| Previous changeset 9:715fe77be601 (2023-05-25) Next changeset 11:ae45992f969e (2023-10-12) |
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Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e |
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modified:
formatter.py macros.xml matchms_formatter.xml test-data/convert/harmonized_msp_out.msp test-data/convert/harmonized_msp_peakcomments_out.msp test-data/scores.json test-data/similarity/scores_test1_out.json test-data/similarity/scores_test2_out.json test-data/similarity/scores_test3_out.json test-data/similarity/scores_test4_out.json test-data/similarity/scores_test5_out.json test-data/split/chunk-size/chunk_0.msp test-data/split/chunk-size/chunk_1.msp test-data/split/chunk-size/chunk_2.msp test-data/split/num-chunks/chunk_0.msp test-data/split/num-chunks/chunk_1.msp test-data/split/one-per-file/1NITROPYRENE.msp test-data/split/one-per-file/23DICHLOROPHENOL.msp test-data/split/one-per-file/245TRICHLOROPHENOL.msp test-data/split/one-per-file/246TRICHLOROPHENOL.msp test-data/split/one-per-file/24DICHLOROPHENOL.msp test-data/split/one-per-file/24DINITROPHENOL.msp test-data/split/one-per-file/25DICHLOROPHENOL.msp test-data/split/one-per-file/26DICHLOROPHENOL.msp test-data/split/one-per-file/34DICHLOROPHENOL.msp test-data/split/one-per-file/35DICHLOROPHENOL.msp |
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added:
help.xml matchms_filtering_wrapper.py matchms_networking_wrapper.py matchms_similarity_wrapper.py matchms_split.py test-data/fingerprints/cosine.json test-data/fingerprints/dice.json test-data/fingerprints/jaccard_scores.json test-data/formatter/fill2_formatted.tsv test-data/formatter/fill2_trunc_scores_with_metadata_match.json test-data/formatter/test4_formatted.tsv test-data/metadata_match/inchi_key_inner.json test-data/metadata_match/inner_join_ri_20.json test-data/metadata_match/left_join_ri_20.json test-data/metadata_match/ri_match_60.json test-data/metadata_match/smiles.json test-data/similarity/rcx_exposome_pesticides_subset.msp test-data/similarity/rcx_gc-ei_ms_subset.msp test-data/similarity/scores_test6_out.json test-data/similarity/spec2vec/inp_filtered_library.msp test-data/similarity/spec2vec/inp_filtered_spectra.msp test-data/similarity/spec2vec/model.json test-data/similarity/spec2vec/weights_100.binary test-data/spectral_similarity/test1.json test-data/spectral_similarity/test2.json |
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removed:
test-data/formatter/test2_threshold_formatting.tsv test-data/formatter/test2_topk_formatting.tsv |
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| diff -r 715fe77be601 -r 1b09315a3f87 formatter.py --- a/formatter.py Thu May 25 09:06:00 2023 +0000 +++ b/formatter.py Tue Jun 27 14:25:59 2023 +0000 |
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| @@ -3,68 +3,7 @@ from pandas import DataFrame -def create_long_table(data: DataFrame, value_id: str) -> DataFrame: - """Convert the table from compact into long format. - See DataFrame.melt(...). - - Args: - data (DataFrame): The data table to convert. - value_id (str): The name to assign to the added column through conversion to long format. - - Returns: - DataFrame: Table in long format. - """ - return data.transpose().melt(ignore_index=False, var_name='compound', value_name=value_id) - - -def join_df(x: DataFrame, y: DataFrame, on=[], how="inner") -> DataFrame: - """Shortcut functions to join to dataframes on columns and index - - Args: - x (DataFrame): Table X - y (DataFrame): Table Y - on (list, optional): Columns on which to join. Defaults to []. - how (str, optional): Join method, see DataFrame.join(...). Defaults to "inner". - - Returns: - DataFrame: Joined dataframe. - """ - df_x = x.set_index([x.index] + on) - df_y = y.set_index([y.index] + on) - combined = df_x.join(df_y, how=how) - return combined - - -def get_top_k_matches(data: DataFrame, k: int) -> DataFrame: - """Function to get top k matches from dataframe with scores. - - Args: - data (DataFrame): A table with score column. - k (int): Number of top scores to retrieve. - - Returns: - DataFrame: Table containing only the top k best matches for each compound. - """ - return data.groupby(level=0, group_keys=False).apply(DataFrame.nlargest, n=k, columns=['score']) - - -def filter_thresholds(data: DataFrame, t_score: float, t_matches: float) -> DataFrame: - """Filter a dataframe with scores and matches to only contain values above specified thresholds. - - Args: - data (DataFrame): Table to filter. - t_score (float): Score threshold. - t_matches (float): Matches threshold. - - Returns: - DataFrame: Filtered dataframe. - """ - filtered = data[data['score'] > t_score] - filtered = filtered[filtered['matches'] > t_matches] - return filtered - - -def scores_to_dataframes(scores): +def scores_to_dataframe(scores): """Unpack scores from matchms.scores into two dataframes of scores and matches. Args: @@ -74,13 +13,12 @@ DataFrame: Scores DataFrame: Matches """ - query_names = [spectra.metadata['compound_name'] for spectra in scores.queries] - reference_names = [spectra.metadata['compound_name'] for spectra in scores.references] + dataframe = DataFrame(columns=['query', 'reference', *scores.scores.score_names]) - dataframe_scores = DataFrame(data=[entry["score"] for entry in scores.scores], index=reference_names, columns=query_names) - dataframe_matches = DataFrame(data=[entry["matches"] for entry in scores.scores], index=reference_names, columns=query_names) + for i, (row, col) in enumerate(zip(scores.scores.row, scores.scores.col)): + dataframe.loc[i] = [scores.queries[col].metadata['compound_name'], scores.references[row].metadata['compound_name'], *scores.scores.data[i]] - return dataframe_scores, dataframe_matches + return dataframe def load_data(scores_filename: str) -> DataFrame: @@ -93,47 +31,19 @@ DataFrame: Joined dataframe on compounds containing scores and matches in long format. """ scores = scores_from_json(scores_filename) - scores, matches = scores_to_dataframes(scores) + scores = scores_to_dataframe(scores) - scores_long = create_long_table(scores, 'score') - matches_long = create_long_table(matches, 'matches') - - combined = join_df(matches_long, scores_long, on=['compound'], how='inner') - return combined + return scores -@click.group() +@click.group(invoke_without_command=True) @click.option('--sf', 'scores_filename', type=click.Path(exists=True), required=True) @click.option('--o', 'output_filename', type=click.Path(writable=True), required=True) -@click.pass_context -def cli(ctx, scores_filename, output_filename): - ctx.ensure_object(dict) - ctx.obj['data'] = load_data(scores_filename) +def cli(scores_filename, output_filename): + result = load_data(scores_filename) + result.to_csv(output_filename, sep="\t", index=False) pass -@cli.command() -@click.option('--st', 'scores_threshold', type=float, required=True) -@click.option('--mt', 'matches_threshold', type=float, required=True) -@click.pass_context -def get_thresholded_data(ctx, scores_threshold, matches_threshold): - result = filter_thresholds(ctx.obj['data'], scores_threshold, matches_threshold) - return result - - -@cli.command() -@click.option('--k', 'k', type=int, required=True) -@click.pass_context -def get_top_k_data(ctx, k): - result = get_top_k_matches(ctx.obj['data'], k) - return result - - -@cli.result_callback() -def write_output(result: DataFrame, scores_filename, output_filename): - result = result.reset_index().rename(columns={'level_0': 'query', 'compound': 'reference'}) - result.to_csv(output_filename, sep="\t", index=False) - - if __name__ == '__main__': - cli(obj={}) + cli() |
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| diff -r 715fe77be601 -r 1b09315a3f87 help.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/help.xml Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| @@ -0,0 +1,58 @@ +<macros> + <token name="@HELP_matchms@"> + Documentation + The Python library matchms provides functions to convert, filter and compare mass spectrometry data. + For an overview of the different galaxy modules, see the figure below. + For detailed documentation on the tool, see https://github.com/matchms/matchms/blob/master/README.rst + and https://matchms.readthedocs.io/en/latest/ for the Python API. + + To get more familiar with the library, there is a `tutorial`_ available which explains how to build a mass spectrometry data processing + pipeline with matchms. + + .. _tutorial: https://medium.com/escience-center/build-your-own-mass-spectrometry-analysis-pipeline-in-python-using-matchms-part-i-d96c718c68ee + + Overview + .. image:: https://github.com/RECETOX/galaxytools/raw/29e54e69dab6ab1263f56d35ea19f5d7f284d728/tools/matchms/images/matchms_galaxytools.png + :width: 3120 + :height: 1686 + :scale: 30 + :alt: Overview of different matchms galaxytools and how they are connected. + </token> + <token name="@HELP_matchms_networking@"> + <![CDATA[ + Documentation + For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst + and https://matchms.readthedocs.io/en/latest/. + + **Upstream Tools** + + matchms similarity + + **Downstream Tools** + + The output is a network-graph file that can be visualized using graph visualization software (e.g., Cytoscape). + ]]> + </token> + + <token name="@HELP_formatter@"> + <![CDATA[ + Usage + This tool creates user friendly tables from the similarity scores produced by **matchms similarity**. + The tool can be operated on two modes based on (i) thresholds or (ii) top k matches. + + Input Table Format + The tool expects a JSON file containing serialized matchms Scores object. + + Output Table Format + +----------+-----------+---------+--------+ + | query | reference | matches | scores | + +==========+===========+=========+========+ + | C001 | Glycine | 6 | 0.5 | + +----------+-----------+---------+--------+ + | C002 | Glycine | 3 | 0.34 | + +----------+-----------+---------+--------+ + | ... | ... | ... | ... | + +----------+-----------+---------+--------+ + ]]> + </token> +</macros> \ No newline at end of file |
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| diff -r 715fe77be601 -r 1b09315a3f87 macros.xml --- a/macros.xml Thu May 25 09:06:00 2023 +0000 +++ b/macros.xml Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">0.17.0</token> + <token name="@TOOL_VERSION@">0.20.0</token> <xml name="creator"> <creator> @@ -31,69 +31,75 @@ </creator> </xml> - <token name="@HELP_matchms@"> - <![CDATA[ - Documentation - For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst - and https://matchms.readthedocs.io/en/latest/. + <xml name="bio.tools"> + <xrefs> + <xref type="bio.tools">matchms</xref> + </xrefs> + </xml> - Upstream Tools - +-----------+---------------+--------+-----------+ - | Name | Output File | Format | Parameter | - +===========+===============+========+===========+ - | RAMClustR | Mass spectra | msp | references| - +-----------+---------------+--------+-----------+ - | RAMClustR | Mass spectra | msp | queries | - +-----------+---------------+--------+-----------+ + <xml name="similarity_metrics"> + <option value="CosineGreedy" selected="true">CosineGreedy</option> + <option value="CosineHungarian">CosineHungarian</option> + <option value="ModifiedCosine">ModifiedCosine</option> + <option value="NeutralLossesCosine">NeutralLossesCosine</option> + </xml> - Downstream Tools - The output is a JSON file containing serialized matchMS Scores object. The file can be processed by **matchMS output formatter**. - ]]> - </token> - - <token name="@HELP_matchms_networking@"> - <![CDATA[ - Documentation - For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst - and https://matchms.readthedocs.io/en/latest/. - - **Upstream Tools** + <xml name="similarity_algorithm_params"> + <section name="algorithm" title="Algorithm Parameters" expanded="true"> + <param label="tolerance [Da]" name="tolerance" type="float" value="0.1" + help="Peaks will be considered a match when less than tolerance apart. Absolute m/z value, not in ppm."/> + <param label="mz_power" name="mz_power" type="float" value="0.0" + help="The power to raise mz to in the cosine function."/> + <param label="intensity_power" name="intensity_power" type="float" value="1.0" + help="The power to raise intensity to in the cosine function."/> + </section> + </xml> - matchMS similarity - - **Downstream Tools** - - The output is a network-graph file that can be visualized using graph visualization software (e.g., Cytoscape). - ]]> - </token> - - <token name="@HELP_formatter@"> - <![CDATA[ - Usage - This tool creates user friendly tables from the similarity scores produced by **matchMS similarity**. - The tool can be operated on two modes based on (i) thresholds or (ii) top k matches. - - Input Table Format - The tool expects a JSON file containing serialized matchMS Scores object. + <xml name="input_param"> + <conditional name="scores"> + <param name="use_scores" label="Use Scores Object" type="boolean" truevalue="TRUE" falsevalue="FALSE" + checked="false"/> + <when value="TRUE"> + <param label="Scores object" name="scores_in" type="data" format="json" + help="Scores objects calculated previously using one of the matchms similarity tools." /> + <param label="join type" name="join_type" type="select" display="radio" + help="The join type to use for appending scores - see [1] for details."> + <option value="left" selected="true">left</option> + <option value="inner">inner</option> + <option value="right">right</option> + <option value="outer">outer</option> + </param> + </when> + <when value="FALSE"> + <param label="Queries spectra" name="queries" type="data" format="msp" + help="Query mass spectra to match against references."/> + <param label="Reference spectra" name="references" type="data" format="msp" + help="Reference mass spectra to match against as library."/> + </when> + </conditional> + </xml> - Output Table Format - +----------+-----------+---------+--------+ - | query | reference | matches | scores | - +==========+===========+=========+========+ - | C001 | Glycine | 6 | 0.5 | - +----------+-----------+---------+--------+ - | C002 | Glycine | 3 | 0.34 | - +----------+-----------+---------+--------+ - | ... | ... | ... | ... | - +----------+-----------+---------+--------+ - ]]> - </token> - - <xml name="citations"> - <citations> - <citation type="doi">10.5281/zenodo.7178586</citation> - <citation type="doi">10.21105/joss.02411</citation> - </citations> - </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.5281/zenodo.7178586</citation> + <citation type="doi">10.21105/joss.02411</citation> + </citations> + </xml> +<token name="@init_scores@"> +from matchms.importing import load_from_msp, scores_from_json +from matchms import Scores +#if $scores.use_scores +scores = scores_from_json("$scores_in") +join_type = "$scores.join_type" +#else +scores = Scores(references=list(load_from_msp("$references")), queries=list(load_from_msp("$queries")), is_symmetric=False) +join_type = "left" +#end if +</token> + +<token name="@init_logger@"> +from matchms import set_matchms_logger_level +set_matchms_logger_level("WARNING") +</token> </macros> |
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| diff -r 715fe77be601 -r 1b09315a3f87 matchms_filtering_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/matchms_filtering_wrapper.py Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| @@ -0,0 +1,77 @@ +import argparse +import sys + +from matchms.exporting import save_as_mgf, save_as_msp +from matchms.filtering import add_compound_name, add_fingerprint, add_losses, add_parent_mass, add_precursor_mz,\ + add_retention_index, add_retention_time, clean_compound_name +from matchms.filtering import default_filters, normalize_intensities, select_by_mz, select_by_relative_intensity +from matchms.importing import load_from_mgf, load_from_msp + + +def main(argv): + parser = argparse.ArgumentParser(description="Compute MSP similarity scores") + parser.add_argument("--spectra", type=str, required=True, help="Mass spectra file to be filtered.") + parser.add_argument("--spectra_format", type=str, required=True, help="Format of spectra file.") + parser.add_argument("--output", type=str, required=True, help="Filtered mass spectra file.") + parser.add_argument("-normalise_intensities", action='store_true', + help="Normalize intensities of peaks (and losses) to unit height.") + parser.add_argument("-default_filters", action='store_true', + help="Collection of filters that are considered default and that do no require any (factory) arguments.") + parser.add_argument("-clean_metadata", action='store_true', + help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata.") + parser.add_argument("-relative_intensity", action='store_true', + help="Keep only peaks within set relative intensity range (keep if to_intensity >= intensity >= from_intensity).") + parser.add_argument("--from_intensity", type=float, help="Lower bound for intensity filter") + parser.add_argument("--to_intensity", type=float, help="Upper bound for intensity filter") + parser.add_argument("-mz_range", action='store_true', + help="Keep only peaks between set m/z range (keep if to_mz >= m/z >= from_mz).") + parser.add_argument("--from_mz", type=float, help="Lower bound for m/z filter") + parser.add_argument("--to_mz", type=float, help="Upper bound for m/z filter") + args = parser.parse_args() + + if not (args.normalise_intensities + or args.default_filters + or args.clean_metadata + or args.relative_intensity + or args.mz_range): + raise ValueError('No filter selected.') + + if args.spectra_format == 'msp': + spectra = list(load_from_msp(args.spectra)) + elif args.queries_format == 'mgf': + spectra = list(load_from_mgf(args.spectra)) + else: + raise ValueError(f'File format {args.spectra_format} not supported for mass spectra file.') + + filtered_spectra = [] + for spectrum in spectra: + if args.normalise_intensities: + spectrum = normalize_intensities(spectrum) + + if args.default_filters: + spectrum = default_filters(spectrum) + + if args.clean_metadata: + filters = [add_compound_name, add_precursor_mz, add_fingerprint, add_losses, add_parent_mass, + add_retention_index, add_retention_time, clean_compound_name] + for metadata_filter in filters: + spectrum = metadata_filter(spectrum) + + if args.relative_intensity: + spectrum = select_by_relative_intensity(spectrum, args.from_intensity, args.to_intensity) + + if args.mz_range: + spectrum = select_by_mz(spectrum, args.from_mz, args.to_mz) + + filtered_spectra.append(spectrum) + + if args.spectra_format == 'msp': + save_as_msp(filtered_spectra, args.output) + else: + save_as_mgf(filtered_spectra, args.output) + + return 0 + + +if __name__ == "__main__": + main(argv=sys.argv[1:]) |
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| diff -r 715fe77be601 -r 1b09315a3f87 matchms_formatter.xml --- a/matchms_formatter.xml Thu May 25 09:06:00 2023 +0000 +++ b/matchms_formatter.xml Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| @@ -1,10 +1,15 @@ -<tool id="matchms_formatter" name="matchms output formatter" version="0.1.4" python_template_version="3.5"> - <description>reformat output tables of matchms</description> +<tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy0" profile="21.09"> + <description>reformat scores object of matchms to long format table</description> <macros> <import>macros.xml</import> + <import>help.xml</import> </macros> <expand macro="creator"/> + <edam_operations> + <edam_operation>operation_0335</edam_operation> + </edam_operations> + <expand macro="bio.tools"/> <requirements> <requirement type="package" version="@TOOL_VERSION@">matchms</requirement> @@ -24,61 +29,32 @@ <configfiles> <configfile name="matchms_formatter_cli"> python3 ${__tool_directory__}/formatter.py \ - --sf "$scores" \ - --o "$output" \ - $method.selection \ - #if $method.selection == "get-thresholded-data" - --st $method.scores_threshold \ - --mt $method.matches_threshold - #else - --k $method.k - #end if + --sf '$scores' \ + --o '$output' </configfile> </configfiles> <inputs> - <param label="Scores object" name="scores" type="data" format="json" help="MatchMS Scores json file." /> - - <conditional name="method"> - <param name="selection" type="select" label="Formatting method"> - <option value="get-thresholded-data" selected="true">Thresholding</option> - <option value="get-top-k-data">Top K Matches</option> - </param> - <when value="get-thresholded-data"> - <param label="Scores Threshold" name="scores_threshold" type="float" value="0.6" min="0.0" max="1.0" - help="Threshold for matching score."/> - <param label="Matches Threshold" name="matches_threshold" type="integer" value="3" min="0" - help="Threshold for number of matches ions."/> - </when> - <when value="get-top-k-data"> - <param label="Top K" name="k" type="integer" value="5" help="K for top k match selection."/> - </when> - </conditional> - + <param label="Scores object" name="scores" type="data" format="json" help="matchms Scores json file." /> </inputs> <outputs> - <data label="${tool.name} (${method.selection}) on ${on_string}" name="output" format="tsv"/> + <data label="${tool.name} on ${on_string}" name="output" format="tsv"/> </outputs> <tests> <test> - <param name="scores" value="similarity/scores_test2_out.json" ftype="json"/> - <param name="selection" value="get-thresholded-data"/> - <param name="scores_threshold" value="0.4"/> - <param name="matches_threshold" value="2"/> - <output name="output" file="formatter/test2_threshold_formatting.tsv" ftype="tsv" - checksum="md5$db18b3f3dd5d8dea4db0fc1d59d3db3b"/> + <param name="scores" value="formatter/fill2_trunc_scores_with_metadata_match.json" ftype="json"/> + <output name="output" value="formatter/fill2_formatted.tsv" ftype="tsv" + checksum="md5$4f0d83da381b8a403d807d26a9dd0f34"/> </test> <test> - <param name="scores" value="similarity/scores_test2_out.json" ftype="json"/> - <param name="selection" value="get-top-k-data"/> - <param name="k" value="3"/> - <output name="output" file="formatter/test2_topk_formatting.tsv" ftype="tsv" - checksum="md5$ff827ec7413acac3d2394330935ace99"/> + <param name="scores" value="similarity/scores_test4_out.json" ftype="json"/> + <output name="output" file="formatter/test4_formatted.tsv" ftype="tsv"/> </test> </tests> - <help><![CDATA[ + <help> @HELP_formatter@ - ]]></help> + @HELP_matchms@ + </help> </tool> |
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| diff -r 715fe77be601 -r 1b09315a3f87 matchms_networking_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/matchms_networking_wrapper.py Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| @@ -0,0 +1,39 @@ +import argparse +import sys + +from matchms.importing import scores_from_json +from matchms.networking import SimilarityNetwork + + +def main(argv): + parser = argparse.ArgumentParser(description="Create network-graph from similarity scores.") + parser.add_argument("--graph_format", type=str, help="Format of the output similarity network.") + parser.add_argument("--score_name", type=str, help="Name of the score layer to use for creating the network graph.") + parser.add_argument("--identifier", type=str, help="Unique metadata identifier of each spectrum from which scores are computed.") + parser.add_argument("--top_n", type=int, help="Number of highest-score edges to keep.") + parser.add_argument("--max_links", type=int, help="Maximum number of links to add per node.") + parser.add_argument("--score_cutoff", type=float, help="Minimum similarity score value to link two spectra.") + parser.add_argument("--link_method", type=str, help="Method for selecting top N edges for each node.") + parser.add_argument("--keep_unconnected_nodes", help="Keep unconnected nodes in the network.", action="store_true") + parser.add_argument("scores", type=str, help="Path to matchms similarity-scores .json file.") + parser.add_argument("output_filename", type=str, help="Path where to store the output similarity network.") + args = parser.parse_args() + + scores = scores_from_json(args.scores) + + network = SimilarityNetwork(identifier_key=args.identifier, + top_n=args.top_n, + max_links=args.max_links, + score_cutoff=args.score_cutoff, + link_method=args.link_method, + keep_unconnected_nodes=args.keep_unconnected_nodes) + + network.create_network(scores, args.score_name) + network.export_to_file(filename=args.output_filename, graph_format=args.graph_format) + + return 0 + + +if __name__ == "__main__": + main(argv=sys.argv[1:]) + pass |
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| diff -r 715fe77be601 -r 1b09315a3f87 matchms_similarity_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/matchms_similarity_wrapper.py Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| @@ -0,0 +1,136 @@ +import argparse +import json +import sys + +from matchms import calculate_scores +from matchms.importing import load_from_mgf, load_from_msp +from matchms.similarity import (CosineGreedy, CosineHungarian, MetadataMatch, + ModifiedCosine, NeutralLossesCosine) +from spec2vec import Spec2Vec +from spec2vec.serialization.model_importing import load_weights, Word2VecLight + + +def convert_precursor_mz(spectrum): + """ + Check the presence of precursor m/z since it is needed for ModifiedCosine similarity metric. Convert to float if + needed, raise error if missing. + """ + + if "precursor_mz" in spectrum.metadata: + metadata = spectrum.metadata + metadata["precursor_mz"] = float(metadata["precursor_mz"]) + spectrum.metadata = metadata + return spectrum + else: + raise ValueError("Precursor_mz missing. Apply 'add_precursor_mz' filter first.") + + +def load_model(model_file, weights_file) -> Word2VecLight: + """ + Read a lightweight version of a :class:`~gensim.models.Word2Vec` model from disk. + + Parameters + ---------- + model_file: + A path of json file to load the model. + weights_file: + A path of `.npy` file to load the model's weights. + + Returns + ------- + :class:`~spec2vec.serialization.model_importing.Word2VecLight` – a lightweight version of a + :class:`~gensim.models.Word2Vec` + """ + with open(model_file, "r", encoding="utf-8") as f: + model: dict = json.load(f) + del (model["mapfile_path"]) + + weights = load_weights(weights_file, model["__weights_format"]) + return Word2VecLight(model, weights) + + +def main(argv): + parser = argparse.ArgumentParser(description="Compute MSP similarity scores") + parser.add_argument("-r", dest="ri_tolerance", type=float, help="Use RI filtering with given tolerance.") + parser.add_argument("-s", dest="symmetric", action='store_true', help="Computation is symmetric.") + parser.add_argument("--array_type", type=str, help="Type of array to use for storing scores (numpy or sparse).") + parser.add_argument("--ref", dest="references_filename", type=str, help="Path to reference spectra library.") + parser.add_argument("--ref_format", dest="references_format", type=str, help="Reference spectra library file format.") + parser.add_argument("--spec2vec_model", dest="spec2vec_model", type=str, help="Path to spec2vec model.") + parser.add_argument("--spec2vec_weights", dest="spec2vec_weights", type=str, help="Path to spec2vec weights.") + parser.add_argument("--allow_missing_percentage", dest="allowed_missing_percentage", type=lambda x: float(x) * 100.0, help="Maximum percentage of missing peaks in model corpus.") + parser.add_argument("queries_filename", type=str, help="Path to query spectra.") + parser.add_argument("queries_format", type=str, help="Query spectra file format.") + parser.add_argument("similarity_metric", type=str, help='Metric to use for matching.') + parser.add_argument("tolerance", type=float, help="Tolerance to use for peak matching.") + parser.add_argument("mz_power", type=float, help="The power to raise mz to in the cosine function.") + parser.add_argument("intensity_power", type=float, help="The power to raise intensity to in the cosine function.") + parser.add_argument("output_filename_scores", type=str, help="Path where to store the output .json scores.") + args = parser.parse_args() + + if args.queries_format == 'msp': + queries_spectra = list(load_from_msp(args.queries_filename)) + elif args.queries_format == 'mgf': + queries_spectra = list(load_from_mgf(args.queries_filename)) + else: + raise ValueError(f'File format {args.queries_format} not supported for query spectra.') + + if args.symmetric: + reference_spectra = queries_spectra.copy() + else: + if args.references_format == 'msp': + reference_spectra = list(load_from_msp(args.references_filename)) + elif args.references_format == 'mgf': + reference_spectra = list(load_from_mgf(args.references_filename)) + else: + raise ValueError(f'File format {args.references_format} not supported for reference spectra library.') + + if args.similarity_metric == 'CosineGreedy': + similarity_metric = CosineGreedy(args.tolerance, args.mz_power, args.intensity_power) + elif args.similarity_metric == 'CosineHungarian': + similarity_metric = CosineHungarian(args.tolerance, args.mz_power, args.intensity_power) + elif args.similarity_metric == 'ModifiedCosine': + similarity_metric = ModifiedCosine(args.tolerance, args.mz_power, args.intensity_power) + reference_spectra = list(map(convert_precursor_mz, reference_spectra)) + queries_spectra = list(map(convert_precursor_mz, queries_spectra)) + elif args.similarity_metric == 'NeutralLossesCosine': + similarity_metric = NeutralLossesCosine(args.tolerance, args.mz_power, args.intensity_power) + reference_spectra = list(map(convert_precursor_mz, reference_spectra)) + queries_spectra = list(map(convert_precursor_mz, queries_spectra)) + elif args.similarity_metric == 'Spec2Vec': + model = load_model(args.spec2vec_model, args.spec2vec_weights) + similarity_metric = Spec2Vec(model, intensity_weighting_power=args.intensity_power, allowed_missing_percentage=args.allowed_missing_percentage) + else: + return -1 + + print("Calculating scores...") + scores = calculate_scores( + references=reference_spectra, + queries=queries_spectra, + array_type=args.array_type, + similarity_function=similarity_metric, + is_symmetric=args.symmetric + ) + + if args.ri_tolerance is not None: + print("RI filtering with tolerance ", args.ri_tolerance) + ri_matches = calculate_scores(references=reference_spectra, + queries=queries_spectra, + similarity_function=MetadataMatch("retention_index", "difference", args.ri_tolerance), + array_type="numpy", + is_symmetric=args.symmetric).scores + scores.scores.add_coo_matrix(ri_matches, "MetadataMatch", join_type="inner") + + write_outputs(args, scores) + return 0 + + +def write_outputs(args, scores): + """Write Scores to json file.""" + print("Storing outputs...") + scores.to_json(args.output_filename_scores) + + +if __name__ == "__main__": + main(argv=sys.argv[1:]) + pass |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 matchms_split.