| Next changeset 1:0009acc67c12 (2023-04-27) |
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Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2 |
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added:
macros.xml matchms_networking.xml matchms_networking_wrapper.py test-data/filtering/clean_metadata.msp test-data/filtering/default_filters.msp test-data/filtering/input.msp test-data/filtering/mz_range.msp test-data/filtering/normalise_intensities.msp test-data/filtering/relative_intensity.msp test-data/formatter/test2_threshold_formatting.tsv test-data/formatter/test2_topk_formatting.tsv test-data/scores.json test-data/similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp test-data/similarity/fill.mgf test-data/similarity/fill2.msp test-data/similarity/recetox_gc-ei_ms_20201028.msp 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 |
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| diff -r 000000000000 -r e4ec3592507f macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Oct 18 13:23:28 2022 +0000 |
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| @@ -0,0 +1,94 @@ +<macros> + <token name="@TOOL_VERSION@">0.17.0</token> + + <xml name="creator"> + <creator> + <yield/> + <person + givenName="Helge" + familyName="Hecht" + url="https://github.com/hechth" + identifier="0000-0001-6744-996X" /> + <person + givenName="Maksym" + familyName="Skoryk" + url="https://github.com/maximskorik" + identifier="0000-0003-2056-8018" /> + <person + givenName="Zargham" + familyName="Ahmad" + url="https://github.com/zargham-ahmad" + identifier="0000-0002-6096-224X" /> + <organization + url="https://www.recetox.muni.cz/" + email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" + name="RECETOX MUNI" /> + </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/. + + Upstream Tools + +-----------+---------------+--------+-----------+ + | Name | Output File | Format | Parameter | + +===========+===============+========+===========+ + | RAMClustR | Mass spectra | msp | references| + +-----------+---------------+--------+-----------+ + | RAMClustR | Mass spectra | msp | queries | + +-----------+---------------+--------+-----------+ + + 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** + + 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> + + <xml name="citations"> + <citations> + <citation type="doi">10.5281/zenodo.7178586</citation> + <citation type="doi">10.21105/joss.02411</citation> + </citations> + </xml> + +</macros> |
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| diff -r 000000000000 -r e4ec3592507f matchms_networking.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/matchms_networking.xml Tue Oct 18 13:23:28 2022 +0000 |
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| b'@@ -0,0 +1,192 @@\n+<tool id="matchms_networking" name="matchMS networking" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">\n+ <description>create similarity network graph from matchMS similarity scores</description>\n+\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="creator"/>\n+\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>\n+ </requirements>\n+\n+ <environment_variables>\n+ <environment_variable name="MPLCONFIGDIR">\\$_GALAXY_JOB_TMP_DIR</environment_variable>\n+ <environment_variable name="XDG_CACHE_HOME">\\$_GALAXY_JOB_TMP_DIR</environment_variable>\n+ </environment_variables>\n+\n+ <command detect_errors="aggressive"><![CDATA[\n+ sh ${matchms_networking_cli}\n+ ]]></command>\n+\n+ <configfiles>\n+ <configfile name="matchms_networking_cli">\n+ python3 ${__tool_directory__}/matchms_networking_wrapper.py \\\n+ --graph_format "$graph_format" \\\n+ --identifier "$identifier_key" \\\n+ --top_n "$top_n" \\\n+ --max_links "$max_links" \\\n+ --score_cutoff "$score_cutoff" \\\n+ --link_method "$link_method" \\\n+ #if $keep_unconnected_nodes\n+ --keep_unconnected_nodes \\\n+ #end if\n+ "$scores" \\\n+ "$similarity_network_file"\n+ </configfile>\n+ </configfiles>\n+\n+ <inputs>\n+ <param label="Similarity scores" name="scores" type="data" format="json"\n+ help="matchMS similarity-scores file."/>\n+ <param label="Network-graph format" name="graph_format" type="select"\n+ help="Output format of the similarity network.">\n+ <option value="graphml">graphml</option>\n+ <option value="cyjs">cyjs</option>\n+ <option value="gexf">gexf</option>\n+ <option value="gml">gml</option>\n+ <option value="json">json</option>\n+ </param>\n+ <param label="Identifier key" name="identifier_key" type="text"\n+ help="Unique metadata identifier of each spectrum from which scores are computed."/>\n+ <param label="Number of top edges to keep" name="top_n" type="integer" value="20"\n+ help="The number of highest-score edges to keep between a pair of nodes. Depending on \'Link method\' parameter the top N edges will be selected either from disjoined\n+ sets of individual specta or joined subset of scores between the given pair of spectra. This value has to be higher than the \'Maximum number of links\'."/>\n+ <param label="Maximum number of links per node" name="max_links" type="integer" value="10"\n+ help="Maximum number of links to add per node."/>\n+ <param label="Score cutoff" name="score_cutoff" type="float" value="0.7" min="0.0" max="1.0"\n+ help="Minimum similarity score value to link two spectra."/>\n+ <param label="Link method" name="link_method" type="select" display="radio"\n+ help="Method for computing top N edges for each node.\n+ If selected \'Single\', top N nodes will be selected from disjoined sets of highest scores for nodes of a given pair (i.e., if a given edge belongs to top N scores of at least one node, it is kept).\n+ If selected \'Mutual\', top N nodes will be selected from a joined subset of a given spectra pair (i.e., if and only if a given edge belongs to top N scores of both nodes, it is kept).">\n+ <option value="single" selected="true">Single</option>\n+ <option value="mutual">Mutual</option>\n+ </param>\n+ <param label="Keep unconnected nodes" name="keep_unconnected_nodes" type="boolean" checked="true"\n+ help="If set to No all unconnected nodes will be removed."