Mercurial > repos > recetox > biotransformer
changeset 0:0b86600b715e draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
| author | recetox |
|---|---|
| date | Tue, 06 Jun 2023 11:23:51 +0000 |
| parents | |
| children | 296bd426527f |
| files | biotransformer.xml macros.xml test-data/output1.tsv test-data/output2.tsv test-data/output3.tsv test-data/smiles.csv wrapper_biotransformer.py |
| diffstat | 7 files changed, 812 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biotransformer.xml Tue Jun 06 11:23:51 2023 +0000 @@ -0,0 +1,70 @@ +<tool id="biotransformer" name="BioTransformer" version="@TOOL_VERSION@+galaxy0" profile="21.09"> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="creator"/> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">biotransformer</requirement> + <requirement type="package" version="3.1.1">openbabel</requirement> + <requirement type="package" version="1.1.1">pandas</requirement> + </requirements> + <command detect_errors="aggressive"><![CDATA[ + python3 '${__tool_directory__}/wrapper_biotransformer.py' + -k $k + -b $b + -s $steps + -t $tolerance + -a + -icsv $input_file + -ocsv $output_file + -ocsvDup $output_file2 + -ocsvDup2 $output_file3 + ]]> + </command> + <inputs> + <param name="k" type="select" value="pred" + label="The task to be permed [pred=prediction, cid=compound identification]."> + <option value="pred" selected="true">pred</option> + <option value="cid">cid</option> + </param> + <param name="b" type="select" value="ecbased" label="The type of description."> + <option value="ecbased" selected="true">EC-based</option> + <option value="cyp450">CYP450</option> + <option value="phaseII">Phase II</option> + <option value="hgut">Human gut microbial</option> + <option value="superbio">Human super transformer 1 (superbio)</option> + <option value="allHuman">Human super transformer 2 (allHuman)</option> + <option value="envimicro">Environmental microbial</option> + </param> + <param name="steps" type="integer" value="1" label=" The number of steps for the prediction."/> + <param name="tolerance" type="float" value="0.01" label="Mass tolerance for metabolite identification."/> + <param name="input_file" type="data" format="csv" label="Input CSV file."/> + </inputs> + + <outputs> + <data format="tsv" name="output_file" label="BioTransformer on ${on_string}"/> + <data format="tsv" name="output_file2" label="BioTransformer with filter on ${on_string}"/> + <data format="tsv" name="output_file3" label="BioTransformer with super filter on ${on_string}"/> + </outputs> + + <tests> + <test> + <param name="k" value="pred"/> + <param name="b" value="allHuman"/> + <param name="steps" value="1"/> + <param name="tolerance" value="0.01"/> + <param name="input_file" value="smiles.csv"/> + <output name="output_file" value="output1.tsv"/> + <output name="output_file2" value="output2.tsv"/> + <output name="output_file3" value="output3.tsv"/> + </test> + </tests> + <help> + <![CDATA[ + @HELP@ + ]]> + </help> + <citations> + <citation type="doi">https://doi.org/10.1186/s13321-018-0324-5</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jun 06 11:23:51 2023 +0000 @@ -0,0 +1,57 @@ +<macros> + <token name="@TOOL_VERSION@">3.0_20230403</token> + <xml name="creator"> + <creator> + <person + givenName="Martin" + familyName="Čech" + url="https://github.com/martenson" + identifier="0000-0002-9318-1781" /> + <person + givenName="Karolína" + familyName="Trachtová" + url="https://github.com/trachtok" /> + <organization + url="https://www.recetox.muni.cz/" + email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" + name="RECETOX MUNI" /> + </creator> + </xml> + <token name="@HELP@"> + <![CDATA[ + BioTransformer is a software tool that predicts small molecule metabolism in mammals, their gut micr obiota, + as well as the soil/aquatic microbiota. BioTransformer also assists scientists in