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/matchms_split.py Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| @@ -0,0 +1,90 @@ +import argparse +import itertools +import os +from typing import List + +from matchms.exporting import save_as_msp +from matchms.importing import load_from_msp + + +def get_spectra_names(spectra: list) -> List[str]: + """Read the keyword 'compound_name' from a spectra. + + Args: + spectra (list): List of individual spectra. + + Returns: + List[str]: List with 'compoud_name' of individual spectra. + """ + return [x.get("compound_name") for x in spectra] + + +def make_outdir(outdir: str): + """Create destination directory. + + Args: + outdir (str): Path to destination directory where split spectra files are generated. + """ + return os.mkdir(outdir) + + +def write_spectra(spectra, outdir): + """Generates MSP files of individual spectra. + + Args: + spectra (List[Spectrum]): Spectra to write to file + outdir (str): Path to destination directory. + """ + names = get_spectra_names(spectra) + for i in range(len(spectra)): + outpath = assemble_outpath(names[i], outdir) + save_as_msp(spectra[i], outpath) + + +def assemble_outpath(name, outdir): + """Filter special chracteres from name. + + Args: + name (str): Name to be filetered. + outdir (str): Path to destination directory. + """ + filename = ''.join(filter(str.isalnum, name)) + outfile = str(filename) + ".msp" + outpath = os.path.join(outdir, outfile) + return outpath + + +def split_round_robin(iterable, num_chunks): + chunks = [list() for _ in range(num_chunks)] + index = itertools.cycle(range(num_chunks)) + for value in iterable: + chunks[next(index)].append(value) + chunks = filter(lambda x: len(x) > 0, chunks) + return chunks + + +listarg = argparse.ArgumentParser() +listarg.add_argument('--filename', type=str) +listarg.add_argument('--method', type=str) +listarg.add_argument('--outdir', type=str) +listarg.add_argument('--parameter', type=int) +args = listarg.parse_args() +outdir = args.outdir +filename = args.filename +method = args.method +parameter = args.parameter + + +if __name__ == "__main__": + spectra = load_from_msp(filename, metadata_harmonization=True) + make_outdir(outdir) + + if method == "one-per-file": + write_spectra(list(spectra), outdir) + else: + if method == "chunk-size": + chunks = iter(lambda: list(itertools.islice(spectra, parameter)), []) + elif method == "num-chunks": + chunks = split_round_robin(spectra, parameter) + for i, x in enumerate(chunks): + save_as_msp(x, os.path.join(outdir, f"chunk_{i}.msp")) |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/convert/harmonized_msp_out.msp --- a/test-data/convert/harmonized_msp_out.msp Thu May 25 09:06:00 2023 +0000 +++ b/test-data/convert/harmonized_msp_out.msp Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -3,18 +3,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C4H10NO3PS\n INCHIKEY: YASYVMFAVPKPKE-SECBINFHSA-N\n-INCHI: \n SMILES: COP(=O)(N=C(O)C)SC\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Acephate\n RETENTION_TIME: 1.232997\n PRECURSOR_MZ: 184.0194\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 16\n 90.09368 1128.0\n@@ -39,18 +36,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C12H11NO2\n INCHIKEY: CVXBEEMKQHEXEN-UHFFFAOYSA-N\n-INCHI: \n SMILES: CN=C(Oc1cccc2c1cccc2)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Carbaryl\n RETENTION_TIME: 5.259445\n PRECURSOR_MZ: 202.0863\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 1\n 145.06491 1326147.0\n@@ -60,18 +54,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C8H16NO5P\n INCHIKEY: VEENJGZXVHKXNB-UHFFFAOYSA-N\n-INCHI: \n SMILES: COP(=O)(OC(=CC(=O)N(C)C)C)OC\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Dicrotophos\n RETENTION_TIME: 2.025499\n PRECURSOR_MZ: 238.0844\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 5\n 112.074 102027.0\n@@ -85,18 +76,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C5H12NO3PS2\n INCHIKEY: MCWXGJITAZMZEV-UHFFFAOYSA-N\n-INCHI: \n SMILES: CN=C(CSP(=S)(OC)OC)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Dimethoate\n RETENTION_TIME: 2.866696\n PRECURSOR_MZ: 230.0072\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 8\n 88.0219 548446.0\n@@ -113,18 +101,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C21H22NO4Cl\n INCHIKEY: QNBTYORWCCMPQP-UHFFFAOYSA-N\n-INCHI: \n SMILES: COc1cc(ccc1OC)C(=CC(=O)N1CCOCC1)c1ccc(cc1)Cl\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Dimethomorph\n RETENTION_TIME: 7.060486\n PRECURSOR_MZ: 388.1316\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 22\n 114.05532 468862.0\n@@ -155,18 +140,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C2H8NO2PS\n INCHIKEY: NNKVPIKMPCQWCG-ZCFIWIBFSA-N\n-INCHI: \n SMILES: COP(=O)(SC)N\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Methamidophos\n RETENTION_TIME: 1.153307\n PRECURSOR_MZ: 142.0089\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 4\n 98.00042 37721.0\n@@ -179,18 +161,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C7H13O6P\n INCHIKEY: GEPDYQSQVLXLEU-UHFFFAOYSA-N\n-INCHI: \n SMILES: COC(=O)C=C(OP(=O)(OC)OC)C\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Mevinphos\n RETENTION_TIME: 2.876307\n PRECURSOR_MZ: 225.0525\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 4\n 99.04416 295529.0\n@@ -203,18 +182,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C5H12NO4PS\n INCHIKEY: PZXOQEXFMJCDPG-UHFFFAOYSA-N\n-INCHI: \n SMILES: CN=C(CSP(=O)(OC)OC)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Omethoate\n RETENTION_TIME: 1.33423\n PRECURSOR_MZ: 214.0303\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 5\n 104.01654 86844.0\n@@ -228,1'..b'CHIKEY: WZZLDXDUQPOXNW-UHFFFAOYSA-N\n-INCHI: \n SMILES: CCCOC(=NCCCN(C)C)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Propamocarb_1\n RETENTION_TIME: 0.7535679\n PRECURSOR_MZ: 189.1603\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 2\n 86.0966 201548.0\n@@ -6366,18 +5877,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C9H20N2O2\n INCHIKEY: WZZLDXDUQPOXNW-UHFFFAOYSA-N\n-INCHI: \n SMILES: CCCOC(=NCCCN(C)C)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Propamocarb_2\n RETENTION_TIME: 1.081971\n PRECURSOR_MZ: 189.1603\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 2\n 86.0966 107829.0\n@@ -6388,18 +5896,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C11H15N3O2\n INCHIKEY: MYPKGPZHHQEODQ-UHFFFAOYSA-N\n-INCHI: \n SMILES: CN=C(Oc1cccc(c1)N=CN(C)C)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Formetanate_1\n RETENTION_TIME: 0.7730471\n PRECURSOR_MZ: 222.1239\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 13\n 93.03365 1796.0\n@@ -6421,18 +5926,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C11H15N3O2\n INCHIKEY: MYPKGPZHHQEODQ-UHFFFAOYSA-N\n-INCHI: \n SMILES: CN=C(Oc1cccc(c1)N=CN(C)C)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Formetanate_2\n RETENTION_TIME: 1.13043\n PRECURSOR_MZ: 222.1239\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 15\n 91.05441 6330.0\n@@ -6456,18 +5958,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C12H18N2O2\n INCHIKEY: YNEVBPNZHBAYOA-UHFFFAOYSA-N\n-INCHI: \n SMILES: CN=C(Oc1cc(C)c(c(c1)C)N(C)C)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Mexacarbate\n RETENTION_TIME: 1.682191\n PRECURSOR_MZ: 223.1443\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 5\n 134.07283 2632951.0\n@@ -6481,18 +5980,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C19H21N2OCl\n INCHIKEY: OGYFATSSENRIKG-UHFFFAOYSA-N\n-INCHI: \n SMILES: Clc1ccc(cc1)CN(C(=Nc1ccccc1)O)C1CCCC1\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Monceren\n RETENTION_TIME: 7.14553\n PRECURSOR_MZ: 329.1426\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 5\n 89.03881 550831.0\n@@ -6506,18 +6002,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C16H16N2O4\n INCHIKEY: WZJZMXBKUWKXTQ-UHFFFAOYSA-N\n-INCHI: \n SMILES: CCOC(=Nc1cccc(c1)OC(=Nc1ccccc1)O)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Desmedipham\n RETENTION_TIME: 6.430396\n PRECURSOR_MZ: 301.1192\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 3\n 136.03947 1773399.0\n@@ -6529,18 +6022,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C16H16N2O4\n INCHIKEY: IDOWTHOLJBTAFI-UHFFFAOYSA-N\n-INCHI: \n SMILES: COC(=Nc1cccc(c1)OC(=Nc1cccc(c1)C)O)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Phenmedipham\n RETENTION_TIME: 6.570995\n PRECURSOR_MZ: 301.1185\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 2\n 136.03947 2596929.0\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/convert/harmonized_msp_peakcomments_out.msp --- a/test-data/convert/harmonized_msp_peakcomments_out.msp Thu May 25 09:06:00 2023 +0000 +++ b/test-data/convert/harmonized_msp_peakcomments_out.msp Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -3,18 +3,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C4H10NO3PS\n INCHIKEY: YASYVMFAVPKPKE-SECBINFHSA-N\n-INCHI: \n SMILES: COP(=O)(N=C(O)C)SC\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Acephate\n RETENTION_TIME: 1.232997\n PRECURSOR_MZ: 184.0194\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 16\n 90.09368 1128.0\n@@ -39,18 +36,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C12H11NO2\n INCHIKEY: CVXBEEMKQHEXEN-UHFFFAOYSA-N\n-INCHI: \n SMILES: CN=C(Oc1cccc2c1cccc2)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Carbaryl\n RETENTION_TIME: 5.259445\n PRECURSOR_MZ: 202.0863\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 1\n 145.06491 1326147.0 "Theoretical m/z 145.064787, Mass diff 0 (0.85 ppm), SMILES OC1=CC=CC=2C=CC=CC12, Annotation [C10H8O+H]+, Rule of HR True"\n@@ -60,18 +54,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C8H16NO5P\n INCHIKEY: VEENJGZXVHKXNB-UHFFFAOYSA-N\n-INCHI: \n SMILES: COP(=O)(OC(=CC(=O)N(C)C)C)OC\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Dicrotophos\n RETENTION_TIME: 2.025499\n PRECURSOR_MZ: 238.0844\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 5\n 112.074 102027.0\n@@ -85,18 +76,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C5H12NO3PS2\n INCHIKEY: MCWXGJITAZMZEV-UHFFFAOYSA-N\n-INCHI: \n SMILES: CN=C(CSP(=S)(OC)OC)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Dimethoate\n RETENTION_TIME: 2.866696\n PRECURSOR_MZ: 230.0072\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 8\n 88.0219 548446.0 "Theoretical m/z 88.021549, Mass diff 0 (3.99 ppm), SMILES SCC=NC, Annotation [C3H7NS-H]+, Rule of HR True"\n@@ -113,18 +101,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C21H22NO4Cl\n INCHIKEY: QNBTYORWCCMPQP-UHFFFAOYSA-N\n-INCHI: \n SMILES: COc1cc(ccc1OC)C(=CC(=O)N1CCOCC1)c1ccc(cc1)Cl\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Dimethomorph\n RETENTION_TIME: 7.060486\n PRECURSOR_MZ: 388.1316\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 22\n 114.05532 468862.0 "Theoretical m/z 114.054958, Mass diff 0 (3.17 ppm), SMILES O=CN1CCOCC1, Annotation [C5H9NO2-H]+, Rule of HR True"\n@@ -155,18 +140,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C2H8NO2PS\n INCHIKEY: NNKVPIKMPCQWCG-ZCFIWIBFSA-N\n-INCHI: \n SMILES: COP(=O)(SC)N\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Methamidophos\n RETENTION_TIME: 1.153307\n PRECURSOR_MZ: 142.0089\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 4\n 98.00042 37721.0\n@@ -179,18 +161,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C7H13O6P\n INCHIKEY: GEPDYQSQVLXLEU-UHFFFAOYSA-N\n-INCHI: \n SMILES: COC(=O)C=C(OP(=O)(OC)OC)C\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Mevinphos\n RETENTION_TIME: 2.876307\n PRECURSOR_MZ: 225.0525\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 4\n 99.04416 295529.0 "Theoretical m/z 99.044056, Mass diff 0 (1.05 ppm), SMILES O=C(OC)C=CC, Annotation [C5H8O2-H]+, Rule of HR True"\n@@ -203,18 +182,15 @@\n SPECTRUMTY'..b'1971\n PRECURSOR_MZ: 189.1603\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 2\n 86.0966 107829.0 "Theoretical m/z 86.096424, Mass diff 0 (2.05 ppm), SMILES N(C)(C)CCC, Annotation [C5H13N-H]+, Rule of HR True"\n@@ -6388,18 +5896,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C11H15N3O2\n INCHIKEY: MYPKGPZHHQEODQ-UHFFFAOYSA-N\n-INCHI: \n SMILES: CN=C(Oc1cccc(c1)N=CN(C)C)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Formetanate_1\n RETENTION_TIME: 0.7730471\n PRECURSOR_MZ: 222.1239\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 13\n 93.03365 1796.0 "Theoretical m/z 93.033489, Mass diff 0 (1.73 ppm), SMILES OC=1C=CC=CC1, Annotation [C6H6O-H]+, Rule of HR True"\n@@ -6421,18 +5926,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C11H15N3O2\n INCHIKEY: MYPKGPZHHQEODQ-UHFFFAOYSA-N\n-INCHI: \n SMILES: CN=C(Oc1cccc(c1)N=CN(C)C)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Formetanate_2\n RETENTION_TIME: 1.13043\n PRECURSOR_MZ: 222.1239\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 15\n 91.05441 6330.0 "Theoretical m/z 91.054775, Mass diff 0 (0 ppm), Formula C7H7"\n@@ -6456,18 +5958,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C12H18N2O2\n INCHIKEY: YNEVBPNZHBAYOA-UHFFFAOYSA-N\n-INCHI: \n SMILES: CN=C(Oc1cc(C)c(c(c1)C)N(C)C)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Mexacarbate\n RETENTION_TIME: 1.682191\n PRECURSOR_MZ: 223.1443\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 5\n 134.07283 2632951.0 "Theoretical m/z 134.072623, Mass diff 0 (1.55 ppm), SMILES O(C=1C=C(C=C(C1)C)C)C, Annotation [C9H12O-2H]+, Rule of HR False"\n@@ -6481,18 +5980,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C19H21N2OCl\n INCHIKEY: OGYFATSSENRIKG-UHFFFAOYSA-N\n-INCHI: \n SMILES: Clc1ccc(cc1)CN(C(=Nc1ccccc1)O)C1CCCC1\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Monceren\n RETENTION_TIME: 7.14553\n PRECURSOR_MZ: 329.1426\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 5\n 89.03881 550831.0 "Theoretical m/z 89.038575, Mass diff 0 (2.63 ppm), SMILES C=1C=CC(=CC1)C, Annotation [C7H8-3H]+, Rule of HR True"\n@@ -6506,18 +6002,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C16H16N2O4\n INCHIKEY: WZJZMXBKUWKXTQ-UHFFFAOYSA-N\n-INCHI: \n SMILES: CCOC(=Nc1cccc(c1)OC(=Nc1ccccc1)O)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Desmedipham\n RETENTION_TIME: 6.430396\n PRECURSOR_MZ: 301.1192\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 3\n 136.03947 1773399.0 "Theoretical m/z 136.03931, Mass diff 0 (1.18 ppm), SMILES OC(O)=NC=1C=CC=CC1, Annotation [C7H7NO2-H]+, Rule of HR True"\n@@ -6529,18 +6022,15 @@\n SPECTRUMTYPE: Centroid\n FORMULA: C16H16N2O4\n INCHIKEY: IDOWTHOLJBTAFI-UHFFFAOYSA-N\n-INCHI: \n SMILES: COC(=Nc1cccc(c1)OC(=Nc1cccc(c1)C)O)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n-COMMENT: \n COMPOUND_NAME: Phenmedipham\n RETENTION_TIME: 6.570995\n PRECURSOR_MZ: 301.1185\n ADDUCT: [M+H]+\n-COLLISION_ENERGY: \n INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 2\n 136.03947 2596929.0 "Theoretical m/z 136.03931, Mass diff 0 (1.18 ppm), SMILES OC(O)=NC=1C=CC=CC1, Annotation [C7H7NO2-H]+, Rule of HR True"\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/fingerprints/cosine.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fingerprints/cosine.json Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"__Scores__": true, "is_symmetric": false, "references": [{"scannumber": "1161", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C4H10NO3PS", "inchikey": "YASYVMFAVPKPKE-SECBINFHSA-N", "smiles": "COP(=O)(N=C(O)C)SC", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "ionization": "ESI+", "license": "CC BY-NC", "num_peaks": "16", "compound_name": "Acephate", "retention_time": 1.232997, "precursor_mz": 184.0194, "adduct": "[M+H]+", "instrument_type": "LC-ESI-Orbitrap", "peaks_json": [[90.09368, 1128.0], [93.11512, 1241.0], [95.10279, 1118.0], [101.31465, 1152.0], [102.90688, 1322.0], [103.98039, 1201.0], [112.01607, 12289.0], [112.99994, 38027.0], [115.00399, 1634.0], [124.98121, 922.0], [128.97701, 9208.0], [132.57193, 1350.0], [135.84808, 1428.0], [142.99275, 16419.0], [147.94205, 1750.0], [173.5094, 2353.0]]}, {"scannumber": "2257", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C12H11NO2", "inchikey": "CVXBEEMKQHEXEN-UHFFFAOYSA-N", "smiles": "CN=C(Oc1cccc2c1cccc2)O", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "ionization": "ESI+", "license": "CC BY-NC", "peak_comments": {"145.06491": "Theoretical m/z 145.064787, Mass diff 0 (0.85 ppm), SMILES OC1=CC=CC=2C=CC=CC12, Annotation [C10H8O+H]+, Rule of HR True"}, "num_peaks": "1", "compound_name": "Carbaryl", "retention_time": 5.259445, "precursor_mz": 202.0863, "adduct": "[M+H]+", "instrument_type": "LC-ESI-Orbitrap", "peaks_json": [[145.06491, 1326147.0]]}, {"scannumber": "1516", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C8H16NO5P", "inchikey": "VEENJGZXVHKXNB-UHFFFAOYSA-N", "smiles": "COP(=O)(OC(=CC(=O)N(C)C)C)OC", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "ionization": "ESI+", "license": "CC BY-NC", "peak_comments": {"112.07591": "Theoretical m/z 112.075687, Mass diff 0 (1.99 ppm), SMILES O=C(C=CC)N(C)C, Annotation [C6H11NO-H]+, Rule of HR True", "127.01563": "Theoretical m/z 127.01547, Mass diff 0 (1.26 ppm), SMILES O=P(O)(OC)OC, Annotation [C2H7O4P+H]+, Rule of HR True", "193.02605": "Theoretical m/z 193.026035, Mass diff 0 (0.08 ppm), SMILES O=CC=C(OP(=O)(OC)OC)C, Annotation [C6H11O5P-H]+, Rule of HR True", "238.08437": "Theoretical m/z 238.083891, Mass diff 0 (2.01 ppm), SMILES O=C(C=C(OP(=O)(OC)OC)C)N(C)C, Annotation [C8H16NO5P+H]+, Rule of HR True"}, "num_peaks": "5", "compound_name": "Dicrotophos", "retention_time": 2.025499, "precursor_mz": 238.0844, "adduct": "[M+H]+", "instrument_type": "LC-ESI-Orbitrap", "peaks_json": [[112.074, 102027.0], [112.07591, 9070987.0], [127.01563, 3230337.0], [193.02605, 7897744.0], [238.08437, 2973124.0]]}, {"scannumber": "1865", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C5H12NO3PS2", "inchikey": "MCWXGJITAZMZEV-UHFFFAOYSA-N", "smiles": "CN=C(CSP(=S)(OC)OC)O", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "ionization": "ESI+", "license": "CC BY-NC", "peak_comments": {"88.0219": "Theoretical m/z 88.021549, Mass diff 0 (3.99 ppm), SMILES SCC=NC, Annotation [C3H7NS-H]+, Rule of HR True", "124.98233": "Theoretical m/z 124.982067, Mass diff 0 (2.11 ppm), SMILES S=P(OC)OC, Annotation [C2H7O2PS-H]+, Rule of HR True", "142.99275": "Theoretical m/z 142.993177, Mass diff 0 (0 ppm), Formula C2H8O3PS", "156.95422": "Theoretical m/z 156.954136, Mass diff 0 (0.54 ppm), SMILES S=P(S)(OC)OC, Annotation [C2H7O2PS2-H]+, Rule of HR True", "170.97": "Theoretical m/z 170.969791, Mass diff 0 (1.22 ppm), SMILES S=P(OC)(OC)SC, Annotation [C3H9O2PS2-H]+, Rule of HR True", "197.98123": "Theoretical m/z 197.980686, Mass diff 0.001 (2.75 ppm), SMILES S=P(OC)SCC(O)=NC, Annotation [C4H10NO2PS2-H]+, Rule of HR True", "198.96501": "Theoretical m/z 198'..b'), Formula C15H7", "189.06969": "Theoretical m/z 189.070425, Mass diff 0 (0 ppm), Formula C15H9", "201.06973": "Theoretical m/z 201.070425, Mass diff 0 (0 ppm), Formula C16H9", "233.04245": "Theoretical m/z 233.042496, Mass diff -0.001 (0 ppm), Formula C16H9S", "234.04965": "Theoretical m/z 234.049775, Mass diff 0 (0.53 ppm), SMILES S1C=2C=CC=CC2C=3C=CC=4C=CC=CC4C13, Annotation [C16H10S]+, Rule of HR False"}, "num_peaks": "23", "compound_name": "Benzo[b]naphtho[2,1-d]thiophene", "retention_time": null, "retention_index": 2419.3, "precursor_mz": 234.04965, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[91.05425, 49130.0], [93.52686, 61653.0], [94.53469, 76638.0], [104.01679, 126871.0], [116.01675, 112547.0], [117.02459, 99108.0], [162.04623, 54491.0], [163.05408, 136418.0], [164.06198, 56321.0], [187.05406, 273349.0], [188.06189, 200750.0], [189.06969, 453336.0], [190.07306, 77884.0], [200.06189, 135620.0], [201.06973, 74692.0], [202.07758, 425058.0], [203.08086, 72058.0], [226.07762, 63460.0], [232.03409, 769638.0], [233.04245, 382457.0], [234.04965, 4404102.0], [235.05304, 725574.0], [236.04547, 251450.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C17H12", "inchikey": "HAPOJKSPCGLOOD-UHFFFAOYSA-N", "smiles": "C1C2=CC=CC=C2C2=C1C=C1C=CC=CC1=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": {"163.05414": "Theoretical m/z 163.054775, Mass diff 0 (0 ppm), Formula C13H7", "187.05412": "Theoretical m/z 187.054775, Mass diff 0 (0 ppm), Formula C15H7", "189.06975": "Theoretical m/z 189.070425, Mass diff 0 (0 ppm), Formula C15H9", "211.05426": "Theoretical m/z 211.054775, Mass diff 0 (0 ppm), Formula C17H7", "213.0699": "Theoretical m/z 213.070425, Mass diff 0 (0 ppm), Formula C17H9", "215.0855": "Theoretical m/z 215.086075, Mass diff 0 (0 ppm), Formula C17H11", "216.09326": "Theoretical m/z 216.093354, Mass diff 0 (0.44 ppm), SMILES C=1C=CC=2C=C3C(=CC2C1)C=4C=CC=CC4C3, Annotation [C17H12]+, Rule of HR False"}, "num_peaks": "21", "compound_name": "2,3-Benzofluorene", "retention_time": null, "retention_index": 2257.5, "precursor_mz": 216.09326, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[93.52689, 122035.0], [94.53471, 241743.0], [95.03638, 42130.0], [105.52688, 47526.0], [106.53471, 171653.0], [107.03639, 60004.0], [107.5425, 180288.0], [108.03385, 97471.0], [163.05414, 68194.0], [187.05412, 167183.0], [188.06201, 86262.0], [189.06975, 239421.0], [190.07321, 37778.0], [211.05426, 117044.0], [212.06215, 60813.0], [213.0699, 808499.0], [214.07317, 202222.0], [215.0855, 3634570.0], [216.09326, 2535030.0], [217.09671, 444170.0], [218.09999, 37976.0]]}], "n_row": 5, "n_col": 7, "row": [0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4], "col": [0, 1, 2, 3, 4, 5, 6, 0, 1, 2, 3, 4, 5, 6, 0, 1, 2, 3, 4, 5, 6, 0, 1, 2, 3, 4, 5, 6, 0, 1, 2, 3, 4, 5, 6], "data": [[0.0563436169819011], [0.05741692517632146], [0.1213570784945665], [0.0563436169819011], [0.06510467359823571], [0.06311869632330808], [0.161218884399274], [0.4023956421624664], [0.4011466400553764], [0.27508612307793867], [0.4023956421624664], [0.1549884934836848], [0.27137377914817884], [0.2569780843750233], [0.08328129877731794], [0.08486775178136235], [0.14708952027694389], [0.08328129877731794], [0.07698478818604926], [0.12056651728064088], [0.1588647043434069], [0.06928995160692483], [0.07060987881136029], [0.11939348655940786], [0.06928995160692483], [0.09912695235553014], [0.09724046213130343], [0.14728100877622677], [0.16031154731160938], [0.1520987974102627], [0.22384378823632398], [0.16031154731160938], [0.13626771391646142], [0.2000718754617515], [0.36485712884822324]], "dtype": [["FingerprintSimilarity_cosine", "<f8"]]}\n\\ No newline at end of file\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/fingerprints/dice.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fingerprints/dice.json Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"__Scores__": true, "is_symmetric": false, "references": [{"scannumber": "1161", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C4H10NO3PS", "inchikey": "YASYVMFAVPKPKE-SECBINFHSA-N", "smiles": "COP(=O)(N=C(O)C)SC", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "ionization": "ESI+", "license": "CC BY-NC", "num_peaks": "16", "compound_name": "Acephate", "retention_time": 1.232997, "precursor_mz": 184.0194, "adduct": "[M+H]+", "instrument_type": "LC-ESI-Orbitrap", "peaks_json": [[90.09368, 1128.0], [93.11512, 1241.0], [95.10279, 1118.0], [101.31465, 1152.0], [102.90688, 1322.0], [103.98039, 1201.0], [112.01607, 12289.0], [112.99994, 38027.0], [115.00399, 1634.0], [124.98121, 922.0], [128.97701, 9208.0], [132.57193, 1350.0], [135.84808, 1428.0], [142.99275, 16419.0], [147.94205, 1750.0], [173.5094, 2353.0]]}, {"scannumber": "2257", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C12H11NO2", "inchikey": "CVXBEEMKQHEXEN-UHFFFAOYSA-N", "smiles": "CN=C(Oc1cccc2c1cccc2)O", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "ionization": "ESI+", "license": "CC BY-NC", "peak_comments": {"145.06491": "Theoretical m/z 145.064787, Mass diff 0 (0.85 ppm), SMILES OC1=CC=CC=2C=CC=CC12, Annotation [C10H8O+H]+, Rule of HR True"}, "num_peaks": "1", "compound_name": "Carbaryl", "retention_time": 5.259445, "precursor_mz": 202.0863, "adduct": "[M+H]+", "instrument_type": "LC-ESI-Orbitrap", "peaks_json": [[145.06491, 1326147.0]]}, {"scannumber": "1516", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C8H16NO5P", "inchikey": "VEENJGZXVHKXNB-UHFFFAOYSA-N", "smiles": "COP(=O)(OC(=CC(=O)N(C)C)C)OC", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "ionization": "ESI+", "license": "CC BY-NC", "peak_comments": {"112.07591": "Theoretical m/z 112.075687, Mass diff 0 (1.99 ppm), SMILES O=C(C=CC)N(C)C, Annotation [C6H11NO-H]+, Rule of HR True", "127.01563": "Theoretical m/z 127.01547, Mass diff 0 (1.26 ppm), SMILES O=P(O)(OC)OC, Annotation [C2H7O4P+H]+, Rule of HR True", "193.02605": "Theoretical m/z 193.026035, Mass diff 0 (0.08 ppm), SMILES O=CC=C(OP(=O)(OC)OC)C, Annotation [C6H11O5P-H]+, Rule of HR True", "238.08437": "Theoretical m/z 238.083891, Mass diff 0 (2.01 ppm), SMILES O=C(C=C(OP(=O)(OC)OC)C)N(C)C, Annotation [C8H16NO5P+H]+, Rule of HR True"}, "num_peaks": "5", "compound_name": "Dicrotophos", "retention_time": 2.025499, "precursor_mz": 238.0844, "adduct": "[M+H]+", "instrument_type": "LC-ESI-Orbitrap", "peaks_json": [[112.074, 102027.0], [112.07591, 9070987.0], [127.01563, 3230337.0], [193.02605, 7897744.0], [238.08437, 2973124.0]]}, {"scannumber": "1865", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C5H12NO3PS2", "inchikey": "MCWXGJITAZMZEV-UHFFFAOYSA-N", "smiles": "CN=C(CSP(=S)(OC)OC)O", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "ionization": "ESI+", "license": "CC BY-NC", "peak_comments": {"88.0219": "Theoretical m/z 88.021549, Mass diff 0 (3.99 ppm), SMILES SCC=NC, Annotation [C3H7NS-H]+, Rule of HR True", "124.98233": "Theoretical m/z 124.982067, Mass diff 0 (2.11 ppm), SMILES S=P(OC)OC, Annotation [C2H7O2PS-H]+, Rule of HR True", "142.99275": "Theoretical m/z 142.993177, Mass diff 0 (0 ppm), Formula C2H8O3PS", "156.95422": "Theoretical m/z 156.954136, Mass diff 0 (0.54 ppm), SMILES S=P(S)(OC)OC, Annotation [C2H7O2PS2-H]+, Rule of HR True", "170.97": "Theoretical m/z 170.969791, Mass diff 0 (1.22 ppm), SMILES S=P(OC)(OC)SC, Annotation [C3H9O2PS2-H]+, Rule of HR True", "197.98123": "Theoretical m/z 197.980686, Mass diff 0.001 (2.75 ppm), SMILES S=P(OC)SCC(O)=NC, Annotation [C4H10NO2PS2-H]+, Rule of HR True", "198.96501": "Theoretical m/z 198'..b'la C15H7", "189.06969": "Theoretical m/z 189.070425, Mass diff 0 (0 ppm), Formula C15H9", "201.06973": "Theoretical m/z 201.070425, Mass diff 0 (0 ppm), Formula C16H9", "233.04245": "Theoretical m/z 233.042496, Mass diff -0.001 (0 ppm), Formula C16H9S", "234.04965": "Theoretical m/z 234.049775, Mass diff 0 (0.53 ppm), SMILES S1C=2C=CC=CC2C=3C=CC=4C=CC=CC4C13, Annotation [C16H10S]+, Rule of HR False"}, "num_peaks": "23", "compound_name": "Benzo[b]naphtho[2,1-d]thiophene", "retention_time": null, "retention_index": 2419.3, "precursor_mz": 234.04965, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[91.05425, 49130.0], [93.52686, 61653.0], [94.53469, 76638.0], [104.01679, 126871.0], [116.01675, 112547.0], [117.02459, 99108.0], [162.04623, 54491.0], [163.05408, 136418.0], [164.06198, 56321.0], [187.05406, 273349.0], [188.06189, 200750.0], [189.06969, 453336.0], [190.07306, 77884.0], [200.06189, 135620.0], [201.06973, 74692.0], [202.07758, 425058.0], [203.08086, 72058.0], [226.07762, 63460.0], [232.03409, 769638.0], [233.04245, 382457.0], [234.04965, 4404102.0], [235.05304, 725574.0], [236.04547, 251450.