/>\n+ </inputs>\n+\n+ <outputs>\n+ <data label="Similarity network of ${scores.name}" name="similarity_network_file">\n+ <change_format>\n+ <when input'..b'/.\' n="138"/>\n+ <has_line_matching expression=\'\\s*.edge source="C[0-9]*" target="C[0-9]*" id="[0-9]*" weight="0.[0-9]*" \\/.\' n="16"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="scores" value="scores.json" ftype="json"/>\n+ <param name="graph_format" value="gml"/>\n+ <param name="identifier_key" value="compound_name"/>\n+ <output name="similarity_network_file" ftype="gml">\n+ <assert_contents>\n+ <has_line_matching expression=\'\\s*node \\[\\n\\s*id [0-9]*\\n\\s*label "C[0-9]*"\\n\\s*\\]\' n="138"/>\n+ <has_line_matching expression=\'\\s*edge \\[\\n\\s*source [0-9]*\\n\\s*target [0-9]*\\n\\s*weight 0\\.[0-9]*\\n\\s*\\]\' n="16"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="scores" value="scores.json" ftype="json"/>\n+ <param name="graph_format" value="json"/>\n+ <param name="identifier_key" value="compound_name"/>\n+ <output name="similarity_network_file" ftype="json">\n+ <assert_contents>\n+ <has_text_matching expression=\'{"id": "C[0-9]*"}\' n="138"/>\n+ <has_text_matching expression=\'{"weight": 0\\.[0-9]*, "source": "C[0-9]*", "target": "C[0-9]*"}\' n="16"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="scores" value="scores.json" ftype="json"/>\n+ <param name="graph_format" value="graphml"/>\n+ <param name="identifier_key" value="compound_name"/>\n+ <param name="keep_unconnected_nodes" value="false"/>\n+ <output name="similarity_network_file" ftype="graphml">\n+ <assert_contents>\n+ <is_valid_xml />\n+ <has_line_matching expression=\'.*node id="C[0-9]*"\\/.\' n="25"/>\n+ <has_line_matching expression=\'.*edge source="C[0-9]*" target="C[0-9]*".\' n="16"/>\n+ <has_line_matching expression=\'\\s*.data key="d0".0\\.[0-9]*.*\' n="16"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="scores" value="scores.json" ftype="json"/>\n+ <param name="graph_format" value="graphml"/>\n+ <param name="identifier_key" value="compound_name"/>\n+ <param name="score_cutoff" value="0.4"/>\n+ <param name="keep_unconnected_nodes" value="false"/>\n+ <output name="similarity_network_file" ftype="graphml">\n+ <assert_contents>\n+ <is_valid_xml />\n+ <has_line_matching expression=\'.*node id="C[0-9]*"\\/.\' n="59"/>\n+ <has_line_matching expression=\'.*edge source="C[0-9]*" target="C[0-9]*".\' n="52"/>\n+ <has_line_matching expression=\'\\s*.data key="d0".0\\.[0-9]*.*\' n="52"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="scores" value="scores.json" ftype="json"/>\n+ <param name="graph_format" value="cyjs"/>\n+ <param name="identifier_key" value="compound_name"/>\n+ <param name="score_cutoff" value="0.8"/>\n+ <param name="link_method" value="mutual"/>\n+ <param name="keep_unconnected_nodes" value="false"/>\n+ <output name="similarity_network_file" ftype="cyjs">\n+ <assert_contents>\n+ <has_text_matching expression=\'{"data": {"id": "C[0-9]*", "value": "C[0-9]*", "name": "C[0-9]*"}}\' n="18"/>\n+ <has_text_matching expression=\'{"data": {"weight": 0\\.[0-9]*, "source": "C[0-9]*", "target": "C[0-9]*"}}\' n="9"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+\n+ <help><![CDATA[\n+ @HELP_matchms_networking@\n+ ]]></help>\n+\n+ <expand macro="citations"/>\n+\n+</tool>\n' |
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| diff -r 000000000000 -r e4ec3592507f matchms_networking_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/matchms_networking_wrapper.py Tue Oct 18 13:23:28 2022 +0000 |
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| @@ -0,0 +1,38 @@ +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("--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) + 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 000000000000 -r e4ec3592507f test-data/filtering/clean_metadata.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtering/clean_metadata.msp Tue Oct 18 13:23:28 2022 +0000 |
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| @@ -0,0 +1,197 @@ +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C001 +RETENTION_TIME: 38.74 +RETENTION_INDEX: None +NUM PEAKS: 57 +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 +COMPOUND_NAME: C002 +RETENTION_TIME: 520.25 +RETENTION_INDEX: 1234.5 +NUM PEAKS: 35 +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 +COMPOUND_NAME: C003 +RETENTION_TIME: 483.67 +RETENTION_INDEX: None +NUM PEAKS: 26 +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 +COMPOUND_NAME: C004 +RETENTION_TIME: 473.48 +RETENTION_INDEX: None +NUM PEAKS: 24 +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 8009033.0 +950.6274 3674694.0 +991.6726 1420557258.0 +992.6749 763118028.0 +993.6787 239161906.0 +994.6801 53549573.0 +1017.6897 168186952.0 +1018.6656 120599518.0 +1019.6555 57647644.0 +1020.6591 12469103.0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C005 +RETENTION_TIME: 41.72 +RETENTION_INDEX: None +NUM PEAKS: 20 +218.1386 14009249.0 +337.0623 88672453.0 +338.0654 8770055.0 +353.0361 37061354.0 +359.0443 48435582.0 +360.0459 5025128.0 +375.018 29159485.0 +376.0216 2740193.0 +381.0261 13522755.0 +396.9999 10317665.0 +417.0027 13822994.0 +418.9966 4386311.0 +432.9764 9779399.0 +438.9851 11307111.0 +440.9796 3364168.0 +454.9592 9820452.0 +456.9603 3774845.0 +470.9263 3632486.0 +512.8989 4072570.0 +572.871 3485486.0 + |
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| diff -r 000000000000 -r e4ec3592507f test-data/filtering/default_filters.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtering/default_filters.msp Tue Oct 18 13:23:28 2022 +0000 |
| b |
