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
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 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)TODO
Write comprehensive tests using pytest
1 maintainer
Metadata
1 maintainer
Release files for pyms-nist-search 0.8.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| pyms-nist-search-0.8.0.tar.gz | 1.8 MB | Without provenance | Details for pyms-nist-search-0.8.0.tar.gz |
Built distributions (wheels)
Total release size: 74.0 MB
Release files / pyms-nist-search-0.8.0.tar.gz
| Download URL | pyms-nist-search-0.8.0.tar.gz |
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| Size | 1.8 MB |
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| Download URL | pyms_nist_search-0.8.0-cp312-cp312-win_amd64.whl |
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| Size | 2.3 MB |
| Tags | CPython 3.12 Windows x86-64 |
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| Size | 2.3 MB |
| Tags | CPython 3.11 Windows x86-64 |
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| Size | 1.8 MB |
| Tags | CPython 3.11 Linux glibc 2.24+ x86-64 Linux glibc 2.5+ x86-64 |
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| Download URL | pyms_nist_search-0.8.0-cp311-cp311-manylinux1_x86_64.manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.whl |
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| Size | 2.3 MB |
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| Tags | CPython 3.10 Linux glibc 2.24+ x86-64 Linux glibc 2.5+ x86-64 |
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| Download URL | pyms_nist_search-0.8.0-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl |
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| Tags | CPython 3.10 Linux glibc 2.12+ x86-64 Linux glibc 2.24+ x86-64 Linux glibc 2.5+ x86-64 |
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| Tags | CPython 3.10 Linux glibc 2.17+ x86-64 Linux glibc 2.5+ x86-64 |
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| Size | 1.8 MB |
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| Size | 1.8 MB |
| Tags | CPython 3.9 Linux glibc 2.24+ x86-64 Linux glibc 2.5+ x86-64 |
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| Download URL | pyms_nist_search-0.8.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl |
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| Size | 1.8 MB |
| Tags | CPython 3.9 Linux glibc 2.12+ x86-64 Linux glibc 2.24+ x86-64 Linux glibc 2.5+ x86-64 |
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| Size | 1.8 MB |
| Tags | CPython 3.9 Linux glibc 2.17+ x86-64 Linux glibc 2.5+ x86-64 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
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twine/6.1.0 CPython/3.9.23
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Release files / pyms_nist_search-0.8.0-cp39-cp39-manylinux1_x86_64.manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.manylinux_2_24_x86_64.whl
| Download URL | pyms_nist_search-0.8.0-cp39-cp39-manylinux1_x86_64.manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.manylinux_2_24_x86_64.whl |
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No |
| Uploaded via |
twine/6.1.0 CPython/3.9.23
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Release files / pyms_nist_search-0.8.0-cp39-cp39-manylinux1_x86_64.manylinux2010_x86_64.manylinux2014_x86_64.manylinux_2_12_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.whl
| Download URL | pyms_nist_search-0.8.0-cp39-cp39-manylinux1_x86_64.manylinux2010_x86_64.manylinux2014_x86_64.manylinux_2_12_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.whl |
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Uploaded using Trusted Publishing? What is trusted publishing? |
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| Uploaded via |
twine/6.1.0 CPython/3.9.23
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Release files / pyms_nist_search-0.8.0-cp39-cp39-manylinux1_x86_64.manylinux2010_x86_64.manylinux2014_x86_64.manylinux_2_12_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.manylinux_2_24_x86_64.whl
| Download URL | pyms_nist_search-0.8.0-cp39-cp39-manylinux1_x86_64.manylinux2010_x86_64.manylinux2014_x86_64.manylinux_2_12_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.manylinux_2_24_x86_64.whl |
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No |
| Uploaded via |
twine/6.1.0 CPython/3.9.23
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Release files / pyms_nist_search-0.8.0-cp38-cp38-win_amd64.whl
| Download URL | pyms_nist_search-0.8.0-cp38-cp38-win_amd64.whl |
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| Size | 2.3 MB |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.8.10
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Release files / pyms_nist_search-0.8.0-cp38-cp38-win32.whl