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C17H12", "inchikey": "HAPOJKSPCGLOOD-UHFFFAOYSA-N", "smiles": "C1C2=CC=CC=C2C2=C1C=C1C=CC=CC1=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": {"163.05414": "Theoretical m/z 163.054775, Mass diff 0 (0 ppm), Formula C13H7", "187.05412": "Theoretical m/z 187.054775, Mass diff 0 (0 ppm), Formula C15H7", "189.06975": "Theoretical m/z 189.070425, Mass diff 0 (0 ppm), Formula C15H9", "211.05426": "Theoretical m/z 211.054775, Mass diff 0 (0 ppm), Formula C17H7", "213.0699": "Theoretical m/z 213.070425, Mass diff 0 (0 ppm), Formula C17H9", "215.0855": "Theoretical m/z 215.086075, Mass diff 0 (0 ppm), Formula C17H11", "216.09326": "Theoretical m/z 216.093354, Mass diff 0 (0.44 ppm), SMILES C=1C=CC=2C=C3C(=CC2C1)C=4C=CC=CC4C3, Annotation [C17H12]+, Rule of HR False"}, "num_peaks": "21", "compound_name": "2,3-Benzofluorene", "retention_time": null, "retention_index": 2257.5, "precursor_mz": 216.09326, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[93.52689, 122035.0], [94.53471, 241743.0], [95.03638, 42130.0], [105.52688, 47526.0], [106.53471, 171653.0], [107.03639, 60004.0], [107.5425, 180288.0], [108.03385, 97471.0], [163.05414, 68194.0], [187.05412, 167183.0], [188.06201, 86262.0], [189.06975, 239421.0], [190.07321, 37778.0], [211.05426, 117044.0], [212.06215, 60813.0], [213.0699, 808499.0], [214.07317, 202222.0], [215.0855, 3634570.0], [216.09326, 2535030.0], [217.09671, 444170.0], [218.09999, 37976.0]]}], "n_row": 5, "n_col": 7, "row": [0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4], "col": [0, 1, 2, 3, 4, 5, 6, 0, 1, 2, 3, 4, 5, 6, 0, 1, 2, 3, 4, 5, 6, 0, 1, 2, 3, 4, 5, 6, 0, 1, 2, 3, 4, 5, 6], "data": [[0.045454545454545456], [0.04580152671755725], [0.11976047904191617], [0.045454545454545456], [0.059800664451827246], [0.06310679611650485], [0.1549053356282272], [0.3108108108108108], [0.30612244897959184], [0.27392120075046905], [0.3108108108108108], [0.13813813813813813], [0.2702702702702703], [0.25122349102773245], [0.06230529595015576], [0.06269592476489028], [0.14695340501792115], [0.06230529595015576], [0.0670391061452514], [0.11940298507462686], [0.15673981191222572], [0.05761316872427984], [0.058091286307053944], [0.11666666666666667], [0.05761316872427984], [0.09285714285714286], [0.09718670076726342], [0.1392857142857143], [0.08787878787878788], [0.08206686930091185], [0.20958751393534003], [0.08787878787878788], [0.09182209469153516], [0.17326732673267325], [0.3541453428863869]], "dtype": [["FingerprintSimilarity_dice", "<f8"]]}\n\\ No newline at end of file\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/fingerprints/jaccard_scores.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fingerprints/jaccard_scores.json Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"__Scores__": true, "is_symmetric": false, "references": [{"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C14H10", "inchikey": "YNPNZTXNASCQKK-UHFFFAOYSA-N", "smiles": "C1=CC2=C(C=C1)C1=C(C=CC=C1)C=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "19", "compound_name": "Phenanthrene", "retention_time": null, "retention_index": 1832.9, "precursor_mz": 178.0775, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[74.01508, 137808.0], [75.02295, 278714.0], [76.03075, 608417.0], [87.02295, 304266.0], [88.03076, 497050.0], [89.03857, 441168.0], [98.01511, 150478.0], [150.04633, 868927.0], [151.05415, 546351.0], [152.0619, 2275502.0], [153.06528, 276320.0], [169.06468, 272559.0], [174.04636, 365846.0], [175.05423, 272039.0], [176.062, 3370523.0], [177.06982, 1751846.0], [178.0775, 13724432.0], [179.08078, 2250119.0], [180.08412, 138203.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C14H10", "inchikey": "MWPLVEDNUUSJAV-UHFFFAOYSA-N", "smiles": "C1=CC2=CC3=C(C=CC=C3)C=C2C=C1", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "21", "compound_name": "Anthracene", "retention_time": null, "retention_index": 1844.4, "precursor_mz": 178.07754, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[74.0151, 117371.0], [75.02296, 245305.0], [76.03077, 632686.0], [87.02297, 236214.0], [88.03078, 347832.0], [89.0386, 507288.0], [91.05425, 130861.0], [126.04636, 128356.0], [149.04478, 126331.0], [150.04637, 641829.0], [151.05415, 403195.0], [152.06195, 1369833.0], [153.06534, 175290.0], [169.06471, 228827.0], [174.04639, 255716.0], [175.05423, 198784.0], [176.06204, 2563053.0], [177.06984, 1182037.0], [178.07754, 11002398.0], [179.08081, 1778803.0], [180.08418, 132922.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C16H10", "inchikey": "GVEPBJHOBDJJJI-UHFFFAOYSA-N", "smiles": "C1=CC2=C(C=C1)C1=C3C2=CC=CC3=CC=C1", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "17", "compound_name": "Fluoranthene", "retention_time": null, "retention_index": 2102.7, "precursor_mz": 202.07756, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[75.02299, 112456.0], [87.02298, 183640.0], [88.03079, 367434.0], [99.02296, 124952.0], [100.03078, 376079.0], [101.03863, 381288.0], [150.04642, 86059.0], [174.04634, 246963.0], [176.06194, 141676.0], [198.0464, 244370.0], [199.05429, 285767.0], [200.06207, 1958890.0], [201.06982, 1103710.0], [202.07756, 8104188.0], [203.08084, 1377015.0], [204.08421, 98067.0], [219.08043, 186623.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C16H10", "inchikey": "BBEAQIROQSPTKN-UHFFFAOYSA-N", "smiles": "C1=CC2=C3C(C=CC4=CC=CC(C=C2)=C34)=C1", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "16", "compound_name": "Pyrene", "retention_time": null, "retention_index": 2154.5, "precursor_mz": 202.07759, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[87.02299, 147113.0], [88.0308, 305149.0], [99.02298, 137042.0], [100.0308, 508914.0], [101.03864, 472094.0], [101.54032, 82430.0], [150.04637, 80741.0], [174.04631, 212706.0], [198.04643, 262925.0], [199.05429, 295144.0], [200.06209, 1960712.0], [201.06982, 1270466.0], [202.'..b' [201.06982, 1270466.0], [202.07759, 7974712.0], [203.08086, 1335645.0], [204.0843, 121774.0], [219.08044, 182944.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C18H14", "inchikey": "XJKSTNDFUHDPQJ-UHFFFAOYSA-N", "smiles": "C1=CC=C(C=C1)C2=CC=C(C=C2)C3=CC=CC=C3", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "25", "compound_name": "para-Terphenyl", "retention_time": null, "retention_index": 2207.5, "precursor_mz": 230.10886, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[88.03077, 233962.0], [101.03861, 353544.0], [113.03854, 437845.0], [115.05423, 690291.0], [128.062, 293046.0], [151.05412, 266397.0], [152.06195, 961184.0], [153.06976, 409346.0], [176.06192, 232793.0], [189.06972, 408734.0], [200.0619, 342984.0], [201.06986, 238974.0], [202.07758, 1292332.0], [203.08093, 374439.0], [213.06973, 256631.0], [215.08548, 1220866.0], [216.08881, 217320.0], [224.062, 181393.0], [226.07771, 1503774.0], [227.08588, 1198323.0], [228.09344, 2885510.0], [229.10123, 1791323.0], [230.10886, 17890056.0], [231.11214, 3536976.0], [232.11542, 320231.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C16H10S", "inchikey": "YEUHHUCOSQOCIX-UHFFFAOYSA-N", "smiles": "S1C2=C(C=CC=C2)C2=C1C1=CC=CC=C1C=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "23", "compound_name": "Benzo[b]naphtho[2,1-d]thiophene", "retention_time": null, "retention_index": 2419.3, "precursor_mz": 234.04965, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[91.05425, 49130.0], [93.52686, 61653.0], [94.53469, 76638.0], [104.01679, 126871.0], [116.01675, 112547.0], [117.02459, 99108.0], [162.04623, 54491.0], [163.05408, 136418.0], [164.06198, 56321.0], [187.05406, 273349.0], [188.06189, 200750.0], [189.06969, 453336.0], [190.07306, 77884.0], [200.06189, 135620.0], [201.06973, 74692.0], [202.07758, 425058.0], [203.08086, 72058.0], [226.07762, 63460.0], [232.03409, 769638.0], [233.04245, 382457.0], [234.04965, 4404102.0], [235.05304, 725574.0], [236.04547, 251450.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C17H12", "inchikey": "HAPOJKSPCGLOOD-UHFFFAOYSA-N", "smiles": "C1C2=CC=CC=C2C2=C1C=C1C=CC=CC1=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "21", "compound_name": "2,3-Benzofluorene", "retention_time": null, "retention_index": 2257.5, "precursor_mz": 216.09326, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[93.52689, 122035.0], [94.53471, 241743.0], [95.03638, 42130.0], [105.52688, 47526.0], [106.53471, 171653.0], [107.03639, 60004.0], [107.5425, 180288.0], [108.03385, 97471.0], [163.05414, 68194.0], [187.05412, 167183.0], [188.06201, 86262.0], [189.06975, 239421.0], [190.07321, 37778.0], [211.05426, 117044.0], [212.06215, 60813.0], [213.0699, 808499.0], [214.07317, 202222.0], [215.0855, 3634570.0], [216.09326, 2535030.0], [217.09671, 444170.0], [218.09999, 37976.0]]}], "n_row": 7, "n_col": 7, "row": [0, 0, 1, 1, 2, 3, 4, 5, 6], "col": [0, 1, 0, 1, 2, 3, 4, 5, 6], "data": [[true, true, 1.0], [true, true, 0.9629629629629629], [true, true, 0.9629629629629629], [true, true, 1.0], [true, true, 1.0], [true, true, 1.0], [true, true, 1.0], [true, true, 1.0], [true, true, 1.0]], "dtype": [["MetadataMatch_retention_index_difference_60.0_f0", "|b1"], ["MetadataMatch_retention_index_difference_20.0_f0", "|b1"], ["FingerprintSimilarity_jaccard", "<f8"]]}\n\\ No newline at end of file\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/formatter/fill2_formatted.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/formatter/fill2_formatted.tsv Tue Jun 27 14:25:59 2023 +0000 |
| b |
| @@ -0,0 +1,8 @@ +query reference CosineGreedy_score CosineGreedy_matches MetadataMatch_MetadataMatch +C001 C001 0.9999999999999994 160 1.0 +C002 C001 0.009949950543146832 45 1.0 +C001 C002 0.009949950543146832 45 1.0 +C002 C002 1.0 154 1.0 +C003 C002 0.051811021915120416 49 1.0 +C002 C003 0.051811021915120416 49 1.0 +C003 C003 1.0000000000000002 135 1.0 |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/formatter/fill2_trunc_scores_with_metadata_match.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/formatter/fill2_trunc_scores_with_metadata_match.json Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"__Scores__": true, "is_symmetric": false, "references": [{"ionmode": "negative", "spectrumtype": "Centroid", "num_peaks": "160", "compound_name": "C001", "retention_time": 268.99, "retention_index": 1800.989583, "peaks_json": [[72.0389617714179, 56416115.0], [76.0256553376053, 49220925.0], [76.0295086554853, 17884882.0], [77.0053275563467, 26589154.0], [83.0127800769552, 72764369.0], [83.031134902227, 10179311.0], [86.7773291870617, 23734479.0], [87.0624748029292, 7498889.0], [93.7759098981009, 12284319.0], [97.0468722156908, 49324192.0], [99.0260406168298, 118701269.0], [103.002983736029, 18397693.0], [106.894754414816, 8004841.0], [111.007632749245, 107433124.0], [117.018501739727, 52467543.0], [131.034273710906, 359133132.0], [133.013526291087, 493499083.0], [133.031172492717, 17650343.0], [135.01033343891, 29110842.0], [135.029247366931, 21569969.0], [135.046364355946, 10818621.0], [136.941594609304, 50570227.0], [138.939618370595, 53903907.0], [139.002532294836, 49931624.0], [139.056768289213, 98175121.0], [141.036538750422, 115707572.0], [141.084158860874, 74023269.0], [142.104641843961, 441884594.0], [143.015834635052, 48987316.0], [143.052340331432, 420396997.0], [143.10428859825, 31762860.0], [143.107947705172, 44080773.0], [145.049469553608, 40966670.0], [147.065597668017, 3426705457.0], [148.066687703799, 456715218.0], [149.044686744287, 2485055493.0], [149.051982158561, 15135407.0], [149.062214633403, 244773900.0], [149.068434618167, 23246006.0], [150.04583614918, 369731636.0], [150.064532557665, 20279235.0], [151.023931616767, 305971501.0], [151.041613361558, 216314524.0], [152.023573104507, 39184709.0], [155.052170983022, 14728905.0], [157.031392134453, 61582084.0], [157.049811244805, 28679691.0], [159.046994608899, 9542515.0], [159.112043200462, 43124161.0], [163.096936467212, 259054581.0], [164.096242459652, 39496478.0], [165.093540352647, 75534890.0], [167.05522365918, 82592725.0], [168.054993436637, 9530750.0], [169.031329681702, 63326558.0], [171.010634911705, 74220303.0], [173.044685418755, 35853332.0], [177.039641177724, 20626924.0], [183.047097257536, 4559958550.0], [183.057249262756, 17431309.0], [184.046358120662, 106511561.0], [184.050443416, 414898624.0], [185.026407772471, 30996555.0], [185.043991660752, 154888217.0], [185.050867499577, 29446895.0], [185.062853536402, 75038250.0], [186.047199218887, 20807119.0], [191.037148572664, 28320845.0], [191.05526102196, 16327982.0], [195.094677873356, 7614346.0], [197.059793589486, 8688331.0], [201.039634295494, 20060252.0], [201.057764327742, 27419375.0], [211.041705745044, 1447339674.0], [212.041045979022, 25597653.0], [212.046025666707, 122581545.0], [213.021020474351, 91489413.0], [213.0391072084, 57195084.0], [214.144261002848, 35457490.0], [215.05549778228, 201625005.0], [215.091952078065, 46374386.0], [216.055525333011, 17909976.0], [217.03448664281, 74746711.0], [217.052170715974, 20626232.0], [218.071997852185, 19993432.0], 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[274.099806030141, 2287536'..b'272989142, 3424764.0], [119.060398059581, 5015688.0], [123.055298722957, 6914458.0], [126.036934304886, 7725659.0], [127.068555548084, 6308443.0], [129.036692025662, 122379411.0], [129.065799497037, 22459026.0], [129.072869578599, 357742590.0], [129.084157333304, 8540678.0], [130.068355771428, 19512498.0], [130.072660895986, 17001807.0], [130.076400507348, 21643851.0], [131.076042114677, 42394426.0], [132.075235945687, 15098771.0], [132.083789835617, 26794170.0], [137.070988883611, 9859706.0], [138.05493224095, 3165654.0], [139.051175003371, 7069320.0], [141.047778003792, 23946731.0], [141.065923570004, 9330027.0], [142.055705069575, 6974963.0], [144.08382621206, 24138104.0], [152.052612709208, 12445682.0], [153.047862201653, 13551007.0], [153.06050104986, 5683251.0], [154.031798596314, 9702495.0], [154.068135836281, 22462918.0], [155.063488378907, 17345256.0], [157.067778706704, 305000842.0], [157.079041955576, 23421863.0], [158.063049350607, 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[211.089848595549, 23856594.0], [212.097009756898, 13775311.0], [213.105228486782, 73929890.0], [219.09527736534, 8505195.0], [221.074300407885, 14508487.0], [225.105533091326, 19016199.0], [233.102475979575, 15389167.0], [242.10246806473, 19687380.0], [242.126657609235, 11066324.0], [243.134206462776, 50646552.0], [244.119452816047, 30022076.0], [245.114820894281, 11088338.0], [254.102870594529, 5350655.0], [255.134441237269, 46732255.0], [269.113908264442, 46534893.0], [270.134437529958, 7090136.0], [271.128972048701, 37425633.0], [273.144669229945, 9722721.0], [274.128730992046, 139451474.0], [275.131908166958, 15282348.0], [284.113416878425, 8739042.0], [284.137011207473, 19427028.0], [301.139887685895, 13069124.0], [303.156554156078, 27321286.0], [309.144715592211, 11863564.0], [315.155169787866, 65230453.0], [319.157101342607, 733557628.0], [320.158352325734, 176280305.0], [321.153241677135, 74811478.0], [322.157191869663, 33601762.0], [327.155355207603, 17725445.0], [333.166397555812, 53890077.0], [334.168322787397, 15415305.0], [360.184205186806, 23337977.0], [374.163526061853, 21552675.0], [399.195205285978, 19867111.0], [401.174241468972, 35504809.0], [417.205717817748, 23250105.0], [417.241711757457, 19573381.0], [418.207654920137, 17403027.0], [418.243205616146, 12152742.0], [475.229231161579, 2756806.0], [489.245871828029, 38098072.0], [490.247019499098, 8845886.0], [491.244269926889, 10775524.0], [523.250368109965, 33514393.0], [579.297280589764, 6860747.0], [595.292757936577, 18386300.0], [596.292128391308, 11382024.0], [597.290217290809, 5672650.0]]}], "n_row": 3, "n_col": 3, "row": [0, 0, 1, 1, 1, 2, 2], "col": [0, 1, 0, 1, 2, 1, 2], "data": [[0.9999999999999994, 160, 1.0], [0.009949950543146832, 45, 1.0], [0.009949950543146832, 45, 1.0], [1.0, 154, 1.0], [0.051811021915120416, 49, 1.0], [0.051811021915120416, 49, 1.0], [1.0000000000000002, 135, 1.0]], "dtype": [["CosineGreedy_score", "<f8"], ["CosineGreedy_matches", "<i8"], ["MetadataMatch_MetadataMatch", "<f8"]]}\n\\ No newline at end of file\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/formatter/test2_threshold_formatting.tsv --- a/test-data/formatter/test2_threshold_formatting.tsv Thu May 25 09:06:00 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,21 +0,0 @@ -query reference matches score -C038 Temephos 3 0.4479813614745304 -C041 Tebuthiuron 3 0.8149016029858368 -C029 Tebuthiuron 4 0.7578160314442438 -C022 Tebuthiuron 5 0.5445755137228012 -C039 Chloroxuron 5 0.7904224091921885 -C005 Forchlorfenuron 3 0.4718886768467089 -C034 Fenuron 4 0.4133963957082293 -C029 Ametryn 5 0.42431125511334006 -C041 Dimoxystrobin 5 0.8072997046898676 -C029 Dimoxystrobin 4 0.7523284529176055 -C015 Dimoxystrobin 4 0.42066129038267897 -C022 Dimoxystrobin 3 0.41284063372275814 -C005 Dinotefuran 4 0.48748010990419266 -C034 Tebufenpyrad 6 0.49374627461317955 -C120 Tebufenpyrad 4 0.40579598696856434 -C010 Mefenacet 4 0.43004982863660707 -C029 Simetryn 4 0.43277920021386995 -C001 Sulfentrazone 18 0.5628769859493975 -C025 Fuberidazole 6 0.52564792144262 -C002 Fuberidazole 10 0.42228986210263 |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/formatter/test2_topk_formatting.tsv --- a/test-data/formatter/test2_topk_formatting.tsv Thu May 25 09:06:00 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,154 +0,0 @@ -query reference matches score -C001 Sulfentrazone 18 0.5628769859493975 -C001 Dimethomorph 13 0.21123947571230445 -C001 Fenpropimorph 3 0.1724402539509388 -C002 Fuberidazole 10 0.42228986210263 -C002 Triflumuron 6 0.18301808160264693 -C002 Metribuzin 34 0.15483736628225514 -C003 Dinotefuran 7 0.36371270405069533 -C003 Forchlorfenuron 6 0.2900844630219365 -C003 Fuberidazole 9 0.2402739206276594 -C004 Boscalid 14 0.21701029457716275 -C004 Chloroxuron 11 0.15146088555482382 -C004 Fenarimol 15 0.1512102787330488 -C005 Dinotefuran 4 0.48748010990419266 -C005 Forchlorfenuron 3 0.4718886768467089 -C005 Triadimefon 11 0.25350626006111326 -C006 Propamocarb_1 1 0.04514131624669475 -C006 Propamocarb_2 1 0.04513568618897746 -C006 Thidiazuron 2 0.04361907635713056 -C007 Thiamethoxam 3 0.10069871056874392 -C007 Carfentrazone ethyl 21 0.058073633733907754 -C007 Azoxystrobin 15 0.04162201690293011 -C008 Nuarimol 19 0.24001108056690446 -C008 Carfentrazone ethyl 16 0.20226312595456533 -C008 Mepanipyrim 24 0.14228820913983994 -C009 Prometon_1 6 0.12091917830942694 -C009 Terbumeton_1 6 0.12091917830942694 -C009 Secbumeton_1 6 0.12091917830942694 -C010 Mefenacet 4 0.43004982863660707 -C010 Formetanate_2 5 0.29457761231941254 -C010 Formetanate_1 5 0.2905090298183795 -C011 Rotenone 16 0.120259993042822 -C011 Fluoxastrobin 15 0.061285197294993043 -C011 Diniconazole 11 0.05699612472380787 -C012 Mandipropamid 1 0.13126222394516718 -C012 Rotenone 8 0.0903130722741197 -C012 Boscalid 2 0.0729005850693225 -C013 Nuarimol 7 0.3025283295712756 -C013 Mepanipyrim 15 0.15526164028147613 -C013 Spirodiclofen 1 0.106955576332115 -C014 Fenarimol 8 0.32179033663818823 -C014 Diniconazole 15 0.15092951638007948 -C014 Triticonazole 11 0.14093053319713594 -C015 Tebuthiuron 2 0.42543841896130863 -C015 Dimoxystrobin 4 0.42066129038267897 -C015 Fenoxycarb 1 0.39730936680367507 -C016 Metaflumizone 7 0.1623382878576429 -C016 Tebufenpyrad 5 0.11500039861447153 -C016 Oxadixyl 3 0.08380136073062606 -C017 Diuron 1 0.40599269142482014 -C017 Neburon 1 0.37730332574966885 -C017 Metalaxyl 2 0.35998019446636254 -C018 Imidacloprid 5 0.38696080636127844 -C018 Diethofencarb 1 0.23518926887912128 -C018 Cyprodinil 5 0.22889204773489977 -C019 Dimethomorph 2 0.1531086374240407 -C019 Methabenzthiazuron 2 0.12163052809382871 -C019 Difenoconazole 3 0.11921837741737686 -C020 Metaflumizone 1 0.23108904445185505 -C020 Pyraclostrobin 2 0.1156909160450248 -C020 Flufenacet 1 0.09961048597871851 -C021 Fluoxastrobin 14 0.19390172961614233 -C021 Fenarimol 11 0.10371603681379983 -C021 Diniconazole 6 0.08088792564439248 -C022 Tebuthiuron 5 0.5445755137228012 -C022 Spiroxamine_2 1 0.5411902751987046 -C022 Spiroxamine_1 1 0.5316646078580738 -C023 Imidacloprid 3 0.14836980800858451 -C023 Mandipropamid 1 0.11566173860759153 -C023 3-Hydroxycarbofuran 1 0.11552221933479846 -C024 Flonicamid 4 0.21759028714740403 -C024 Imidacloprid 5 0.17807908901049269 -C024 Thiabendazole 1 0.11784109029164849 -C025 Fuberidazole 6 0.52564792144262 -C025 Thiamethoxam 2 0.43521398714077664 -C025 Dinotefuran 5 0.2544714861099532 -C026 Acibenzolar-S-methyl 1 0.27294451049290036 -C026 Ethofumesate 2 0.243921969041657 -C026 Tricyclazole 1 0.21870788794062254 -C027 Aminocarb_2 1 0.14452637381616495 -C027 Aminocarb_1 1 0.14452459002891235 -C027 Pyriproxyfen 1 0.143443143210623 -C028 Nuarimol 7 0.09525157976370839 -C028 Hydramethylnon 7 0.07386760517124663 -C028 Mevinphos 2 0.05351024774800468 -C029 Tebuthiuron 4 0.7578160314442438 -C029 Dimoxystrobin 4 0.7523284529176055 -C029 Fenoxycarb 2 0.7362883237809213 -C030 Fluoxastrobin 5 0.024671788239558207 -C030 Azoxystrobin 3 0.00805772872563839 -C030 Imazalil 1 0.006118222556281094 -C031 Thiabendazole 3 0.32542772940407816 -C031 Indoxacarb 3 0.11181300878614284 -C031 Fenpyroximate 11 0.09496750784008315 -C032 Chloroxuron 3 0.23099832140782792 -C032 Metaflumizone 4 0.15811807538527828 -C032 Clothianidin 3 0.15597953103591186 -C033 Triflumizole 1 0.12293170145864117 -C033 Fenoxycarb 1 0.03427456690960066 -C033 Hydramethylnon 4 0.02714227769520051 -C034 Tebufenpyrad 6 0.49374627461317955 -C034 Fenuron 4 0.4133963957082293 -C034 Carbaryl 1 0.3632254452201241 -C035 Fenarimol 7 0.09384407157367812 -C035 Diniconazole 3 0.0769387737847929 -C035 Furalaxyl 1 0.06844880759579586 -C036 Temephos 1 0.18474730701395245 -C036 Boscalid 2 0.1555080166548933 -C036 Difenoconazole 1 0.12573965018277433 -C037 Spiroxamine_1 1 0.17748544814941167 -C037 Spiroxamine_2 1 0.17459305075844642 -C037 Prometon_2 2 0.13300447820659206 -C038 Temephos 3 0.4479813614745304 -C038 Cyprodinil 11 0.38945132482337325 -C038 Tebufenpyrad 1 0.3230268544205335 -C039 Chloroxuron 5 0.7904224091921885 -C039 Metaflumizone 4 0.20495514559344025 -C039 Indoxacarb 4 0.06499320980489846 -C040 Nuarimol 7 0.3282707805775684 -C040 Hydramethylnon 8 0.2348918036086256 -C040 Dimoxystrobin 3 0.16614009139106203 -C041 Tebuthiuron 3 0.8149016029858368 -C041 Dimoxystrobin 5 0.8072997046898676 -C041 Fenoxycarb 1 0.7659786346098226 -C042 Fuberidazole 2 0.5857766323253869 -C042 Tebuthiuron 2 0.21955707467985677 -C042 Fenoxycarb 1 0.20659543701873473 -C043 Boscalid 2 0.06825376275669572 -C043 Pyrimethanil 3 0.057216918628908514 -C043 Dicrotophos 1 0.03384456583647226 -C045 Boscalid 3 0.1957440269836893 -C045 Carfentrazone ethyl 12 0.18490605424898302 -C045 Fipronil 8 0.15156444609388484 -C046 Nuarimol 4 0.3305281148374125 -C046 Methiocarb 1 0.15050994460485362 -C046 Clothianidin 2 0.1485039064562506 -C047 Methamidophos 2 0.13774763771211443 -C047 Ethirimol 3 0.1034867151296582 -C047 Dicrotophos 1 0.09639598176270271 -C048 Methoprotryne 1 0.15549799127470398 -C048 Prometon_2 1 0.10192628653945639 -C048 Terbumeton_2 1 0.10192628653945639 -C050 Propamocarb_1 1 0.995253153453804 -C050 Propamocarb_2 1 0.9951290247583393 -C050 Thidiazuron 2 0.9615972463125247 -C069 Metalaxyl 10 0.35854283629234446 -C069 Diuron 1 0.29921097365528254 -C069 Neburon 2 0.2796612168022523 -C106 Ethiofencarb 1 0.09746429231898772 -C106 Chlortoluron 1 0.05338627217152306 -C106 Ethirimol 2 0.04411148813226952 -C120 Tebufenpyrad 4 0.40579598696856434 -C120 Fenamidone 2 0.206943065684131 -C120 Isoproturon 6 0.15000239728413484 |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/formatter/test4_formatted.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/formatter/test4_formatted.tsv Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b"@@ -0,0 +1,11916 @@\n+query\treference\tNeutralLossesCosine_score\tNeutralLossesCosine_matches\n+Perylene\tPerylene\t1.0\t16\n+Phenanthrene\tPerylene\t0.7594055481290253\t6\n+Anthracene\tPerylene\t0.7816811045895042\t6\n+Acenaphthene\tPerylene\t0.5690164471890379\t5\n+Fluoranthene\tPerylene\t0.8546237198996057\t7\n+Pyrene\tPerylene\t0.8185192159559384\t5\n+para-Terphenyl\tPerylene\t0.7343454316376467\t7\n+Benzo[b]naphtho[2,1-d]thiophene\tPerylene\t0.6425661177089488\t2\n+2,3-Benzofluorene\tPerylene\t0.2525670085697937\t6\n+Benzofluoranthene\tPerylene\t0.8938819006775962\t10\n+Benzo(k)fluoranthene\tPerylene\t0.985274599682159\t13\n+Indeno[1,2,3-cd]pyrene\tPerylene\t0.7922540002305708\t7\n+Dibenzanthracene\tPerylene\t0.8172966984973474\t9\n+Benzophenone\tPerylene\t0.08849313203633093\t3\n+4-Methylbenzophenone\tPerylene\t0.0040900408841154\t2\n+2,6-Dichloro-4-nitroaniline\tPerylene\t0.06076643210788908\t4\n+1-Methylphenanthrene\tPerylene\t0.42348807105444636\t7\n+Triclosan\tPerylene\t0.029360869411532375\t4\n+Drometrizole\tPerylene\t0.0587027706971795\t2\n+Enzacamene\tPerylene\t0.11863743194394825\t7\n+2,2',3,4,5,5',6-Heptachlorobiphenyl\tPerylene\t0.001966468710916666\t2\n+2,2',3,3',4,5',6,6'-Octachlorobiphenyl\tPerylene\t0.000764358229746351\t1\n+beta-Hexachlorocyclohexane\tPerylene\t0.008413733301153947\t2\n+alpha-1,2,3,4,5,6-Hexachlorocyclohexane\tPerylene\t0.0005491770202375849\t1\n+Lindane\tPerylene\t0.0008209590469777335\t1\n+delta-Hexachlorocyclohexane\tPerylene\t0.0005388743414914208\t1\n+epsilon-Hexachlorocyclohexane\tPerylene\t0.0006026403861762904\t1\n+Pentachlorobenzene\tPerylene\t0.019757127107049986\t2\n+Hexachlorobenzene\tPerylene\t0.0022473490727107207\t1\n+2,4'-Dichlorodiphenyldichloroethane\tPerylene\t0.013157945063149563\t2\n+2,4'-Dichlorodiphenyltrichloroethane\tPerylene\t0.013347565755229026\t3\n+2,2',4,5,5'-Pentachlorobiphenyl\tPerylene\t0.0003958854222256223\t1\n+2,2',3,4,4',5'-Hexachlorobiphenyl\tPerylene\t0.0005077696302166955\t1\n+2,2',4,4',5,5'-Hexachlorobiphenyl\tPerylene\t0.07521910915424485\t4\n+2,2',3,4,4',5,5'-Heptachlorobiphenyl\tPerylene\t0.0014636617538366383\t2\n+2,2',5,5'-Tetrachlorobiphenyl\tPerylene\t0.00042116604751712907\t1\n+2,2',3,4',5-Pentachlorobiphenyl\tPerylene\t0.00072829765065908\t1\n+2,3,3',4,5,6-Hexachlorobiphenyl\tPerylene\t0.0005346121023576851\t1\n+2,3,3',4',5,5',6-Heptachlorobiphenyl\tPerylene\t0.0005961644717473801\t1\n+trans-Prallethrin\tPerylene\t0.0013033208643460548\t1\n+Fenpropathrin\tPerylene\t0.022271646454031933\t2\n+Chlorpyrifos oxon\tPerylene\t0.036296460167888005\t9\n+Transfluthrin\tPerylene\t0.018431113763733808\t3\n+cis-Cyfluthrin_isomer2\tPerylene\t0.015875450516702534\t2\n+trans-Cyfluthrin_Isomer2\tPerylene\t0.0057284317883735565\t1\n+1,2,3,4,7,8-Hexachlorodibenzo-p-dioxin\tPerylene\t0.35713628898895355\t2\n+1,2,3,4,6,7,8-Heptachlorodibenzo-p-dioxin\tPerylene\t0.6004738760543434\t4\n+Estragole\tPerylene\t0.1274354945159494\t3\n+Benzyl salicylate\tPerylene\t0.0025487592367612172\t1\n+Eucalyptol\tPerylene\t0.0014044497521836833\t1\n+Coumarin\tPerylene\t0.06516422811768255\t1\n+Limonene\tPerylene\t0.00249747607765285\t2\n+Isomethyl-alpha-ionone\tPerylene\t0.029962167865351642\t2\n+delta-Iraldeine\tPerylene\t0.010722361197213872\t4\n+Safrole\tPerylene\t0.0653442903989148\t4\n+Cashmeran\tPerylene\t0.029760402289703447\t5\n+Celestolide\tPerylene\t0.00632853603000457\t3\n+Phantolide\tPerylene\t0.005171685189631448\t3\n+Thiobencarb\tPerylene\t0.005102702742696307\t1\n+Isoprocarb\tPerylene\t0.012488960236250022\t1\n+Linuron\tPerylene\t0.010317618084000975\t1\n+Metobromuron\tPerylene\t0.007456310296289823\t2\n+Monolinuron\tPerylene\t0.015775168176517546\t3\n+Pirimicarb\tPerylene\t0.005765295246724256\t1\n+Boscalid\tPerylene\t0.00321731217654157\t2\n+Butafenacil\tPerylene\t0.002533257463670457\t1\n+Myclobutanil\tPerylene\t0.0015717545649436182\t1\n+Terbumeton\tPerylene\t0.012379273705355584\t5\n+Rotenone\tPerylene\t0.0044024783401794935\t2\n+Enilconazole\tPerylene\t0.002087916382540429\t1\n+Acibenzolar-S-methyl\tPerylene\t0.003087426600635205\t1\n+Buprofezin\tPerylene\t0.0016122911027146008\t1\n+Ethofumesate\tPerylene\t0.002652615111824328\t1\n+Fenamidone\tPerylene\t0.003528882271834487\t1\n+Perylene\tPhenanthrene\t0.7594055481290253\t6\n+Phenanthrene\tPhenanthrene\t1.0"..b"iphenyl\tFenamidone\t0.0009962252275582525\t2\n+3,3',4,5,5'-Pentachlorobiphenyl\tFenamidone\t0.0007132215414105701\t1\n+2,3',4,4',5',6-Hexachlorobiphenyl\tFenamidone\t0.003941192991095589\t3\n+2,3,3',4,5,6-Hexachlorobiphenyl\tFenamidone\t0.0032602230184353796\t4\n+2,3,3',4',5',6-Hexachlorobiphenyl\tFenamidone\t0.003902911013387605\t3\n+2,3,3',4',5,6-Hexachlorobiphenyl\tFenamidone\t0.0028816112771112476\t3\n+2,3,3',4',5,5',6-Heptachlorobiphenyl\tFenamidone\t0.004129652769687335\t4\n+cis-Prallethrin\tFenamidone\t0.02063893548098056\t6\n+trans-Prallethrin\tFenamidone\t0.0636896775821581\t18\n+cis-Resmethrin\tFenamidone\t0.004385623187808619\t8\n+trans-Resmethrin\tFenamidone\t0.0037438584101095406\t3\n+cis-Tetramethrin\tFenamidone\t0.01457741637519401\t10\n+trans-Tetramethrin\tFenamidone\t0.01998288532279959\t5\n+Bifenthrin\tFenamidone\t0.016943871184680423\t3\n+Fenpropathrin\tFenamidone\t0.020485320040871696\t12\n+cis-Phenothrin\tFenamidone\t6.285139330345371e-05\t1\n+cis-Cyphenothrin\tFenamidone\t0.01577650392972678\t12\n+Flucythrinate_isomer1\tFenamidone\t0.011702041332335697\t2\n+Flucythrinate_isomer2\tFenamidone\t0.010479081997924272\t3\n+cis-Fenvalerate\tFenamidone\t0.0026839418346610074\t4\n+trans-Fenvalerate\tFenamidone\t0.005168753640460431\t7\n+Deltamethrin\tFenamidone\t0.02538556396055245\t8\n+Chlorpyrifos oxon\tFenamidone\t0.008017165415374613\t6\n+lambda-Cyhalothrin\tFenamidone\t0.004129170239233964\t2\n+Tefluthrin\tFenamidone\t0.048329475132303006\t9\n+Transfluthrin\tFenamidone\t0.00434534268029665\t5\n+cis-Permethrin\tFenamidone\t0.0336080987239482\t12\n+trans-Permethrin\tFenamidone\t0.037158313842249\t12\n+cis-Allethrin\tFenamidone\t0.029034992247889045\t6\n+trans-Allethrin\tFenamidone\t0.08565057856307288\t16\n+cis-Cypermethrin_isomer1\tFenamidone\t0.10145493598365102\t13\n+trans-Cypermethrin_isomer1\tFenamidone\t0.018538092241168595\t9\n+cis-Cypermethrin_isomer2\tFenamidone\t0.09931273097453466\t12\n+trans-Cypermethrin_isomer2\tFenamidone\t0.06070353397555056\t14\n+cis-Cyfluthrin_isomer1\tFenamidone\t0.002741342514267584\t9\n+trans-Cyfluthrin_isomer1\tFenamidone\t0.00460623189175496\t6\n+cis-Cyfluthrin_isomer2\tFenamidone\t0.013560322081058994\t12\n+trans-Cyfluthrin_Isomer2\tFenamidone\t0.012723588396856826\t11\n+1,2,3,4,7,8-Hexachlorodibenzo-p-dioxin\tFenamidone\t0.0014932550806373572\t2\n+1,2,3,4,6,7,8-Heptachlorodibenzo-p-dioxin\tFenamidone\t0.007463259062288398\t4\n+Estragole\tFenamidone\t0.1412047674540015\t8\n+Benzyl benzoate\tFenamidone\t0.003501755080485208\t3\n+Benzyl cinnamate\tFenamidone\t0.01046473315565069\t5\n+Benzyl salicylate\tFenamidone\t0.0003965607968942006\t1\n+Camphor\tFenamidone\t0.20590013512001082\t7\n+Eucalyptol\tFenamidone\t0.35784239189966305\t8\n+Coumarin\tFenamidone\t0.04127530460264906\t3\n+Limonene\tFenamidone\t0.4549680796955883\t5\n+Isomethyl-alpha-ionone\tFenamidone\t0.023153444567903744\t5\n+delta-Iraldeine\tFenamidone\t0.014791952326994103\t7\n+Safrole\tFenamidone\t0.033972430110607105\t7\n+Cashmeran\tFenamidone\t0.3711542904483082\t10\n+Celestolide\tFenamidone\t0.03604508634054142\t6\n+Phantolide\tFenamidone\t0.04706388584812521\t6\n+Propham\tFenamidone\t0.058857146107057945\t5\n+Thiobencarb\tFenamidone\t0.001747548159513367\t5\n+Isoprocarb\tFenamidone\t0.044272293314883686\t3\n+Linuron\tFenamidone\t0.04061042591948574\t11\n+Metobromuron\tFenamidone\t0.052801064317870655\t8\n+Monolinuron\tFenamidone\t0.03570076858640123\t5\n+Pirimicarb\tFenamidone\t0.09776996663893509\t6\n+Benalaxyl\tFenamidone\t0.04001833146441783\t15\n+Benzoximate\tFenamidone\t0.0014714555648693989\t4\n+Boscalid\tFenamidone\t0.0004504195432699507\t4\n+Myclobutanil\tFenamidone\t0.11173292584219889\t10\n+Oxadixyl\tFenamidone\t0.00309658302518114\t7\n+Picoxystrobin\tFenamidone\t0.011345966685709261\t11\n+Piperonyl butoxide\tFenamidone\t0.015934410043558587\t7\n+Terbumeton\tFenamidone\t0.014135762445538736\t5\n+Rotenone\tFenamidone\t0.001702586530993099\t3\n+Enilconazole\tFenamidone\t0.0021231289122006507\t7\n+Acibenzolar-S-methyl\tFenamidone\t0.0022815011051092924\t2\n+Bupirimate\tFenamidone\t0.3391095176584686\t16\n+Buprofezin\tFenamidone\t0.0166891482966783\t15\n+Carboxin\tFenamidone\t0.002867840748348977\t2\n+Ethofumesate\tFenamidone\t0.021945212693018183\t14\n+Fenamidone\tFenamidone\t0.9999999999999996\t47\n" |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/metadata_match/inchi_key_inner.