| @@ -0,0 +1,199 @@ +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C001 +RETENTION_TIME: 38.74 +RETENTION_INDEX: None +CHARGE: -1 +NUM PEAKS: 57 +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 +COMPOUND_NAME: C002 +RETENTION_TIME: 520.25 +RETENTION_INDEX: 1234.5 +CHARGE: -1 +NUM PEAKS: 35 +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 +COMPOUND_NAME: C003 +RETENTION_TIME: 483.67 +CHARGE: -1 +NUM PEAKS: 26 +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 +COMPOUND_NAME: C004 +RETENTION_TIME: 473.48 +CHARGE: -1 +NUM PEAKS: 24 +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 8009033.0 +950.6274 3674694.0 +991.6726 1420557258.0 +992.6749 763118028.0 +993.6787 239161906.0 +994.6801 53549573.0 +1017.6897 168186952.0 +1018.6656 120599518.0 +1019.6555 57647644.0 +1020.6591 12469103.0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C005 +RETENTION_TIME: 41.72 +CHARGE: -1 +NUM PEAKS: 20 +218.1386 14009249.0 +337.0623 88672453.0 +338.0654 8770055.0 +353.0361 37061354.0 +359.0443 48435582.0 +360.0459 5025128.0 +375.018 29159485.0 +376.0216 2740193.0 +381.0261 13522755.0 +396.9999 10317665.0 +417.0027 13822994.0 +418.9966 4386311.0 +432.9764 9779399.0 +438.9851 11307111.0 +440.9796 3364168.0 +454.9592 9820452.0 +456.9603 3774845.0 +470.9263 3632486.0 +512.8989 4072570.0 +572.871 3485486.0 + |
| b |
| diff -r 000000000000 -r e4ec3592507f test-data/filtering/input.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtering/input.msp Tue Oct 18 13:23:28 2022 +0000 |
| b |
| @@ -0,0 +1,193 @@ +NAME:C001 +IONMODE:Negative +RETENTIONTIME:38.74 +RETENTIONINDEX: -1 +SPECTRUMTYPE:Centroid +Num Peaks:57 +216.9205 32607700 +256.8215 31377637 +175.0641 26780143 +206.9034 26130980 +254.8252 23747536 +198.8647 21688594 +196.8658 21390430 +372.7383 19374863 +258.8237 15532799 +382.8218 12815572 +488.6825 12267966 +392.7685 10913351 +316.7777 10734168 +440.7322 10603010 +138.9121 10186226 +312.7841 10051801 +434.7287 9943329 +266.8652 9805546 +370.7418 9765463 +450.7016 8762673 +324.9549 8619910 +428.7834 8554675 +384.8177 8311500 +442.7401 8271752 +200.8848 7742528 +492.744 7662344 +494.8953 7188793 +546.6093 7177067 +498.8794 6811405 +500.8484 6520691 +322.8157 6317648 +350.9875 6150799 +550.6949 6104789 +426.7772 5431633 +566.5977 5171811 +510.763 4989757 +486.7743 4886062 +460.7076 4528973 +484.7242 4273989 +518.7415 4243468 +334.849 4178412 +413.2664 3965867 +436.8161 3705247 +502.7832 3567833 +342.8093 3285552 +366.8281 3253770 +306.9914 3169316 +268.8537 3090354 +800.4451 2792137 +186.1095 2675456 +234.0134 2550129 +462.7862 2123666 +349.9455 2050695 +612.6927 2005587 +676.6436 1982714 +351.941 1965882 +148.9337 1008656 + +NAME:C002 +IONMODE:Negative +RETENTIONTIME:520.25 +RETENTIONINDEX: 1234.5 +SPECTRUMTYPE:Centroid +Num Peaks:35 +525.375 1073323842 +310.1623 295359836 +526.3783 181668883 +1047.7378 150394804 +551.3321 111616808 +1048.7399 90978863 +289.6491 46498377 +312.0296 38757284 +1075.1968 33352763 +1049.7432 29946438 +552.3348 28340614 +813.5403 25060147 +527.3812 23642795 +309.1649 18045974 +301.1565 15185412 +311.1658 13124727 +330.6757 12666597 +624.296 11790213 +1076.2004 10417953 +578.2905 7578406 +562.3269 7538206 +1050.7453 6807767 +267.2688 6103973 +814.5336 5865975 +1069.7158 5074652 +619.3008 4742103 +1216.8041 4439324 +1206.3127 3738816 +1217.807 3565334 +1074.1979 3402288 +553.3314 2609936 +955.1171 2322927 +1101.6535 2023916 +131.1733 1971789 +279.0196 1946255 + +NAME:C003 +IONMODE:Negative +RETENTIONTIME:483.67 +SPECTRUMTYPE:Centroid +Num Peaks:26 +522.3565 4089569222 +523.354 1201714423 +288.6414 202172046 +1043.7028 144351468 +1044.7068 83271854 +549.3267 63300808 +279.6362 29849749 +1045.706 27998321 +1058.1594 20718345 +1071.1639 15461047 +378.2093 15309961 +796.9808 13576738 +809.9883 12596682 +265.2529 11366224 +280.6546 8848921 +576.2749 7386007 +1059.1626 6608764 +810.9916 6601055 +1046.7131 6505178 +797.9841 6368973 +1072.1671 5096642 +625.4543 4040374 +379.1966 2902366 +577.3074 2354251 +617.2778 2323470 +266.2564 1420444 + +NAME:C004 +IONMODE:Negative +RETENTIONTIME:473.48 +SPECTRUMTYPE:Centroid +Num Peaks:24 +496.34 12577588056 +497.3442 3337125302 +991.6726 1420557258 +992.6749 763118028 +498.3462 532285213 +993.6787 239161906 +296.147 190395687 +1017.6897 168186952 +482.3247 145772322 +1018.6656 120599518 +499.3493 68176083 +1019.6555 57647644 +994.6801 53549573 +770.964 49250157 +483.3283 36245876 +275.6336 28001849 +771.9675 22666873 +1020.6591 12469103 +783.9721 9839299 +949.6233 8009033 +124.1405 6517662 +950.6274 3674694 +784.9749 3622908 +170.2437 1237313 + +NAME:C005 +IONMODE:Negative +RETENTIONTIME:41.72 +SPECTRUMTYPE:Centroid +Num Peaks:20 +337.0623 88672453 +359.0443 48435582 +353.0361 37061354 +375.018 29159485 +218.1386 14009249 +417.0027 13822994 +381.0261 13522755 +438.9851 11307111 +396.9999 10317665 +454.9592 9820452 +432.9764 9779399 +338.0654 8770055 +360.0459 5025128 +418.9966 4386311 +512.8989 4072570 +456.9603 3774845 +470.9263 3632486 +572.871 3485486 +440.9796 3364168 +376.0216 2740193 |
| b |
| diff -r 000000000000 -r e4ec3592507f test-data/filtering/mz_range.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtering/mz_range.msp Tue Oct 18 13:23:28 2022 +0000 |
| b |
| @@ -0,0 +1,129 @@ +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C001 +RETENTION_TIME: 38.74 +RETENTION_INDEX: None +NUM PEAKS: 41 +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 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C002 +RETENTION_TIME: 520.25 +RETENTION_INDEX: 1234.5 +NUM PEAKS: 16 +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 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C003 +RETENTION_TIME: 483.67 +NUM PEAKS: 11 +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 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C004 +RETENTION_TIME: 473.48 +NUM PEAKS: 10 +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 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C005 +RETENTION_TIME: 41.72 +NUM PEAKS: 19 +337.0623 88672453.0 +338.0654 8770055.0 +353.0361 37061354.0 +359.0443 48435582.0 +360.0459 5025128.0 +375.018 29159485.0 +376.0216 2740193.0 +381.0261 13522755.0 +396.9999 10317665.0 +417.0027 13822994.0 +418.9966 4386311.0 +432.9764 9779399.0 +438.9851 11307111.0 +440.9796 3364168.0 +454.9592 9820452.0 +456.9603 3774845.0 +470.9263 3632486.0 +512.8989 4072570.0 +572.871 3485486.0 + |
| b |
| diff -r 000000000000 -r e4ec3592507f test-data/filtering/normalise_intensities.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtering/normalise_intensities.msp Tue Oct 18 13:23:28 2022 +0000 |
