Add rule-based fragmentation #17
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jackgisby
commented
Jul 14, 2022
jackgisby
commented
- Add rule-based fragmentation
- Restructure modules
- Switch to conda-incubator for setting up Actions CI
- Remove unused dependencies
…ate mc, exact_mass, MSn masses
…or the correlated query
Codecov Report
@@ Coverage Diff @@
## dev #17 +/- ##
==========================================
- Coverage 94.86% 94.62% -0.25%
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Files 7 8 +1
Lines 955 1190 +235
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+ Hits 906 1126 +220
- Misses 49 64 +15
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jackgisby
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Nov 7, 2022
* Compatibility with conda version of geng; remove geng tool from package * Incorporate pkl files into connectivity database * Add nauty as dependency * Add pickle as test dependency * Switch from strings to pickles for connectivity graphs * Use blob instead of text to store pickled dictionary * No longer write substructures to .smi * Add option to build to select only frequent substructures * Add connectivity filter to k_configs * Incorporate connectivity filter into MSn build method * Build substructures for each set of masses independently * Call itertools.product on substructures within multiprocessing portion of build * Configure run script for current create_isomorphism_database inputs * Built subsets should be empty list, not None * Update variable names, remove debug options, update docstrings * Add annotate_msn and generate_structures user functions * Move stage at which multiprocessing step is performed * Allow for multiple output options in build * Remove ppm option for retrieving elemental composition from substructure db * Allow list of mc/exact_mass to be passed to generate_structures * Use TemporaryDirectory to store unittest results * Let generate_structures return/yield smiles * Implement build_msn to incorporate considerations for building structures from MS/MS * Implement annotate_msn to provide an interface to build_msn * Add/update build docstrings * Remove unnecessary build parameters * Pass data dictionary to user-facing build functions rather than separate mc, exact_mass, MSn masses * Update variable naming conventions * Add newline between smiles in out file * Update SubstructureDb for removal of .pkl files * Add function create_substructure_database * Bring tests up to date with variable renaming * Bring scripts up to date with variable renaming * Simplify loading of test data and remove teardown * Remove unused class ConnectivityDb and update SubstructureDb parameters * Implement additional non-msn build tests * Improve temporary table cleaning logic * Fix issues with new build functions * Allow tests to load auxiliary test data * Implement msn tests and update k_config test for new parameter * Correctly specify ppm in generate_structures * Minor docstring and code reformatting * Add binder dir * Add example notebook * Remove scripts * Implement basic notebook * Add small substructures to database prior to msn annotation * Complete notebook example * Fix logic for when smi_out_dir is None * Rename example_msms.ipynb to workflow.ipynb * Add pip to install metaboblend * Add data dir, remove databases dir, move test data to data dir * Write notebook databases to notebook_data * Unzip test data * Simplify test paths * Remove databases from gitignore * Use test databases for notebook * Implement simple hydrogenation rules * Get bond types rather than number of available atoms for hydrogen rule calculations * Don't count dummy atoms for bond type calculations * Remove dummy atom mass * Use max_degree of 6 and 2 available_atoms by default for create_substructure_database * Account for the fact we use neutral peaks (i.e. have removed adduct ion) * Modify hydrogen re-arrangement rules for doulbe bonds * Update databases tests * Implement test for calculate_possible_hydrogenations using reference numbers * Add test for calculate_hydrogen_rearrangements * Update hydrogen re-arrangement calculation function documentation * Update remaining unit tests * Add hydrogen re-arrangement compound HMDB XMLs * Record even substructures * Record even substructures in results DB * Add indexes to improve combine_ecs function performance * Improve results DB hierarchy and implement aggregation of scoring metrics * Define SQLite functions to calculate scores via queries alone * Record max BDE in spectra results table * Calculate frequency in the absence of scores (for non-MSn method) * Retain substructures does not cause substructures not to be initially recorded * Add additional scoring metrics * Update results db test data * Define ppm error and valence of fragment prior to re-ordering * Configure checks on recording of putative structure information * Calculate scores at substructure combination level * Convert True to 1 and False to 0 for conversion to SQLite boolean type * Index results DB * Use a loop in place of pool.map * Minor performance improvements * Merge minor performance improvements * Use the minimum absolute error for getting possible fragment ions * Add separate absolute error options for MSn peak and full structure * Use 0.005 for abs_error_precursor * Drop indexes before inserting into results DB * Add results table index on ms_id_num and structure_smiles * Update results DB tests * Add table for generating unique structure smiles IDs * Calculate cosine spectrum similarity * Allow for the specification of weights for the results database scoring calculations * Aggregate structure scores but force floating point division * Select fragment and substructure id when calculating results scores for the correlated query * Update results DB tests with updated scores * Don't create indexes until structure scoring * Don't include valence=0 substructures in the substructure database * Add max BDE parameter for building * Remove redundant connectivity graphs * Update data to test filter records function * Update dictionary pickle with Python 3.7 * Update file header * Update contact information * Update setup.py * Update tests for RDKit changes * Update README * Keep functioning buttons * Update testing workflow * Use python 3.7 * Remove unused dependencies * Use only the channel conda-forge * Add pillow and pyqt dependencies * Remove list definition in function arguments * Add algorithms test * Merge database tests into single file * Restructure modules * Restructure tests * Update outdated imports * Omit notebooks from coverage Co-authored-by: Ralf Weber <[email protected]>
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