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/metadata_match/inchi_key_inner.json Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"__Scores__": true, "is_symmetric": false, "references": [{"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C14H10", "inchikey": "YNPNZTXNASCQKK-UHFFFAOYSA-N", "smiles": "C1=CC2=C(C=C1)C1=C(C=CC=C1)C=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "19", "compound_name": "Phenanthrene", "retention_time": null, "retention_index": 1832.9, "precursor_mz": 178.0775, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[74.01508, 137808.0], [75.02295, 278714.0], [76.03075, 608417.0], [87.02295, 304266.0], [88.03076, 497050.0], [89.03857, 441168.0], [98.01511, 150478.0], [150.04633, 868927.0], [151.05415, 546351.0], [152.0619, 2275502.0], [153.06528, 276320.0], [169.06468, 272559.0], [174.04636, 365846.0], [175.05423, 272039.0], [176.062, 3370523.0], [177.06982, 1751846.0], [178.0775, 13724432.0], [179.08078, 2250119.0], [180.08412, 138203.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C14H10", "inchikey": "MWPLVEDNUUSJAV-UHFFFAOYSA-N", "smiles": "C1=CC2=CC3=C(C=CC=C3)C=C2C=C1", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "21", "compound_name": "Anthracene", "retention_time": null, "retention_index": 1844.4, "precursor_mz": 178.07754, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[74.0151, 117371.0], [75.02296, 245305.0], [76.03077, 632686.0], [87.02297, 236214.0], [88.03078, 347832.0], [89.0386, 507288.0], [91.05425, 130861.0], [126.04636, 128356.0], [149.04478, 126331.0], [150.04637, 641829.0], [151.05415, 403195.0], [152.06195, 1369833.0], [153.06534, 175290.0], [169.06471, 228827.0], [174.04639, 255716.0], [175.05423, 198784.0], [176.06204, 2563053.0], [177.06984, 1182037.0], [178.07754, 11002398.0], [179.08081, 1778803.0], [180.08418, 132922.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C16H10", "inchikey": "GVEPBJHOBDJJJI-UHFFFAOYSA-N", "smiles": "C1=CC2=C(C=C1)C1=C3C2=CC=CC3=CC=C1", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "17", "compound_name": "Fluoranthene", "retention_time": null, "retention_index": 2102.7, "precursor_mz": 202.07756, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[75.02299, 112456.0], [87.02298, 183640.0], [88.03079, 367434.0], [99.02296, 124952.0], [100.03078, 376079.0], [101.03863, 381288.0], [150.04642, 86059.0], [174.04634, 246963.0], [176.06194, 141676.0], [198.0464, 244370.0], [199.05429, 285767.0], [200.06207, 1958890.0], [201.06982, 1103710.0], [202.07756, 8104188.0], [203.08084, 1377015.0], [204.08421, 98067.0], [219.08043, 186623.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C16H10", "inchikey": "BBEAQIROQSPTKN-UHFFFAOYSA-N", "smiles": "C1=CC2=C3C(C=CC4=CC=CC(C=C2)=C34)=C1", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "16", "compound_name": "Pyrene", "retention_time": null, "retention_index": 2154.5, "precursor_mz": 202.07759, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[87.02299, 147113.0], [88.0308, 305149.0], [99.02298, 137042.0], [100.0308, 508914.0], [101.03864, 472094.0], [101.54032, 82430.0], [150.04637, 80741.0], [174.04631, 212706.0], [198.04643, 262925.0], [199.05429, 295144.0], [200.06209, 1960712.0], [201.06982, 1270466.0], [202.'..b'2.0], [100.0308, 508914.0], [101.03864, 472094.0], [101.54032, 82430.0], [150.04637, 80741.0], [174.04631, 212706.0], [198.04643, 262925.0], [199.05429, 295144.0], [200.06209, 1960712.0], [201.06982, 1270466.0], [202.07759, 7974712.0], [203.08086, 1335645.0], [204.0843, 121774.0], [219.08044, 182944.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C18H14", "inchikey": "XJKSTNDFUHDPQJ-UHFFFAOYSA-N", "smiles": "C1=CC=C(C=C1)C2=CC=C(C=C2)C3=CC=CC=C3", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "25", "compound_name": "para-Terphenyl", "retention_time": null, "retention_index": 2207.5, "precursor_mz": 230.10886, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[88.03077, 233962.0], [101.03861, 353544.0], [113.03854, 437845.0], [115.05423, 690291.0], [128.062, 293046.0], [151.05412, 266397.0], [152.06195, 961184.0], [153.06976, 409346.0], [176.06192, 232793.0], [189.06972, 408734.0], [200.0619, 342984.0], [201.06986, 238974.0], [202.07758, 1292332.0], [203.08093, 374439.0], [213.06973, 256631.0], [215.08548, 1220866.0], [216.08881, 217320.0], [224.062, 181393.0], [226.07771, 1503774.0], [227.08588, 1198323.0], [228.09344, 2885510.0], [229.10123, 1791323.0], [230.10886, 17890056.0], [231.11214, 3536976.0], [232.11542, 320231.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C16H10S", "inchikey": "YEUHHUCOSQOCIX-UHFFFAOYSA-N", "smiles": "S1C2=C(C=CC=C2)C2=C1C1=CC=CC=C1C=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "23", "compound_name": "Benzo[b]naphtho[2,1-d]thiophene", "retention_time": null, "retention_index": 2419.3, "precursor_mz": 234.04965, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[91.05425, 49130.0], [93.52686, 61653.0], [94.53469, 76638.0], [104.01679, 126871.0], [116.01675, 112547.0], [117.02459, 99108.0], [162.04623, 54491.0], [163.05408, 136418.0], [164.06198, 56321.0], [187.05406, 273349.0], [188.06189, 200750.0], [189.06969, 453336.0], [190.07306, 77884.0], [200.06189, 135620.0], [201.06973, 74692.0], [202.07758, 425058.0], [203.08086, 72058.0], [226.07762, 63460.0], [232.03409, 769638.0], [233.04245, 382457.0], [234.04965, 4404102.0], [235.05304, 725574.0], [236.04547, 251450.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C17H12", "inchikey": "HAPOJKSPCGLOOD-UHFFFAOYSA-N", "smiles": "C1C2=CC=CC=C2C2=C1C=C1C=CC=CC1=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "21", "compound_name": "2,3-Benzofluorene", "retention_time": null, "retention_index": 2257.5, "precursor_mz": 216.09326, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[93.52689, 122035.0], [94.53471, 241743.0], [95.03638, 42130.0], [105.52688, 47526.0], [106.53471, 171653.0], [107.03639, 60004.0], [107.5425, 180288.0], [108.03385, 97471.0], [163.05414, 68194.0], [187.05412, 167183.0], [188.06201, 86262.0], [189.06975, 239421.0], [190.07321, 37778.0], [211.05426, 117044.0], [212.06215, 60813.0], [213.0699, 808499.0], [214.07317, 202222.0], [215.0855, 3634570.0], [216.09326, 2535030.0], [217.09671, 444170.0], [218.09999, 37976.0]]}], "n_row": 7, "n_col": 7, "row": [0, 1, 2, 3, 4, 5, 6], "col": [0, 1, 2, 3, 4, 5, 6], "data": [[true, true], [true, true], [true, true], [true, true], [true, true], [true, true], [true, true]], "dtype": [["MetadataMatch_smiles_equal_match", "|b1"], ["MetadataMatch_inchikey_equal_match", "|b1"]]}\n\\ No newline at end of file\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/metadata_match/inner_join_ri_20.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/metadata_match/inner_join_ri_20.json Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"__Scores__": true, "is_symmetric": false, "references": [{"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C14H10", "inchikey": "YNPNZTXNASCQKK-UHFFFAOYSA-N", "smiles": "C1=CC2=C(C=C1)C1=C(C=CC=C1)C=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "19", "compound_name": "Phenanthrene", "retention_time": null, "retention_index": 1832.9, "precursor_mz": 178.0775, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[74.01508, 137808.0], [75.02295, 278714.0], [76.03075, 608417.0], [87.02295, 304266.0], [88.03076, 497050.0], [89.03857, 441168.0], [98.01511, 150478.0], [150.04633, 868927.0], [151.05415, 546351.0], [152.0619, 2275502.0], [153.06528, 276320.0], [169.06468, 272559.0], [174.04636, 365846.0], [175.05423, 272039.0], [176.062, 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"retention_time": null, "retention_index": 2257.5, "precursor_mz": 216.09326, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[93.52689, 122035.0], [94.53471, 241743.0], [95.03638, 42130.0], [105.52688, 47526.0], [106.53471, 171653.0], [107.03639, 60004.0], [107.5425, 180288.0], [108.03385, 97471.0], [163.05414, 68194.0], [187.05412, 167183.0], [188.06201, 86262.0], [189.06975, 239421.0], [190.07321, 37778.0], [211.05426, 117044.0], [212.06215, 60813.0], [213.0699, 808499.0], [214.07317, 202222.0], [215.0855, 3634570.0], [216.09326, 2535030.0], [217.09671, 444170.0], [218.09999, 37976.0]]}], "n_row": 7, "n_col": 7, "row": [0, 0, 1, 1, 2, 3, 4, 5, 6], "col": [0, 1, 0, 1, 2, 3, 4, 5, 6], "data": [[true, true], [true, true], [true, true], [true, true], [true, true], [true, true], [true, true], [true, true], [true, true]], "dtype": [["MetadataMatch_retention_index_difference_60.0_f0", "|b1"], ["MetadataMatch_retention_index_difference_20.0_f0", "|b1"]]}\n\\ No newline at end of file\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/metadata_match/left_join_ri_20.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/metadata_match/left_join_ri_20.json Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"__Scores__": true, "is_symmetric": false, "references": [{"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C14H10", "inchikey": "YNPNZTXNASCQKK-UHFFFAOYSA-N", "smiles": "C1=CC2=C(C=C1)C1=C(C=CC=C1)C=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "19", "compound_name": "Phenanthrene", "retention_time": null, "retention_index": 1832.9, "precursor_mz": 178.0775, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[74.01508, 137808.0], [75.02295, 278714.0], [76.03075, 608417.0], [87.02295, 304266.0], [88.03076, 497050.0], [89.03857, 441168.0], [98.01511, 150478.0], [150.04633, 868927.0], [151.05415, 546351.0], [152.0619, 2275502.0], [153.06528, 276320.0], [169.06468, 272559.0], [174.04636, 365846.0], [175.05423, 272039.0], [176.062, 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[201.06982, 1270466.0], [202.'..b'82, 1270466.0], [202.07759, 7974712.0], [203.08086, 1335645.0], [204.0843, 121774.0], [219.08044, 182944.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C18H14", "inchikey": "XJKSTNDFUHDPQJ-UHFFFAOYSA-N", "smiles": "C1=CC=C(C=C1)C2=CC=C(C=C2)C3=CC=CC=C3", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "25", "compound_name": "para-Terphenyl", "retention_time": null, "retention_index": 2207.5, "precursor_mz": 230.10886, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[88.03077, 233962.0], [101.03861, 353544.0], [113.03854, 437845.0], [115.05423, 690291.0], [128.062, 293046.0], [151.05412, 266397.0], [152.06195, 961184.0], [153.06976, 409346.0], [176.06192, 232793.0], [189.06972, 408734.0], [200.0619, 342984.0], [201.06986, 238974.0], [202.07758, 1292332.0], [203.08093, 374439.0], [213.06973, 256631.0], [215.08548, 1220866.0], [216.08881, 217320.0], [224.062, 181393.0], [226.07771, 1503774.0], [227.08588, 1198323.0], [228.09344, 2885510.0], [229.10123, 1791323.0], [230.10886, 17890056.0], [231.11214, 3536976.0], [232.11542, 320231.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C16H10S", "inchikey": "YEUHHUCOSQOCIX-UHFFFAOYSA-N", "smiles": "S1C2=C(C=CC=C2)C2=C1C1=CC=CC=C1C=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "23", "compound_name": "Benzo[b]naphtho[2,1-d]thiophene", "retention_time": null, "retention_index": 2419.3, "precursor_mz": 234.04965, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[91.05425, 49130.0], [93.52686, 61653.0], [94.53469, 76638.0], [104.01679, 126871.0], [116.01675, 112547.0], [117.02459, 99108.0], [162.04623, 54491.0], [163.05408, 136418.0], [164.06198, 56321.0], [187.05406, 273349.0], [188.06189, 200750.0], [189.06969, 453336.0], [190.07306, 77884.0], [200.06189, 135620.0], [201.06973, 74692.0], [202.07758, 425058.0], [203.08086, 72058.0], [226.07762, 63460.0], [232.03409, 769638.0], [233.04245, 382457.0], [234.04965, 4404102.0], [235.05304, 725574.0], [236.04547, 251450.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C17H12", "inchikey": "HAPOJKSPCGLOOD-UHFFFAOYSA-N", "smiles": "C1C2=CC=CC=C2C2=C1C=C1C=CC=CC1=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "21", "compound_name": "2,3-Benzofluorene", "retention_time": null, "retention_index": 2257.5, "precursor_mz": 216.09326, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[93.52689, 122035.0], [94.53471, 241743.0], [95.03638, 42130.0], [105.52688, 47526.0], [106.53471, 171653.0], [107.03639, 60004.0], [107.5425, 180288.0], [108.03385, 97471.0], [163.05414, 68194.0], [187.05412, 167183.0], [188.06201, 86262.0], [189.06975, 239421.0], [190.07321, 37778.0], [211.05426, 117044.0], [212.06215, 60813.0], [213.0699, 808499.0], [214.07317, 202222.0], [215.0855, 3634570.0], [216.09326, 2535030.0], [217.09671, 444170.0], [218.09999, 37976.0]]}], "n_row": 7, "n_col": 7, "row": [0, 0, 1, 1, 2, 2, 3, 3, 3, 4, 4, 4, 5, 6, 6], "col": [0, 1, 0, 1, 2, 3, 2, 3, 4, 3, 4, 6, 5, 4, 6], "data": [[true, true], [true, true], [true, true], [true, true], [true, true], [true, false], [true, false], [true, true], [true, false], [true, false], [true, true], [true, false], [true, true], [true, false], [true, true]], "dtype": [["MetadataMatch_retention_index_difference_60.0_f0", "|b1"], ["MetadataMatch_retention_index_difference_20.0_f0", "|b1"]]}\n\\ No newline at end of file\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/metadata_match/ri_match_60.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/metadata_match/ri_match_60.json Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"__Scores__": true, "is_symmetric": false, "references": [{"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C14H10", "inchikey": "YNPNZTXNASCQKK-UHFFFAOYSA-N", "smiles": "C1=CC2=C(C=C1)C1=C(C=CC=C1)C=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": {"74.01508": "Theoretical m/z 74.01565, Mass diff 0 (0 ppm), Formula C6H2", "75.02295": "Theoretical m/z 75.023475, Mass diff 0 (0 ppm), Formula C6H3", "76.03075": "Theoretical m/z 76.0313, Mass diff 0 (0 ppm), Formula C6H4", "87.02295": "Theoretical m/z 87.023475, Mass diff 0 (0 ppm), Formula C7H3", "88.03076": "Theoretical m/z 88.0313, Mass diff 0 (0 ppm), Formula C7H4", "89.03857": "Theoretical m/z 89.039125, Mass diff 0 (0 ppm), Formula C7H5", "151.05415": "Theoretical m/z 151.054775, Mass diff 0 (0 ppm), Formula C12H7", "175.05423": "Theoretical m/z 175.054775, Mass diff 0 (0 ppm), Formula C14H7", "176.062": "Theoretical m/z 176.0626, Mass diff 0 (0 ppm), Formula C14H8", "177.06982": "Theoretical m/z 177.070425, Mass diff 0 (0 ppm), Formula C14H9", "178.0775": "Theoretical m/z 178.077698, Mass diff 0 (1.11 ppm), SMILES C=1C=CC2=C(C1)C=CC=3C=CC=CC32, Annotation [C14H10]+, Rule of HR False"}, "num_peaks": "19", "compound_name": "Phenanthrene", "retention_time": null, "retention_index": 1832.9, "precursor_mz": 178.0775, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[74.01508, 137808.0], [75.02295, 278714.0], [76.03075, 608417.0], [87.02295, 304266.0], [88.03076, 497050.0], [89.03857, 441168.0], [98.01511, 150478.0], [150.04633, 868927.0], [151.05415, 546351.0], [152.0619, 2275502.0], [153.06528, 276320.0], [169.06468, 272559.0], [174.04636, 365846.0], [175.05423, 272039.0], [176.062, 3370523.0], [177.06982, 1751846.0], [178.0775, 13724432.0], [179.08078, 2250119.0], [180.08412, 138203.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C14H10", "inchikey": "MWPLVEDNUUSJAV-UHFFFAOYSA-N", "smiles": "C1=CC2=CC3=C(C=CC=C3)C=C2C=C1", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": {"74.0151": "Theoretical m/z 74.01565, Mass diff 0 (0 ppm), Formula C6H2", "75.02296": "Theoretical m/z 75.023475, Mass diff 0 (0 ppm), Formula C6H3", "76.03077": "Theoretical m/z 76.0313, Mass diff 0 (0 ppm), Formula C6H4", "87.02297": "Theoretical m/z 87.023475, Mass diff 0 (0 ppm), Formula C7H3", "88.03078": "Theoretical m/z 88.0313, Mass diff 0 (0 ppm), Formula C7H4", "89.0386": "Theoretical m/z 89.039125, Mass diff 0 (0 ppm), Formula C7H5", "91.05425": "Theoretical m/z 91.054775, Mass diff 0 (0 ppm), Formula C7H7", "151.05415": "Theoretical m/z 151.054775, Mass diff 0 (0 ppm), Formula C12H7", "175.05423": "Theoretical m/z 175.054775, Mass diff 0 (0 ppm), Formula C14H7", "176.06204": "Theoretical m/z 176.0626, Mass diff 0 (0 ppm), Formula C14H8", "177.06984": "Theoretical m/z 177.070425, Mass diff 0 (0 ppm), Formula C14H9", "178.07754": "Theoretical m/z 178.077698, Mass diff 0 (0.89 ppm), SMILES C=1C=CC=2C=C3C=CC=CC3=CC2C1, Annotation [C14H10]+, Rule of HR False"}, "num_peaks": "21", "compound_name": "Anthracene", "retention_time": null, "retention_index": 1844.4, "precursor_mz": 178.07754, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[74.0151, 117371.0], [75.02296, 245305.0], [76.03077, 632686.0], [87.02297, 236214.0], [88.03078, 347832.0], [89.0386, 507288.0], [91.05425, 130861.0], [126.04636, 128356.0], [149.04478, 126331.0], [150.04637, 641829.0], [151.05415, 403195.0], [152.06195, 1369833.0], [153.06534, 175290.0], [169.06471, 228827.0], [174.04639, 255716.0], [175.05423, 198784.0], [176.06204, 2563053.0], [177.06984, 1182037.0], [178.07754, 11002398.0], [179.080'..b'320.0], [224.062, 181393.0], [226.07771, 1503774.0], [227.08588, 1198323.0], [228.09344, 2885510.0], [229.10123, 1791323.0], [230.10886, 17890056.0], [231.11214, 3536976.0], [232.11542, 320231.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C16H10S", "inchikey": "YEUHHUCOSQOCIX-UHFFFAOYSA-N", "smiles": "S1C2=C(C=CC=C2)C2=C1C1=CC=CC=C1C=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": {"91.05425": "Theoretical m/z 91.054775, Mass diff 0 (0 ppm), Formula C7H7", "163.05408": "Theoretical m/z 163.054775, Mass diff 0 (0 ppm), Formula C13H7", "187.05406": "Theoretical m/z 187.054775, Mass diff 0 (0 ppm), Formula C15H7", "189.06969": "Theoretical m/z 189.070425, Mass diff 0 (0 ppm), Formula C15H9", "201.06973": "Theoretical m/z 201.070425, Mass diff 0 (0 ppm), Formula C16H9", "233.04245": "Theoretical m/z 233.042496, Mass diff -0.001 (0 ppm), Formula C16H9S", "234.04965": "Theoretical m/z 234.049775, Mass diff 0 (0.53 ppm), SMILES S1C=2C=CC=CC2C=3C=CC=4C=CC=CC4C13, Annotation [C16H10S]+, Rule of HR False"}, "num_peaks": "23", "compound_name": "Benzo[b]naphtho[2,1-d]thiophene", "retention_time": null, "retention_index": 2419.3, "precursor_mz": 234.04965, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[91.05425, 49130.0], [93.52686, 61653.0], [94.53469, 76638.0], [104.01679, 126871.0], [116.01675, 112547.0], [117.02459, 99108.0], [162.04623, 54491.0], [163.05408, 136418.0], [164.06198, 56321.0], [187.05406, 273349.0], [188.06189, 200750.0], [189.06969, 453336.0], [190.07306, 77884.0], [200.06189, 135620.0], [201.06973, 74692.0], [202.07758, 425058.0], [203.08086, 72058.0], [226.07762, 63460.0], [232.03409, 769638.0], [233.04245, 382457.0], [234.04965, 4404102.0], [235.05304, 725574.0], [236.04547, 251450.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C17H12", "inchikey": "HAPOJKSPCGLOOD-UHFFFAOYSA-N", "smiles": "C1C2=CC=CC=C2C2=C1C=C1C=CC=CC1=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": {"163.05414": "Theoretical m/z 163.054775, Mass diff 0 (0 ppm), Formula C13H7", "187.05412": "Theoretical m/z 187.054775, Mass diff 0 (0 ppm), Formula C15H7", "189.06975": "Theoretical m/z 189.070425, Mass diff 0 (0 ppm), Formula C15H9", "211.05426": "Theoretical m/z 211.054775, Mass diff 0 (0 ppm), Formula C17H7", "213.0699": "Theoretical m/z 213.070425, Mass diff 0 (0 ppm), Formula C17H9", "215.0855": "Theoretical m/z 215.086075, Mass diff 0 (0 ppm), Formula C17H11", "216.09326": "Theoretical m/z 216.093354, Mass diff 0 (0.44 ppm), SMILES C=1C=CC=2C=C3C(=CC2C1)C=4C=CC=CC4C3, Annotation [C17H12]+, Rule of HR False"}, "num_peaks": "21", "compound_name": "2,3-Benzofluorene", "retention_time": null, "retention_index": 2257.5, "precursor_mz": 216.09326, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[93.52689, 122035.0], [94.53471, 241743.0], [95.03638, 42130.0], [105.52688, 47526.0], [106.53471, 171653.0], [107.03639, 60004.0], [107.5425, 180288.0], [108.03385, 97471.0], [163.05414, 68194.0], [187.05412, 167183.0], [188.06201, 86262.0], [189.06975, 239421.0], [190.07321, 37778.0], [211.05426, 117044.0], [212.06215, 60813.0], [213.0699, 808499.0], [214.07317, 202222.0], [215.0855, 3634570.0], [216.09326, 2535030.0], [217.09671, 444170.0], [218.09999, 37976.0]]}], "n_row": 7, "n_col": 7, "row": [0, 0, 1, 1, 2, 2, 3, 3, 3, 4, 4, 4, 5, 6, 6], "col": [0, 1, 0, 1, 2, 3, 2, 3, 4, 3, 4, 6, 5, 4, 6], "data": [[true], [true], [true], [true], [true], [true], [true], [true], [true], [true], [true], [true], [true], [true], [true]], "dtype": [["MetadataMatch_retention_index_difference_60.0_f0", "|b1"]]}\n\\ No newline at end of file\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/metadata_match/smiles.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/metadata_match/smiles.json Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"__Scores__": true, "is_symmetric": false, "references": [{"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C14H10", "inchikey": "YNPNZTXNASCQKK-UHFFFAOYSA-N", "smiles": "C1=CC2=C(C=C1)C1=C(C=CC=C1)C=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": {"74.01508": "Theoretical m/z 74.01565, Mass diff 0 (0 ppm), Formula C6H2", "75.02295": "Theoretical m/z 75.023475, Mass diff 0 (0 ppm), Formula C6H3", "76.03075": "Theoretical m/z 76.0313, Mass diff 0 (0 ppm), Formula C6H4", "87.02295": "Theoretical m/z 87.023475, Mass diff 0 (0 ppm), Formula C7H3", "88.03076": "Theoretical m/z 88.0313, Mass diff 0 (0 ppm), Formula C7H4", "89.03857": "Theoretical m/z 89.039125, Mass diff 0 (0 ppm), Formula C7H5", "151.05415": "Theoretical m/z 151.054775, Mass diff 0 (0 ppm), Formula C12H7", "175.05423": "Theoretical m/z 175.054775, Mass diff 0 (0 ppm), Formula C14H7", "176.062": "Theoretical m/z 176.0626, Mass diff 0 (0 ppm), Formula C14H8", "177.06982": "Theoretical m/z 177.070425, Mass diff 0 (0 ppm), Formula C14H9", "178.0775": "Theoretical m/z 178.077698, Mass diff 0 (1.11 ppm), SMILES C=1C=CC2=C(C1)C=CC=3C=CC=CC32, Annotation [C14H10]+, Rule of HR False"}, "num_peaks": "19", "compound_name": "Phenanthrene", "retention_time": null, "retention_index": 1832.9, "precursor_mz": 178.0775, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[74.01508, 137808.0], [75.02295, 278714.0], [76.03075, 608417.0], [87.02295, 304266.0], [88.03076, 497050.0], [89.03857, 441168.0], [98.01511, 150478.0], [150.04633, 868927.0], [151.05415, 546351.0], [152.0619, 2275502.0], [153.06528, 276320.0], [169.06468, 272559.0], [174.04636, 365846.0], [175.05423, 272039.0], [176.062, 3370523.0], [177.06982, 1751846.0], [178.0775, 13724432.0], [179.08078, 2250119.0], [180.08412, 138203.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C14H10", "inchikey": "MWPLVEDNUUSJAV-UHFFFAOYSA-N", "smiles": "C1=CC2=CC3=C(C=CC=C3)C=C2C=C1", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": {"74.0151": "Theoretical m/z 74.01565, Mass diff 0 (0 ppm), Formula C6H2", "75.02296": "Theoretical m/z 75.023475, Mass diff 0 (0 ppm), Formula C6H3", "76.03077": "Theoretical m/z 76.0313, Mass diff 0 (0 ppm), Formula C6H4", "87.02297": "Theoretical m/z 87.023475, Mass diff 0 (0 ppm), Formula C7H3", "88.03078": "Theoretical m/z 88.0313, Mass diff 0 (0 ppm), Formula C7H4", "89.0386": "Theoretical m/z 89.039125, Mass diff 0 (0 ppm), Formula C7H5", "91.05425": "Theoretical m/z 91.054775, Mass diff 0 (0 ppm), Formula C7H7", "151.05415": "Theoretical m/z 151.054775, Mass diff 0 (0 ppm), Formula C12H7", "175.05423": "Theoretical m/z 175.054775, Mass diff 0 (0 ppm), Formula C14H7", "176.06204": "Theoretical m/z 176.0626, Mass diff 0 (0 ppm), Formula C14H8", "177.06984": "Theoretical m/z 177.070425, Mass diff 0 (0 ppm), Formula C14H9", "178.07754": "Theoretical m/z 178.077698, Mass diff 0 (0.89 ppm), SMILES C=1C=CC=2C=C3C=CC=CC3=CC2C1, Annotation [C14H10]+, Rule of HR False"}, "num_peaks": "21", "compound_name": "Anthracene", "retention_time": null, "retention_index": 1844.4, "precursor_mz": 178.07754, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[74.0151, 117371.0], [75.02296, 245305.0], [76.03077, 632686.0], [87.02297, 236214.0], [88.03078, 347832.0], [89.0386, 507288.0], [91.05425, 130861.0], [126.04636, 128356.0], [149.04478, 126331.0], [150.04637, 641829.0], [151.05415, 403195.0], [152.06195, 1369833.0], [153.06534, 175290.0], [169.06471, 228827.0], [174.04639, 255716.0], [175.05423, 198784.0], [176.06204, 2563053.0], [177.06984, 1182037.0], [178.07754, 11002398.0], [179.080'..b'.06986, 238974.0], [202.07758, 1292332.0], [203.08093, 374439.0], [213.06973, 256631.0], [215.08548, 1220866.0], [216.08881, 217320.0], [224.062, 181393.0], [226.07771, 1503774.0], [227.08588, 1198323.0], [228.09344, 2885510.0], [229.10123, 1791323.0], [230.10886, 17890056.0], [231.11214, 3536976.0], [232.11542, 320231.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C16H10S", "inchikey": "YEUHHUCOSQOCIX-UHFFFAOYSA-N", "smiles": "S1C2=C(C=CC=C2)C2=C1C1=CC=CC=C1C=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": {"91.05425": "Theoretical m/z 91.054775, Mass diff 0 (0 ppm), Formula C7H7", "163.05408": "Theoretical m/z 163.054775, Mass diff 0 (0 ppm), Formula C13H7", "187.05406": "Theoretical m/z 187.054775, Mass diff 0 (0 ppm), Formula C15H7", "189.06969": "Theoretical m/z 189.070425, Mass diff 0 (0 ppm), Formula C15H9", "201.06973": "Theoretical m/z 201.070425, Mass diff 0 (0 ppm), Formula C16H9", "233.04245": "Theoretical m/z 233.042496, Mass diff -0.001 (0 ppm), Formula C16H9S", "234.04965": "Theoretical m/z 234.049775, Mass diff 0 (0.53 ppm), SMILES S1C=2C=CC=CC2C=3C=CC=4C=CC=CC4C13, Annotation [C16H10S]+, Rule of HR False"}, "num_peaks": "23", "compound_name": "Benzo[b]naphtho[2,1-d]thiophene", "retention_time": null, "retention_index": 2419.3, "precursor_mz": 234.04965, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[91.05425, 49130.0], [93.52686, 61653.0], [94.53469, 76638.0], [104.01679, 126871.0], [116.01675, 112547.0], [117.02459, 99108.0], [162.04623, 54491.0], [163.05408, 136418.0], [164.06198, 56321.0], [187.05406, 273349.0], [188.06189, 200750.0], [189.06969, 453336.0], [190.07306, 77884.0], [200.06189, 135620.0], [201.06973, 74692.0], [202.07758, 425058.0], [203.08086, 72058.0], [226.07762, 63460.0], [232.03409, 769638.0], [233.04245, 382457.0], [234.04965, 4404102.0], [235.05304, 725574.0], [236.04547, 251450.