| b |
| @@ -0,0 +1,194 @@ +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C001 +RETENTION_TIME: 38.74 +RETENTION_INDEX: None +NUM PEAKS: 57 +138.9121 0.31238713555387226 +148.9337 0.03093306182282099 +175.0641 0.8212827951680125 +186.1095 0.08204982258791635 +196.8658 0.6559932163262051 +198.8647 0.6651371915222478 +200.8848 0.23744477531380626 +206.9034 0.8013745219687375 +216.9205 1.0 +234.0134 0.0782063439003671 +254.8252 0.7282800074828951 +256.8215 0.9622769161885076 +258.8237 0.4763537140000675 +266.8652 0.30071259242448867 +268.8537 0.09477374975849262 +306.9914 0.09719532503059093 +312.7841 0.30826464301376666 +316.7777 0.3291912033047409 +322.8157 0.1937471210787636 +324.9549 0.2643519782137348 +334.849 0.12814188059875428 +342.8093 0.10076000453880525 +349.9455 0.06288990023828728 +350.9875 0.18863026217733847 +351.941 0.06028888882073866 +366.8281 0.09978532677864431 +370.7418 0.29948334289140294 +372.7383 0.5941806076478868 +382.8218 0.3930228749651156 +384.8177 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| b |
| diff -r 000000000000 -r e4ec3592507f test-data/filtering/relative_intensity.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtering/relative_intensity.msp Tue Oct 18 13:23:28 2022 +0000 |
| b |
| @@ -0,0 +1,51 @@ +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C001 +RETENTION_TIME: 38.74 +RETENTION_INDEX: None +NUM PEAKS: 16 +138.9121 10186226.0 +175.0641 26780143.0 +196.8658 21390430.0 +198.8647 21688594.0 +206.9034 26130980.0 +254.8252 23747536.0 +258.8237 15532799.0 +266.8652 9805546.0 +312.7841 10051801.0 +316.7777 10734168.0 +372.7383 19374863.0 +382.8218 12815572.0 +392.7685 10913351.0 +434.7287 9943329.0 +440.7322 10603010.0 +488.6825 12267966.0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C002 +RETENTION_TIME: 520.25 +RETENTION_INDEX: 1234.5 +NUM PEAKS: 0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C003 +RETENTION_TIME: 483.67 +NUM PEAKS: 0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C004 +RETENTION_TIME: 473.48 +NUM PEAKS: 0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C005 +RETENTION_TIME: 41.72 +NUM PEAKS: 3 +353.0361 37061354.0 +359.0443 48435582.0 +375.018 29159485.0 + |
| b |
| diff -r 000000000000 -r e4ec3592507f test-data/formatter/test2_threshold_formatting.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/formatter/test2_threshold_formatting.tsv Tue Oct 18 13:23:28 2022 +0000 |
| b |
| @@ -0,0 +1,21 @@ +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 000000000000 -r e4ec3592507f test-data/formatter/test2_topk_formatting.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/formatter/test2_topk_formatting.tsv Tue Oct 18 13:23:28 2022 +0000 |
| b |
| @@ -0,0 +1,154 @@ +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 000000000000 -r e4ec3592507f test-data/scores.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scores.json Tue Oct 18 13:23:28 2022 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\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, 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[0.07254436753789326, 7], [1.0, 45]]]}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r e4ec3592507f test-data/similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp Tue Oct 18 13:23:28 2022 +0000 |
| [ |
| b'@@ -0,0 +1,6547 @@\n+NAME: Acephate\r\n+SCANNUMBER: 1161\r\n+RETENTIONTIME: 1.232997\r\n+PRECURSORMZ: 184.0194\r\n+PRECURSORTYPE: [M+H]+\r\n+IONMODE: Positive\r\n+SPECTRUMTYPE: Centroid\r\n+FORMULA: C4H10NO3PS\r\n+INCHIKEY: YASYVMFAVPKPKE-SECBINFHSA-N\r\n+INCHI: \r\n+SMILES: COP(=O)(N=C(O)C)SC\r\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\r\n+COLLISIONENERGY: \r\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\r\n+INSTRUMENTTYPE: LC-ESI-Orbitrap\r\n+IONIZATION: ESI+\r\n+LICENSE: CC BY-NC\r\n+COMMENT: \r\n+Num Peaks: 16\r\n+90.09368\t1128\r\n+93.11512\t1241\r\n+95.10279\t1118\r\n+101.31465\t1152\r\n+102.90688\t1322\r\n+103.98039\t1201\r\n+112.01607\t12289\r\n+112.99994\t38027\r\n+115.00399\t1634\r\n+124.98121\t922\r\n+128.97701\t9208\r\n+132.57193\t1350\r\n+135.84808\t1428\r\n+142.99275\t16419\r\n+147.94205\t1750\r\n+173.5094\t2353\r\n+\r\n+NAME: Carbaryl\r\n+SCANNUMBER: 2257\r\n+RETENTIONTIME: 5.259445\r\n+PRECURSORMZ: 202.0863\r\n+PRECURSORTYPE: [M+H]+\r\n+IONMODE: Positive\r\n+SPECTRUMTYPE: Centroid\r\n+FORMULA: C12H11NO2\r\n+INCHIKEY: CVXBEEMKQHEXEN-UHFFFAOYSA-N\r\n+INCHI: \r\n+SMILES: CN=C(Oc1cccc2c1cccc2)O\r\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\r\n+COLLISIONENERGY: \r\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\r\n+INSTRUMENTTYPE: LC-ESI-Orbitrap\r\n+IONIZATION: ESI+\r\n+LICENSE: CC BY-NC\r\n+COMMENT: \r\n+Num Peaks: 1\r\n+145.06491\t1326147\t"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"\r\n+\r\n+NAME: Dicrotophos\r\n+SCANNUMBER: 1516\r\n+RETENTIONTIME: 2.025499\r\n+PRECURSORMZ: 238.0844\r\n+PRECURSORTYPE: [M+H]+\r\n+IONMODE: Positive\r\n+SPECTRUMTYPE: Centroid\r\n+FORMULA: C8H16NO5P\r\n+INCHIKEY: VEENJGZXVHKXNB-UHFFFAOYSA-N\r\n+INCHI: \r\n+SMILES: COP(=O)(OC(=CC(=O)N(C)C)C)OC\r\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\r\n+COLLISIONENERGY: \r\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\r\n+INSTRUMENTTYPE: LC-ESI-Orbitrap\r\n+IONIZATION: ESI+\r\n+LICENSE: CC BY-NC\r\n+COMMENT: \r\n+Num Peaks: 5\r\n+112.074\t102027\r\n+112.07591\t9070987\t"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"\r\n+127.01563\t3230337\t"Theoretical m/z 127.01547, Mass diff 0 (1.26 ppm), SMILES O=P(O)(OC)OC, Annotation [C2H7O4P+H]+, Rule of HR True"\r\n+193.02605\t7897744\t"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"\r\n+238.08437\t2973124\t"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"\r\n+\r\n+NAME: Dimethoate\r\n+SCANNUMBER: 1865\r\n+RETENTIONTIME: 2.866696\r\n+PRECURSORMZ: 230.0072\r\n+PRECURSORTYPE: [M+H]+\r\n+IONMODE: Positive\r\n+SPECTRUMTYPE: Centroid\r\n+FORMULA: C5H12NO3PS2\r\n+INCHIKEY: MCWXGJITAZMZEV-UHFFFAOYSA-N\r\n+INCHI: \r\n+SMILES: CN=C(CSP(=S)(OC)OC)O\r\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\r\n+COLLISIONENERGY: \r\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\r\n+INSTRUMENTTYPE: LC-ESI-Orbitrap\r\n+IONIZATION: ESI+\r\n+LICENSE: CC BY-NC\r\n+COMMENT: \r\n+Num Peaks: 8\r\n+88.0219\t548446\t"Theoretical m/z 88.021549, Mass diff 0 (3.99 ppm), SMILES SCC=NC, Annotation [C3H7NS-H]+, Rule of HR True"\r\n+124.98233\t183861\t"Theoretical m/z 124.982067, Mass diff 0 (2.11 ppm), SMILES S=P(OC)OC, Annotation [C2H7O2PS-H]+, Rule of HR True"\r\n+142.99275\t722053\t"Theoretical m/z 142.993177, Mass diff 0 (0 ppm), Formula C2H8O3PS"\r\n+156.95422\t80792\t"Theoretical m/z 156.954136, Mass diff 0 (0.54 ppm), SMILES S=P(S)(OC)OC, Annotation [C2H7O2PS2-H]+, Rule of HR True"\r\n+170.97\t1426256\t"Theoretical m/z 170.969791, Mass diff 0 (1.22 ppm), SMILES S=P(OC)(OC)SC, Annotation [C3H9O2PS2-H]+, Rule of HR True"\r\n+197.98123\t240915\t"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"\r\n+198.96501\t5415933\t"Theoretical m/z 198.965248, Mass diff 0 (0 ppm), Formula C4H8O3PS2"\r\n+230.00722\t497851\t"Theoretical m/z 230.006895, Mass diff 0 (1.41 ppm), SMILES S=P(OC)(OC)SCC(O)=NC'..b'PRECURSORMZ: 223.1443\r\n+PRECURSORTYPE: [M+H]+\r\n+IONMODE: Positive\r\n+SPECTRUMTYPE: Centroid\r\n+FORMULA: C12H18N2O2\r\n+INCHIKEY: YNEVBPNZHBAYOA-UHFFFAOYSA-N\r\n+INCHI: \r\n+SMILES: CN=C(Oc1cc(C)c(c(c1)C)N(C)C)O\r\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\r\n+COLLISIONENERGY: \r\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\r\n+INSTRUMENTTYPE: LC-ESI-Orbitrap\r\n+IONIZATION: ESI+\r\n+LICENSE: CC BY-NC\r\n+COMMENT: \r\n+Num Peaks: 5\r\n+134.07283\t2632951\t"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"\r\n+136.07611\t26036728\t"Theoretical m/z 136.076239, Mass diff 0 (0 ppm), Formula C8H10NO"\r\n+150.092\t1572118\t"Theoretical m/z 150.091343, Mass diff 0.001 (4.38 ppm), SMILES OC1=CC=C(C(=C1)C)N(C)C, Annotation [C9H13NO-H]+, Rule of HR True"\r\n+151.09932\t54847764\t"Theoretical m/z 151.099168, Mass diff 0 (1.01 ppm), SMILES OC1=CC=C(C(=C1)C)N(C)C, Annotation [C9H13NO]+, Rule of HR False"\r\n+166.12282\t1541928\t"Theoretical m/z 166.122633, Mass diff 0 (1.13 ppm), SMILES OC=1C=C(C(=C(C1)C)N(C)C)C, Annotation [C10H15NO+H]+, Rule of HR True"\r\n+\r\n+NAME: Monceren\r\n+SCANNUMBER: 3999\r\n+RETENTIONTIME: 7.14553\r\n+PRECURSORMZ: 329.1426\r\n+PRECURSORTYPE: [M+H]+\r\n+IONMODE: Positive\r\n+SPECTRUMTYPE: Centroid\r\n+FORMULA: C19H21N2OCl\r\n+INCHIKEY: OGYFATSSENRIKG-UHFFFAOYSA-N\r\n+INCHI: \r\n+SMILES: Clc1ccc(cc1)CN(C(=Nc1ccccc1)O)C1CCCC1\r\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\r\n+COLLISIONENERGY: \r\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\r\n+INSTRUMENTTYPE: LC-ESI-Orbitrap\r\n+IONIZATION: ESI+\r\n+LICENSE: CC BY-NC\r\n+COMMENT: \r\n+Num Peaks: 5\r\n+89.03881\t550831\t"Theoretical m/z 89.038575, Mass diff 0 (2.63 ppm), SMILES C=1C=CC(=CC1)C, Annotation [C7H8-3H]+, Rule of HR True"\r\n+94.06543\t635265\t"Theoretical m/z 94.065123, Mass diff 0 (3.27 ppm), SMILES NC=1C=CC=CC1, Annotation [C6H7N+H]+, Rule of HR True"\r\n+106.06545\t446416\t"Theoretical m/z 106.065123, Mass diff 0 (3.09 ppm), SMILES N(=C)C=1C=CC=CC1, Annotation [C7H7N+H]+, Rule of HR True"\r\n+125.01307\t512150\r\n+125.01532\t37442116\t"Theoretical m/z 125.015255, Mass diff 0 (0.52 ppm), SMILES ClC1=CC=C(C=C1)C, Annotation [C7H7Cl-H]+, Rule of HR True"\r\n+\r\n+NAME: Desmedipham\r\n+SCANNUMBER: 2271\r\n+RETENTIONTIME: 6.430396\r\n+PRECURSORMZ: 301.1192\r\n+PRECURSORTYPE: [M+H]+\r\n+IONMODE: Positive\r\n+SPECTRUMTYPE: Centroid\r\n+FORMULA: C16H16N2O4\r\n+INCHIKEY: WZJZMXBKUWKXTQ-UHFFFAOYSA-N\r\n+INCHI: \r\n+SMILES: CCOC(=Nc1cccc(c1)OC(=Nc1ccccc1)O)O\r\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\r\n+COLLISIONENERGY: \r\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\r\n+INSTRUMENTTYPE: LC-ESI-Orbitrap\r\n+IONIZATION: ESI+\r\n+LICENSE: CC BY-NC\r\n+COMMENT: \r\n+Num Peaks: 3\r\n+136.03947\t1773399\t"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"\r\n+154.04993\t1002798\t"Theoretical m/z 154.049864, Mass diff 0 (0.43 ppm), SMILES OC(O)=NC=1C=CC=C(O)C1, Annotation [C7H7NO3+H]+, Rule of HR True"\r\n+182.08162\t6480130\t"Theoretical m/z 182.081175, Mass diff 0 (2.45 ppm), SMILES OC(=NC=1C=CC=C(O)C1)OCC, Annotation [C9H11NO3+H]+, Rule of HR True"\r\n+\r\n+NAME: Phenmedipham\r\n+SCANNUMBER: 2458\r\n+RETENTIONTIME: 6.570995\r\n+PRECURSORMZ: 301.1185\r\n+PRECURSORTYPE: [M+H]+\r\n+IONMODE: Positive\r\n+SPECTRUMTYPE: Centroid\r\n+FORMULA: C16H16N2O4\r\n+INCHIKEY: IDOWTHOLJBTAFI-UHFFFAOYSA-N\r\n+INCHI: \r\n+SMILES: COC(=Nc1cccc(c1)OC(=Nc1cccc(c1)C)O)O\r\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\r\n+COLLISIONENERGY: \r\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\r\n+INSTRUMENTTYPE: LC-ESI-Orbitrap\r\n+IONIZATION: ESI+\r\n+LICENSE: CC BY-NC\r\n+COMMENT: \r\n+Num Peaks: 2\r\n+136.03947\t2596929\t"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"\r\n+168.06587\t7038054\t"Theoretical m/z 168.065519, Mass diff 0 (2.09 ppm), SMILES OC(=NC=1C=CC=C(O)C1)OC, Annotation [C8H9NO3+H]+, Rule of HR True"\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r e4ec3592507f test-data/similarity/fill.mgf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/fill.mgf Tue Oct 18 13:23:28 2022 +0000 |
| b |
