mona_data)	Construct an object from Massbank of North America json data that has been loaded into a dictionary.
`from_pynist`(pynist_dict)	Create a `ReferenceData` object from the raw data returned by the C extension.
`to_dict`()	Convert the object to a dictionary.
`to_json`()	Convert the object to JSON.
`to_msp`()	Returns the ReferenceData object as an MSP file similar to that produced by NIST MS Search’s export function.

Attributes:

`contributor`	The name of the contributor to the library.
`exact_mass`	The exact mass of the compound.
`formula`	The formula of the compound.
`id`	The ID of the compound.
`mass_spec`	The mass spectrum of the compound.
`mw`	The molecular weight of the compound.
`nist_no`	The NIST number of the compund.
`synonyms`	A list of synonyms for the compound.

__repr__()[source]¶

Return a string representation of the ReferenceData.

Return type: str

property contributor¶

The name of the contributor to the library.

Return type: str

property exact_mass¶

The exact mass of the compound.

Return type: float

property formula¶

The formula of the compound.

Return type: str

classmethod from_jcamp(file_name, ignore_warnings=True)[source]¶

Create a ReferenceData object from a JCAMP-DX file.

Parameters

file_name (Union[str, Path, PathLike]) – Path of the file to read.
ignore_warnings (bool) – Whether warnings about invalid tags should be shown. Default True.

Authors

Qiao Wang, Andrew Isaac, Vladimir Likic, David Kainer, Dominic Davis-Foster

Return type

ReferenceData

classmethod from_json(json_data)[source]¶

Construct an object from JSON data.

Parameters: json_data (str)

classmethod from_mona_dict(mona_data)[source]¶

Construct an object from Massbank of North America json data that has been loaded into a dictionary.

Parameters: mona_data (Dict) – dict
Return type: ReferenceData

classmethod from_pynist(pynist_dict)[source]¶

Create a ReferenceData object from the raw data returned by the C extension.

Parameters: pynist_dict (Dict[str, Any])
Return type: ReferenceData

property id¶

The ID of the compound.

Return type: str

property mass_spec¶

The mass spectrum of the compound.

Return type: Optional[MassSpectrum]

property mw¶

The molecular weight of the compound.

Return type: int

property nist_no¶

The NIST number of the compund.

Return type: int

property synonyms¶

A list of synonyms for the compound.

Return type: List[str]

to_dict()[source]¶

Convert the object to a dictionary.

New in version 0.6.0.

Return type: Dict[str, Any]

to_json()[source]¶

Convert the object to JSON.

Return type: str

to_msp()[source]¶

Returns the ReferenceData object as an MSP file similar to that produced by NIST MS Search’s export function.

Return type: str

`search_result`¶

Class to store search results from NIST MS Search.

class SearchResult(name='', cas='---', match_factor=0, reverse_match_factor=0, hit_prob=0.0, spec_loc=0)[source]¶

Bases: NISTBase

Class to store search results from NIST MS Search.

Parameters

name (str) – The name of the compound. Default ''.
cas (Union[str, int]) – The CAS number of the compound. Default '---'.
match_factor (float) – Default 0.
reverse_match_factor (float) – Default 0.
hit_prob (float) – Default 0.0.
spec_loc (float) – The location of the reference spectrum in the library. Default 0.

Methods:

`from_pynist`(pynist_dict)	Create a `SearchResult` object from the raw data returned by the C extension.
`to_dict`()	Convert the object to a dictionary.

Attributes:

`hit_prob`	Returns the probability of the hit being the compound responsible for the mass spectrum.
`match_factor`	Returns a score (out of 1000) representing the similarity of the searched mass spectrum to the search result.
`reverse_match_factor`	A score (out of 1000) representing the similarity of the searched mass spectrum to the search result, but ignoring any peaks that are in the searched mass spectrum but not in the library spectrum.
`spec_loc`	The location of the reference spectrum in the library.

classmethod from_pynist(pynist_dict)[source]¶

Create a SearchResult object from the raw data returned by the C extension.

Parameters: pynist_dict (Dict[str, Any])
Return type: SearchResult

property hit_prob¶

Returns the probability of the hit being the compound responsible for the mass spectrum.

Return type: float

property match_factor¶

Returns a score (out of 1000) representing the similarity of the searched mass spectrum to the search result.

Return type: int

property reverse_match_factor¶

A score (out of 1000) representing the similarity of the searched mass spectrum to the search result, but ignoring any peaks that are in the searched mass spectrum but not in the library spectrum.

Return type: int

property spec_loc¶

The location of the reference spectrum in the library.

This can then be searched using the get_reference_data() method of the search engine to obtain the reference data.

Return type: int

to_dict()[source]¶

Convert the object to a dictionary.

New in version 0.6.0.

Return type: Dict[str, Any]

`utils`¶

General utilities.

Functions:

`pack`(mass_spec[, top])	Convert a pyms.Spectrum.MassSpectrum object into a string.
`parse_name_chars`(name_char_list)	Takes a list of Unicode character codes and converts them to characters, taking into account the special codes used by the NIST DLL.

pack(mass_spec, top=20)[source]¶

Convert a pyms.Spectrum.MassSpectrum object into a string.

Adapted from https://sourceforge.net/projects/mzapi-live/

Parameters

mass_spec (MassSpectrum)
top (int) – The number of largest peaks to identify. Default 20.