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C17H12", "inchikey": "HAPOJKSPCGLOOD-UHFFFAOYSA-N", "smiles": "C1C2=CC=CC=C2C2=C1C=C1C=CC=CC1=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": {"163.05414": "Theoretical m/z 163.054775, Mass diff 0 (0 ppm), Formula C13H7", "187.05412": "Theoretical m/z 187.054775, Mass diff 0 (0 ppm), Formula C15H7", "189.06975": "Theoretical m/z 189.070425, Mass diff 0 (0 ppm), Formula C15H9", "211.05426": "Theoretical m/z 211.054775, Mass diff 0 (0 ppm), Formula C17H7", "213.0699": "Theoretical m/z 213.070425, Mass diff 0 (0 ppm), Formula C17H9", "215.0855": "Theoretical m/z 215.086075, Mass diff 0 (0 ppm), Formula C17H11", "216.09326": "Theoretical m/z 216.093354, Mass diff 0 (0.44 ppm), SMILES C=1C=CC=2C=C3C(=CC2C1)C=4C=CC=CC4C3, Annotation [C17H12]+, Rule of HR False"}, "num_peaks": "21", "compound_name": "2,3-Benzofluorene", "retention_time": null, "retention_index": 2257.5, "precursor_mz": 216.09326, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[93.52689, 122035.0], [94.53471, 241743.0], [95.03638, 42130.0], [105.52688, 47526.0], [106.53471, 171653.0], [107.03639, 60004.0], [107.5425, 180288.0], [108.03385, 97471.0], [163.05414, 68194.0], [187.05412, 167183.0], [188.06201, 86262.0], [189.06975, 239421.0], [190.07321, 37778.0], [211.05426, 117044.0], [212.06215, 60813.0], [213.0699, 808499.0], [214.07317, 202222.0], [215.0855, 3634570.0], [216.09326, 2535030.0], [217.09671, 444170.0], [218.09999, 37976.0]]}], "n_row": 7, "n_col": 7, "row": [0, 1, 2, 3, 4, 5, 6], "col": [0, 1, 2, 3, 4, 5, 6], "data": [[true], [true], [true], [true], [true], [true], [true]], "dtype": [["MetadataMatch_smiles_equal_match", "|b1"]]}\n\\ No newline at end of file\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/scores.json --- a/test-data/scores.json Thu May 25 09:06:00 2023 +0000 +++ b/test-data/scores.json Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -1,1 +1,24885 @@\n-{"__Scores__": true, "similarity_function": {"__Similarity__": "CosineGreedy", "tolerance": 0.1, "mz_power": 0.0, "intensity_power": 1.0}, "is_symmetric": true, "references": [{"ionmode": "negative", "spectrumtype": "Centroid", "num_peaks": "32", "compound_name": "C041", "retention_time": 122.44, "retention_index": 1079.198718, "peaks_json": [[73.0841293753643, 962537.0], [92.9922681974622, 25809589.0], [93.5236243719193, 7832508.0], [93.9918503397022, 4037554.0], [94.9892593290089, 9273560.0], [102.528897846033, 5258508.0], [103.032878700634, 5618676.0], [106.048287181011, 17919228.0], [116.082937025519, 19358163.0], [116.088997408008, 2749072817.0], [116.093789141941, 21174548.0], [117.085953932526, 5958559.0], [117.088526521735, 137197201.0], [117.09226575013, 144026411.0], [117.095343138483, 3078493.0], [118.085738968471, 93658275.0], [118.091857064635, 7792967.0], [118.095506285782, 3082221.0], [120.088840757968, 158124.0], [129.052817882804, 2757896.0], [144.047597981883, 6935455.0], [154.03180616847, 40749504.0], [155.035134922158, 4354801.0], [156.011148185837, 2560241.0], [172.042203916163, 16922092.0], [178.047197818956, 372134.0], [190.107642341182, 143044792.0], [191.109992585577, 20336483.0], [192.104283767627, 9359612.0], [204.050979060253, 4818700.0], [205.059630310281, 24572956.0], [244.042971889438, 1521120.0]]}, {"ionmode": "negative", "spectrumtype": "Centroid", "num_peaks": "19", "compound_name": "C078", "retention_time": 123.01, "retention_index": 1084.222756, "peaks_json": [[75.010394066048, 41579966.0], [76.0137882041242, 2876047.0], [76.0181929768627, 28340717.0], [77.0259504577085, 2087987.0], [78.0338979909698, 183026502.0], [78.5690293876576, 1621521.0], [78.8681599478139, 1487893.0], [79.0376938452989, 30093264.0], [79.0416552579741, 2825081311.0], [79.0447459388332, 28320503.0], [79.0501993561375, 4270687.0], [79.2157179170819, 1455165.0], [79.5185598181509, 1593839.0], [80.0386557190469, 10075569.0], [80.0450063493877, 149614748.0], [81.0483295726077, 3268158.0], [89.9974943554148, 1961794.0], [95.0365701495921, 4214292.0], [96.0443688524812, 20830699.0]]}, {"ionmode": "negative", "spectrumtype": "Centroid", "num_peaks": "12", "compound_name": "C115", "retention_time": 123.7, "retention_index": 1090.304487, "peaks_json": [[77.9912808985361, 1430046.0], [78.0150262817737, 37531039.0], [84.0934034839136, 3045143.0], [85.1012069274801, 7651144.0], [86.1044999837715, 502049.0], [127.023946499139, 21672536.0], [155.015395274682, 50181759.0], [173.025818014551, 19321056.0], [225.059247121035, 54449419.0], [240.031884101672, 47027617.0], [278.105692656594, 44448528.0], [332.077037506685, 36734393.0]]}, {"ionmode": "negative", "spectrumtype": "Centroid", "num_peaks": "20", "compound_name": "C072", "retention_time": 126.02, "retention_index": 1105.809524, "peaks_json": [[75.026123979198, 434239353.0], [76.0294479264598, 10769681.0], [79.0184721827801, 4406598.0], [79.0228409649542, 3040911.0], [86.0420715774215, 69402087.0], [93.9412902191997, 4117357.0], [95.0446916434486, 4401744.0], [95.9392474302401, 3764925.0], [120.033807681496, 1445863.0], [122.943972830176, 4871174.0], [131.088643222278, 12343251.0], [134.108939486662, 1310131.0], [137.026000929413, 1710939.0], [168.950062688366, 1235026.0], [176.091958662459, 68901069.0], [177.09146256329, 9695519.0], [184.040024671153, 13159137.0], [206.084125728074, 4028572.0], [249.138642058545, 13543889.0], [251.137167813194, 1490829.0]]}, {"ionmode": "negative", "spectrumtype": "Centroid", "num_peaks": "26", "compound_name": "C050", "retention_time": 128.53, "retention_index": 1117.761905, "peaks_json": [[72.0264235348245, 4721310.0], [75.0234110401587, 7374271.0], [75.0288404069534, 9420937.0], [86.9717728755449, 9553539.0], [88.9509947069327, 6380434.0], [97.088645546243, 920854.0], [100.00330732202, 18214503.0], [102.073359041231, 484549126.0], [103.002973695426, 21838182.0], [105.0182950443, 11385761.0], [108.947110640446, 3717342.0]'..b' 10\n+ ],\n+ [\n+ 0.02721712700818484,\n+ 2\n+ ],\n+ [\n+ 0.01604776148430577,\n+ 4\n+ ],\n+ [\n+ 0.004643459359286748,\n+ 1\n+ ],\n+ [\n+ 0.06028384723921053,\n+ 5\n+ ],\n+ [\n+ 0.010182216968476942,\n+ 2\n+ ],\n+ [\n+ 0.015514294506382824,\n+ 7\n+ ],\n+ [\n+ 0.006159930050479137,\n+ 1\n+ ],\n+ [\n+ 0.16161703455381496,\n+ 6\n+ ],\n+ [\n+ 0.0040750621823237455,\n+ 1\n+ ],\n+ [\n+ 0.00035959474689346225,\n+ 1\n+ ],\n+ [\n+ 0.004410365100501621,\n+ 1\n+ ],\n+ [\n+ 0.19629045559553993,\n+ 7\n+ ],\n+ [\n+ 2.183361903331013e-05,\n+ 1\n+ ],\n+ [\n+ 0.00874020096442854,\n+ 6\n+ ],\n+ [\n+ 0.05339849611313036,\n+ 3\n+ ],\n+ [\n+ 0.07241757799207088,\n+ 9\n+ ],\n+ [\n+ 1.0,\n+ 57\n+ ],\n+ [\n+ 0.1532083156483457,\n+ 9\n+ ],\n+ [\n+ 0.07254436753789326,\n+ 7\n+ ],\n+ [\n+ 0.001955368426994351,\n+ 2\n+ ],\n+ [\n+ 0.0025872639272902275,\n+ 4\n+ ],\n+ [\n+ 0.0013204445873728583,\n+ 1\n+ ],\n+ [\n+ 0.0038473569260636577,\n+ 2\n+ ],\n+ [\n+ 2.3474291172828106e-05,\n+ 1\n+ ],\n+ [\n+ 0.0026965131583056297,\n+ 1\n+ ],\n+ [\n+ 0.006365332254288743,\n+ 5\n+ ],\n+ [\n+ 0.00029988255581130476,\n+ 1\n+ ],\n+ [\n+ 0.007912892888665144,\n+ 1\n+ ],\n+ [\n+ 0.0010730602771333662,\n+ 1\n+ ],\n+ [\n+ 0.016989615322438187,\n+ 9\n+ ],\n+ [\n+ 0.003161355905982341,\n+ 3\n+ ],\n+ [\n+ 0.0016932596421780554,\n+ 4\n+ ],\n+ [\n+ 0.12277955682638493,\n+ 2\n+ ],\n+ [\n+ 0.0010876843418038634,\n+ 2\n+ ],\n+ [\n+ 0.006154982701162679,\n+ 6\n+ ],\n+ [\n+ 0.008208323843919407,\n+ 3\n+ ],\n+ [\n+ 0.0022656923270095238,\n+ 1\n+ ],\n+ [\n+ 0.00024388889524274332,\n+ 1\n+ ],\n+ [\n+ 0.02730466120239496,\n+ 3\n+ ],\n+ [\n+ 0.0006430820485323683,\n+ 1\n+ ],\n+ [\n+ 0.020922814133647005,\n+ 2\n+ ],\n+ [\n+ 0.02997880004616917,\n+ 1\n+ ],\n+ [\n+ 0.012077049920079725,\n+ 1\n+ ],\n+ [\n+ 0.002011546918083829,\n+ 1\n+ ],\n+ [\n+ 0.01644817444407394,\n+ 3\n+ ],\n+ [\n+ 0.034476184479167796,\n+ 3\n+ ],\n+ [\n+ 0.01192804514810923,\n+ 2\n+ ],\n+ [\n+ 0.0008393606283062712,\n+ 1\n+ ],\n+ [\n+ 0.008295825799065532,\n+ 1\n+ ],\n+ [\n+ 0.004505223629535381,\n+ 3\n+ ],\n+ [\n+ 0.1532083156483457,\n+ 9\n+ ],\n+ [\n+ 1.0,\n+ 43\n+ ]\n+ ],\n+ "dtype": [\n+ [\n+ "CosineGreedy_score",\n+ "<f8"\n+ ],\n+ [\n+ "CosineGreedy_matches",\n+ "<i8"\n+ ]\n+ ]\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/similarity/rcx_exposome_pesticides_subset.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/rcx_exposome_pesticides_subset.msp Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| @@ -0,0 +1,151 @@ +NAME: Acephate +SCANNUMBER: 1161 +RETENTIONTIME: 1.232997 +PRECURSORMZ: 184.0194 +PRECURSORTYPE: [M+H]+ +IONMODE: Positive +SPECTRUMTYPE: Centroid +FORMULA: C4H10NO3PS +INCHIKEY: YASYVMFAVPKPKE-SECBINFHSA-N +INCHI: +SMILES: COP(=O)(N=C(O)C)SC +AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ) +COLLISIONENERGY: +INSTRUMENT: LC Orbitrap Fusion Tribrid MS +INSTRUMENTTYPE: LC-ESI-Orbitrap +IONIZATION: ESI+ +LICENSE: CC BY-NC +COMMENT: +Num Peaks: 16 +90.09368 1128 +93.11512 1241 +95.10279 1118 +101.31465 1152 +102.90688 1322 +103.98039 1201 +112.01607 12289 +112.99994 38027 +115.00399 1634 +124.98121 922 +128.97701 9208 +132.57193 1350 +135.84808 1428 +142.99275 16419 +147.94205 1750 +173.5094 2353 + +NAME: Carbaryl +SCANNUMBER: 2257 +RETENTIONTIME: 5.259445 +PRECURSORMZ: 202.0863 +PRECURSORTYPE: [M+H]+ +IONMODE: Positive +SPECTRUMTYPE: Centroid +FORMULA: C12H11NO2 +INCHIKEY: CVXBEEMKQHEXEN-UHFFFAOYSA-N +INCHI: +SMILES: CN=C(Oc1cccc2c1cccc2)O +AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ) +COLLISIONENERGY: +INSTRUMENT: LC Orbitrap Fusion Tribrid MS +INSTRUMENTTYPE: LC-ESI-Orbitrap +IONIZATION: ESI+ +LICENSE: CC BY-NC +COMMENT: +Num Peaks: 1 +145.06491 1326147 "Theoretical m/z 145.064787, Mass diff 0 (0.85 ppm), SMILES OC1=CC=CC=2C=CC=CC12, Annotation [C10H8O+H]+, Rule of HR True" + +NAME: Dicrotophos +SCANNUMBER: 1516 +RETENTIONTIME: 2.025499 +PRECURSORMZ: 238.0844 +PRECURSORTYPE: [M+H]+ +IONMODE: Positive +SPECTRUMTYPE: Centroid +FORMULA: C8H16NO5P +INCHIKEY: VEENJGZXVHKXNB-UHFFFAOYSA-N +INCHI: +SMILES: COP(=O)(OC(=CC(=O)N(C)C)C)OC +AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ) +COLLISIONENERGY: +INSTRUMENT: LC Orbitrap Fusion Tribrid MS +INSTRUMENTTYPE: LC-ESI-Orbitrap +IONIZATION: ESI+ +LICENSE: CC BY-NC +COMMENT: +Num Peaks: 5 +112.074 102027 +112.07591 9070987 "Theoretical m/z 112.075687, Mass diff 0 (1.99 ppm), SMILES O=C(C=CC)N(C)C, Annotation [C6H11NO-H]+, Rule of HR True" +127.01563 3230337 "Theoretical m/z 127.01547, Mass diff 0 (1.26 ppm), SMILES O=P(O)(OC)OC, Annotation [C2H7O4P+H]+, Rule of HR True" +193.02605 7897744 "Theoretical m/z 193.026035, Mass diff 0 (0.08 ppm), SMILES O=CC=C(OP(=O)(OC)OC)C, Annotation [C6H11O5P-H]+, Rule of HR True" +238.08437 2973124 "Theoretical m/z 238.083891, Mass diff 0 (2.01 ppm), SMILES O=C(C=C(OP(=O)(OC)OC)C)N(C)C, Annotation [C8H16NO5P+H]+, Rule of HR True" + +NAME: Dimethoate +SCANNUMBER: 1865 +RETENTIONTIME: 2.866696 +PRECURSORMZ: 230.0072 +PRECURSORTYPE: [M+H]+ +IONMODE: Positive +SPECTRUMTYPE: Centroid +FORMULA: C5H12NO3PS2 +INCHIKEY: MCWXGJITAZMZEV-UHFFFAOYSA-N +INCHI: +SMILES: CN=C(CSP(=S)(OC)OC)O +AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ) +COLLISIONENERGY: +INSTRUMENT: LC Orbitrap Fusion Tribrid MS +INSTRUMENTTYPE: LC-ESI-Orbitrap +IONIZATION: ESI+ +LICENSE: CC BY-NC +COMMENT: +Num Peaks: 8 +88.0219 548446 "Theoretical m/z 88.021549, Mass diff 0 (3.99 ppm), SMILES SCC=NC, Annotation [C3H7NS-H]+, Rule of HR True" +124.98233 183861 "Theoretical m/z 124.982067, Mass diff 0 (2.11 ppm), SMILES S=P(OC)OC, Annotation [C2H7O2PS-H]+, Rule of HR True" +142.99275 722053 "Theoretical m/z 142.993177, Mass diff 0 (0 ppm), Formula C2H8O3PS" +156.95422 80792 "Theoretical m/z 156.954136, Mass diff 0 (0.54 ppm), SMILES S=P(S)(OC)OC, Annotation [C2H7O2PS2-H]+, Rule of HR True" +170.97 1426256 "Theoretical m/z 170.969791, Mass diff 0 (1.22 ppm), SMILES S=P(OC)(OC)SC, Annotation [C3H9O2PS2-H]+, Rule of HR True" +197.98123 240915 "Theoretical m/z 197.980686, Mass diff 0.001 (2.75 ppm), SMILES S=P(OC)SCC(O)=NC, Annotation [C4H10NO2PS2-H]+, Rule of HR True" +198.96501 5415933 "Theoretical m/z 198.965248, Mass diff 0 (0 ppm), Formula C4H8O3PS2" +230.00722 497851 "Theoretical m/z 230.006895, Mass diff 0 (1.41 ppm), SMILES S=P(OC)(OC)SCC(O)=NC, Annotation [C5H12NO3PS2+H]+, Rule of HR True" + +NAME: Dimethomorph +SCANNUMBER: 3852 +RETENTIONTIME: 7.060486 +PRECURSORMZ: 388.1316 +PRECURSORTYPE: [M+H]+ +IONMODE: Positive +SPECTRUMTYPE: Centroid +FORMULA: C21H22NO4Cl +INCHIKEY: QNBTYORWCCMPQP-UHFFFAOYSA-N +INCHI: +SMILES: COc1cc(ccc1OC)C(=CC(=O)N1CCOCC1)c1ccc(cc1)Cl +AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ) +COLLISIONENERGY: +INSTRUMENT: LC Orbitrap Fusion Tribrid MS +INSTRUMENTTYPE: LC-ESI-Orbitrap +IONIZATION: ESI+ +LICENSE: CC BY-NC +COMMENT: +Num Peaks: 22 +114.05532 468862 "Theoretical m/z 114.054958, Mass diff 0 (3.17 ppm), SMILES O=CN1CCOCC1, Annotation [C5H9NO2-H]+, Rule of HR True" +125.01571 886745 "Theoretical m/z 125.015255, Mass diff 0 (3.64 ppm), SMILES ClC1=CC=C(C=C1)C, Annotation [C7H7Cl-H]+, Rule of HR True" +138.99484 4138370 "Theoretical m/z 138.995067, Mass diff 0 (0 ppm), Formula C7H4ClO" +155.0705 425164 "Theoretical m/z 155.070819, Mass diff 0 (0 ppm), Formula C8H11O3" +165.05519 15513399 "Theoretical m/z 165.055169, Mass diff -0.001 (0 ppm), Formula C9H9O3" +165.06543 350695 +195.08057 386226 "Theoretical m/z 195.08099, Mass diff 0 (0 ppm), Formula C14H11O" +215.0262 490061 "Theoretical m/z 215.026368, Mass diff 0 (0 ppm), Formula C13H8ClO" +223.07544 702025 "Theoretical m/z 223.075837, Mass diff 0 (1.78 ppm), SMILES O=C(C=CC1=CC=C(Cl)C=C1)N(C)CC, Annotation [C12H14ClNO]+, Rule of HR False" +227.02576 230514 "Theoretical m/z 227.026368, Mass diff 0 (0 ppm), Formula C14H8ClO" +229.04225 216308 "Theoretical m/z 229.041467, Mass diff 0.001 (3.42 ppm), SMILES ClC1=CC=C(C=C1)CC2=CC=C(OC)C=C2, Annotation [C14H13ClO-3H]+, Rule of HR True" +235.07555 241142 "Theoretical m/z 235.075842, Mass diff 0 (1.24 ppm), SMILES O=C(C=CC1=CC=C(Cl)C=C1)N(CC)CC, Annotation [C13H16ClNO-2H]+, Rule of HR False" +238.09914 1323577 "Theoretical m/z 238.099317, Mass diff 0 (0.75 ppm), SMILES O=C(C=CC1=CC=C(Cl)C=C1)N(CC)CC, Annotation [C13H16ClNO+H]+, Rule of HR True" +242.04929 2449236 +243.02142 891584 "Theoretical m/z 243.021282, Mass diff -0.001 (0 ppm), Formula C14H8ClO2" +257.03726 578874 "Theoretical m/z 257.036371, Mass diff 0.001 (3.46 ppm), SMILES ClC1=CC=C(C=C1)C(=C)C2=CC=C(OC)C(O)=C2, Annotation [C15H13ClO2-3H]+, Rule of HR True" +258.04443 3232295 +266.0943 358273 "Theoretical m/z 266.093756, Mass diff 0.001 (2.04 ppm), SMILES O=CC=C(C=1C=CC=CC1)C2=CC=C(OC)C(OC)=C2, Annotation [C17H16O3-2H]+, Rule of HR False" +270.04492 608851 +273.06772 3866006 "Theoretical m/z 273.067676, Mass diff 0 (0.16 ppm), SMILES ClC1=CC=C(C=C1)C(=C)C2=CC=C(OC)C(OC)=C2, Annotation [C16H15ClO2-H]+, Rule of HR True" +286.03912 483547 +301.06311 4060551 "Theoretical m/z 301.06261, Mass diff 0 (1.66 ppm), SMILES O=CC=C(C1=CC=C(Cl)C=C1)C2=CC=C(OC)C(OC)=C2, Annotation [C17H15ClO3-H]+, Rule of HR True" |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/similarity/rcx_gc-ei_ms_subset.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/rcx_gc-ei_ms_subset.msp Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -0,0 +1,288 @@\n+NAME: Phenanthrene\n+SCANNUMBER: -1\n+RETENTIONTIME: -1\n+RETENTIONINDEX: 1832.9\n+PRECURSORMZ: 178.0775\n+PRECURSORTYPE: [M]+\n+IONMODE: Positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C14H10\n+INCHIKEY: YNPNZTXNASCQKK-UHFFFAOYSA-N\n+INCHI: \n+SMILES: C1=CC2=C(C=C1)C1=C(C=CC=C1)C=C2\n+AUTHORS: Price et al., RECETOX, Masaryk University (CZ)\n+COLLISIONENERGY: 70eV\n+INSTRUMENT: Q Exactive GC Orbitrap GC-MS/MS\n+INSTRUMENTTYPE: GC-EI-Orbitrap\n+IONIZATION: EI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+Num Peaks: 19\n+74.01508\t137808\t"Theoretical m/z 74.01565, Mass diff 0 (0 ppm), Formula C6H2"\n+75.02295\t278714\t"Theoretical m/z 75.023475, Mass diff 0 (0 ppm), Formula C6H3"\n+76.03075\t608417\t"Theoretical m/z 76.0313, Mass diff 0 (0 ppm), Formula C6H4"\n+87.02295\t304266\t"Theoretical m/z 87.023475, Mass diff 0 (0 ppm), Formula C7H3"\n+88.03076\t497050\t"Theoretical m/z 88.0313, Mass diff 0 (0 ppm), Formula C7H4"\n+89.03857\t441168\t"Theoretical m/z 89.039125, Mass diff 0 (0 ppm), Formula C7H5"\n+98.01511\t150478\n+150.04633\t868927\n+151.05415\t546351\t"Theoretical m/z 151.054775, Mass diff 0 (0 ppm), Formula C12H7"\n+152.0619\t2275502\n+153.06528\t276320\n+169.06468\t272559\n+174.04636\t365846\n+175.05423\t272039\t"Theoretical m/z 175.054775, Mass diff 0 (0 ppm), Formula C14H7"\n+176.062\t3370523\t"Theoretical m/z 176.0626, Mass diff 0 (0 ppm), Formula C14H8"\n+177.06982\t1751846\t"Theoretical m/z 177.070425, Mass diff 0 (0 ppm), Formula C14H9"\n+178.0775\t13724432\t"Theoretical m/z 178.077698, Mass diff 0 (1.11 ppm), SMILES C=1C=CC2=C(C1)C=CC=3C=CC=CC32, Annotation [C14H10]+, Rule of HR False"\n+179.08078\t2250119\n+180.08412\t138203\n+\n+NAME: Anthracene\n+SCANNUMBER: -1\n+RETENTIONTIME: -1\n+RETENTIONINDEX: 1844.4\n+PRECURSORMZ: 178.07754\n+PRECURSORTYPE: [M]+\n+IONMODE: Positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C14H10\n+INCHIKEY: MWPLVEDNUUSJAV-UHFFFAOYSA-N\n+INCHI: \n+SMILES: C1=CC2=CC3=C(C=CC=C3)C=C2C=C1\n+AUTHORS: Price et al., RECETOX, Masaryk University (CZ)\n+COLLISIONENERGY: 70eV\n+INSTRUMENT: Q Exactive GC Orbitrap GC-MS/MS\n+INSTRUMENTTYPE: GC-EI-Orbitrap\n+IONIZATION: EI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+Num Peaks: 21\n+74.0151\t117371\t"Theoretical m/z 74.01565, Mass diff 0 (0 ppm), Formula C6H2"\n+75.02296\t245305\t"Theoretical m/z 75.023475, Mass diff 0 (0 ppm), Formula C6H3"\n+76.03077\t632686\t"Theoretical m/z 76.0313, Mass diff 0 (0 ppm), Formula C6H4"\n+87.02297\t236214\t"Theoretical m/z 87.023475, Mass diff 0 (0 ppm), Formula C7H3"\n+88.03078\t347832\t"Theoretical m/z 88.0313, Mass diff 0 (0 ppm), Formula C7H4"\n+89.0386\t507288\t"Theoretical m/z 89.039125, Mass diff 0 (0 ppm), Formula C7H5"\n+91.05425\t130861\t"Theoretical m/z 91.054775, Mass diff 0 (0 ppm), Formula C7H7"\n+126.04636\t128356\n+149.04478\t126331\n+150.04637\t641829\n+151.05415\t403195\t"Theoretical m/z 151.054775, Mass diff 0 (0 ppm), Formula C12H7"\n+152.06195\t1369833\n+153.06534\t175290\n+169.06471\t228827\n+174.04639\t255716\n+175.05423\t198784\t"Theoretical m/z 175.054775, Mass diff 0 (0 ppm), Formula C14H7"\n+176.06204\t2563053\t"Theoretical m/z 176.0626, Mass diff 0 (0 ppm), Formula C14H8"\n+177.06984\t1182037\t"Theoretical m/z 177.070425, Mass diff 0 (0 ppm), Formula C14H9"\n+178.07754\t11002398\t"Theoretical m/z 178.077698, Mass diff 0 (0.89 ppm), SMILES C=1C=CC=2C=C3C=CC=CC3=CC2C1, Annotation [C14H10]+, Rule of HR False"\n+179.08081\t1778803\n+180.08418\t132922\n+\n+NAME: Fluoranthene\n+SCANNUMBER: -1\n+RETENTIONTIME: -1\n+RETENTIONINDEX: 2102.7\n+PRECURSORMZ: 202.07756\n+PRECURSORTYPE: [M]+\n+IONMODE: Positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C16H10\n+INCHIKEY: GVEPBJHOBDJJJI-UHFFFAOYSA-N\n+INCHI: \n+SMILES: C1=CC2=C(C=C1)C1=C3C2=CC=CC3=CC=C1\n+AUTHORS: Price et al., RECETOX, Masaryk University (CZ)\n+COLLISIONENERGY: 70eV\n+INSTRUMENT: Q Exactive GC Orbitrap GC-MS/MS\n+INSTRUMENTTYPE: GC-EI-Orbitrap\n+IONIZATION: EI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+Num Peaks: 17\n+75.02299\t112456\t"Theoretical m/z 75.023475, Mass diff 0 (0 ppm), Formula C6H3"\n+87.02298\t183640\t"Theoretical m/z 87.023475, Mass diff 0 (0 ppm), Formula C7H3"\n+88.03079\t367434\t"Theoretical m/z 88.0313, Mas'..b'046\t"Theoretical m/z 128.0626, Mass diff 0 (0 ppm), Formula C10H8"\n+151.05412\t266397\t"Theoretical m/z 151.054775, Mass diff 0 (0 ppm), Formula C12H7"\n+152.06195\t961184\n+153.06976\t409346\t"Theoretical m/z 153.069873, Mass diff 0 (0.74 ppm), SMILES *C=1C=CC(=CC1)C=2C=CC=CC2, Annotation [C12H10-H]+, Rule of HR True"\n+176.06192\t232793\t"Theoretical m/z 176.0626, Mass diff 0 (0 ppm), Formula C14H8"\n+189.06972\t408734\t"Theoretical m/z 189.070425, Mass diff 0 (0 ppm), Formula C15H9"\n+200.0619\t342984\n+201.06986\t238974\t"Theoretical m/z 201.070425, Mass diff 0 (0 ppm), Formula C16H9"\n+202.07758\t1292332\n+203.08093\t374439\n+213.06973\t256631\t"Theoretical m/z 213.070425, Mass diff 0 (0 ppm), Formula C17H9"\n+215.08548\t1220866\t"Theoretical m/z 215.086075, Mass diff 0 (0 ppm), Formula C17H11"\n+216.08881\t217320\n+224.062\t181393\n+226.07771\t1503774\n+227.08588\t1198323\t"Theoretical m/z 227.086075, Mass diff 0 (0 ppm), Formula C18H11"\n+228.09344\t2885510\n+229.10123\t1791323\n+230.10886\t17890056\t"Theoretical m/z 230.108994, Mass diff 0 (0.58 ppm), SMILES C=1C=CC(=CC1)C=2C=CC(=CC2)C=3C=CC=CC3, Annotation [C18H14]+, Rule of HR False"\n+231.11214\t3536976\n+232.11542\t320231\n+\n+NAME: Benzo[b]naphtho[2,1-d]thiophene\n+SCANNUMBER: -1\n+RETENTIONTIME: -1\n+RETENTIONINDEX: 2419.3\n+PRECURSORMZ: 234.04965\n+PRECURSORTYPE: [M]+\n+IONMODE: Positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C16H10S\n+INCHIKEY: YEUHHUCOSQOCIX-UHFFFAOYSA-N\n+INCHI: \n+SMILES: S1C2=C(C=CC=C2)C2=C1C1=CC=CC=C1C=C2\n+AUTHORS: Price et al., RECETOX, Masaryk University (CZ)\n+COLLISIONENERGY: 70eV\n+INSTRUMENT: Q Exactive GC Orbitrap GC-MS/MS\n+INSTRUMENTTYPE: GC-EI-Orbitrap\n+IONIZATION: EI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+Num Peaks: 23\n+91.05425\t49130\t"Theoretical m/z 91.054775, Mass diff 0 (0 ppm), Formula C7H7"\n+93.52686\t61653\n+94.53469\t76638\n+104.01679\t126871\n+116.01675\t112547\n+117.02459\t99108\n+162.04623\t54491\n+163.05408\t136418\t"Theoretical m/z 163.054775, Mass diff 0 (0 ppm), Formula C13H7"\n+164.06198\t56321\n+187.05406\t273349\t"Theoretical m/z 187.054775, Mass diff 0 (0 ppm), Formula C15H7"\n+188.06189\t200750\n+189.06969\t453336\t"Theoretical m/z 189.070425, Mass diff 0 (0 ppm), Formula C15H9"\n+190.07306\t77884\n+200.06189\t135620\n+201.06973\t74692\t"Theoretical m/z 201.070425, Mass diff 0 (0 ppm), Formula C16H9"\n+202.07758\t425058\n+203.08086\t72058\n+226.07762\t63460\n+232.03409\t769638\n+233.04245\t382457\t"Theoretical m/z 233.042496, Mass diff -0.001 (0 ppm), Formula C16H9S"\n+234.04965\t4404102\t"Theoretical m/z 234.049775, Mass diff 0 (0.53 ppm), SMILES S1C=2C=CC=CC2C=3C=CC=4C=CC=CC4C13, Annotation [C16H10S]+, Rule of HR False"\n+235.05304\t725574\n+236.04547\t251450\n+\n+NAME: 2,3-Benzofluorene\n+SCANNUMBER: -1\n+RETENTIONTIME: -1\n+RETENTIONINDEX: 2257.5\n+PRECURSORMZ: 216.09326\n+PRECURSORTYPE: [M]+\n+IONMODE: Positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C17H12\n+INCHIKEY: HAPOJKSPCGLOOD-UHFFFAOYSA-N\n+INCHI: \n+SMILES: C1C2=CC=CC=C2C2=C1C=C1C=CC=CC1=C2\n+AUTHORS: Price et al., RECETOX, Masaryk University (CZ)\n+COLLISIONENERGY: 70eV\n+INSTRUMENT: Q Exactive GC Orbitrap GC-MS/MS\n+INSTRUMENTTYPE: GC-EI-Orbitrap\n+IONIZATION: EI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+Num Peaks: 21\n+93.52689\t122035\n+94.53471\t241743\n+95.03638\t42130\n+105.52688\t47526\n+106.53471\t171653\n+107.03639\t60004\n+107.5425\t180288\n+108.03385\t97471\n+163.05414\t68194\t"Theoretical m/z 163.054775, Mass diff 0 (0 ppm), Formula C13H7"\n+187.05412\t167183\t"Theoretical m/z 187.054775, Mass diff 0 (0 ppm), Formula C15H7"\n+188.06201\t86262\n+189.06975\t239421\t"Theoretical m/z 189.070425, Mass diff 0 (0 ppm), Formula C15H9"\n+190.07321\t37778\n+211.05426\t117044\t"Theoretical m/z 211.054775, Mass diff 0 (0 ppm), Formula C17H7"\n+212.06215\t60813\n+213.0699\t808499\t"Theoretical m/z 213.070425, Mass diff 0 (0 ppm), Formula C17H9"\n+214.07317\t202222\n+215.0855\t3634570\t"Theoretical m/z 215.086075, Mass diff 0 (0 ppm), Formula C17H11"\n+216.09326\t2535030\t"Theoretical m/z 216.093354, Mass diff 0 (0.44 ppm), SMILES C=1C=CC=2C=C3C(=CC2C1)C=4C=CC=CC4C3, Annotation [C17H12]+, Rule of HR False"\n+217.09671\t444170\n+218.09999\t37976\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/similarity/scores_test1_out.json --- a/test-data/similarity/scores_test1_out.json Thu May 25 09:06:00 2023 +0000 +++ b/test-data/similarity/scores_test1_out.json Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -1,1 +1,1 @@\n-{"__Scores__": true, "similarity_function": {"__Similarity__": "CosineGreedy", "tolerance": 0.1, "mz_power": 0.0, "intensity_power": 1.0}, "is_symmetric": false, "references": [{"ionmode": "negative", "spectrumtype": "Centroid", "num_peaks": "57", "compound_name": "C001", "retention_time": 38.74, "retention_index": null, "peaks_json": [[138.9121, 10186226.0], [148.9337, 1008656.0], [175.0641, 26780143.0], [186.1095, 2675456.0], [196.8658, 21390430.0], [198.8647, 21688594.0], [200.8848, 7742528.0], [206.9034, 26130980.0], [216.9205, 32607700.0], [234.0134, 2550129.0], [254.8252, 23747536.0], [256.8215, 31377637.0], [258.8237, 15532799.0], [266.8652, 9805546.0], [268.8537, 3090354.0], [306.9914, 3169316.0], [312.7841, 10051801.0], [316.7777, 10734168.0], [322.8157, 6317648.0], [324.9549, 8619910.0], [334.849, 4178412.0], [342.8093, 3285552.0], [349.9455, 2050695.0], [350.9875, 6150799.0], [351.941, 1965882.0], [366.8281, 3253770.0], [370.7418, 9765463.0], [372.7383, 19374863.0], [382.8218, 12815572.0], [384.8177, 8311500.0], [392.7685, 10913351.0], [413.2664, 3965867.0], [426.7772, 5431633.0], [428.7834, 8554675.0], [434.7287, 9943329.0], [436.8161, 3705247.0], [440.7322, 10603010.0], [442.7401, 8271752.0], [450.7016, 8762673.0], [460.7076, 4528973.0], [462.7862, 2123666.0], [484.7242, 4273989.0], [486.7743, 4886062.0], [488.6825, 12267966.0], [492.744, 7662344.0], [494.8953, 7188793.0], [498.8794, 6811405.0], [500.8484, 6520691.0], [502.7832, 3567833.0], [510.763, 4989757.0], [518.7415, 4243468.0], [546.6093, 7177067.0], [550.6949, 6104789.0], [566.5977, 5171811.0], [612.6927, 2005587.0], [676.6436, 1982714.0], [800.4451, 2792137.0]]}, {"ionmode": "negative", "spectrumtype": "Centroid", "num_peaks": "35", "compound_name": "C002", "retention_time": 520.25, "retention_index": null, "peaks_json": [[131.1733, 1971789.0], [267.2688, 6103973.0], [279.0196, 1946255.0], [289.6491, 46498377.0], [301.1565, 15185412.0], [309.1649, 18045974.0], [310.1623, 295359836.0], [311.1658, 13124727.0], [312.0296, 38757284.0], [330.6757, 12666597.0], [525.375, 1073323842.0], [526.3783, 181668883.0], [527.3812, 23642795.0], [551.3321, 111616808.0], [552.3348, 28340614.0], [553.3314, 2609936.0], [562.3269, 7538206.0], [578.2905, 7578406.0], [619.3008, 4742103.0], [624.296, 11790213.0], [813.5403, 25060147.0], [814.5336, 5865975.0], [955.1171, 2322927.0], [1047.7378, 150394804.0], [1048.7399, 90978863.0], [1049.7432, 29946438.0], [1050.7453, 6807767.0], [1069.7158, 5074652.0], [1074.1979, 3402288.0], [1075.1968, 33352763.0], [1076.2004, 10417953.0], [1101.6535, 2023916.0], [1206.3127, 3738816.0], [1216.8041, 4439324.0], [1217.807, 3565334.0]]}, {"ionmode": "negative", "spectrumtype": "Centroid", "num_peaks": "26", "compound_name": "C003", "retention_time": 483.67, "retention_index": null, "peaks_json": [[265.2529, 11366224.0], [266.2564, 1420444.0], [279.6362, 29849749.0], [280.6546, 8848921.0], [288.6414, 202172046.0], [378.2093, 15309961.0], [379.1966, 2902366.0], [522.3565, 4089569222.0], [523.354, 1201714423.0], [549.3267, 63300808.0], [576.2749, 7386007.0], [577.3074, 2354251.0], [617.2778, 2323470.0], [625.4543, 4040374.0], [796.9808, 13576738.0], [797.9841, 6368973.0], [809.9883, 12596682.0], [810.9916, 6601055.0], [1043.7028, 144351468.0], [1044.7068, 83271854.0], [1045.706, 27998321.0], [1046.7131, 6505178.0], [1058.1594, 20718345.0], [1059.1626, 6608764.0], [1071.1639, 15461047.0], [1072.1671, 5096642.0]]}, {"ionmode": "negative", "spectrumtype": "Centroid", "num_peaks": "24", "compound_name": "C004", "retention_time": 473.48, "retention_index": null, "peaks_json": [[124.1405, 6517662.0], [170.2437, 1237313.0], [275.6336, 28001849.0], [296.147, 190395687.0], [482.3247, 145772322.0], [483.3283, 36245876.0], [496.34, 12577588056.0], [497.3442, 3337125302.0], [498.3462, 532285213.0], [499.3493, 68176083.0], [770.964, 49250157.0], [771.9675, 22666873.0], [783.9721, 9839299.0], [784.9749, 3622908.0], [949.6233, 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30, 6, 10, 19, 21, 22, 31, 38, 1, 2, 5, 14, 15, 18, 20, 21, 22, 23, 24, 27, 40, 43, 49, 50, 28, 38], "data": [[0.0018399092347892974, 1], [0.0003737432507248734, 2], [0.002261095921649124, 1], [0.0006772781844061508, 1], [0.005210287483991151, 3], [0.0011367653250466707, 1], [0.0005519181707221115, 1], [0.0019222675998802402, 1], [0.006361969507425509, 2], [0.020274153669902494, 3], [0.017517104899474972, 1], [0.011955078756829818, 2], [0.011381869280662654, 2], [0.040543958124585944, 1], [0.0008178767212134002, 1], [0.005670274191001168, 1], [0.017313471143856486, 2], [0.0008514601258333194, 1], [0.026334935904595114, 1], [0.00039771420418687587, 1], [4.920409691033264e-05, 1], [0.0013688419859179705, 1], [0.0012932520287310416, 1], [0.0010350795213821488, 1], [0.005220131896413382, 2], [0.00041700791188063903, 2], [0.00042911042717726856, 3], [0.00810426228305399, 1], [0.0017914424466763802, 1], [0.000558207243274732, 