| @@ -0,0 +1,234 @@ +BEGIN IONS +NAME=C001 +IONMODE=Negative +RETENTIONTIME=38.74 +RETENTIONINDEX= +SPECTRUMTYPE=Centroid +NUM PEAKS=57 +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 +END IONS + +BEGIN IONS +NAME=C002 +IONMODE=Negative +RETENTIONTIME=520.25 +RETENTIONINDEX= +SPECTRUMTYPE=Centroid +NUM PEAKS=35 +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 +END IONS + +BEGIN IONS +NAME=C003 +IONMODE=Negative +RETENTIONTIME=483.67 +RETENTIONINDEX= +SPECTRUMTYPE=Centroid +NUM PEAKS=26 +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 +END IONS + +BEGIN IONS +NAME=C004 +IONMODE=Negative +RETENTIONTIME=473.48 +RETENTIONINDEX= +SPECTRUMTYPE=Centroid +NUM PEAKS=24 +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 8009033.0 +950.6274 3674694.0 +991.6726 1420557258.0 +992.6749 763118028.0 +993.6787 239161906.0 +994.6801 53549573.0 +1017.6897 168186952.0 +1018.6656 120599518.0 +1019.6555 57647644.0 +1020.6591 12469103.0 +END IONS + +BEGIN IONS +NAME=C005 +IONMODE=Negative +RETENTIONTIME=41.72 +RETENTIONINDEX= +SPECTRUMTYPE=Centroid +NUM PEAKS=20 +218.1386 14009249.0 +337.0623 88672453.0 +338.0654 8770055.0 +353.0361 37061354.0 +359.0443 48435582.0 +360.0459 5025128.0 +375.018 29159485.0 +376.0216 2740193.0 +381.0261 13522755.0 +396.9999 10317665.0 +417.0027 13822994.0 +418.9966 4386311.0 +432.9764 9779399.0 +438.9851 11307111.0 +440.9796 3364168.0 +454.9592 9820452.0 +456.9603 3774845.0 +470.9263 3632486.0 +512.8989 4072570.0 +572.871 3485486.0 +END IONS + +BEGIN IONS +NAME=C006 +IONMODE=Negative +RETENTIONTIME=452.08 +RETENTIONINDEX= +SPECTRUMTYPE=Centroid +NUM PEAKS=19 +265.6196 4371245.0 +274.6257 21694276.0 +290.6256 9704443.0 +471.1945 2160605.0 +484.3311 5283943.0 +494.3249 803829845.0 +495.3278 207959661.0 +516.3076 24092471.0 +542.3239 193323900.0 +543.3276 55501736.0 +987.6411 7453650.0 +988.6455 3739523.0 +1001.658 11852076.0 +1037.6578 7076912.0 +1061.6562 9417442.0 +1062.6592 5657208.0 +1087.6715 34676828.0 +1088.6773 21466528.0 +1089.682 9948820.0 +END IONS |
| b |
| diff -r 000000000000 -r e4ec3592507f test-data/similarity/fill2.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/fill2.msp Tue Oct 18 13:23:28 2022 +0000 |
| b |
| b'@@ -0,0 +1,3117 @@\n+\n+NAME: C019\n+IONMODE: Negative\n+SPECTRUMTYPE: Centroid\n+RETENTIONTIME: 688.11\n+RETENTIONINDEX: 4135.446429\n+NUM PEAKS: 45\n+70.261357375322 1769331.0\n+82.0777101637279 1721684.0\n+92.0256956423549 1063403.0\n+104.057597689888 2564581.0\n+106.07773010104 1697865.0\n+118.073139793174 3070732.0\n+135.080430341161 1465718.0\n+144.946939559008 1208427.0\n+145.046705119092 2856482.0\n+164.985419247789 16217649.0\n+179.033979756352 10865004.0\n+180.980322946522 4830502.0\n+191.070496682473 3188459.0\n+192.078428243192 3993484.0\n+194.04893073403 5942766.0\n+195.046783458568 4544081.0\n+211.026857856803 2083491.0\n+213.039588698474 3950087.0\n+213.998834302427 1664182.0\n+248.988380501455 23053112.0\n+251.037178293 10860752.0\n+265.054817014529 3722747.0\n+265.089588392487 3283162.0\n+283.099929585291 13668779.0\n+313.053040045895 8388200.0\n+329.031653006854 6682061.0\n+341.157248840923 18181095.0\n+385.022947628725 6484159.0\n+399.075287615392 4270821.0\n+401.053681557414 30562249.0\n+401.124275228471 4559258.0\n+403.051400482668 5874830.0\n+415.106669687654 54985895.0\n+416.107049345269 18386437.0\n+417.104122333661 8837789.0\n+476.073864807294 4515967.0\n+489.124198650628 43332063.0\n+535.10922525834 9870959.0\n+536.110887614382 4207959.0\n+550.163296442538 12203065.0\n+551.161445828019 6205283.0\n+564.146181690587 6031009.0\n+609.130287444605 3608658.0\n+623.183150220198 13681871.0\n+638.166995588673 2404616.0\n+\n+NAME: C008\n+IONMODE: Negative\n+SPECTRUMTYPE: Centroid\n+RETENTIONTIME: 383.25\n+RETENTIONINDEX: 2436.111111\n+NUM PEAKS: 102\n+78.7781680742475 2556976.0\n+82.0287864194648 8611959.0\n+85.0104542195255 4745054.0\n+92.0495708428228 5241931.0\n+95.0491933558967 2316015.0\n+96.0078464060989 4720367.0\n+99.0260585452107 42333146.0\n+100.025652771381 2210104.0\n+100.029460129111 1981052.0\n+101.005418898448 6144105.0\n+101.02272083003 3343084.0\n+106.894747495922 3789804.0\n+108.892716700199 4700928.0\n+108.910416566696 4697413.0\n+110.908317235236 3641673.0\n+111.026121150586 7898189.0\n+113.034483087363 1496932.0\n+116.02876233702 10183471.0\n+119.015881013881 1977959.0\n+120.04434550515 4465533.0\n+125.034561908395 2616569.0\n+125.041780188163 5642602.0\n+126.036944910833 5772477.0\n+128.076372883456 5931740.0\n+136.941645253989 15500747.0\n+138.000329453771 4425123.0\n+138.939672935419 14601520.0\n+140.065140977456 18496952.0\n+142.044407303719 9098154.0\n+144.053483905356 7606120.0\n+145.067857890803 7879741.0\n+148.039287263976 7328850.0\n+153.036553916572 14858551.0\n+153.047854996355 18125030.0\n+156.059954180827 5934059.0\n+159.065697727649 7272776.0\n+167.06348032557 99885797.0\n+168.047501694808 12449580.0\n+168.068381413815 19985484.0\n+169.042872715042 111801595.0\n+170.045964437299 9501453.0\n+170.069851541155 17765150.0\n+171.039411915043 2980892.0\n+171.04718236227 9542984.0\n+177.039637442155 5983921.0\n+181.042632909891 3502669.0\n+183.058412555312 14609802.0\n+184.090614336983 12693765.0\n+185.073952424469 56878550.0\n+187.05314814224 24897096.0\n+187.070922888834 7169841.0\n+196.065548645302 32801154.0\n+201.076259513554 6881178.0\n+202.082996186392 9963473.0\n+203.091832141757 11700196.0\n+209.037561708176 19568054.0\n+215.091944217113 45540404.0\n+222.057912826487 2321839.0\n+224.061333736415 316557240.0\n+225.065854975194 19218426.0\n+226.057739905584 '..b'4038 3016933.0\n+346.046486912175 1754291.0\n+346.973191534072 1590963.0\n+382.97408022551 1514772.0\n+386.969422084375 2096957.0\n+402.964369782575 1172149.0\n+493.152823320977 2513229.0\n+\n+NAME: C012\n+IONMODE: Negative\n+SPECTRUMTYPE: Centroid\n+RETENTIONTIME: 687.83\n+RETENTIONINDEX: 4134.613095\n+NUM PEAKS: 57\n+78.0419846383593 1742200.0\n+79.0497716096318 1893817.0\n+85.0284186196566 2191757.0\n+121.046741626167 6162741.0\n+142.078087888737 3381352.0\n+192.997735629267 9539743.0\n+195.029110650825 3772846.0\n+205.016711322548 5926636.0\n+207.066696618797 3714385.0\n+209.098935410027 6173585.0\n+213.05754958053 13341991.0\n+219.06802937228 2601724.0\n+253.016653119059 43935840.0\n+269.047850642358 4644691.0\n+271.027137265637 6759639.0\n+281.085992168442 2140320.0\n+284.047997947258 8403825.0\n+311.073606748707 3371803.0\n+313.113777264345 2391990.0\n+325.985953604199 8513850.0\n+327.03525664153 49155384.0\n+328.035343658 13109000.0\n+329.014530869431 3595462.0\n+331.063707530223 2063612.0\n+343.084122931946 3769846.0\n+345.046169172075 8812838.0\n+353.090427317747 2832675.0\n+359.09769204202 9873384.0\n+360.028136457829 10686927.0\n+360.169639740951 3818378.0\n+371.040514349465 1472266.0\n+387.002413998209 12940469.0\n+387.071825807939 15096984.0\n+389.068871345424 1810336.0\n+402.055174276849 12479459.0\n+404.05195192305 1405422.0\n+458.971973456131 1214840.0\n+459.041861218696 1286084.0\n+460.952039584771 