Return type

str

parse_name_chars(name_char_list)[source]¶

Takes a list of Unicode character codes and converts them to characters, taking into account the special codes used by the NIST DLL.

Parameters: name_char_list (Sequence[int])
Return type: str
Returns: The parsed name.

`win_engine`¶

Search engine for Windows systems.

class Engine(lib_path, lib_type=1, work_dir=None, debug=False)[source]¶

Bases: object

Search engine for Windows systems.

Parameters

lib_path (Union[str, Path, PathLike]) – The path to the mass spectral library.
lib_type (int) – The type of library. One of NISTMS_MAIN_LIB, NISTMS_USER_LIB, NISTMS_REP_LIB. Default 1.
work_dir (Union[str, Path, PathLike, None]) – The path to the working directory. Default None.

Methods:

`full_search_with_ref_data`(mass_spec[, n_hits])	Perform a Full Spectrum Search of the mass spectral library, including reference data.
`full_spectrum_search`(mass_spec[, n_hits])	Perform a Full Spectrum Search of the mass spectral library.
`get_reference_data`(spec_loc)	Get reference data from the library for the compound at the given location.
`spectrum_search`(mass_spec[, n_hits])	Perform a Quick Spectrum Search of the mass spectral library.
`uninit`()	Uninitialize the Search Engine.

full_search_with_ref_data(mass_spec, n_hits=5)[source]¶

Perform a Full Spectrum Search of the mass spectral library, including reference data.

Parameters

mass_spec (MassSpectrum) – The mass spectrum to search against the library.
n_hits (int) – The number of hits to return. Default 5.

Return type

List[Tuple[SearchResult, ReferenceData]]

Returns

List of tuples containing possible identities for the mass spectrum, and the reference data

static full_spectrum_search(mass_spec, n_hits=5)[source]¶

Perform a Full Spectrum Search of the mass spectral library.

Parameters

mass_spec (MassSpectrum) – The mass spectrum to search against the library.
n_hits (int) – The number of hits to return. Default 5.

Return type

List[SearchResult]

Returns

List of possible identities for the mass spectrum.

static get_reference_data(spec_loc)[source]¶

Get reference data from the library for the compound at the given location.

Parameters: spec_loc (int)
Return type: ReferenceData

static spectrum_search(mass_spec, n_hits=5)[source]¶

Perform a Quick Spectrum Search of the mass spectral library.

Parameters

mass_spec (MassSpectrum) – The mass spectrum to search against the library.
n_hits (int) – The number of hits to return. Default 5.

Return type

List[SearchResult]

Returns

List of possible identities for the mass spectrum.

uninit()[source]¶: Uninitialize the Search Engine.

Contributing¶

pyms-nist-search uses tox to automate testing and packaging, and pre-commit to maintain code quality.

Install pre-commit with pip and install the git hook:

python -m pip install pre-commit
pre-commit install

Coding style¶

formate is used for code formatting.

It can be run manually via pre-commit:

pre-commit run formate -a

Or, to run the complete autoformatting suite:

pre-commit run -a

Automated tests¶

Tests are run with tox and pytest. To run tests for a specific Python version, such as Python 3.6:

tox -e py36

To run tests for all Python versions, simply run:

tox

Type Annotations¶

Type annotations are checked using mypy. Run mypy using tox:

tox -e mypy

Build documentation locally¶

The documentation is powered by Sphinx. A local copy of the documentation can be built with tox:

tox -e docs

License¶

pyms-nist-search is licensed under the GNU Lesser General Public License v3.0

Permissions of this copyleft license are conditioned on making available complete source code of licensed works and modifications under the same license or the GNU GPLv3. Copyright and license notices must be preserved. Contributors provide an express grant of patent rights. However, a larger work using the licensed work through interfaces provided by the licensed work may be distributed under different terms and without source code for the larger work.

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Commercial use Modification Distribution Patent use Private use	License and copyright notice Disclose source State changes Same license (library)	Liability Warranty

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Downloading source code¶

The pyms-nist-search source code is available on GitHub, and can be accessed from the following URL: https://github.com/domdfcoding/pynist

If you have git installed, you can clone the repository with the following command:

git clone https://github.com/domdfcoding/pynist

Cloning into 'pynist'...
remote: Enumerating objects: 47, done.
remote: Counting objects: 100% (47/47), done.
remote: Compressing objects: 100% (41/41), done.
remote: Total 173 (delta 16), reused 17 (delta 6), pack-reused 126
Receiving objects: 100% (173/173), 126.56 KiB | 678.00 KiB/s, done.
Resolving deltas: 100% (66/66), done.

Alternatively, the code can be downloaded in a ‘zip’ file by clicking:

Clone or download –> Download Zip

Downloading a ‘zip’ file of the source code¶

Building from source¶

The recommended way to build pyms-nist-search is to use tox:

tox -e build

The source and wheel distributions will be in the directory dist.

If you wish, you may also use pep517.build or another PEP 517-compatible build tool.

View the Function Index or browse the Source Code.

Browse the GitHub Repository

PyMassSpec NIST Search¶

Installation¶

Contents¶

Usage¶

API Reference¶

base¶

docker_engine¶

reference_data¶

search_result¶

utils¶

win_engine¶

Contributing¶

Coding style¶

Automated tests¶

Type Annotations¶

Build documentation locally¶

License¶

Downloading source code¶

Building from source¶

`base`¶

`docker_engine`¶

`reference_data`¶

`search_result`¶

`utils`¶

`win_engine`¶