1], [3.0727899170534577e-06, 1], [0.001200605516845171, 1], [0.016205568468406192, 3], [0.0003490131371939824, 1], [0.0012777731679730743, 1], [1.5186307992169529e-05, 1], [0.0009349245322469299, 3], [0.0002621230171312692, 1], [0.0004253169742294291, 1], [6.58229030248094e-05, 1], [2.446654442400292e-05, 1], [2.158432356442278e-05, 1], [1.042176430293052e-06, 1], [1.0756853043872807e-05, 2], [1.0328107820449307e-06, 1], [0.0011763296355585277, 1], [0.0015107038247838176, 2], [0.0005521035532025616, 1], [0.006960910397590913, 1], [0.008227393532896343, 3], [0.003108683139316554, 1], [0.007409589227651824, 1], [0.09234973475736206, 1], [0.022252246905890102, 4], [0.019737608617704024, 1], [0.00031096878396815933, 1], [0.0345091397314379, 1], [0.11775324981062069, 1], [0.28004814632763314, 3], [0.026281168576484135, 1], [0.0018303163274005687, 1], [0.0008172798650456041, 1], [0.06035755813969004, 3], [0.011673031727211581, 2], [1.9721604555814565e-05, 1], [0.00039664571613187715, 1]], "dtype": [["CosineGreedy_score", "<f8"], ["CosineGreedy_matches", "<i8"]]}\n\\ No newline at end of file\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/similarity/scores_test2_out.json --- a/test-data/similarity/scores_test2_out.json Thu May 25 09:06:00 2023 +0000 +++ b/test-data/similarity/scores_test2_out.json Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -1,1 +1,1 @@\n-{"__Scores__": true, "similarity_function": {"__Similarity__": "CosineGreedy", "tolerance": 0.1, "mz_power": 0.0, "intensity_power": 1.0}, "is_symmetric": false, "references": [{"scannumber": "1161", "precursortype": "[M+H]+", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C4H10NO3PS", "inchikey": "YASYVMFAVPKPKE-SECBINFHSA-N", "inchi": "", "smiles": "COP(=O)(N=C(O)C)SC", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "instrumenttype": "LC-ESI-Orbitrap", "ionization": "ESI+", "license": "CC BY-NC", "comment": "", "num_peaks": "16", "compound_name": "Acephate", "retention_time": 1.232997, "precursor_mz": 184.0194, "collision_energy": "", "peaks_json": [[90.09368, 1128.0], [93.11512, 1241.0], [95.10279, 1118.0], [101.31465, 1152.0], [102.90688, 1322.0], [103.98039, 1201.0], [112.01607, 12289.0], [112.99994, 38027.0], [115.00399, 1634.0], [124.98121, 922.0], [128.97701, 9208.0], [132.57193, 1350.0], [135.84808, 1428.0], [142.99275, 16419.0], [147.94205, 1750.0], [173.5094, 2353.0]]}, {"scannumber": "2257", "precursortype": "[M+H]+", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C12H11NO2", "inchikey": "CVXBEEMKQHEXEN-UHFFFAOYSA-N", "inchi": "", "smiles": "CN=C(Oc1cccc2c1cccc2)O", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "instrumenttype": "LC-ESI-Orbitrap", "ionization": "ESI+", "license": "CC BY-NC", "comment": "", "peak_comments": {"145.06491": "Theoretical m/z 145.064787, Mass diff 0 (0.85 ppm), SMILES OC1=CC=CC=2C=CC=CC12, Annotation [C10H8O+H]+, Rule of HR True"}, "num_peaks": "1", "compound_name": "Carbaryl", "retention_time": 5.259445, "precursor_mz": 202.0863, "collision_energy": "", "peaks_json": [[145.06491, 1326147.0]]}, {"scannumber": "1516", "precursortype": "[M+H]+", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C8H16NO5P", "inchikey": "VEENJGZXVHKXNB-UHFFFAOYSA-N", "inchi": "", "smiles": "COP(=O)(OC(=CC(=O)N(C)C)C)OC", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "instrumenttype": "LC-ESI-Orbitrap", "ionization": "ESI+", "license": "CC BY-NC", "comment": "", "peak_comments": {"112.07591": "Theoretical m/z 112.075687, Mass diff 0 (1.99 ppm), SMILES O=C(C=CC)N(C)C, Annotation [C6H11NO-H]+, Rule of HR True", "127.01563": "Theoretical m/z 127.01547, Mass diff 0 (1.26 ppm), SMILES O=P(O)(OC)OC, Annotation [C2H7O4P+H]+, Rule of HR True", "193.02605": "Theoretical m/z 193.026035, Mass diff 0 (0.08 ppm), SMILES O=CC=C(OP(=O)(OC)OC)C, Annotation [C6H11O5P-H]+, Rule of HR True", "238.08437": "Theoretical m/z 238.083891, Mass diff 0 (2.01 ppm), SMILES O=C(C=C(OP(=O)(OC)OC)C)N(C)C, Annotation [C8H16NO5P+H]+, Rule of HR True"}, "num_peaks": "5", "compound_name": "Dicrotophos", "retention_time": 2.025499, "precursor_mz": 238.0844, "collision_energy": "", "peaks_json": [[112.074, 102027.0], [112.07591, 9070987.0], [127.01563, 3230337.0], [193.02605, 7897744.0], [238.08437, 2973124.0]]}, {"scannumber": "1865", "precursortype": "[M+H]+", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C5H12NO3PS2", "inchikey": "MCWXGJITAZMZEV-UHFFFAOYSA-N", "inchi": "", "smiles": "CN=C(CSP(=S)(OC)OC)O", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "instrumenttype": "LC-ESI-Orbitrap", "ionization": "ESI+", "license": "CC BY-NC", "comment": "", "peak_comments": {"88.0219": "Theoretical m/z 88.021549, Mass diff 0 (3.99 ppm), SMILES SCC=NC, Annotation [C3H7NS-H]+, Rule of HR True", "124.98233": "Theoretical m/z 124.982067, Mass diff 0 (2.11 ppm), SMILES S=P(OC)OC, Annotation [C2H7O2PS-H]+, Rule of HR True", "142.99275": "Theoretical m/z 142.993177, Mass diff 0 (0 ppm), Formula C2H8O3PS", "156.95422": "Theoretical m/z 156.954136, Mass diff 0'..b'04730671174696972, 3], [0.2905090298183795, 5], [0.0007786069695307855, 1], [0.0005160257799646218, 2], [0.00038736811468175473, 3], [0.004167449964456371, 2], [0.002043269072734401, 2], [0.0007317319771959746, 4], [1.9838321402668794e-05, 1], [8.801820482468617e-06, 1], [9.255871433471165e-05, 1], [0.00027188763979513214, 1], [4.4947603414879724e-05, 1], [0.009400379409723776, 2], [0.005755388742032419, 5], [0.0007186188027915625, 4], [0.0002820277712237843, 1], [0.0021840777388529727, 3], [0.0021623907785408305, 3], [0.0007283436921234106, 1], [0.0008441009586501761, 1], [0.0002073559764999649, 1], [0.0007416252801498897, 1], [0.00015068661266851979, 1], [8.813547345301928e-05, 1], [9.26696450737907e-05, 1], [0.001547967118838771, 1], [0.05550228874171714, 5], [0.02125475011618532, 3], [0.011654725377056363, 2], [0.048940875059941075, 1], [0.09674974767603109, 4], [0.00012831189436302386, 1], [0.01967432143668846, 1], [0.01205243016929935, 1], [0.0023135823935159366, 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[0.018417594020478472, 1], [0.010756665957563824, 1], [0.015590543256883976, 2], [0.04566648744942041, 1], [5.931306182041711e-06, 1], [0.03353471802351476, 2], [0.0016641176911516493, 1], [0.011667998101389831, 2], [0.00013501455706461823, 2], [0.0005641822404665421, 1], [0.013565745106156183, 3], [0.0022081590773529217, 2], [2.755827193743529e-05, 1], [0.0007386957430155464, 1], [0.004966786726868895, 2], [0.0010661461087560196, 2], [0.001063292846857611, 1], [0.000606881881809848, 1], [0.002186896434193792, 1], [0.12865769017257328, 1], [0.028190890883599714, 4], [0.0005044163468766756, 1], [0.002886337967280529, 1], [0.0559715028711476, 1], [0.0002158797917780897, 1], [0.00620360880796666, 2], [0.0007355365822429641, 3], [0.0007942591768873767, 1], [0.00010209303249019821, 2], [0.00019287244985231734, 1], [0.00016324733223990588, 2], [9.721355793156336e-06, 1], [4.652016835129338e-05, 1], [0.019877538355056665, 1], [0.0021026011257930747, 1], [0.0008375181541441654, 3], [2.8019476783829662e-05, 1], [0.00126319178728046, 2], [0.033408666281750724, 1], [0.00022237422701605942, 1], [0.002265272552324613, 1], [0.000234866112352408, 1], [0.0009646911431102235, 2], [0.0001427118212822249, 1], [0.0015640758643172626, 1], [0.027845060459883365, 1], [0.0005869184307697094, 1], [0.002177606309783109, 1], [0.0011879375171201744, 2], [0.00024257932792313028, 2], [0.029015752159248828, 1], [0.012882620708157606, 1], [0.09087822963404141, 1], [0.016369110194600803, 2], [0.0009837491848604097, 1], [0.0010871277430062854, 1], [0.006379222433724256, 2], [0.07844880045683728, 1], [0.003552995338630374, 1], [0.00675497126450081, 1], [0.020492592767589624, 1], [0.0004882302811255579, 1], [0.03692178564115823, 1], [0.05107327151527259, 1], [0.0013454548424030402, 1], [0.00023077527573114648, 1], [0.0034920044529350115, 1], [0.05588674606358348, 1], [0.10402095547417871, 1], [0.004711174266112351, 1]], "dtype": [["CosineGreedy_score", "<f8"], ["CosineGreedy_matches", "<i8"]]}\n\\ No newline at end of file\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/similarity/scores_test3_out.json --- a/test-data/similarity/scores_test3_out.json Thu May 25 09:06:00 2023 +0000 +++ b/test-data/similarity/scores_test3_out.json Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -1,1 +1,1 @@\n-{"__Scores__": true, "similarity_function": {"__Similarity__": "CosineHungarian", "tolerance": 0.1, "mz_power": 0.0, "intensity_power": 1.0}, "is_symmetric": false, "references": [{"ionmode": "negative", "spectrumtype": "Centroid", "num_peaks": "57", "compound_name": "C001", "retention_time": 38.74, "retention_index": null, "peaks_json": [[138.9121, 10186226.0], [148.9337, 1008656.0], [175.0641, 26780143.0], [186.1095, 2675456.0], [196.8658, 21390430.0], [198.8647, 21688594.0], [200.8848, 7742528.0], [206.9034, 26130980.0], [216.9205, 32607700.0], [234.0134, 2550129.0], [254.8252, 23747536.0], [256.8215, 31377637.0], [258.8237, 15532799.0], [266.8652, 9805546.0], [268.8537, 3090354.0], [306.9914, 3169316.0], [312.7841, 10051801.0], [316.7777, 10734168.0], [322.8157, 6317648.0], [324.9549, 8619910.0], [334.849, 4178412.0], [342.8093, 3285552.0], [349.9455, 2050695.0], [350.9875, 6150799.0], [351.941, 1965882.0], [366.8281, 3253770.0], [370.7418, 9765463.0], [372.7383, 19374863.0], [382.8218, 12815572.0], [384.8177, 8311500.0], [392.7685, 10913351.0], [413.2664, 3965867.0], [426.7772, 5431633.0], [428.7834, 8554675.0], [434.7287, 9943329.0], [436.8161, 3705247.0], [440.7322, 10603010.0], [442.7401, 8271752.0], [450.7016, 8762673.0], [460.7076, 4528973.0], [462.7862, 2123666.0], [484.7242, 4273989.0], [486.7743, 4886062.0], [488.6825, 12267966.0], [492.744, 7662344.0], [494.8953, 7188793.0], [498.8794, 6811405.0], [500.8484, 6520691.0], [502.7832, 3567833.0], [510.763, 4989757.0], [518.7415, 4243468.0], [546.6093, 7177067.0], [550.6949, 6104789.0], [566.5977, 5171811.0], [612.6927, 2005587.0], [676.6436, 1982714.0], [800.4451, 2792137.0]]}, {"ionmode": "negative", "spectrumtype": "Centroid", "num_peaks": "35", "compound_name": "C002", "retention_time": 520.25, "retention_index": null, "peaks_json": [[131.1733, 1971789.0], [267.2688, 6103973.0], [279.0196, 1946255.0], [289.6491, 46498377.0], [301.1565, 15185412.0], [309.1649, 18045974.0], 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[949.6233, 8009033.0], [950'..b'312.986211377174, 2448284.0], [313.019993142226, 1479514.0], [326.982724315442, 4863722.0], [344.975776862771, 10267994.0], [345.976092174038, 3016933.0], [346.046486912175, 1754291.0], [346.973191534072, 1590963.0], [382.97408022551, 1514772.0], [386.969422084375, 2096957.0], [402.964369782575, 1172149.0], [493.152823320977, 2513229.0]]}, {"ionmode": "negative", "spectrumtype": "Centroid", "num_peaks": "57", "compound_name": "C012", "retention_time": 687.83, "retention_index": 4134.613095, "peaks_json": [[78.0419846383593, 1742200.0], [79.0497716096318, 1893817.0], [85.0284186196566, 2191757.0], [121.046741626167, 6162741.0], [142.078087888737, 3381352.0], [192.997735629267, 9539743.0], [195.029110650825, 3772846.0], [205.016711322548, 5926636.0], [207.066696618797, 3714385.0], [209.098935410027, 6173585.0], [213.05754958053, 13341991.0], [219.06802937228, 2601724.0], [253.016653119059, 43935840.0], [269.047850642358, 4644691.0], [271.027137265637, 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13026182.0], [477.140480798609, 4944561.0], [478.141485242814, 1506934.0], [479.101672410454, 3603024.0], [490.12632015072, 18188437.0], [491.122346777972, 10290558.0], [549.162553092955, 24746614.0], [563.144239233773, 12735845.0], [624.183209223215, 7134906.0], [637.164550513183, 3866368.0], [698.205944560218, 1919968.0]]}, {"ionmode": "negative", "spectrumtype": "Centroid", "num_peaks": "43", "compound_name": "C020", "retention_time": 687.99, "retention_index": 4135.089286, "peaks_json": [[109.052235628516, 1922885.0], [111.044058476785, 1730416.0], [133.064909307365, 1579533.0], [137.041722086745, 2474039.0], [194.053642118165, 5252308.0], [212.061782732582, 10437319.0], [267.034768010352, 4429084.0], [267.068824022318, 27744081.0], [268.069192256745, 2367920.0], [310.970568727813, 3126083.0], [311.004219192148, 2666091.0], [325.055731606087, 7634729.0], [327.965549188207, 5442532.0], [328.962716535303, 2722019.0], [339.03821058645, 6627839.0], [341.051986399316, 1671451.0], [342.996634492902, 3939816.0], [345.115297423962, 3938049.0], [358.067243216398, 3526875.0], [361.025211906011, 6516476.0], [388.003000430725, 3422825.0], [388.073272089579, 4224454.0], [399.005054559559, 4141766.0], [401.984326631505, 5585170.0], [402.98179623463, 3562508.0], [416.036473280551, 7221552.0], [417.033665098569, 4129234.0], [417.087073648909, 1945166.0], [418.994970709551, 2648178.0], [430.088321970134, 10765018.0], [431.085366629672, 6887942.0], [473.09370665615, 2502410.0], [475.002854889036, 2969642.0], [475.14184210128, 30625723.0], [477.070907310139, 2271450.0], [489.055479984185, 1973511.0], [503.107930410573, 2407435.0], [549.092119293556, 2513579.0], [552.160354111203, 1673065.0], [565.143723544965, 3485979.0], [610.132183060405, 1997085.0], [625.181479977537, 3872339.0], [697.202597429349, 2820429.0]]}], "n_row": 6, "n_col": 51, "row": [], "col": [], "data": [], "dtype": [["CosineHungarian_score", "<f8"], ["CosineHungarian_matches", "<i8"], ["MetadataMatch_MetadataMatch", "<f8"]]}\n\\ No newline at end of file\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/similarity/scores_test4_out.json --- a/test-data/similarity/scores_test4_out.json Thu May 25 09:06:00 2023 +0000 +++ b/test-data/similarity/scores_test4_out.json Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -1,1 +1,1 @@\n-{"__Scores__": true, "similarity_function": {"__Similarity__": "NeutralLossesCosine", "tolerance": 0.1, "mz_power": 0.0, "intensity_power": 1.0, "ignore_peaks_above_precursor": true}, "is_symmetric": true, "references": [{"scannumber": "-1", "precursortype": "[M]+", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C20H12", "inchikey": "CSHWQDPOILHKBI-UHFFFAOYSA-N", "inchi": "", "smiles": "C1=CC2=C3C(=C1)C1=CC=CC4=C1C(=CC=C4)C3=CC=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "instrumenttype": "GC-EI-Orbitrap", "ionization": "EI+", "license": "CC BY-NC", "comment": "", "peak_comments": {"113.03854": "Theoretical m/z 113.039125, Mass diff 0 (0 ppm), Formula C9H5", "125.03855": "Theoretical m/z 125.039125, Mass diff 0 (0 ppm), Formula C10H5", "249.07072": "Theoretical m/z 249.070425, Mass diff -0.001 (0 ppm), Formula C20H9", "252.09323": "Theoretical m/z 252.093354, Mass diff 0 (0.49 ppm), SMILES C1=CC=2C=CC=C3C4=CC=CC5=CC=CC(C(=C1)C23)=C54, Annotation [C20H12]+, Rule of HR False"}, "num_peaks": "19", "compound_name": "Perylene", "retention_time": null, "retention_index": 2886.9, "precursor_mz": 252.09323, "collision_energy": "70eV", "peaks_json": [[112.03071, 49892.0], [113.03854, 87510.0], [124.03076, 100146.0], [124.53242, 24923.0], [125.03855, 179254.0], [125.54019, 49039.0], [126.04636, 131679.0], [126.54804, 36313.0], [222.04645, 28905.0], [224.06192, 55632.0], [226.04175, 37413.0], [246.04646, 23286.0], [248.06204, 140007.0], [249.07072, 62236.0], [250.07765, 641789.0], [251.07967, 137600.0], [252.09323, 1955166.0], [253.09656, 402252.0], [254.09985, 39987.0]]}, {"scannumber": "-1", "precursortype": "[M]+", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C14H10", "inchikey": "YNPNZTXNASCQKK-UHFFFAOYSA-N", "inchi": "", "smiles": "C1=CC2=C(C=C1)C1=C(C=CC=C1)C=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "instrumenttype": "GC-EI-Orbitrap", "ionization": "EI+", "license": "CC BY-NC", "comment": "", "peak_comments": {"74.01508": "Theoretical m/z 74.01565, Mass diff 0 (0 ppm), Formula C6H2", "75.02295": "Theoretical m/z 75.023475, Mass diff 0 (0 ppm), Formula C6H3", "76.03075": "Theoretical m/z 76.0313, Mass diff 0 (0 ppm), Formula C6H4", "87.02295": "Theoretical m/z 87.023475, Mass diff 0 (0 ppm), Formula C7H3", "88.03076": "Theoretical m/z 88.0313, Mass diff 0 (0 ppm), Formula C7H4", "89.03857": "Theoretical m/z 89.039125, Mass diff 0 (0 ppm), Formula C7H5", "151.05415": "Theoretical m/z 151.054775, Mass diff 0 (0 ppm), Formula C12H7", "175.05423": "Theoretical m/z 175.054775, Mass diff 0 (0 ppm), Formula C14H7", "176.062": "Theoretical m/z 176.0626, Mass diff 0 (0 ppm), Formula C14H8", "177.06982": "Theoretical m/z 177.070425, Mass diff 0 (0 ppm), Formula C14H9", "178.0775": "Theoretical m/z 178.077698, Mass diff 0 (1.11 ppm), SMILES C=1C=CC2=C(C1)C=CC=3C=CC=CC32, Annotation [C14H10]+, Rule of HR False"}, "num_peaks": "19", "compound_name": "Phenanthrene", "retention_time": null, "retention_index": 1832.9, "precursor_mz": 178.0775, "collision_energy": "70eV", "peaks_json": [[74.01508, 137808.0], [75.02295, 278714.0], [76.03075, 608417.0], [87.02295, 304266.0], [88.03076, 497050.0], [89.03857, 441168.0], [98.01511, 150478.0], [150.04633, 868927.0], [151.05415, 546351.0], [152.0619, 2275502.0], [153.06528, 276320.0], [169.06468, 272559.0], [174.04636, 365846.0], [175.05423, 272039.0], [176.062, 3370523.0], [177.06982, 1751846.0], [178.0775, 13724432.0], [179.08078, 2250119.0], [180.08412, 138203.0]]}, {"scannumber": "-1", "precursortype": "[M]+", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C14H10", "inchikey": "MWPLVEDNUUSJAV-UHFFFAOYSA-N", "inchi": "", "smiles": "C1=CC2=CC3=C(C=CC=C3)C=C2C=C1", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "instrumenttype": "GC-E'..b', 6], [0.000849016367431184, 1], [0.1164944277710488, 27], [0.013509973424897055, 10], [0.03985367849716299, 8], [0.0012060403391046337, 3], [0.11935916738712983, 12], [0.0019639190156446325, 4], [0.0013748628337669718, 5], [0.0317854774013463, 1], [0.1558977110222132, 19], [0.014345386694957156, 8], [0.015208293160793463, 7], [0.004975840661608583, 4], [0.028830083229516423, 5], [0.0012552816488229767, 4], [0.21426428394497732, 19], [0.009096654439736741, 2], [0.1079410688788675, 23], [0.006130350456356002, 8], [0.007640564541242704, 3], [0.9999999999999988, 48], [0.021945212693018183, 14], [0.003528882271834487, 1], [0.015071423169004209, 4], [0.01752672237557547, 4], [0.0012278672124513919, 1], [0.02457732872594147, 3], [0.028089820111006143, 3], [0.020559718677529624, 5], [0.005829674957204082, 3], [0.0015946384059203665, 2], [0.010535580085179396, 2], [0.007238048072503043, 2], [0.004927768302894852, 2], [0.0071872334678916685, 2], [0.07913720198135349, 3], [0.06304990188039904, 5], [0.006318930777064041, 3], [0.07368259593632372, 6], [0.008442291915136306, 5], [0.00699968309054316, 7], [0.07019719341011542, 9], [0.2398882344714446, 20], [0.0229385340033579, 6], [0.01487726657821838, 6], [0.004929592584065554, 5], [0.014094580531893271, 3], [0.005184721153651502, 3], [0.02402038383021682, 7], [0.005598808948450314, 8], [0.006086228481598814, 7], [0.005641055153174164, 7], [0.0059533976604853696, 8], [0.0012026254671697182, 1], [0.00481561807356803, 1], [0.0008733064074341988, 3], [0.02926724665280256, 9], [0.03973174515467047, 4], [0.0017110803566769432, 2], [0.0004537488222312789, 1], [0.0008768839784626263, 2], [0.002078720093069269, 3], [0.15068343708487614, 5], [0.004534614144447201, 6], [0.0005040922793645043, 2], [0.0006132574916066991, 2], [0.0006023439826045464, 2], [0.0009962252275582525, 2], [0.0007132215414105701, 1], [0.003941192991095589, 3], [0.0032602230184353796, 4], [0.003902911013387605, 3], [0.0028816112771112476, 3], [0.004129652769687335, 4], [0.02063893548098056, 6], [0.0636896775821581, 18], [0.004385623187808619, 8], [0.0037438584101095406, 3], [0.01457741637519401, 10], [0.01998288532279959, 5], [0.016943871184680423, 3], [0.020485320040871696, 12], [6.285139330345371e-05, 1], [0.01577650392972678, 12], [0.011702041332335697, 2], [0.010479081997924272, 3], [0.0026839418346610074, 4], [0.005168753640460431, 7], [0.02538556396055245, 8], [0.008017165415374613, 6], [0.004129170239233964, 2], [0.048329475132303006, 9], [0.00434534268029665, 5], [0.0336080987239482, 12], [0.037158313842249, 12], [0.029034992247889045, 6], [0.08565057856307288, 16], [0.10145493598365102, 13], [0.018538092241168595, 9], [0.09931273097453466, 12], [0.06070353397555056, 14], [0.002741342514267584, 9], [0.00460623189175496, 6], [0.013560322081058994, 12], [0.012723588396856826, 11], [0.0014932550806373572, 2], [0.007463259062288398, 4], [0.1412047674540015, 8], [0.003501755080485208, 3], [0.01046473315565069, 5], [0.0003965607968942006, 1], [0.20590013512001082, 7], [0.35784239189966305, 8], [0.04127530460264906, 3], [0.4549680796955883, 5], [0.023153444567903744, 5], [0.014791952326994103, 7], [0.033972430110607105, 7], [0.3711542904483082, 10], [0.03604508634054142, 6], [0.04706388584812521, 6], [0.058857146107057945, 5], [0.001747548159513367, 5], [0.044272293314883686, 3], [0.04061042591948574, 11], [0.052801064317870655, 8], [0.03570076858640123, 5], [0.09776996663893509, 6], [0.04001833146441783, 15], [0.0014714555648693989, 4], [0.0004504195432699507, 4], [0.11173292584219889, 10], [0.00309658302518114, 7], [0.011345966685709261, 11], [0.015934410043558587, 7], [0.014135762445538736, 5], [0.001702586530993099, 3], [0.0021231289122006507, 7], [0.0022815011051092924, 2], [0.3391095176584686, 16], [0.0166891482966783, 15], [0.002867840748348977, 2], [0.021945212693018183, 14], [0.9999999999999996, 47]], "dtype": [["NeutralLossesCosine_score", "<f8"], ["NeutralLossesCosine_matches", "<i8"]]}\n\\ No newline at end of file\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/similarity/scores_test5_out.json --- a/test-data/similarity/scores_test5_out.json Thu May 25 09:06:00 2023 +0000 +++ b/test-data/similarity/scores_test5_out.json Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -1,1 +1,1 @@\n-{"__Scores__": true, "similarity_function": {"__Similarity__": "ModifiedCosine", "tolerance": 0.1, "mz_power": 0.0, "intensity_power": 1.0}, "is_symmetric": true, "references": [{"scannumber": "-1", "precursortype": "[M]+", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C20H12", "inchikey": "CSHWQDPOILHKBI-UHFFFAOYSA-N", "inchi": "", "smiles": "C1=CC2=C3C(=C1)C1=CC=CC4=C1C(=CC=C4)C3=CC=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "instrumenttype": "GC-EI-Orbitrap", "ionization": "EI+", "license": "CC BY-NC", "comment": "", "peak_comments": {"113.03854": "Theoretical m/z 113.039125, Mass diff 0 (0 ppm), Formula C9H5", "125.03855": "Theoretical m/z 125.039125, Mass diff 0 (0 ppm), Formula C10H5", "249.07072": "Theoretical m/z 249.070425, Mass diff -0.001 (0 ppm), Formula C20H9", "252.09323": "Theoretical m/z 252.093354, Mass diff 0 (0.49 ppm), SMILES C1=CC=2C=CC=C3C4=CC=CC5=CC=CC(C(=C1)C23)=C54, Annotation [C20H12]+, Rule of HR False"}, "num_peaks": "19", "compound_name": "Perylene", "retention_time": null, "retention_index": 2886.9, "precursor_mz": 252.09323, "collision_energy": "70eV", "peaks_json": [[112.03071, 49892.0], [113.03854, 87510.0], [124.03076, 100146.0], [124.53242, 24923.0], [125.03855, 179254.0], [125.54019, 49039.0], [126.04636, 131679.0], [126.54804, 36313.0], [222.04645, 28905.0], [224.06192, 55632.0], [226.04175, 37413.0], [246.04646, 23286.0], [248.06204, 140007.0], [249.07072, 62236.0], [250.07765, 641789.0], [251.07967, 137600.0], [252.09323, 1955166.0], [253.09656, 402252.0], [254.09985, 39987.0]]}, {"scannumber": "-1", "precursortype": "[M]+", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C14H10", "inchikey": "YNPNZTXNASCQKK-UHFFFAOYSA-N", "inchi": "", "smiles": "C1=CC2=C(C=C1)C1=C(C=CC=C1)C=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "instrumenttype": "GC-EI-Orbitrap", "ionization": "EI+", "license": "CC BY-NC", "comment": "", "peak_comments": {"74.01508": "Theoretical m/z 74.01565, Mass diff 0 (0 ppm), Formula C6H2", "75.02295": "Theoretical m/z 75.023475, Mass diff 0 (0 ppm), Formula C6H3", "76.03075": "Theoretical m/z 76.0313, Mass diff 0 (0 ppm), Formula C6H4", "87.02295": "Theoretical m/z 87.023475, Mass diff 0 (0 ppm), Formula C7H3", "88.03076": "Theoretical m/z 88.0313, Mass diff 0 (0 ppm), Formula C7H4", "89.03857": "Theoretical m/z 89.039125, Mass diff 0 (0 ppm), Formula C7H5", "151.05415": "Theoretical m/z 151.054775, Mass diff 0 (0 ppm), Formula C12H7", "175.05423": "Theoretical m/z 175.054775, Mass diff 0 (0 ppm), Formula C14H7", "176.062": "Theoretical m/z 176.0626, Mass diff 0 (0 ppm), Formula C14H8", "177.06982": "Theoretical m/z 177.070425, Mass diff 0 (0 ppm), Formula C14H9", "178.0775": "Theoretical m/z 178.077698, Mass diff 0 (1.11 ppm), SMILES C=1C=CC2=C(C1)C=CC=3C=CC=CC32, Annotation [C14H10]+, Rule of HR False"}, "num_peaks": "19", "compound_name": "Phenanthrene", "retention_time": null, "retention_index": 1832.9, "precursor_mz": 178.0775, "collision_energy": "70eV", "peaks_json": [[74.01508, 137808.0], [75.02295, 278714.0], [76.03075, 608417.0], [87.02295, 304266.0], [88.03076, 497050.0], [89.03857, 441168.0], [98.01511, 150478.0], [150.04633, 868927.0], [151.05415, 546351.0], [152.0619, 2275502.0], [153.06528, 276320.0], [169.06468, 272559.0], [174.04636, 365846.0], [175.05423, 272039.0], [176.062, 3370523.0], [177.06982, 1751846.0], [178.0775, 13724432.0], [179.08078, 2250119.0], [180.08412, 138203.0]]}, {"scannumber": "-1", "precursortype": "[M]+", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C14H10", "inchikey": "MWPLVEDNUUSJAV-UHFFFAOYSA-N", "inchi": "", "smiles": "C1=CC2=CC3=C(C=CC=C3)C=C2C=C1", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "instrumenttype": "GC-EI-Orbitrap", "ionization": "EI+", "license"'..b'0], [0.0028730971640638244, 4, 1.0], [0.0031611093785701995, 3, 1.0], [0.07809000356411269, 24, 1.0], [0.011339523303273511, 11, 1.0], [0.1816760057075885, 45, 1.0], [0.015161639879948667, 10, 1.0], [0.02217259430184349, 14, 1.0], [0.03016187459010991, 15, 1.0], [0.05429349969259654, 20, 1.0], [0.21156692241257447, 22, 1.0], [0.06330592536098255, 20, 1.0], [0.37756373251668857, 22, 1.0], [0.1824545636663668, 17, 1.0], [0.9999999999999989, 61, 1.0], [0.03487408174852443, 18, 1.0], [0.0031530335453573023, 5, 1.0], [0.07421964444934627, 14, 1.0], [0.0072896351039373666, 8, 1.0], [0.02223307394055662, 14, 1.0], [0.02257124600169508, 16, 1.0], [0.027963268346603974, 17, 1.0], [0.023381830669040555, 9, 1.0], [0.026962291591070775, 11, 1.0], [0.01658660054533858, 7, 1.0], [0.010178493180153044, 13, 1.0], [0.37373952662816223, 18, 1.0], [0.9999999999999998, 37, 1.0], [0.02777631464351049, 12, 1.0], [0.1447639137740579, 24, 1.0], [0.03147233467542128, 17, 1.0], [0.03668676267612972, 14, 1.0], [0.020961417223860423, 6, 1.0], [0.014547506975992702, 7, 1.0], [0.7165448092914788, 27, 1.0], [0.7077717691138634, 26, 1.0], [0.14841215335964056, 22, 1.0], [0.9999999999999986, 49, 1.0], [0.15478920576000488, 8, 1.0], [0.1525091787681603, 8, 1.0], [1.0, 75, 1.0], [0.013960480414345186, 7, 1.0], [0.012898053940131163, 5, 1.0], [0.02934740784150951, 10, 1.0], [0.048383174738395124, 26, 1.0], [0.015570817504218529, 16, 1.0], [0.029506747379838084, 20, 1.0], [0.01039090462946715, 18, 1.0], [0.012832752777152854, 19, 1.0], [0.0372296294007929, 21, 1.0], [0.19471605273580178, 18, 1.0], [0.022182739554052363, 10, 1.0], [0.09428821665388754, 36, 1.0], [0.03487408174852443, 18, 1.0], [1.0, 57, 1.0], [0.3581452270515483, 19, 1.0], [0.02692737752602113, 29, 1.0], [0.015614695013710414, 5, 1.0], [0.5621299506007804, 15, 1.0], [0.5899393930827314, 16, 1.0], [0.009549214615669823, 6, 1.0], [0.013182084190193821, 10, 1.0], [0.013450993184542724, 14, 1.0], [0.0012715157671517663, 3, 1.0], [0.0025645094667376784, 5, 1.0], [0.08804375656589408, 25, 1.0], [0.01220117358353883, 13, 1.0], [0.013115830082688965, 8, 1.0], [1.0, 35, 1.0], [0.04168219452723639, 18, 1.0], [0.13815332243425266, 5, 1.0], [0.1454824342075702, 12, 1.0], [0.09634874816811735, 6, 1.0], [0.0908731699433544, 18, 1.0], [0.0714806286065652, 14, 1.0], [0.0685535992926502, 14, 1.0], [0.0011191911101418256, 3, 1.0], [0.259743494306901, 29, 1.0], [0.3581452270515483, 19, 1.0], [1.0, 60, 1.0], [0.024836905223525062, 25, 1.0], [0.06659189766227433, 8, 1.0], [0.033368714192638226, 6, 1.0], [0.029776983139679143, 8, 1.0], [0.014386598516398983, 7, 1.0], [0.0174029922991385, 14, 1.0], [0.13635394439889434, 22, 1.0], [0.07045920127432331, 31, 1.0], [0.02692737752602113, 29, 1.0], [0.024836905223525062, 25, 1.0], [1.0, 82, 1.0], [0.038530836114745656, 12, 1.0], [0.37715574987564204, 6, 1.0], [0.21925449641312258, 4, 1.0], [0.2897578505717055, 5, 1.0], [0.18214368073680545, 10, 1.0], [0.17367471503469017, 10, 1.0], [0.01802858781741649, 7, 1.0], [0.057634459588011146, 11, 1.0], [0.06659189766227433, 8, 1.0], [0.038530836114745656, 12, 1.0], [0.9999999999999997, 20, 1.0], [0.13338495790962168, 9, 1.0], [0.13394438395989552, 14, 1.0], [0.08015473107805055, 15, 1.0], [0.1041070691955264, 16, 1.0], [0.0982258184690084, 14, 1.0], [0.04243089164102407, 20, 1.0], [0.14167032653965456, 22, 1.0], [0.06118585359929772, 10, 1.0], [0.27102141235736116, 36, 1.0], [0.01967212182056244, 9, 1.0], [0.04168219452723639, 18, 1.0], [0.9999999999999988, 51, 1.0], [0.02253416942501213, 12, 1.0], [0.018822784115202575, 20, 1.0], [0.007606153593747367, 13, 1.0], [0.0067533077336432434, 11, 1.0], [0.030397959311646662, 10, 1.0], [0.020386018142265136, 6, 1.0], [0.05336186216280011, 22, 1.0], [0.018724366773580196, 14, 1.0], [0.016595252772073396, 11, 1.0], [0.9999999999999994, 48, 1.0]], "dtype": [["ModifiedCosine_score", "<f8"], ["ModifiedCosine_matches", "<i8"], ["MetadataMatch_MetadataMatch", "<f8"]]}\n\\ No newline at end of file\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/similarity/scores_test6_out.