4371596.0\n+461.021207128847 2869881.0\n+461.090256355859 17842323.0\n+461.951796665319 1222018.0\n+462.091555156095 6970195.0\n+463.088708091285 2556050.0\n+475.072310244956 13564752.0\n+476.003821454759 1471505.0\n+476.143434019655 13026182.0\n+477.140480798609 4944561.0\n+478.141485242814 1506934.0\n+479.101672410454 3603024.0\n+490.12632015072 18188437.0\n+491.122346777972 10290558.0\n+549.162553092955 24746614.0\n+563.144239233773 12735845.0\n+624.183209223215 7134906.0\n+637.164550513183 3866368.0\n+698.205944560218 1919968.0\n+\n+NAME: C020\n+IONMODE: Negative\n+SPECTRUMTYPE: Centroid\n+RETENTIONTIME: 687.99\n+RETENTIONINDEX: 4135.089286\n+NUM PEAKS: 43\n+109.052235628516 1922885.0\n+111.044058476785 1730416.0\n+133.064909307365 1579533.0\n+137.041722086745 2474039.0\n+194.053642118165 5252308.0\n+212.061782732582 10437319.0\n+267.034768010352 4429084.0\n+267.068824022318 27744081.0\n+268.069192256745 2367920.0\n+310.970568727813 3126083.0\n+311.004219192148 2666091.0\n+325.055731606087 7634729.0\n+327.965549188207 5442532.0\n+328.962716535303 2722019.0\n+339.03821058645 6627839.0\n+341.051986399316 1671451.0\n+342.996634492902 3939816.0\n+345.115297423962 3938049.0\n+358.067243216398 3526875.0\n+361.025211906011 6516476.0\n+388.003000430725 3422825.0\n+388.073272089579 4224454.0\n+399.005054559559 4141766.0\n+401.984326631505 5585170.0\n+402.98179623463 3562508.0\n+416.036473280551 7221552.0\n+417.033665098569 4129234.0\n+417.087073648909 1945166.0\n+418.994970709551 2648178.0\n+430.088321970134 10765018.0\n+431.085366629672 6887942.0\n+473.09370665615 2502410.0\n+475.002854889036 2969642.0\n+475.14184210128 30625723.0\n+477.070907310139 2271450.0\n+489.055479984185 1973511.0\n+503.107930410573 2407435.0\n+549.092119293556 2513579.0\n+552.160354111203 1673065.0\n+565.143723544965 3485979.0\n+610.132183060405 1997085.0\n+625.181479977537 3872339.0\n+697.202597429349 2820429.0\n' |
| b |
| diff -r 000000000000 -r e4ec3592507f test-data/similarity/recetox_gc-ei_ms_20201028.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/recetox_gc-ei_ms_20201028.msp Tue Oct 18 13:23:28 2022 +0000 |
| [ |
| b'@@ -0,0 +1,10214 @@\n+NAME: Perylene\r\n+SCANNUMBER: -1\r\n+RETENTIONTIME: -1\r\n+RETENTIONINDEX: 2886.9\r\n+PRECURSORMZ: 252.09323\r\n+PRECURSORTYPE: [M]+\r\n+IONMODE: Positive\r\n+SPECTRUMTYPE: Centroid\r\n+FORMULA: C20H12\r\n+INCHIKEY: CSHWQDPOILHKBI-UHFFFAOYSA-N\r\n+INCHI: \r\n+SMILES: C1=CC2=C3C(=C1)C1=CC=CC4=C1C(=CC=C4)C3=CC=C2\r\n+AUTHORS: Price et al., RECETOX, Masaryk University (CZ)\r\n+COLLISIONENERGY: 70eV\r\n+INSTRUMENT: Q Exactive GC Orbitrap GC-MS/MS\r\n+INSTRUMENTTYPE: GC-EI-Orbitrap\r\n+IONIZATION: EI+\r\n+LICENSE: CC BY-NC\r\n+COMMENT: \r\n+Num Peaks: 19\r\n+112.03071\t49892\r\n+113.03854\t87510\t"Theoretical m/z 113.039125, Mass diff 0 (0 ppm), Formula C9H5"\r\n+124.03076\t100146\r\n+124.53242\t24923\r\n+125.03855\t179254\t"Theoretical m/z 125.039125, Mass diff 0 (0 ppm), Formula C10H5"\r\n+125.54019\t49039\r\n+126.04636\t131679\r\n+126.54804\t36313\r\n+222.04645\t28905\r\n+224.06192\t55632\r\n+226.04175\t37413\r\n+246.04646\t23286\r\n+248.06204\t140007\r\n+249.07072\t62236\t"Theoretical m/z 249.070425, Mass diff -0.001 (0 ppm), Formula C20H9"\r\n+250.07765\t641789\r\n+251.07967\t137600\r\n+252.09323\t1955166\t"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"\r\n+253.09656\t402252\r\n+254.09985\t39987\r\n+\r\n+NAME: Phenanthrene\r\n+SCANNUMBER: -1\r\n+RETENTIONTIME: -1\r\n+RETENTIONINDEX: 1832.9\r\n+PRECURSORMZ: 178.0775\r\n+PRECURSORTYPE: [M]+\r\n+IONMODE: Positive\r\n+SPECTRUMTYPE: Centroid\r\n+FORMULA: C14H10\r\n+INCHIKEY: YNPNZTXNASCQKK-UHFFFAOYSA-N\r\n+INCHI: \r\n+SMILES: C1=CC2=C(C=C1)C1=C(C=CC=C1)C=C2\r\n+AUTHORS: Price et al., RECETOX, Masaryk University (CZ)\r\n+COLLISIONENERGY: 70eV\r\n+INSTRUMENT: Q Exactive GC Orbitrap GC-MS/MS\r\n+INSTRUMENTTYPE: GC-EI-Orbitrap\r\n+IONIZATION: EI+\r\n+LICENSE: CC BY-NC\r\n+COMMENT: \r\n+Num Peaks: 19\r\n+74.01508\t137808\t"Theoretical m/z 74.01565, Mass diff 0 (0 ppm), Formula C6H2"\r\n+75.02295\t278714\t"Theoretical m/z 75.023475, Mass diff 0 (0 ppm), Formula C6H3"\r\n+76.03075\t608417\t"Theoretical m/z 76.0313, Mass diff 0 (0 ppm), Formula C6H4"\r\n+87.02295\t304266\t"Theoretical m/z 87.023475, Mass diff 0 (0 ppm), Formula C7H3"\r\n+88.03076\t497050\t"Theoretical m/z 88.0313, Mass diff 0 (0 ppm), Formula C7H4"\r\n+89.03857\t441168\t"Theoretical m/z 89.039125, Mass diff 0 (0 ppm), Formula C7H5"\r\n+98.01511\t150478\r\n+150.04633\t868927\r\n+151.05415\t546351\t"Theoretical m/z 151.054775, Mass diff 0 (0 ppm), Formula C12H7"\r\n+152.0619\t2275502\r\n+153.06528\t276320\r\n+169.06468\t272559\r\n+174.04636\t365846\r\n+175.05423\t272039\t"Theoretical m/z 175.054775, Mass diff 0 (0 ppm), Formula C14H7"\r\n+176.062\t3370523\t"Theoretical m/z 176.0626, Mass diff 0 (0 ppm), Formula C14H8"\r\n+177.06982\t1751846\t"Theoretical m/z 177.070425, Mass diff 0 (0 ppm), Formula C14H9"\r\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"\r\n+179.08078\t2250119\r\n+180.08412\t138203\r\n+\r\n+NAME: Anthracene\r\n+SCANNUMBER: -1\r\n+RETENTIONTIME: -1\r\n+RETENTIONINDEX: 1844.4\r\n+PRECURSORMZ: 178.07754\r\n+PRECURSORTYPE: [M]+\r\n+IONMODE: Positive\r\n+SPECTRUMTYPE: Centroid\r\n+FORMULA: C14H10\r\n+INCHIKEY: MWPLVEDNUUSJAV-UHFFFAOYSA-N\r\n+INCHI: \r\n+SMILES: C1=CC2=CC3=C(C=CC=C3)C=C2C=C1\r\n+AUTHORS: Price et al., RECETOX, Masaryk University (CZ)\r\n+COLLISIONENERGY: 70eV\r\n+INSTRUMENT: Q Exactive GC Orbitrap GC-MS/MS\r\n+INSTRUMENTTYPE: GC-EI-Orbitrap\r\n+IONIZATION: EI+\r\n+LICENSE: CC BY-NC\r\n+COMMENT: \r\n+Num Peaks: 21\r\n+74.0151\t117371\t"Theoretical m/z 74.01565, Mass diff 0 (0 ppm), Formula C6H2"\r\n+75.02296\t245305\t"Theoretical m/z 75.023475, Mass diff 0 (0 ppm), Formula C6H3"\r\n+76.03077\t632686\t"Theoretical m/z 76.0313, Mass diff 0 (0 ppm), Formula C6H4"\r\n+87.02297\t236214\t"Theoretical m/z 87.023475, Mass diff 0 (0 ppm), Formula C7H3"\r\n+88.03078\t347832\t"Theoretical m/z 88.0313, Mass diff 0 (0 ppm), Formula C7H4"\r\n+89.0386\t507288\t"Theoretical m/z 89.039125, Mass diff 0 (0 ppm), Formula