| Download URL | pyms_nist_search-0.8.0-cp38-cp38-win32.whl |
|---|---|
| Size | 2.3 MB |
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No |
| Uploaded via |
twine/6.1.0 CPython/3.8.10
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Release files / pyms_nist_search-0.8.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_24_x86_64.whl
| Download URL | pyms_nist_search-0.8.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_24_x86_64.whl |
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No |
| Uploaded via |
twine/6.1.0 CPython/3.9.23
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Release files / pyms_nist_search-0.8.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl
| Download URL | pyms_nist_search-0.8.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl |
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No |
| Uploaded via |
twine/6.1.0 CPython/3.9.23
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Release files / pyms_nist_search-0.8.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_24_x86_64.whl
| Download URL | pyms_nist_search-0.8.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_24_x86_64.whl |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.9.23
|
Release files / pyms_nist_search-0.8.0-cp38-cp38-manylinux1_x86_64.manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.whl
| Download URL | pyms_nist_search-0.8.0-cp38-cp38-manylinux1_x86_64.manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.whl |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.9.23
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Release files / pyms_nist_search-0.8.0-cp38-cp38-manylinux1_x86_64.manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.manylinux_2_24_x86_64.whl
| Download URL | pyms_nist_search-0.8.0-cp38-cp38-manylinux1_x86_64.manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.manylinux_2_24_x86_64.whl |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.9.23
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Release files / pyms_nist_search-0.8.0-cp38-cp38-manylinux1_x86_64.manylinux2010_x86_64.manylinux2014_x86_64.manylinux_2_12_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.whl
| Download URL | pyms_nist_search-0.8.0-cp38-cp38-manylinux1_x86_64.manylinux2010_x86_64.manylinux2014_x86_64.manylinux_2_12_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.whl |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.9.23
|
Release files / pyms_nist_search-0.8.0-cp38-cp38-manylinux1_x86_64.manylinux2010_x86_64.manylinux2014_x86_64.manylinux_2_12_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.manylinux_2_24_x86_64.whl
| Download URL | pyms_nist_search-0.8.0-cp38-cp38-manylinux1_x86_64.manylinux2010_x86_64.manylinux2014_x86_64.manylinux_2_12_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.manylinux_2_24_x86_64.whl |
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| Size | 1.8 MB |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.9.23
|
Release files / pyms_nist_search-0.8.0-cp37-cp37m-win_amd64.whl
| Download URL | pyms_nist_search-0.8.0-cp37-cp37m-win_amd64.whl |
|---|---|
| Size | 2.3 MB |
| Tags | CPython 3.7 CPython 3.7 pymalloc Windows x86-64 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.7.9
|
Release files / pyms_nist_search-0.8.0-cp37-cp37m-win32.whl
| Download URL | pyms_nist_search-0.8.0-cp37-cp37m-win32.whl |
|---|---|
| Size | 2.3 MB |
| Tags | CPython 3.7 CPython 3.7 pymalloc Windows x86-32 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.7.9
|
Release files / pyms_nist_search-0.8.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_24_x86_64.whl
| Download URL | pyms_nist_search-0.8.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_24_x86_64.whl |
|---|---|
| Size | 1.8 MB |
| Tags | CPython 3.7 CPython 3.7 pymalloc Linux glibc 2.24+ x86-64 Linux glibc 2.5+ x86-64 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.9.23
|
Release files / pyms_nist_search-0.8.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl
| Download URL | pyms_nist_search-0.8.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl |
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| Size | 1.8 MB |
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|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.9.23
|
Release files / pyms_nist_search-0.8.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_24_x86_64.whl
| Download URL | pyms_nist_search-0.8.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_24_x86_64.whl |
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| Size | 1.8 MB |
| Tags | CPython 3.7 CPython 3.7 pymalloc Linux glibc 2.12+ x86-64 Linux glibc 2.24+ x86-64 Linux glibc 2.5+ x86-64 |
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SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.9.23
|
Security for pyms-nist-search 0.8.0
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