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/scores_test6_out.json Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"__Scores__": true, "is_symmetric": false, "references": [{"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C20H12", "inchikey": "CSHWQDPOILHKBI-UHFFFAOYSA-N", "smiles": "C1=CC2=C3C(=C1)C1=CC=CC4=C1C(=CC=C4)C3=CC=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "compound_name": "Perylene", "retention_time": null, "retention_index": 2886.9, "precursor_mz": 252.09323, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "charge": 1, "parent_mass": "251.08595400000002", "peak_comments": {"252.09323": "Theoretical m/z 252.093354, Mass diff 0 (0.49 ppm), SMILES C1=CC=2C=CC=C3C4=CC=CC5=CC=CC(C(=C1)C23)=C54, Annotation [C20H12]+, Rule of HR False"}, "num_peaks": "3", "peaks_json": [[250.07765, 0.3282529462971431], [252.09323, 1.0], [253.09656, 0.20573802940517583]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C14H10", "inchikey": "YNPNZTXNASCQKK-UHFFFAOYSA-N", "smiles": "C1=CC2=C(C=C1)C1=C(C=CC=C1)C=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "compound_name": "Phenanthrene", "retention_time": null, "retention_index": 1832.9, "precursor_mz": 178.0775, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "charge": 1, "parent_mass": "177.070224", "peak_comments": {"176.062": "Theoretical m/z 176.0626, Mass diff 0 (0 ppm), Formula C14H8", "177.06982": "Theoretical m/z 177.070425, Mass diff 0 (0 ppm), Formula C14H9", "178.0775": "Theoretical m/z 178.077698, Mass diff 0 (1.11 ppm), SMILES C=1C=CC2=C(C1)C=CC=3C=CC=CC32, Annotation [C14H10]+, Rule of HR False"}, "num_peaks": "5", "peaks_json": [[152.0619, 0.1657993569424221], [176.062, 0.24558560966311757], [177.06982, 0.12764433529926775], [178.0775, 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[176.06204, 0.23295403420236208], [177.06984, 0.1074344883724439], [178.07754, 1.0], [179.08081, 0.1616741186784917]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C12H10", "inchikey": "CWRYPZZKDGJXCA-UHFFFAOYSA-N", "smiles": "C1CC2=C3C1=CC=CC3=CC=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "compound_name": "Acenaphthene", "retention_time": null, "retention_index": 1528.3, "precursor_mz": 154.07741, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "charge": 1, "parent_mass": "153.070134", "peak_comments": {"151.05418": "Theoretical m/z 151.054775, Mass diff 0 (0 ppm), Formula C12H7", "153.06969": "Theoretical m/z 153.070425, Mass diff 0 (0 ppm), Formula C12H9", "154.07741": "Theoretical m/z 154.077698, Mass diff 0 (1.87 ppm), SMILES C=1C=C2C=CC=C3C2=C(C1)CC3, Annotation [C12H10]+, Rule of HR False"}, 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newline at end of file\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/similarity/spec2vec/inp_filtered_library.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/spec2vec/inp_filtered_library.msp Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -0,0 +1,4205 @@\n+SCANNUMBER: -1\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C20H12\n+INCHIKEY: CSHWQDPOILHKBI-UHFFFAOYSA-N\n+SMILES: C1=CC2=C3C(=C1)C1=CC=CC4=C1C(=CC=C4)C3=CC=C2\n+AUTHORS: Price et al., RECETOX, Masaryk University (CZ)\n+INSTRUMENT: Q Exactive GC Orbitrap GC-MS/MS\n+IONIZATION: EI+\n+LICENSE: CC BY-NC\n+COMPOUND_NAME: Perylene\n+RETENTION_TIME: None\n+RETENTION_INDEX: 2886.9\n+PRECURSOR_MZ: 252.09323\n+ADDUCT: [M]+\n+COLLISION_ENERGY: 70eV\n+INSTRUMENT_TYPE: GC-EI-Orbitrap\n+CHARGE: 1\n+PARENT_MASS: 251.08595400000002\n+NUM PEAKS: 3\n+250.07765 0.3282529462971431\n+252.09323 1.0 "Theoretical m/z 252.093354, Mass diff 0 (0.49 ppm), SMILES C1=CC=2C=CC=C3C4=CC=CC5=CC=CC(C(=C1)C23)=C54, Annotation [C20H12]+, Rule of HR False"\n+253.09656 0.20573802940517583\n+\n+SCANNUMBER: -1\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C14H10\n+INCHIKEY: YNPNZTXNASCQKK-UHFFFAOYSA-N\n+SMILES: C1=CC2=C(C=C1)C1=C(C=CC=C1)C=C2\n+AUTHORS: Price et al., RECETOX, Masaryk University (CZ)\n+INSTRUMENT: Q Exactive GC Orbitrap GC-MS/MS\n+IONIZATION: EI+\n+LICENSE: CC BY-NC\n+COMPOUND_NAME: Phenanthrene\n+RETENTION_TIME: None\n+RETENTION_INDEX: 1832.9\n+PRECURSOR_MZ: 178.0775\n+ADDUCT: [M]+\n+COLLISION_ENERGY: 70eV\n+INSTRUMENT_TYPE: GC-EI-Orbitrap\n+CHARGE: 1\n+PARENT_MASS: 177.070224\n+NUM PEAKS: 5\n+152.0619 0.1657993569424221\n+176.062 0.24558560966311757 "Theoretical m/z 176.0626, Mass diff 0 (0 ppm), Formula C14H8"\n+177.06982 0.12764433529926775 "Theoretical m/z 177.070425, Mass diff 0 (0 ppm), Formula C14H9"\n+178.0775 1.0 "Theoretical m/z 178.077698, Mass diff 0 (1.11 ppm), SMILES C=1C=CC2=C(C1)C=CC=3C=CC=CC32, Annotation [C14H10]+, Rule of HR False"\n+179.08078 0.16394988149600653\n+\n+SCANNUMBER: -1\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C14H10\n+INCHIKEY: MWPLVEDNUUSJAV-UHFFFAOYSA-N\n+SMILES: C1=CC2=CC3=C(C=CC=C3)C=C2C=C1\n+AUTHORS: Price et al., RECETOX, Masaryk University (CZ)\n+INSTRUMENT: Q Exactive GC Orbitrap GC-MS/MS\n+IONIZATION: EI+\n+LICENSE: CC BY-NC\n+COMPOUND_NAME: Anthracene\n+RETENTION_TIME: None\n+RETENTION_INDEX: 1844.4\n+PRECURSOR_MZ: 178.07754\n+ADDUCT: [M]+\n+COLLISION_ENERGY: 70eV\n+INSTRUMENT_TYPE: GC-EI-Orbitrap\n+CHARGE: 1\n+PARENT_MASS: 177.070264\n+NUM PEAKS: 5\n+152.06195 0.12450313104470498\n+176.06204 0.23295403420236208 "Theoretical m/z 176.0626, Mass diff 0 (0 ppm), Formula C14H8"\n+177.06984 0.1074344883724439 "Theoretical m/z 177.070425, Mass diff 0 (0 ppm), Formula C14H9"\n+178.07754 1.0 "Theoretical m/z 178.077698, Mass diff 0 (0.89 ppm), SMILES C=1C=CC=2C=C3C=CC=CC3=CC2C1, Annotation [C14H10]+, Rule of HR False"\n+179.08081 0.1616741186784917\n+\n+SCANNUMBER: -1\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C12H10\n+INCHIKEY: CWRYPZZKDGJXCA-UHFFFAOYSA-N\n+SMILES: C1CC2=C3C1=CC=CC3=CC=C2\n+AUTHORS: Price et al., RECETOX, Masaryk University (CZ)\n+INSTRUMENT: Q Exactive GC Orbitrap GC-MS/MS\n+IONIZATION: EI+\n+LICENSE: CC BY-NC\n+COMPOUND_NAME: Acenaphthene\n+RETENTION_TIME: None\n+RETENTION_INDEX: 1528.3\n+PRECURSOR_MZ: 154.07741\n+ADDUCT: [M]+\n+COLLISION_ENERGY: 70eV\n+INSTRUMENT_TYPE: GC-EI-Orbitrap\n+CHARGE: 1\n+PARENT_MASS: 153.070134\n+NUM PEAKS: 4\n+151.05418 0.10238389021994407 "Theoretical m/z 151.054775, Mass diff 0 (0 ppm), Formula C12H7"\n+152.06194 0.4817565861859871\n+153.06969 1.0 "Theoretical m/z 153.070425, Mass diff 0 (0 ppm), Formula C12H9"\n+154.07741 0.6474388804646675 "Theoretical m/z 154.077698, Mass diff 0 (1.87 ppm), SMILES C=1C=C2C=CC=C3C2=C(C1)CC3, Annotation [C12H10]+, Rule of HR False"\n+\n+SCANNUMBER: -1\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C16H10\n+INCHIKEY: GVEPBJHOBDJJJI-UHFFFAOYSA-N\n+SMILES: C1=CC2=C(C=C1)C1=C3C2=CC=CC3=CC=C1\n+AUTHORS: Price et al., RECETOX, Masaryk University (CZ)\n+INSTRUMENT: Q Exactive GC Orbitrap GC-MS/MS\n+IONIZATION: EI+\n+LICENSE: CC BY-NC\n+COMPOUND_NAME: Fluoranthene\n+RETENTION_TIME: None\n+RETENTION_INDEX: 2102.7\n+PRECURSOR_MZ: 202.07756\n+ADDUCT: [M]+\n+COLLISION_ENERGY: 70eV\n'..b' "Theoretical m/z 235.066148, Mass diff 0 (0.18 ppm), SMILES O=C(NC1=CC=CC=C1)C2=C(OCCS2)C, Annotation [C12H13NO2S]+, Rule of HR False"\n+\n+SCANNUMBER: -1\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C13H18O5S\n+INCHIKEY: IRCMYGHHKLLGHV-UHFFFAOYSA-N\n+SMILES: CCOC1C(C2=C(O1)C=CC(=C2)OS(=O)(=O)C)(C)C\n+AUTHORS: Price et al., RECETOX, Masaryk University (CZ)\n+INSTRUMENT: Q Exactive GC Orbitrap GC-MS/MS\n+IONIZATION: EI+\n+LICENSE: CC BY-NC\n+COMPOUND_NAME: Ethofumesate\n+RETENTION_TIME: None\n+RETENTION_INDEX: 1954.4\n+PRECURSOR_MZ: 286.08679\n+ADDUCT: [M]+\n+COLLISION_ENERGY: 70eV\n+INSTRUMENT_TYPE: GC-EI-Orbitrap\n+CHARGE: 1\n+PARENT_MASS: 285.079514\n+NUM PEAKS: 13\n+79.05419 0.1392834489952906 "Theoretical m/z 79.054228, Mass diff 0 (0.48 ppm), SMILES C1=CC=CC=C1, Annotation [C6H6+H]+, Rule of HR True"\n+91.0542 0.1456948233889637 "Theoretical m/z 91.054775, Mass diff 0 (0 ppm), Formula C7H7"\n+105.06984 0.29471655075385655 "Theoretical m/z 105.070425, Mass diff 0 (0 ppm), Formula C8H9"\n+115.05416 0.14265948876449097 "Theoretical m/z 115.054229, Mass diff 0 (0.6 ppm), SMILES C1=CC=C(C=C1)C(C)C, Annotation [C9H12-5H]+, Rule of HR True"\n+133.0647 0.3868381358475808 "Theoretical m/z 133.064798, Mass diff 0 (0.73 ppm), SMILES OC=1C=CC=C(C=1)C(C)C, Annotation [C9H12O-3H]+, Rule of HR True"\n+137.05962 0.565607729176301 "Theoretical m/z 137.060255, Mass diff 0 (0 ppm), Formula C8H9O2"\n+161.0596 1.0 "Theoretical m/z 161.059701, Mass diff 0 (0.63 ppm), SMILES OC=1C=CC=2OCC(C=2(C=1))(C)C, Annotation [C10H12O2-3H]+, Rule of HR True"\n+162.06293 0.1395183569693118\n+163.07518 0.1571750863529426 "Theoretical m/z 163.075351, Mass diff 0 (1.05 ppm), SMILES OC=1C=CC=2OCC(C=2(C=1))(C)C, Annotation [C10H12O2-H]+, Rule of HR True"\n+179.07016 0.3858738890199595 "Theoretical m/z 179.07027, Mass diff 0 (0.62 ppm), SMILES OC=1C=CC=2OC(O)C(C=2(C=1))(C)C, Annotation [C10H12O3-H]+, Rule of HR True"\n+207.1015 0.9146502804597079 "Theoretical m/z 207.101566, Mass diff 0 (0.32 ppm), SMILES OC=1C=CC=2OC(OCC)C(C=2(C=1))(C)C, Annotation [C12H16O3-H]+, Rule of HR True"\n+208.1048 0.1224932435932507\n+286.08679 0.294378369815484 "Theoretical m/z 286.086945, Mass diff 0 (0.54 ppm), SMILES O=S(=O)(OC=1C=CC=2OC(OCC)C(C=2(C=1))(C)C)C, Annotation [C13H18O5S]+, Rule of HR False"\n+\n+SCANNUMBER: -1\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C17H17N3OS\n+INCHIKEY: LMVPQMGRYSRMIW-KRWDZBQOSA-N\n+SMILES: CC1(C(=O)N(C(=N1)SC)NC2=CC=CC=C2)C3=CC=CC=C3\n+AUTHORS: Price et al., RECETOX, Masaryk University (CZ)\n+INSTRUMENT: Q Exactive GC Orbitrap GC-MS/MS\n+IONIZATION: EI+\n+LICENSE: CC BY-NC\n+COMPOUND_NAME: Fenamidone\n+RETENTION_TIME: None\n+RETENTION_INDEX: 2516.1\n+PRECURSOR_MZ: 311.10815\n+ADDUCT: [M]+\n+COLLISION_ENERGY: 70eV\n+INSTRUMENT_TYPE: GC-EI-Orbitrap\n+CHARGE: 1\n+PARENT_MASS: 310.10087400000003\n+NUM PEAKS: 10\n+77.03851 0.1341728006141734 "Theoretical m/z 77.038578, Mass diff 0 (0.88 ppm), SMILES C1=CC=CC=C1, Annotation [C6H6-H]+, Rule of HR True"\n+91.04161 0.14196713486951465 "Theoretical m/z 91.041647, Mass diff 0 (0.41 ppm), SMILES NC1=CC=CC=C1, Annotation [C6H7N-2H]+, Rule of HR False"\n+103.05415 0.13231626786608644 "Theoretical m/z 103.054223, Mass diff 0 (0.71 ppm), SMILES C1=CC=C(C=C1)CC, Annotation [C8H10-3H]+, Rule of HR True"\n+206.07457 0.2477103476704148 "Theoretical m/z 206.07464, Mass diff 0 (0.34 ppm), SMILES N(=C(NN)SC)C(C1=CC=CC=C1)C, Annotation [C10H15N3S-3H]+, Rule of HR True"\n+210.11507 0.1254196447843151\n+237.10208 0.5638187350251782 "Theoretical m/z 237.102243, Mass diff 0 (0.69 ppm), SMILES O=C(NNC1=CC=CC=C1)C(C2=CC=CC=C2)C, Annotation [C15H16N2O-3H]+, Rule of HR True"\n+238.10997 0.737876380592742\n+239.11317 0.12354824276317873\n+268.09 1.0 "Theoretical m/z 268.090295, Mass diff 0 (1.1 ppm), SMILES N(=C(NNC1=CC=CC=C1)S)C(C2=CC=CC=C2)C, Annotation [C15H17N3S-3H]+, Rule of HR True"\n+269.09351 0.15574634382295574\n+\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/similarity/spec2vec/inp_filtered_spectra.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/spec2vec/inp_filtered_spectra.msp Tue Jun 27 14:25:59 2023 +0000 |
| b |
| b'@@ -0,0 +1,1008 @@\n+IONMODE: negative\n+SPECTRUMTYPE: Centroid\n+COMPOUND_NAME: C019\n+RETENTION_TIME: 688.11\n+RETENTION_INDEX: 4135.446429\n+CHARGE: -1\n+NUM PEAKS: 21\n+164.985419247789 0.2949419846671587\n+179.033979756352 0.1975962017168221\n+194.04893073403 0.1080780080055076\n+248.988380501455 0.4192550107623055\n+251.037178293 0.1975188727945594\n+283.099929585291 0.24858700581303622\n+313.053040045895 0.15255184988804857\n+329.031653006854 0.12152318335456756\n+341.157248840923 0.33065016037294653\n+385.022947628725 0.11792404215662944\n+401.053681557414 0.5558197970588639\n+403.051400482668 0.10684249115159443\n+415.106669687654 1.0\n+416.107049345269 0.3343846089983622\n+417.104122333661 0.16072829222839785\n+489.124198650628 0.7880577919119076\n+535.10922525834 0.17951802003040962\n+550.163296442538 0.22193082425956692\n+551.161445828019 0.11285226875001307\n+564.146181690587 0.10968283775320925\n+623.183150220198 0.24882510323783946\n+\n+IONMODE: negative\n+SPECTRUMTYPE: Centroid\n+COMPOUND_NAME: C008\n+RETENTION_TIME: 383.25\n+RETENTION_INDEX: 2436.111111\n+CHARGE: -1\n+NUM PEAKS: 10\n+167.06348032557 0.2012680241749571\n+169.042872715042 0.22527813564183466\n+185.073952424469 0.1146092209329471\n+224.061333736415 0.637856954108077\n+241.084284214072 0.5378362429201462\n+243.086918863664 0.8440889152136807\n+245.102418520421 1.0\n+257.113614660022 0.7014464407039914\n+258.111154671539 0.45403443749116\n+315.119168534318 0.2802677742648726\n+\n+IONMODE: negative\n+SPECTRUMTYPE: Centroid\n+COMPOUND_NAME: C001\n+RETENTION_TIME: 268.99\n+RETENTION_INDEX: 1800.989583\n+CHARGE: -1\n+NUM PEAKS: 7\n+147.065597668017 0.20713460605355152\n+149.044686744287 0.15021454193335101\n+183.047097257536 0.2756365347787095\n+257.066031671279 0.16716705800250425\n+273.097313808265 1.0\n+274.099806030141 0.1382750943677773\n+347.116266654718 0.10796331331103011\n+\n+IONMODE: negative\n+SPECTRUMTYPE: Centroid\n+COMPOUND_NAME: C010\n+RETENTION_TIME: 271.76\n+RETENTION_INDEX: 1815.416667\n+CHARGE: -1\n+NUM PEAKS: 12\n+76.0323849976885 0.5337096603553363\n+107.129167494293 0.17750725429827036\n+120.05545372843 0.732323548309492\n+132.054968772294 0.6582449478277536\n+136.084083848357 0.18110012219874336\n+138.177598969977 0.10980088538234019\n+311.387345297053 0.3149229368865709\n+312.394070075839 1.0\n+313.396963036504 0.1996701454734163\n+329.397982197985 0.17215789049120694\n+330.403963356557 0.5441264876224288\n+331.407288294656 0.1075489761979763\n+\n+IONMODE: negative\n+SPECTRUMTYPE: Centroid\n+COMPOUND_NAME: C009\n+RETENTION_TIME: 224.1\n+RETENTION_INDEX: 1606.578947\n+CHARGE: -1\n+NUM PEAKS: 5\n+128.088974937905 0.30238672398872746\n+142.104728421893 0.13125344469355718\n+230.102912184687 0.13629903834332716\n+246.13394892703 1.0\n+247.135560589937 0.1027800448922141\n+\n+IONMODE: negative\n+SPECTRUMTYPE: Centroid\n+COMPOUND_NAME: C011\n+RETENTION_TIME: 322.28\n+RETENTION_INDEX: 2083.777778\n+CHARGE: -1\n+NUM PEAKS: 8\n+191.091545005862 0.3661694612326083\n+204.099524919261 0.1379655416395176\n+217.107439740029 0.8659676702439103\n+221.084188869749 0.13224939836684152\n+265.110639707297 0.12404535021125133\n+305.141591931944 1.0\n+306.142075983677 0.19894438269593562\n+318.149353523284 0.5161780338363837\n+\n+IONMODE: negative\n+SPECTRUMTYPE: Centroid\n+COMPOUND_NAME: C013\n+RETENTION_TIME: 471.03\n+RETENTION_INDEX: 3168.684211\n+CHARGE: -1\n+NUM PEAKS: 6\n+78.0464517452347 0.13019193533313522\n+155.087332200892 0.16981875175936348\n+207.101729466849 1.0\n+313.053036971607 0.12108100658431745\n+353.320009154806 0.2895861096886366\n+624.30876303981 0.14852029190801175\n'..b'349696378594456\n+196.992752093539 0.3065603768824057\n+197.974508055988 0.395078144825856\n+198.95441899853 0.20984023997622794\n+212.970014961884 0.312364140356306\n+213.006147303489 0.3451086913299261\n+214.98560992714 0.5058106319186024\n+220.957069324217 0.1741467403445935\n+222.936453968368 0.1925777417566011\n+229.019119616188 1.0\n+230.00074243328 0.4313373151032761\n+236.98832473252 0.17144823687024496\n+240.946899738586 0.37016492220221137\n+253.982966844011 0.2619026170220304\n+269.977845781938 0.369206087321791\n+270.975426915952 0.26702156040941716\n+270.993770069105 0.5558156567281477\n+297.079403794841 0.3276080388276794\n+298.934550867121 0.27505460413538213\n+328.980928284848 0.30053783536988743\n+330.960641905517 0.36106011190503906\n+372.953096157169 0.24565144306023193\n+\n+IONMODE: negative\n+SPECTRUMTYPE: Centroid\n+COMPOUND_NAME: C018\n+RETENTION_TIME: 687.52\n+RETENTION_INDEX: 4133.690476\n+CHARGE: -1\n+NUM PEAKS: 9\n+209.011554808631 0.6525630494040975\n+209.029113642814 0.10839584784422365\n+210.990970491228 0.15000447517519525\n+226.041539764125 0.3130785916148705\n+227.039590062704 0.17080278851135594\n+265.020169474237 0.2407632085362116\n+281.051364215883 1.0\n+282.049803555434 0.21798058347517868\n+285.009414657485 0.12222513080126347\n+\n+IONMODE: negative\n+SPECTRUMTYPE: Centroid\n+COMPOUND_NAME: C012\n+RETENTION_TIME: 687.83\n+RETENTION_INDEX: 4134.613095\n+CHARGE: -1\n+NUM PEAKS: 27\n+121.046741626167 0.12537265500763864\n+192.997735629267 0.1940732067111916\n+205.016711322548 0.12056941717717026\n+209.098935410027 0.12559326156418593\n+213.05754958053 0.27142481482801556\n+253.016653119059 0.8938154160284864\n+271.027137265637 0.1375157398831428\n+284.047997947258 0.1709644868199992\n+325.985953604199 0.17320279707305308\n+327.03525664153 1.0\n+328.035343658 0.26668492712822667\n+345.046169172075 0.17928530473894783\n+359.09769204202 0.2008606829314974\n+360.028136457829 0.21741111817985187\n+387.002413998209 0.2632563912022333\n+387.071825807939 0.3071277807533759\n+402.055174276849 0.2538777644377674\n+461.090256355859 0.3629780005380489\n+462.091555156095 0.14179921776218857\n+475.072310244956 0.27595658697326014\n+476.143434019655 0.2650001066007337\n+477.140480798609 0.10059042565917092\n+490.12632015072 0.3700192231231476\n+491.122346777972 0.20934752539009766\n+549.162553092955 0.5034364902937184\n+563.144239233773 0.2590935918637112\n+624.183209223215 0.1451500409395642\n+\n+IONMODE: negative\n+SPECTRUMTYPE: Centroid\n+COMPOUND_NAME: C020\n+RETENTION_TIME: 687.99\n+RETENTION_INDEX: 4135.089286\n+CHARGE: -1\n+NUM PEAKS: 24\n+194.053642118165 0.17149988589657134\n+212.061782732582 0.3408023706085241\n+267.034768010352 0.14461973681405008\n+267.068824022318 0.9059077886912253\n+310.970568727813 0.10207376981761378\n+325.055731606087 0.2492913881575955\n+327.965549188207 0.17771113517875153\n+339.03821058645 0.2164141235131004\n+342.996634492902 0.12864401601229136\n+345.115297423962 0.12858631941521836\n+358.067243216398 0.11516054657713713\n+361.025211906011 0.21277786650130676\n+388.003000430725 0.1117630757647746\n+388.073272089579 0.1379380986368877\n+399.005054559559 0.13523814605127854\n+401.984326631505 0.18236859257167579\n+402.98179623463 0.11632404563967355\n+416.036473280551 0.23580021278191537\n+417.033665098569 0.13482894754843827\n+430.088321970134 0.3515024935084798\n+431.085366629672 0.22490708219361874\n+475.14184210128 1.0\n+565.143723544965 0.11382519851041557\n+625.181479977537 0.1264407374154073\n+\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/similarity/spec2vec/model.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/spec2vec/model.json Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"vector_size": 100, "index_to_key": ["peak@95.05", "peak@91.05", "peak@92.05", "peak@115.05", "peak@125.02", "peak@89.04", "peak@173.51", "peak@93.06", "peak@105.07", "peak@105.05", "peak@155.06", "peak@111.04", "peak@120.04", "peak@110.07", "peak@106.07", "peak@118.07", "peak@127.02", "peak@119.06", "peak@119.09", "peak@110.05", "peak@137.02", "peak@149.02", "peak@142.07", "peak@94.07", "peak@107.05", "peak@103.05", "peak@138.08", "peak@96.06", "peak@85.05", "peak@96.04", "peak@158.98", "peak@117.06", "peak@129.07", "peak@139.01", "peak@143.06", "peak@129.01", "peak@120.08", "peak@146.06", "peak@128.06", "peak@119.05", "peak@123.00", "peak@104.05", "peak@131.06", "peak@123.04", "peak@105.04", "peak@163.03", "peak@109.07", "peak@138.99", "peak@117.07", "peak@144.06", "peak@170.10", "peak@110.06", "peak@95.09", "peak@145.06", "peak@85.08", "peak@147.08", "peak@137.06", "peak@151.03", "peak@133.06", "peak@97.04", "peak@165.05", "peak@114.07", "peak@175.03", "peak@132.08", "peak@139.03", "peak@107.09", "peak@99.00", "peak@141.01", "peak@140.03", "peak@113.02", "peak@158.05", "peak@113.08", "peak@109.08", "peak@122.06", "peak@130.07", "peak@168.09", "peak@156.07", "peak@141.07", "peak@167.07", "peak@153.07", "peak@136.04", "peak@165.07", "peak@98.06", "peak@161.06", "peak@164.03", "peak@93.07", "peak@128.05", "peak@157.08", "peak@116.06", "peak@172.99", "peak@86.04", "peak@116.03", "peak@124.08", "peak@118.05", "peak@134.06", "peak@116.05", "peak@150.02", "peak@174.97", "peak@135.08", "peak@184.12", "peak@128.08", "peak@129.05", "peak@100.05", "peak@99.07", "peak@152.06", "peak@148.04", "peak@134.10", "peak@152.07", "peak@121.04", "peak@176.04", "peak@130.03", "peak@94.04", "peak@147.94", "peak@182.08", "peak@121.07", "peak@134.07", "peak@136.08", "peak@186.08", "peak@168.07", "peak@122.10", "peak@123.06", "peak@124.06", "peak@125.01", "peak@91.03", "peak@102.04", "peak@183.06", "peak@91.04", "peak@125.06", "peak@90.03", "peak@130.04", 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"peak@123.02", "peak@219.03", "peak@109.03", "peak@172.96", "peak@139.05", "peak@124.98", "peak@113.00", "peak@142.99", "peak@147.04", "peak@169.10", "peak@99.04", "peak@146.07", "peak@125.05", "peak@176.03", "peak@141.02", "peak@180.10", "peak@102.06", "peak@136.01", "peak@226.17", "peak@215.03", "peak@147.06", "peak@184.99", "peak@99.08", "peak@164.11", "peak@198.08", "peak@208.13", "peak@165.06", "peak@151.11", "peak@192.10", "peak@308.00", "peak@223.01", "peak@156.09", "peak@109.10", "peak@155.00", "peak@132.96", "peak@125.00", "peak@208.10", "peak@171.03", "peak@159.07", "peak@158.04", "peak@159.97", "peak@127.10", "peak@163.04", "peak@142.12", "peak@216.03", "peak@171.04", "peak@148.09", "peak@158.07", "peak@180.03", "peak@144.07", "peak@148.11", "peak@121.09", "peak@127.99", "peak@140.05", "peak@217.02", "peak@87.08", "peak@166.12", "peak@206.08", "peak@179.07", "peak@107.06", "peak@242.08", "peak@162.04", "peak@150.01", "peak@160.11", "peak@110.10", "peak@115.08", "peak@86.10", "peak@138.09", "peak@223.08'..b': 1240, "peak@155.02": 1241, "peak@226.13": 1242, "peak@210.10": 1243, "peak@209.11": 1244, "peak@196.09": 1245, "peak@185.11": 1246, "peak@102.03": 1247, "peak@187.09": 1248, "peak@188.08": 1249, "peak@216.06": 1250, "peak@161.03": 1251, "peak@174.02": 1252, "peak@175.05": 1253, "peak@119.04": 1254, "peak@134.04": 1255, "peak@150.04": 1256, "peak@151.10": 1257, "peak@163.01": 1258, "peak@188.09": 1259, "peak@163.05": 1260, "peak@170.04": 1261, "peak@178.03": 1262, "peak@179.00": 1263, "peak@205.04": 1264, "peak@214.04": 1265, "peak@155.04": 1266, "peak@147.03": 1267, "peak@146.02": 1268, "peak@134.05": 1269, "peak@101.02": 1270, "peak@98.04": 1271, "peak@366.15": 1272, "peak@231.10": 1273, "peak@230.09": 1274, "peak@215.11": 1275, "peak@214.10": 1276, "peak@202.10": 1277, "peak@201.10": 1278, "peak@200.08": 1279, "peak@199.09": 1280, "peak@199.07": 1281, "peak@189.10": 1282, "peak@247.07": 1283, "peak@260.07": 1284, "peak@273.06": 1285, "peak@139.12": 1286, "peak@211.00": 1287, "peak@86.07": 1288, "peak@96.08": 1289, "peak@136.09": 1290, "peak@137.09": 1291, "peak@138.10": 1292, "peak@151.12": 1293, "peak@224.18": 1294, "peak@179.13": 1295, "peak@180.15": 1296, "peak@191.12": 1297, "peak@192.15": 1298, "peak@194.13": 1299, "peak@208.14": 1300, "peak@167.97": 1301, "peak@152.98": 1302, "peak@139.97": 1303, "peak@136.00": 1304, "peak@134.99": 1305, "peak@121.01": 1306, "peak@111.03": 1307, "peak@108.00": 1308, "peak@107.00": 1309, "peak@96.00": 1310, "peak@90.97": 1311, "peak@377.14": 1312, "peak@349.11": 1313, "peak@347.09": 1314, "peak@337.11": 1315, "peak@335.13": 1316, "peak@334.08": 1317, "peak@209.18": 1318, "peak@237.21": 1319, "peak@273.08": 1320, "peak@226.12": 1321, "peak@172.98": 1322, "peak@204.02": 1323, "peak@206.02": 1324, "peak@220.02": 1325, "peak@250.02": 1326, "peak@225.11": 1327, "peak@251.11": 1328, "peak@272.11": 1329, "peak@261.09": 1330, "peak@279.10": 1331, "peak@325.05": 1332, "peak@325.14": 1333, "peak@325.24": 1334, "peak@263.97": 1335, "peak@168.05": 1336, "peak@179.09": 1337, "peak@177.08": 1338, "peak@138.06": 1339, "peak@178.09": 1340, "peak@150.13": 1341, "peak@150.05": 1342, "peak@149.05": 1343, "peak@114.05": 1344, "peak@166.03": 1345, "peak@148.02": 1346, "peak@143.02": 1347, "peak@138.04": 1348, "peak@99.03": 1349, "peak@89.01": 1350, "peak@86.99": 1351, "peak@103.00": 1352, "peak@333.11": 1353, "peak@331.10": 1354, "peak@321.11": 1355, "peak@127.03": 1356, "peak@186.07": 1357, "peak@90.01": 1358, "peak@117.02": 1359, "peak@334.17": 1360, "peak@110.04": 1361, "peak@111.00": 1362, "peak@155.03": 1363, "peak@319.10": 1364, "peak@159.02": 1365, "peak@190.10": 1366, "peak@161.05": 1367, "peak@186.05": 1368, "peak@160.99": 1369, "peak@176.99": 1370, "peak@133.07": 1371, "peak@200.12": 1372, "peak@173.11": 1373, "peak@115.04": 1374, "peak@376.04": 1375, "peak@265.95": 1376, "peak@279.13": 1377, "peak@219.11": 1378, "peak@178.04": 1379, "peak@166.04": 1380, "peak@220.13": 1381, "peak@192.14": 1382, "peak@162.13": 1383, "peak@147.10": 1384, "peak@330.09": 1385, "peak@288.09": 1386, "peak@286.07": 1387, "peak@204.00": 1388, "peak@183.97": 1389, "peak@184.98": 1390, "peak@174.07": 1391, "peak@241.09": 1392, "peak@226.06": 1393, "peak@220.07": 1394, "peak@219.07": 1395, "peak@211.08": 1396, "peak@205.05": 1397, "peak@198.07": 1398, "peak@197.06": 1399, "peak@193.09": 1400, "peak@193.05": 1401, "peak@189.09": 1402, "peak@188.05": 1403, "peak@187.04": 1404, "peak@175.04": 1405, "peak@164.05": 1406, "peak@196.98": 1407, "peak@161.02": 1408, "peak@151.08": 1409, "peak@150.07": 1410, "peak@148.05": 1411, "peak@139.08": 1412, "peak@280.01": 1413, "peak@254.04": 1414, "peak@253.03": 1415, "peak@245.04": 1416, "peak@244.03": 1417, "peak@237.06": 1418, "peak@225.03": 1419, "peak@213.98": 1420, "peak@212.97": 1421, "peak@90.09": 1422}, "norms": null, "mapfile_path": null, "__numpys": [], "__scipys": [], "__ignoreds": [], "__recursive_saveloads": [], "__weights_format": "np.ndarray"}\n\\ No newline at end of file\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/similarity/spec2vec/weights_100.binary |
| b |