C7H5"\r\n+91.05425\t130861\t"Theoretical m/z 91.054775, Mass diff 0 (0 ppm), Formula C7H7"\r\n+126.04636\t128356\r\n+149.04478\t126331\r\n+150.04637\t641829\r\n+1'..b'ES NC1=CC=CC=C1, Annotation [C6H7N-2H]+, Rule of HR False"\r\n+92.04941\t7277821\t"Theoretical m/z 92.049472, Mass diff 0 (0.68 ppm), SMILES NC1=CC=CC=C1, Annotation [C6H7N-H]+, Rule of HR True"\r\n+93.05727\t3978164\t"Theoretical m/z 93.057297, Mass diff 0 (0.3 ppm), SMILES NC1=CC=CC=C1, Annotation [C6H7N]+, Rule of HR False"\r\n+99.11674\t2328901\t"Theoretical m/z 99.117375, Mass diff 0 (0 ppm), Formula C7H15"\r\n+102.04636\t1350028\t"Theoretical m/z 102.046398, Mass diff 0 (0.38 ppm), SMILES C1=CC=C(C=C1)CC, Annotation [C8H10-4H]+, Rule of HR False"\r\n+103.05415\t17174370\t"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"\r\n+104.06195\t9726849\t"Theoretical m/z 104.062048, Mass diff 0 (0.95 ppm), SMILES C1=CC=C(C=C1)CC, Annotation [C8H10-2H]+, Rule of HR False"\r\n+105.06982\t8156076\t"Theoretical m/z 105.069873, Mass diff 0 (0.51 ppm), SMILES C1=CC=C(C=C1)CC, Annotation [C8H10-H]+, Rule of HR True"\r\n+106.06507\t1589715\t"Theoretical m/z 106.065128, Mass diff 0 (0.55 ppm), SMILES NCC1=CC=CC=C1, Annotation [C7H9N-H]+, Rule of HR True"\r\n+113.13237\t1360232\t"Theoretical m/z 113.133026, Mass diff 0 (0 ppm), Formula C8H17"\r\n+118.06498\t7179476\t"Theoretical m/z 118.065126, Mass diff 0 (1.23 ppm), SMILES NC(C1=CC=CC=C1)C, Annotation [C8H11N-3H]+, Rule of HR True"\r\n+119.06025\t1747935\t"Theoretical m/z 119.060373, Mass diff 0 (1.03 ppm), SMILES C1=CC=C(C=C1)NNC, Annotation [C7H10N2-3H]+, Rule of HR True"\r\n+121.01054\t6952288\t"Theoretical m/z 121.011196, Mass diff 0 (0 ppm), Formula C7H5S"\r\n+129.04457\t2381139\t"Theoretical m/z 129.045273, Mass diff 0 (0 ppm), Formula C8H5N2"\r\n+130.06502\t2036222\t"Theoretical m/z 130.065118, Mass diff 0 (0.75 ppm), SMILES N(=C)C(C1=CC=CC=C1)C, Annotation [C9H11N-3H]+, Rule of HR True"\r\n+131.06024\t1694144\t"Theoretical m/z 131.060923, Mass diff 0 (0 ppm), Formula C8H7N2"\r\n+132.05687\t5223785\r\n+133.06467\t1497173\t"Theoretical m/z 133.064792, Mass diff 0 (0.92 ppm), SMILES O=CC(C1=CC=CC=C1)C, Annotation [C9H10O-H]+, Rule of HR True"\r\n+146.05989\t1635793\t"Theoretical m/z 146.060037, Mass diff 0 (1.01 ppm), SMILES O=C(N)C(C1=CC=CC=C1)C, Annotation [C9H11NO-3H]+, Rule of HR True"\r\n+162.03708\t6358848\t"Theoretical m/z 162.037195, Mass diff 0 (0.71 ppm), SMILES N(=CS)C(C1=CC=CC=C1)C, Annotation [C9H11NS-3H]+, Rule of HR True"\r\n+163.03226\t2270290\t"Theoretical m/z 163.032994, Mass diff 0 (0 ppm), Formula C8H7N2S"\r\n+180.0806\t5085106\t"Theoretical m/z 180.08078, Mass diff 0 (-1 ppm), SMILES C1=CC2=CC3=C(C=CC=C3)[NH+]=C2C=C1, Annotation [C13H10N]+, Rule of HR True"\r\n+191.06355\t1931709\t"Theoretical m/z 191.063745, Mass diff 0 (1.02 ppm), SMILES N(=C(N)SC)C(C1=CC=CC=C1)C, Annotation [C10H14N2S-3H]+, Rule of HR True"\r\n+194.09631\t2147028\t"Theoretical m/z 194.096974, Mass diff 0 (0 ppm), Formula C14H12N"\r\n+195.09154\t2761186\r\n+206.07457\t32152276\t"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"\r\n+207.07802\t3378894\r\n+209.10724\t7216709\t"Theoretical m/z 209.107873, Mass diff 0 (0 ppm), Formula C14H13N2"\r\n+210.11507\t16279203\r\n+211.11832\t2385281\r\n+223.08647\t7150340\t"Theoretical m/z 223.086587, Mass diff 0 (0.53 ppm), SMILES O=C(NNC1=CC=CC=C1)CC2=CC=CC=C2, Annotation [C14H14N2O-3H]+, Rule of HR True"\r\n+237.10208\t73182472\t"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"\r\n+238.10997\t95774784\r\n+239.11317\t16036299\r\n+240.11644\t1359291\r\n+253.06654\t1780430\t"Theoretical m/z 253.068711, Mass diff 0.002 (0 ppm), Formula C16H13OS"\r\n+268.09\t129797872\t"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"\r\n+269.09351\t20215544\r\n+270.08588\t6998940\r\n+283.11356\t8692036\r\n+284.11704\t1569478\r\n+311.10815\t1417036\t"Theoretical m/z 311.108674, Mass diff 0.001 (1.68 ppm), SMILES O=C3N(NC1=CC=CC=C1)C(=NC3(C2=CC=CC=C2)C)SC, Annotation [C17H17N3OS]+, Rule of HR False"\r\n' |
| b |
| diff -r 000000000000 -r e4ec3592507f test-data/similarity/scores_test1_out.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/scores_test1_out.json Tue Oct 18 13:23:28 2022 +0000 |
| [ |
| b'@@ -0,0 +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, 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| b |
| diff -r 000000000000 -r e4ec3592507f test-data/similarity/scores_test2_out.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/scores_test2_out.json Tue Oct 18 13:23:28 2022 +0000 |
| [ |
| b'@@ -0,0 +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, 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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, 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0]]]}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r e4ec3592507f test-data/similarity/scores_test3_out.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/scores_test3_out.json Tue Oct 18 13:23:28 2022 +0000 |
| [ |
| b'@@ -0,0 +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], 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0]]]}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r e4ec3592507f test-data/similarity/scores_test4_out.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/scores_test4_out.json Tue Oct 18 13:23:28 2022 +0000 |
| [ |
| b'@@ -0,0 +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 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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'184, 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], [0.0, 0], [0.07913720198135349, 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14], [0.9999999999999996, 47]]]}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r e4ec3592507f test-data/similarity/scores_test5_out.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/scores_test5_out.json Tue Oct 18 13:23:28 2022 +0000 |
| [ |
| b'@@ -0,0 +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": 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[0.0, 23], [0.9999999999999994, 48]]]}\n\\ No newline at end of file\n' |