| Binary file test-data/similarity/spec2vec/weights_100.binary has changed |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/spectral_similarity/test1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/spectral_similarity/test1.json Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"__Scores__": true, "is_symmetric": false, "references": [{"scannumber": "1161", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C4H10NO3PS", "inchikey": "YASYVMFAVPKPKE-SECBINFHSA-N", "smiles": "COP(=O)(N=C(O)C)SC", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "ionization": "ESI+", "license": "CC BY-NC", "num_peaks": "16", "compound_name": "Acephate", "retention_time": 1.232997, "precursor_mz": 184.0194, "adduct": "[M+H]+", "instrument_type": "LC-ESI-Orbitrap", "peaks_json": [[90.09368, 1128.0], [93.11512, 1241.0], [95.10279, 1118.0], [101.31465, 1152.0], [102.90688, 1322.0], [103.98039, 1201.0], [112.01607, 12289.0], [112.99994, 38027.0], [115.00399, 1634.0], [124.98121, 922.0], [128.97701, 9208.0], [132.57193, 1350.0], [135.84808, 1428.0], [142.99275, 16419.0], [147.94205, 1750.0], [173.5094, 2353.0]]}, {"scannumber": "2257", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C12H11NO2", "inchikey": "CVXBEEMKQHEXEN-UHFFFAOYSA-N", "smiles": "CN=C(Oc1cccc2c1cccc2)O", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "ionization": "ESI+", "license": "CC BY-NC", "peak_comments": {"145.06491": "Theoretical m/z 145.064787, Mass diff 0 (0.85 ppm), SMILES OC1=CC=CC=2C=CC=CC12, Annotation [C10H8O+H]+, Rule of HR True"}, "num_peaks": "1", "compound_name": "Carbaryl", "retention_time": 5.259445, "precursor_mz": 202.0863, "adduct": "[M+H]+", "instrument_type": "LC-ESI-Orbitrap", "peaks_json": [[145.06491, 1326147.0]]}, {"scannumber": "1516", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C8H16NO5P", "inchikey": "VEENJGZXVHKXNB-UHFFFAOYSA-N", "smiles": "COP(=O)(OC(=CC(=O)N(C)C)C)OC", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "ionization": "ESI+", "license": "CC BY-NC", "peak_comments": {"112.07591": "Theoretical m/z 112.075687, Mass diff 0 (1.99 ppm), SMILES O=C(C=CC)N(C)C, Annotation [C6H11NO-H]+, Rule of HR True", "127.01563": "Theoretical m/z 127.01547, Mass diff 0 (1.26 ppm), SMILES O=P(O)(OC)OC, Annotation [C2H7O4P+H]+, Rule of HR True", "193.02605": "Theoretical m/z 193.026035, Mass diff 0 (0.08 ppm), SMILES O=CC=C(OP(=O)(OC)OC)C, Annotation [C6H11O5P-H]+, Rule of HR True", "238.08437": "Theoretical m/z 238.083891, Mass diff 0 (2.01 ppm), SMILES O=C(C=C(OP(=O)(OC)OC)C)N(C)C, Annotation [C8H16NO5P+H]+, Rule of HR True"}, "num_peaks": "5", "compound_name": "Dicrotophos", "retention_time": 2.025499, "precursor_mz": 238.0844, "adduct": "[M+H]+", "instrument_type": "LC-ESI-Orbitrap", "peaks_json": [[112.074, 102027.0], [112.07591, 9070987.0], [127.01563, 3230337.0], [193.02605, 7897744.0], [238.08437, 2973124.0]]}, {"scannumber": "1865", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C5H12NO3PS2", "inchikey": "MCWXGJITAZMZEV-UHFFFAOYSA-N", "smiles": "CN=C(CSP(=S)(OC)OC)O", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "ionization": "ESI+", "license": "CC BY-NC", "peak_comments": {"88.0219": "Theoretical m/z 88.021549, Mass diff 0 (3.99 ppm), SMILES SCC=NC, Annotation [C3H7NS-H]+, Rule of HR True", "124.98233": "Theoretical m/z 124.982067, Mass diff 0 (2.11 ppm), SMILES S=P(OC)OC, Annotation [C2H7O2PS-H]+, Rule of HR True", "142.99275": "Theoretical m/z 142.993177, Mass diff 0 (0 ppm), Formula C2H8O3PS", "156.95422": "Theoretical m/z 156.954136, Mass diff 0 (0.54 ppm), SMILES S=P(S)(OC)OC, Annotation [C2H7O2PS2-H]+, Rule of HR True", "170.97": "Theoretical m/z 170.969791, Mass diff 0 (1.22 ppm), SMILES S=P(OC)(OC)SC, Annotation [C3H9O2PS2-H]+, Rule of HR True", "197.98123": "Theoretical m/z 197.980686, Mass diff 0.001 (2.75 ppm), SMILES S=P(OC)SCC(O)=NC, Annotation [C4H10NO2PS2-H]+, Rule of HR True", "198.96501": "Theoretical m/z 198'..b'68404, 2870255.0], [312.986211377174, 2448284.0], [313.019993142226, 1479514.0], [326.982724315442, 4863722.0], [344.975776862771, 10267994.0], [345.976092174038, 3016933.0], [346.046486912175, 1754291.0], [346.973191534072, 1590963.0], [382.97408022551, 1514772.0], [386.969422084375, 2096957.0], [402.964369782575, 1172149.0], [493.152823320977, 2513229.0]]}, {"ionmode": "negative", "spectrumtype": "Centroid", "num_peaks": "57", "compound_name": "C012", "retention_time": 687.83, "retention_index": 4134.613095, "peaks_json": [[78.0419846383593, 1742200.0], [79.0497716096318, 1893817.0], [85.0284186196566, 2191757.0], [121.046741626167, 6162741.0], [142.078087888737, 3381352.0], [192.997735629267, 9539743.0], [195.029110650825, 3772846.0], [205.016711322548, 5926636.0], [207.066696618797, 3714385.0], [209.098935410027, 6173585.0], [213.05754958053, 13341991.0], [219.06802937228, 2601724.0], [253.016653119059, 43935840.0], [269.047850642358, 4644691.0], [271.027137265637, 6759639.0], [281.085992168442, 2140320.0], [284.047997947258, 8403825.0], [311.073606748707, 3371803.0], [313.113777264345, 2391990.0], [325.985953604199, 8513850.0], [327.03525664153, 49155384.0], [328.035343658, 13109000.0], [329.014530869431, 3595462.0], [331.063707530223, 2063612.0], [343.084122931946, 3769846.0], [345.046169172075, 8812838.0], [353.090427317747, 2832675.0], [359.09769204202, 9873384.0], [360.028136457829, 10686927.0], [360.169639740951, 3818378.0], [371.040514349465, 1472266.0], [387.002413998209, 12940469.0], [387.071825807939, 15096984.0], [389.068871345424, 1810336.0], [402.055174276849, 12479459.0], [404.05195192305, 1405422.0], [458.971973456131, 1214840.0], [459.041861218696, 1286084.0], [460.952039584771, 4371596.0], [461.021207128847, 2869881.0], [461.090256355859, 17842323.0], [461.951796665319, 1222018.0], [462.091555156095, 6970195.0], [463.088708091285, 2556050.0], [475.072310244956, 13564752.0], [476.003821454759, 1471505.0], [476.143434019655, 13026182.0], [477.140480798609, 4944561.0], [478.141485242814, 1506934.0], [479.101672410454, 3603024.0], [490.12632015072, 18188437.0], [491.122346777972, 10290558.0], [549.162553092955, 24746614.0], [563.144239233773, 12735845.0], [624.183209223215, 7134906.0], [637.164550513183, 3866368.0], [698.205944560218, 1919968.0]]}, {"ionmode": "negative", "spectrumtype": "Centroid", "num_peaks": "43", "compound_name": "C020", "retention_time": 687.99, "retention_index": 4135.089286, "peaks_json": [[109.052235628516, 1922885.0], [111.044058476785, 1730416.0], [133.064909307365, 1579533.0], [137.041722086745, 2474039.0], [194.053642118165, 5252308.0], [212.061782732582, 10437319.0], [267.034768010352, 4429084.0], [267.068824022318, 27744081.0], [268.069192256745, 2367920.0], [310.970568727813, 3126083.0], [311.004219192148, 2666091.0], [325.055731606087, 7634729.0], [327.965549188207, 5442532.0], [328.962716535303, 2722019.0], [339.03821058645, 6627839.0], [341.051986399316, 1671451.0], [342.996634492902, 3939816.0], [345.115297423962, 3938049.0], [358.067243216398, 3526875.0], [361.025211906011, 6516476.0], [388.003000430725, 3422825.0], [388.073272089579, 4224454.0], [399.005054559559, 4141766.0], [401.984326631505, 5585170.0], [402.98179623463, 3562508.0], [416.036473280551, 7221552.0], [417.033665098569, 4129234.0], [417.087073648909, 1945166.0], [418.994970709551, 2648178.0], [430.088321970134, 10765018.0], [431.085366629672, 6887942.0], [473.09370665615, 2502410.0], [475.002854889036, 2969642.0], [475.14184210128, 30625723.0], [477.070907310139, 2271450.0], [489.055479984185, 1973511.0], [503.107930410573, 2407435.0], [549.092119293556, 2513579.0], [552.160354111203, 1673065.0], [565.143723544965, 3485979.0], [610.132183060405, 1997085.0], [625.181479977537, 3872339.0], [697.202597429349, 2820429.0]]}], "n_row": 170, "n_col": 51, "row": [], "col": [], "data": [], "dtype": [["CosineGreedy_0.1_0.0_1.0_score", "<f8"], ["CosineGreedy_0.1_0.0_1.0_matches", "<i8"]]}\n\\ No newline at end of file\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/spectral_similarity/test2.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/spectral_similarity/test2.json Tue Jun 27 14:25:59 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"__Scores__": true, "is_symmetric": false, "references": [{"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C14H10", "inchikey": "YNPNZTXNASCQKK-UHFFFAOYSA-N", "smiles": "C1=CC2=C(C=C1)C1=C(C=CC=C1)C=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "19", "compound_name": "Phenanthrene", "retention_time": null, "retention_index": 1832.9, "precursor_mz": 178.0775, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[74.01508, 137808.0], [75.02295, 278714.0], [76.03075, 608417.0], [87.02295, 304266.0], [88.03076, 497050.0], [89.03857, 441168.0], [98.01511, 150478.0], [150.04633, 868927.0], [151.05415, 546351.0], [152.0619, 2275502.0], [153.06528, 276320.0], [169.06468, 272559.0], [174.04636, 365846.0], [175.05423, 272039.0], [176.062, 3370523.0], [177.06982, 1751846.0], [178.0775, 13724432.0], [179.08078, 2250119.0], [180.08412, 138203.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C14H10", "inchikey": "MWPLVEDNUUSJAV-UHFFFAOYSA-N", "smiles": "C1=CC2=CC3=C(C=CC=C3)C=C2C=C1", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "21", "compound_name": "Anthracene", "retention_time": null, "retention_index": 1844.4, "precursor_mz": 178.07754, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[74.0151, 117371.0], [75.02296, 245305.0], [76.03077, 632686.0], [87.02297, 236214.0], [88.03078, 347832.0], [89.0386, 507288.0], [91.05425, 130861.0], [126.04636, 128356.0], [149.04478, 126331.0], [150.04637, 641829.0], [151.05415, 403195.0], [152.06195, 1369833.0], [153.06534, 175290.0], [169.06471, 228827.0], [174.04639, 255716.0], [175.05423, 198784.0], [176.06204, 2563053.0], [177.06984, 1182037.0], [178.07754, 11002398.0], [179.08081, 1778803.0], [180.08418, 132922.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C16H10", "inchikey": "GVEPBJHOBDJJJI-UHFFFAOYSA-N", "smiles": "C1=CC2=C(C=C1)C1=C3C2=CC=CC3=CC=C1", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "17", "compound_name": "Fluoranthene", "retention_time": null, "retention_index": 2102.7, "precursor_mz": 202.07756, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[75.02299, 112456.0], [87.02298, 183640.0], [88.03079, 367434.0], [99.02296, 124952.0], [100.03078, 376079.0], [101.03863, 381288.0], [150.04642, 86059.0], [174.04634, 246963.0], [176.06194, 141676.0], [198.0464, 244370.0], [199.05429, 285767.0], [200.06207, 1958890.0], [201.06982, 1103710.0], [202.07756, 8104188.0], [203.08084, 1377015.0], [204.08421, 98067.0], [219.08043, 186623.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C16H10", "inchikey": "BBEAQIROQSPTKN-UHFFFAOYSA-N", "smiles": "C1=CC2=C3C(C=CC4=CC=CC(C=C2)=C34)=C1", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "16", "compound_name": "Pyrene", "retention_time": null, "retention_index": 2154.5, "precursor_mz": 202.07759, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[87.02299, 147113.0], [88.0308, 305149.0], [99.02298, 137042.0], [100.0308, 508914.0], [101.03864, 472094.0], [101.54032, 82430.0], [150.04637, 80741.0], [174.04631, 212706.0], [198.04643, 262925.0], [199.05429, 295144.0], [200.06209, 1960712.0], [201.06982, 1270466.0], [202.'..b'NDFUHDPQJ-UHFFFAOYSA-N", "smiles": "C1=CC=C(C=C1)C2=CC=C(C=C2)C3=CC=CC=C3", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "25", "compound_name": "para-Terphenyl", "retention_time": null, "retention_index": 2207.5, "precursor_mz": 230.10886, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[88.03077, 233962.0], [101.03861, 353544.0], [113.03854, 437845.0], [115.05423, 690291.0], [128.062, 293046.0], [151.05412, 266397.0], [152.06195, 961184.0], [153.06976, 409346.0], [176.06192, 232793.0], [189.06972, 408734.0], [200.0619, 342984.0], [201.06986, 238974.0], [202.07758, 1292332.0], [203.08093, 374439.0], [213.06973, 256631.0], [215.08548, 1220866.0], [216.08881, 217320.0], [224.062, 181393.0], [226.07771, 1503774.0], [227.08588, 1198323.0], [228.09344, 2885510.0], [229.10123, 1791323.0], [230.10886, 17890056.0], [231.11214, 3536976.0], [232.11542, 320231.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C16H10S", "inchikey": "YEUHHUCOSQOCIX-UHFFFAOYSA-N", "smiles": "S1C2=C(C=CC=C2)C2=C1C1=CC=CC=C1C=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "23", "compound_name": "Benzo[b]naphtho[2,1-d]thiophene", "retention_time": null, "retention_index": 2419.3, "precursor_mz": 234.04965, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[91.05425, 49130.0], [93.52686, 61653.0], [94.53469, 76638.0], [104.01679, 126871.0], [116.01675, 112547.0], [117.02459, 99108.0], [162.04623, 54491.0], [163.05408, 136418.0], [164.06198, 56321.0], [187.05406, 273349.0], [188.06189, 200750.0], [189.06969, 453336.0], [190.07306, 77884.0], [200.06189, 135620.0], [201.06973, 74692.0], [202.07758, 425058.0], [203.08086, 72058.0], [226.07762, 63460.0], [232.03409, 769638.0], [233.04245, 382457.0], [234.04965, 4404102.0], [235.05304, 725574.0], [236.04547, 251450.0]]}, {"scannumber": "-1", "ionmode": "positive", "spectrumtype": "Centroid", "formula": "C17H12", "inchikey": "HAPOJKSPCGLOOD-UHFFFAOYSA-N", "smiles": "C1C2=CC=CC=C2C2=C1C=C1C=CC=CC1=C2", "authors": "Price et al., RECETOX, Masaryk University (CZ)", "instrument": "Q Exactive GC Orbitrap GC-MS/MS", "ionization": "EI+", "license": "CC BY-NC", "peak_comments": null, "num_peaks": "21", "compound_name": "2,3-Benzofluorene", "retention_time": null, "retention_index": 2257.5, "precursor_mz": 216.09326, "adduct": "[M]+", "collision_energy": "70eV", "instrument_type": "GC-EI-Orbitrap", "peaks_json": [[93.52689, 122035.0], [94.53471, 241743.0], [95.03638, 42130.0], [105.52688, 47526.0], [106.53471, 171653.0], [107.03639, 60004.0], [107.5425, 180288.0], [108.03385, 97471.0], [163.05414, 68194.0], [187.05412, 167183.0], [188.06201, 86262.0], [189.06975, 239421.0], [190.07321, 37778.0], [211.05426, 117044.0], [212.06215, 60813.0], [213.0699, 808499.0], [214.07317, 202222.0], [215.0855, 3634570.0], [216.09326, 2535030.0], [217.09671, 444170.0], [218.09999, 37976.0]]}], "n_row": 7, "n_col": 7, "row": [0, 0, 1, 1, 2, 2, 3, 3, 3, 4, 4, 4, 5, 6, 6], "col": [0, 1, 0, 1, 2, 3, 2, 3, 4, 3, 4, 6, 5, 4, 6], "data": [[true, 1.0, 19], [true, 0.9986026416952778, 18], [true, 0.9986026416952778, 18], [true, 1.0, 21], [true, 0.9999999999999998, 17], [true, 0.999244339007754, 15], [true, 0.999244339007754, 15], [true, 1.0000000000000002, 16], [true, 0.07545864560115775, 6], [true, 0.07545864560115775, 6], [true, 1.0, 25], [true, 0.061706695748466586, 4], [true, 1.0, 23], [true, 0.061706695748466586, 4], [true, 1.0, 21]], "dtype": [["MetadataMatch_retention_index_difference_60.0_f0", "|b1"], ["CosineHungarian_0.1_0.0_1.0_score", "<f8"], ["CosineHungarian_0.1_0.0_1.0_matches", "<i8"]]}\n\\ No newline at end of file\n' |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/split/chunk-size/chunk_0.msp --- a/test-data/split/chunk-size/chunk_0.msp Thu May 25 09:06:00 2023 +0000 +++ b/test-data/split/chunk-size/chunk_0.msp Tue Jun 27 14:25:59 2023 +0000 |
| b |
| @@ -1,9 +1,6 @@ SYNONYM: 1-NITROPYRENE -DB#: JP000001 INCHIKEY: ALRLPDGCPYIVHP-UHFFFAOYSA-N -MW: 247.063328528 FORMULA: C16H9NO2 -ACCESSION: JP000001 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -19,6 +16,8 @@ MOLECULAR_FORMULA: C16H9NO2 TOTAL_EXACT_MASS: 247.063328528 COMPOUND_NAME: 1-NITROPYRENE +SPECTRUM_ID: JP000001 +NOMINAL_MASS: 247.063328528 PRECURSOR_MZ: 0.0 PARENT_MASS: 247.06333 NUM PEAKS: 75 @@ -99,11 +98,8 @@ 248.0 10.16 SYNONYM: 2,4-DINITROPHENOL -DB#: JP000002 INCHIKEY: UFBJCMHMOXMLKC-UHFFFAOYSA-N -MW: 184.01202122799998 FORMULA: C6H4N2O5 -ACCESSION: JP000002 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -119,6 +115,8 @@ MOLECULAR_FORMULA: C6H4N2O5 TOTAL_EXACT_MASS: 184.01202122799998 COMPOUND_NAME: 2,4-DINITROPHENOL +SPECTRUM_ID: JP000002 +NOMINAL_MASS: 184.01202122799998 PRECURSOR_MZ: 0.0 PARENT_MASS: 184.01202 NUM PEAKS: 64 @@ -188,11 +186,8 @@ 186.0 1.34 SYNONYM: 3,4-DICHLOROPHENOL -DB#: JP000003 INCHIKEY: WDNBURPWRNALGP-UHFFFAOYSA-N -MW: 161.963920108 FORMULA: C6H4Cl2O -ACCESSION: JP000003 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -208,6 +203,8 @@ MOLECULAR_FORMULA: C6H4Cl2O TOTAL_EXACT_MASS: 161.963920108 COMPOUND_NAME: 3,4-DICHLOROPHENOL +SPECTRUM_ID: JP000003 +NOMINAL_MASS: 161.963920108 PRECURSOR_MZ: 0.0 PARENT_MASS: 161.96392 NUM PEAKS: 36 @@ -249,11 +246,8 @@ 166.0 9.78 SYNONYM: 2,5-DICHLOROPHENOL -DB#: JP000004 INCHIKEY: RANCECPPZPIPNO-UHFFFAOYSA-N -MW: 161.963920108 FORMULA: C6H4Cl2O -ACCESSION: JP000004 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -269,6 +263,8 @@ MOLECULAR_FORMULA: C6H4Cl2O TOTAL_EXACT_MASS: 161.963920108 COMPOUND_NAME: 2,5-DICHLOROPHENOL +SPECTRUM_ID: JP000004 +NOMINAL_MASS: 161.963920108 PRECURSOR_MZ: 0.0 PARENT_MASS: 161.96392 NUM PEAKS: 44 |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/split/chunk-size/chunk_1.msp --- a/test-data/split/chunk-size/chunk_1.msp Thu May 25 09:06:00 2023 +0000 +++ b/test-data/split/chunk-size/chunk_1.msp Tue Jun 27 14:25:59 2023 +0000 |
| b |
| @@ -1,9 +1,6 @@ SYNONYM: 2,6-DICHLOROPHENOL -DB#: JP000005 INCHIKEY: HOLHYSJJBXSLMV-UHFFFAOYSA-N -MW: 161.963920108 FORMULA: C6H4Cl2O -ACCESSION: JP000005 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -19,6 +16,8 @@ MOLECULAR_FORMULA: C6H4Cl2O TOTAL_EXACT_MASS: 161.963920108 COMPOUND_NAME: 2,6-DICHLOROPHENOL +SPECTRUM_ID: JP000005 +NOMINAL_MASS: 161.963920108 PRECURSOR_MZ: 0.0 PARENT_MASS: 161.96392 NUM PEAKS: 33 @@ -57,11 +56,8 @@ 166.0 9.91 SYNONYM: 2,3-DICHLOROPHENOL -DB#: JP000006 INCHIKEY: UMPSXRYVXUPCOS-UHFFFAOYSA-N -MW: 161.963920108 FORMULA: C6H4Cl2O -ACCESSION: JP000006 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -77,6 +73,8 @@ MOLECULAR_FORMULA: C6H4Cl2O TOTAL_EXACT_MASS: 161.963920108 COMPOUND_NAME: 2,3-DICHLOROPHENOL +SPECTRUM_ID: JP000006 +NOMINAL_MASS: 161.963920108 PRECURSOR_MZ: 0.0 PARENT_MASS: 161.96392 NUM PEAKS: 42 @@ -124,11 +122,8 @@ 166.0 7.58 SYNONYM: 2,4-DICHLOROPHENOL -DB#: JP000007 INCHIKEY: HFZWRUODUSTPEG-UHFFFAOYSA-N -MW: 161.963920108 FORMULA: C6H4Cl2O -ACCESSION: JP000007 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -144,6 +139,8 @@ MOLECULAR_FORMULA: C6H4Cl2O TOTAL_EXACT_MASS: 161.963920108 COMPOUND_NAME: 2,4-DICHLOROPHENOL +SPECTRUM_ID: JP000007 +NOMINAL_MASS: 161.963920108 PRECURSOR_MZ: 0.0 PARENT_MASS: 161.96392 NUM PEAKS: 37 @@ -186,11 +183,8 @@ 166.0 9.19 SYNONYM: 3,5-DICHLOROPHENOL -DB#: JP000008 INCHIKEY: VPOMSPZBQMDLTM-UHFFFAOYSA-N -MW: 161.963920108 FORMULA: C6H4Cl2O -ACCESSION: JP000008 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -206,6 +200,8 @@ MOLECULAR_FORMULA: C6H4Cl2O TOTAL_EXACT_MASS: 161.963920108 COMPOUND_NAME: 3,5-DICHLOROPHENOL +SPECTRUM_ID: JP000008 +NOMINAL_MASS: 161.963920108 PRECURSOR_MZ: 0.0 PARENT_MASS: 161.96392 NUM PEAKS: 32 |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/split/chunk-size/chunk_2.msp --- a/test-data/split/chunk-size/chunk_2.msp Thu May 25 09:06:00 2023 +0000 +++ b/test-data/split/chunk-size/chunk_2.msp Tue Jun 27 14:25:59 2023 +0000 |
| b |
| @@ -1,9 +1,6 @@ SYNONYM: 2,4,5-TRICHLOROPHENOL -DB#: JP000009 INCHIKEY: LHJGJYXLEPZJPM-UHFFFAOYSA-N -MW: 195.924947756 FORMULA: C6H3Cl3O -ACCESSION: JP000009 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -19,6 +16,8 @@ MOLECULAR_FORMULA: C6H3Cl3O TOTAL_EXACT_MASS: 195.924947756 COMPOUND_NAME: 2,4,5-TRICHLOROPHENOL +SPECTRUM_ID: JP000009 +NOMINAL_MASS: 195.924947756 PRECURSOR_MZ: 0.0 PARENT_MASS: 195.92495 NUM PEAKS: 65 @@ -89,11 +88,8 @@ 202.0 3.15 SYNONYM: 2,4,6-TRICHLOROPHENOL -DB#: JP000010 INCHIKEY: LINPIYWFGCPVIE-UHFFFAOYSA-N -MW: 195.924947756 FORMULA: C6H3Cl3O -ACCESSION: JP000010 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -109,6 +105,8 @@ MOLECULAR_FORMULA: C6H3Cl3O TOTAL_EXACT_MASS: 195.924947756 COMPOUND_NAME: 2,4,6-TRICHLOROPHENOL +SPECTRUM_ID: JP000010 +NOMINAL_MASS: 195.924947756 PRECURSOR_MZ: 0.0 PARENT_MASS: 195.92495 NUM PEAKS: 66 |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/split/num-chunks/chunk_0.msp --- a/test-data/split/num-chunks/chunk_0.msp Thu May 25 09:06:00 2023 +0000 +++ b/test-data/split/num-chunks/chunk_0.msp Tue Jun 27 14:25:59 2023 +0000 |
| b |
| @@ -1,9 +1,6 @@ SYNONYM: 1-NITROPYRENE -DB#: JP000001 INCHIKEY: ALRLPDGCPYIVHP-UHFFFAOYSA-N -MW: 247.063328528 FORMULA: C16H9NO2 -ACCESSION: JP000001 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -19,6 +16,8 @@ MOLECULAR_FORMULA: C16H9NO2 TOTAL_EXACT_MASS: 247.063328528 COMPOUND_NAME: 1-NITROPYRENE +SPECTRUM_ID: JP000001 +NOMINAL_MASS: 247.063328528 PRECURSOR_MZ: 0.0 PARENT_MASS: 247.06333 NUM PEAKS: 75 @@ -99,11 +98,8 @@ 248.0 10.16 SYNONYM: 3,4-DICHLOROPHENOL -DB#: JP000003 INCHIKEY: WDNBURPWRNALGP-UHFFFAOYSA-N -MW: 161.963920108 FORMULA: C6H4Cl2O -ACCESSION: JP000003 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -119,6 +115,8 @@ MOLECULAR_FORMULA: C6H4Cl2O TOTAL_EXACT_MASS: 161.963920108 COMPOUND_NAME: 3,4-DICHLOROPHENOL +SPECTRUM_ID: JP000003 +NOMINAL_MASS: 161.963920108 PRECURSOR_MZ: 0.0 PARENT_MASS: 161.96392 NUM PEAKS: 36 @@ -160,11 +158,8 @@ 166.0 9.78 SYNONYM: 2,6-DICHLOROPHENOL -DB#: JP000005 INCHIKEY: HOLHYSJJBXSLMV-UHFFFAOYSA-N -MW: 161.963920108 FORMULA: C6H4Cl2O -ACCESSION: JP000005 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -180,6 +175,8 @@ MOLECULAR_FORMULA: C6H4Cl2O TOTAL_EXACT_MASS: 161.963920108 COMPOUND_NAME: 2,6-DICHLOROPHENOL +SPECTRUM_ID: JP000005 +NOMINAL_MASS: 161.963920108 PRECURSOR_MZ: 0.0 PARENT_MASS: 161.96392 NUM PEAKS: 33 @@ -218,11 +215,8 @@ 166.0 9.91 SYNONYM: 2,4-DICHLOROPHENOL -DB#: JP000007 INCHIKEY: HFZWRUODUSTPEG-UHFFFAOYSA-N -MW: 161.963920108 FORMULA: C6H4Cl2O -ACCESSION: JP000007 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -238,6 +232,8 @@ MOLECULAR_FORMULA: C6H4Cl2O TOTAL_EXACT_MASS: 161.963920108 COMPOUND_NAME: 2,4-DICHLOROPHENOL +SPECTRUM_ID: JP000007 +NOMINAL_MASS: 161.963920108 PRECURSOR_MZ: 0.0 PARENT_MASS: 161.96392 NUM PEAKS: 37 @@ -280,11 +276,8 @@ 166.0 9.19 SYNONYM: 2,4,5-TRICHLOROPHENOL -DB#: JP000009 INCHIKEY: LHJGJYXLEPZJPM-UHFFFAOYSA-N -MW: 195.924947756 FORMULA: C6H3Cl3O -ACCESSION: JP000009 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -300,6 +293,8 @@ MOLECULAR_FORMULA: C6H3Cl3O TOTAL_EXACT_MASS: 195.924947756 COMPOUND_NAME: 2,4,5-TRICHLOROPHENOL +SPECTRUM_ID: JP000009 +NOMINAL_MASS: 195.924947756 PRECURSOR_MZ: 0.0 PARENT_MASS: 195.92495 NUM PEAKS: 65 |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/split/num-chunks/chunk_1.msp --- a/test-data/split/num-chunks/chunk_1.msp Thu May 25 09:06:00 2023 +0000 +++ b/test-data/split/num-chunks/chunk_1.msp Tue Jun 27 14:25:59 2023 +0000 |
| b |
| @@ -1,9 +1,6 @@ SYNONYM: 2,4-DINITROPHENOL -DB#: JP000002 INCHIKEY: UFBJCMHMOXMLKC-UHFFFAOYSA-N -MW: 184.01202122799998 FORMULA: C6H4N2O5 -ACCESSION: JP000002 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -19,6 +16,8 @@ MOLECULAR_FORMULA: C6H4N2O5 TOTAL_EXACT_MASS: 184.01202122799998 COMPOUND_NAME: 2,4-DINITROPHENOL +SPECTRUM_ID: JP000002 +NOMINAL_MASS: 184.01202122799998 PRECURSOR_MZ: 0.0 PARENT_MASS: 184.01202 NUM PEAKS: 64 @@ -88,11 +87,8 @@ 186.0 1.34 SYNONYM: 2,5-DICHLOROPHENOL -DB#: JP000004 INCHIKEY: RANCECPPZPIPNO-UHFFFAOYSA-N -MW: 161.963920108 FORMULA: C6H4Cl2O -ACCESSION: JP000004 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -108,6 +104,8 @@ MOLECULAR_FORMULA: C6H4Cl2O TOTAL_EXACT_MASS: 161.963920108 COMPOUND_NAME: 2,5-DICHLOROPHENOL +SPECTRUM_ID: JP000004 +NOMINAL_MASS: 161.963920108 PRECURSOR_MZ: 0.0 PARENT_MASS: 161.96392 NUM PEAKS: 44 @@ -157,11 +155,8 @@ 166.0 8.78 SYNONYM: 2,3-DICHLOROPHENOL -DB#: JP000006 INCHIKEY: UMPSXRYVXUPCOS-UHFFFAOYSA-N -MW: 161.963920108 FORMULA: C6H4Cl2O -ACCESSION: JP000006 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -177,6 +172,8 @@ MOLECULAR_FORMULA: C6H4Cl2O TOTAL_EXACT_MASS: 161.963920108 COMPOUND_NAME: 2,3-DICHLOROPHENOL +SPECTRUM_ID: JP000006 +NOMINAL_MASS: 161.963920108 PRECURSOR_MZ: 0.0 PARENT_MASS: 161.96392 NUM PEAKS: 42 @@ -224,11 +221,8 @@ 166.0 7.58 SYNONYM: 3,5-DICHLOROPHENOL -DB#: JP000008 INCHIKEY: VPOMSPZBQMDLTM-UHFFFAOYSA-N -MW: 161.963920108 FORMULA: C6H4Cl2O -ACCESSION: JP000008 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -244,6 +238,8 @@ MOLECULAR_FORMULA: C6H4Cl2O TOTAL_EXACT_MASS: 161.963920108 COMPOUND_NAME: 3,5-DICHLOROPHENOL +SPECTRUM_ID: JP000008 +NOMINAL_MASS: 161.963920108 PRECURSOR_MZ: 0.0 PARENT_MASS: 161.96392 NUM PEAKS: 32 @@ -281,11 +277,8 @@ 166.0 9.68 SYNONYM: 2,4,6-TRICHLOROPHENOL -DB#: JP000010 INCHIKEY: LINPIYWFGCPVIE-UHFFFAOYSA-N -MW: 195.924947756 FORMULA: C6H3Cl3O -ACCESSION: JP000010 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -301,6 +294,8 @@ MOLECULAR_FORMULA: C6H3Cl3O TOTAL_EXACT_MASS: 195.924947756 COMPOUND_NAME: 2,4,6-TRICHLOROPHENOL +SPECTRUM_ID: JP000010 +NOMINAL_MASS: 195.924947756 PRECURSOR_MZ: 0.0 PARENT_MASS: 195.92495 NUM PEAKS: 66 |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/split/one-per-file/1NITROPYRENE.msp --- a/test-data/split/one-per-file/1NITROPYRENE.msp Thu May 25 09:06:00 2023 +0000 +++ b/test-data/split/one-per-file/1NITROPYRENE.msp Tue Jun 27 14:25:59 2023 +0000 |
| b |
| @@ -1,9 +1,6 @@ SYNONYM: 1-NITROPYRENE -DB#: JP000001 INCHIKEY: ALRLPDGCPYIVHP-UHFFFAOYSA-N -MW: 247.063328528 FORMULA: C16H9NO2 -ACCESSION: JP000001 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -19,7 +16,9 @@ MOLECULAR_FORMULA: C16H9NO2 TOTAL_EXACT_MASS: 247.063328528 COMPOUND_NAME: 1-NITROPYRENE -PRECURSOR_MZ: 0 +SPECTRUM_ID: JP000001 +NOMINAL_MASS: 247.063328528 +PRECURSOR_MZ: 0.0 PARENT_MASS: 247.06333 NUM PEAKS: 75 51.0 2.66 |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/split/one-per-file/23DICHLOROPHENOL.msp --- a/test-data/split/one-per-file/23DICHLOROPHENOL.msp Thu May 25 09:06:00 2023 +0000 +++ b/test-data/split/one-per-file/23DICHLOROPHENOL.msp Tue Jun 27 14:25:59 2023 +0000 |
| b |
| @@ -1,9 +1,6 @@ SYNONYM: 2,3-DICHLOROPHENOL -DB#: JP000006 INCHIKEY: UMPSXRYVXUPCOS-UHFFFAOYSA-N -MW: 161.963920108 FORMULA: C6H4Cl2O -ACCESSION: JP000006 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -19,7 +16,9 @@ MOLECULAR_FORMULA: C6H4Cl2O TOTAL_EXACT_MASS: 161.963920108 COMPOUND_NAME: 2,3-DICHLOROPHENOL -PRECURSOR_MZ: 0 +SPECTRUM_ID: JP000006 +NOMINAL_MASS: 161.963920108 +PRECURSOR_MZ: 0.0 PARENT_MASS: 161.96392 NUM PEAKS: 42 51.0 4.43 |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/split/one-per-file/245TRICHLOROPHENOL.msp --- a/test-data/split/one-per-file/245TRICHLOROPHENOL.msp Thu May 25 09:06:00 2023 +0000 +++ b/test-data/split/one-per-file/245TRICHLOROPHENOL.msp Tue Jun 27 14:25:59 2023 +0000 |
| b |
| @@ -1,9 +1,6 @@ SYNONYM: 2,4,5-TRICHLOROPHENOL -DB#: JP000009 INCHIKEY: LHJGJYXLEPZJPM-UHFFFAOYSA-N -MW: 195.924947756 FORMULA: C6H3Cl3O -ACCESSION: JP000009 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -19,7 +16,9 @@ MOLECULAR_FORMULA: C6H3Cl3O TOTAL_EXACT_MASS: 195.924947756 COMPOUND_NAME: 2,4,5-TRICHLOROPHENOL -PRECURSOR_MZ: 0 +SPECTRUM_ID: JP000009 +NOMINAL_MASS: 195.924947756 +PRECURSOR_MZ: 0.0 PARENT_MASS: 195.92495 NUM PEAKS: 65 51.0 2.58 |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/split/one-per-file/246TRICHLOROPHENOL.msp --- a/test-data/split/one-per-file/246TRICHLOROPHENOL.msp Thu May 25 09:06:00 2023 +0000 +++ b/test-data/split/one-per-file/246TRICHLOROPHENOL.msp Tue Jun 27 14:25:59 2023 +0000 |
| b |
| @@ -1,9 +1,6 @@ SYNONYM: 2,4,6-TRICHLOROPHENOL -DB#: JP000010 INCHIKEY: LINPIYWFGCPVIE-UHFFFAOYSA-N -MW: 195.924947756 FORMULA: C6H3Cl3O -ACCESSION: JP000010 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -19,7 +16,9 @@ MOLECULAR_FORMULA: C6H3Cl3O TOTAL_EXACT_MASS: 195.924947756 COMPOUND_NAME: 2,4,6-TRICHLOROPHENOL -PRECURSOR_MZ: 0 +SPECTRUM_ID: JP000010 +NOMINAL_MASS: 195.924947756 +PRECURSOR_MZ: 0.0 PARENT_MASS: 195.92495 NUM PEAKS: 66 53.0 14.63 |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/split/one-per-file/24DICHLOROPHENOL.msp --- a/test-data/split/one-per-file/24DICHLOROPHENOL.msp Thu May 25 09:06:00 2023 +0000 +++ b/test-data/split/one-per-file/24DICHLOROPHENOL.msp Tue Jun 27 14:25:59 2023 +0000 |
| b |
| @@ -1,9 +1,6 @@ SYNONYM: 2,4-DICHLOROPHENOL -DB#: JP000007 INCHIKEY: HFZWRUODUSTPEG-UHFFFAOYSA-N -MW: 161.963920108 FORMULA: C6H4Cl2O -ACCESSION: JP000007 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -19,7 +16,9 @@ MOLECULAR_FORMULA: C6H4Cl2O TOTAL_EXACT_MASS: 161.963920108 COMPOUND_NAME: 2,4-DICHLOROPHENOL -PRECURSOR_MZ: 0 +SPECTRUM_ID: JP000007 +NOMINAL_MASS: 161.963920108 +PRECURSOR_MZ: 0.0 PARENT_MASS: 161.96392 NUM PEAKS: 37 51.0 3.07 |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/split/one-per-file/24DINITROPHENOL.msp --- a/test-data/split/one-per-file/24DINITROPHENOL.msp Thu May 25 09:06:00 2023 +0000 +++ b/test-data/split/one-per-file/24DINITROPHENOL.msp Tue Jun 27 14:25:59 2023 +0000 |
| b |
| @@ -1,9 +1,6 @@ SYNONYM: 2,4-DINITROPHENOL -DB#: JP000002 INCHIKEY: UFBJCMHMOXMLKC-UHFFFAOYSA-N -MW: 184.01202122799998 FORMULA: C6H4N2O5 -ACCESSION: JP000002 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -19,7 +16,9 @@ MOLECULAR_FORMULA: C6H4N2O5 TOTAL_EXACT_MASS: 184.01202122799998 COMPOUND_NAME: 2,4-DINITROPHENOL -PRECURSOR_MZ: 0 +SPECTRUM_ID: JP000002 +NOMINAL_MASS: 184.01202122799998 +PRECURSOR_MZ: 0.0 PARENT_MASS: 184.01202 NUM PEAKS: 64 51.0 27.22 |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/split/one-per-file/25DICHLOROPHENOL.msp --- a/test-data/split/one-per-file/25DICHLOROPHENOL.msp Thu May 25 09:06:00 2023 +0000 +++ b/test-data/split/one-per-file/25DICHLOROPHENOL.msp Tue Jun 27 14:25:59 2023 +0000 |
| b |
| @@ -1,9 +1,6 @@ SYNONYM: 2,5-DICHLOROPHENOL -DB#: JP000004 INCHIKEY: RANCECPPZPIPNO-UHFFFAOYSA-N -MW: 161.963920108 FORMULA: C6H4Cl2O -ACCESSION: JP000004 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -19,7 +16,9 @@ MOLECULAR_FORMULA: C6H4Cl2O TOTAL_EXACT_MASS: 161.963920108 COMPOUND_NAME: 2,5-DICHLOROPHENOL -PRECURSOR_MZ: 0 +SPECTRUM_ID: JP000004 +NOMINAL_MASS: 161.963920108 +PRECURSOR_MZ: 0.0 PARENT_MASS: 161.96392 NUM PEAKS: 44 51.0 5.05 |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/split/one-per-file/26DICHLOROPHENOL.msp --- a/test-data/split/one-per-file/26DICHLOROPHENOL.msp Thu May 25 09:06:00 2023 +0000 +++ b/test-data/split/one-per-file/26DICHLOROPHENOL.msp Tue Jun 27 14:25:59 2023 +0000 |
| b |
| @@ -1,9 +1,6 @@ SYNONYM: 2,6-DICHLOROPHENOL -DB#: JP000005 INCHIKEY: HOLHYSJJBXSLMV-UHFFFAOYSA-N -MW: 161.963920108 FORMULA: C6H4Cl2O -ACCESSION: JP000005 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -19,7 +16,9 @@ MOLECULAR_FORMULA: C6H4Cl2O TOTAL_EXACT_MASS: 161.963920108 COMPOUND_NAME: 2,6-DICHLOROPHENOL -PRECURSOR_MZ: 0 +SPECTRUM_ID: JP000005 +NOMINAL_MASS: 161.963920108 +PRECURSOR_MZ: 0.0 PARENT_MASS: 161.96392 NUM PEAKS: 33 53.0 7.25 |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/split/one-per-file/34DICHLOROPHENOL.msp --- a/test-data/split/one-per-file/34DICHLOROPHENOL.msp Thu May 25 09:06:00 2023 +0000 +++ b/test-data/split/one-per-file/34DICHLOROPHENOL.msp Tue Jun 27 14:25:59 2023 +0000 |
| b |
| @@ -1,9 +1,6 @@ SYNONYM: 3,4-DICHLOROPHENOL -DB#: JP000003 INCHIKEY: WDNBURPWRNALGP-UHFFFAOYSA-N -MW: 161.963920108 FORMULA: C6H4Cl2O -ACCESSION: JP000003 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -19,7 +16,9 @@ MOLECULAR_FORMULA: C6H4Cl2O TOTAL_EXACT_MASS: 161.963920108 COMPOUND_NAME: 3,4-DICHLOROPHENOL -PRECURSOR_MZ: 0 +SPECTRUM_ID: JP000003 +NOMINAL_MASS: 161.963920108 +PRECURSOR_MZ: 0.0 PARENT_MASS: 161.96392 NUM PEAKS: 36 51.0 2.25 |
| b |
| diff -r 715fe77be601 -r 1b09315a3f87 test-data/split/one-per-file/35DICHLOROPHENOL.msp --- a/test-data/split/one-per-file/35DICHLOROPHENOL.msp Thu May 25 09:06:00 2023 +0000 +++ b/test-data/split/one-per-file/35DICHLOROPHENOL.msp Tue Jun 27 14:25:59 2023 +0000 |
| b |
| @@ -1,9 +1,6 @@ SYNONYM: 3,5-DICHLOROPHENOL -DB#: JP000008 INCHIKEY: VPOMSPZBQMDLTM-UHFFFAOYSA-N -MW: 161.963920108 FORMULA: C6H4Cl2O -ACCESSION: JP000008 AUTHOR: KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH LICENSE: CC BY-NC-SA INSTRUMENT: VARIAN MAT-44 @@ -19,7 +16,9 @@ MOLECULAR_FORMULA: C6H4Cl2O TOTAL_EXACT_MASS: 161.963920108 COMPOUND_NAME: 3,5-DICHLOROPHENOL -PRECURSOR_MZ: 0 +SPECTRUM_ID: JP000008 +NOMINAL_MASS: 161.963920108 +PRECURSOR_MZ: 0.0 PARENT_MASS: 161.96392 NUM PEAKS: 32 51.0 1.24 |