metabolite identification, + based on the metabolism prediction. + + BioTransformer is offered to the public as a freely acessible software package under the GNU License GPL v3. + + Users are free to copy and redistribute the material in any medium or format. Moreover, they could modify, and + build upon the material under the condition that they must give appropriate credit, provide links to the license, + and indicate if changes were made. Furthermore, the above copyright notice and this permission notice must be + included. Use and re-distribution of the these resources, in whole or in part, for commercial purposes requires + explicit permission of the authors. We ask that all users of the BioTransformer software tool, the BioTransformer + web server, or BioTransformerDB to cite the BioTransformer reference in any resulting publications, and to + acknowledge the authors. + + Parameters explanation: + + **Input.** Currently, only a CSV file with one SMILES per line is accepted. + + **The type of prediction:** EC-based (ecbased), CYP450 (cyp450), Phase II (phaseII), Human gut + microbial (hgut), human super transformer* (superbio, or allHuman), Environmental microbial (envimicro). + + **The number of steps for the prediction:** this option will be used for the EC-based, CYP450, Phase II, and Environmental + microbial biotransformers. The default value is 1. + + **Mass tolerance for metabolite identification** (default is 0.01). + + **Output of BioTransformer** with CSV as an input are 3 TSV files. One without any filtering, second with filtered + duplicates based on 6 columns (InChI, InChIKey, Synonyms, Molecular formula, Major Isotope Mass, AlogP) and third with + filtered duplicates based on 3 columns (Molecular formula, Major Isotope Mass, AlogP). + + (* ) While the 'superbio' option runs a set number of transformation steps in a pre-defined order (e.g. deconjugation + first, then Oxidation/reduction, etc.), the 'allHuman' option predicts all possible metabolites from any applicable + reaction(Oxidation, reduction, (de-)conjugation) at each step. + ]]> + </token> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output1.tsv Tue Jun 06 11:23:51 2023 +0000 @@ -0,0 +1,215 @@ + SMILES query SMILES target InChI InChIKey SMILES Synonyms PUBCHEM_CID Molecular formula Major Isotope Mass ALogP Lipinski_Violations Insecticide_Likeness_Violations Post_Em_Herbicide_Likeness_Violations Metabolite ID cdk:Title Reaction Reaction ID Enzyme(s) Biosystem Precursor ID Precursor SMILES Precursor InChI Precursor InChIKey Precursor ALogP Precursor Major Isotope Mass +0 CC(C)C1=CC=C(C)C=C1O "CC(C)c1ccc(C)cc1OC1C(C(C(C(C(=O)O)O1)O)O)O +" InChI=1S/C16H22O7/c1-7(2)9-5-4-8(3)6-10(9)22-16-13(19)11(17)12(18)14(23-16)15(20)21/h4-7,11-14,16-19H,1-3H3,(H,20,21) ADQJSAVCKZSGMK-UHFFFAOYSA-N CC(C)C1=CC=C(C)C=C1OC2OC(C(O)=O)C(C(C2O)O)O "NSC404789 +NSC-404789 +(2S,3S,4S,5R)-3,4,5-trihydroxy-6-(5-methyl-2-propan-2-ylphenoxy)oxane-2-carboxylic acid +3,5-trihydroxy-6-(2-isopropyl-5-methyl-phenoxy)tetrahydro-2H-pyran-2-carboxylic acid" 346530 C16H22O7 326.13655304400004 1.5474999999999992 0 1 1 BTM00001 BTM00001 Aromatic OH-glucuronidation BTMR0166 EC 2.4.1.17 HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +1 CC(C)C1=CC=C(C)C=C1O "CC(C)c1ccc(C)cc1OS(=O)(=O)O +" InChI=1S/C10H14O4S/c1-7(2)9-5-4-8(3)6-10(9)14-15(11,12)13/h4-7H,1-3H3,(H,11,12,13) NODSEPOUFZPJEQ-UHFFFAOYSA-N CC(C)C1=CC=C(C)C=C1OS(O)(=O)=O "thymol sulfate +Thymol sulphate +Thymol sulfuric acid +Thymol sulphuric acid +SCHEMBL235717 +CHEBI:82911 +(5-methyl-2-propan-2-ylphenyl) hydrogen sulfate +5-methyl-2-(propan-2-yl)phenyl hydrogen sulfate +Q27156452" 12456386 C10H14O4S 230.061279928 2.5061999999999993 0 0 0 BTM00002 BTM00002 Sulfonation of phenolic compound BTMR1376 EC 2.8.2.1 HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +2 CC(C)C1=CC=C(C)C=C1O "CC(C)c1ccc(C)cc1OC +" InChI=1S/C11H16O/c1-8(2)10-6-5-9(3)7-11(10)12-4/h5-8H,1-4H3 LSQXNMXDFRRDSJ-UHFFFAOYSA-N CC(C)C1=CC=C(C)C=C1OC "Thymol methyl ether +2-Isopropyl-5-methylanisole +1076-56-8 +O-Methylthymol +Thymyl methyl ether +Methyl thymyl ether +3-Methoxy-p-cymene +4-Isopropyl-3-methoxytoluene +1-Isopropyl-2-methoxy-4-methylbenzene +Methyl thymol ether +Benzene, 2-methoxy-4-methyl-1-(1-methylethyl)- +ANISOLE, 2-ISOPROPYL-5-METHYL- +2-methoxy-4-methyl-1-propan-2-ylbenzene +1-Methyl-3-methoxy-4-isopropylbenzene +Benzene,2-methoxy-4-methyl-1-(1-methylethyl)- +methylthymol +FEMA No. 3436 +Thymol methyl +thymol Me ether +2-Methoxy-4-methyl-1-(1-methylethyl)benzene +2-methoxy-4-methyl-1-(propan-2-yl)benzene +Fema3436 +VTE0C4390U +DTXSID5047617 +NSC-404221 +Methylthymol, o- +EINECS 214-063-9 +NSC 404221 +BRN 2042889 +UNII-VTE0C4390U +AI3-03431 +thymyl methyl oxide +Methyl THYMYL oxide +starbld0009587 +Thymol derivative, 21 +4-06-00-03335 (Beilstein Handbook Reference) +3-METHOXY-PARA-CYMENE +SCHEMBL196752 +2-Isopropyl-5-methyl-Anisole +CHEMBL2424841 +DTXCID3027617 +CHEBI:167336 +BDBM248170 +Tox21_302575 +MFCD01674973 +NSC404221 +2-ISO PROPYL-5-METHYLANISOLE +AKOS015914183 +Thymol methyl ether (= methyl thymol) +NCGC00256877-01 +LS-13985 +CAS-1076-56-8 +CS-0335474 +FT-0754651 +I0996 +1-Methyl-3-methoxy-4-isopropylbenzene, 98% +D91215 +Q27292012 +1-METHYL-3-METHOXY-4-ISOPROPYL BENZENE [FHFI] +1-Isopropyl-2-methoxy-4-methylbenzene, analytical standard" 14104 C11H16O 164.120115132 3.493999999999998 0 0 0 BTM00003 BTM00003 Methylation of phenolic compound BTMR1377 EC 2.1.1.25 HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +3 CC(C)C1=CC=C(C)C=C1O "Cc1ccc(c(c1)O)C(C)(C)O +" InChI=1S/C10H14O2/c1-7-4-5-8(9(11)6-7)10(2,3)12/h4-6,11-12H,1-3H3 UWRRYLNXMGBJKK-UHFFFAOYSA-N CC(C)(C1=CC=C(C)C=C1O)O "SCHEMBL22652590 +2-(2-hydroxypropan-2-yl)-5-methylphenol +EN300-1838871 +4478-33-5" 11332674 C10H14O2 166.099379688 2.0267999999999997 0 0 0 BTM00004 BTM00004 Hydroxylation of non-terminal aliphatic carbon adjacent to aromatic ring BTMR1077 "CYP1A2 +CYP2C8 +CYP2C9 +CYP2D6 +CYP3A4" HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +4 CC(C)C1=CC=C(C)C=C1O "CC(C)c1cc(c(C)cc1O)O +" InChI=1S/C10H14O2/c1-6(2)8-5-9(11)7(3)4-10(8)12/h4-6,11-12H,1-3H3 OQIOHYHRGZNZCW-UHFFFAOYSA-N CC(C)C1=CC(=C(C)C=C1O)O "Thymohydroquinone +2217-60-9 +Hydrothymoquinone +Thymoquinol +p-Cymene-2,5-diol +1,4-Benzenediol, 2-methyl-5-(1-methylethyl)- +2-Methyl-5-isopropylhydroquinone +Hydroquinone, 5-isopropyl-2-methyl- +2-methyl-5-(propan-2-yl)benzene-1,4-diol +NSC 34803 +2-ISOPROPYL-5-METHYLBENZENE-1,4-DIOL +1C2ICM1R8V +2-methyl-5-(1-methylethyl)-1,4-benzenediol +NSC-34803 +BRN 2084452 +Thymohydrochinon +2-methyl-5-propan-2-ylbenzene-1,4-diol +2-hydroxythymol +2,5-DIHYDROXY-P-CYMENE +Thymohydroquinone (I) +UNII-1C2ICM1R8V +SCHEMBL69082 +CHEMBL4204349 +2-isopropyl-5-methylhydroquinone +DTXSID70176706 +WLN: QR DQ B1 EY1&1 +NSC34803 +1, 2-methyl-5-(1-methylethyl)- +AKOS006274324 +2-isopropyl-5-methyl-benzene-1,4-diol +CS-0259073 +FT-0700031 +4-HYDROXY-5-ISOPROPYL-2-METHYLPHENOL +EN300-722422 +Z1198148655 +2-Methyl-5-(1-Methylethyl)cyclohexa-2,5-Diene-1,4-Dione +9J9 +IMW" 95779 C10H14O2 166.099379688 2.9756 0 0 0 BTM00005 BTM00005 p-Hydroxylation of phenol BTMR1038 "CYP1A2 +CYP2A6 +CYP2B6 +CYP2C8 +CYP2C9 +CYP2C19 +CYP2D6 +CYP2E1 +CYP3A4" HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +5 CC(C)C1=CC=C(C)C=C1O "CC(C)c1ccc(cc1O)CO +" InChI=1S/C10H14O2/c1-7(2)9-4-3-8(6-11)5-10(9)12/h3-5,7,11-12H,6H2,1-2H3 UNNQYEJIPIBHFS-UHFFFAOYSA-N CC(C)C1=CC=C(CO)C=C1O "77311-68-3 +5-(Hydroxymethyl)-2-(propan-2-yl)phenol +5-hydroxymethyl-2-isopropylphenol +DTXSID70554040 +2-Isopropyl-5-(hydroxymethyl)phenol" 14002478 C10H14O2 166.099379688 2.1523000000000003 0 0 0 BTM00006 BTM00006 Aliphatic hydroxylation of methyl carbon adjacent to aromatic ring BTMR1058 "CYP1A2 +CYP2A6 +CYP2B6 +CYP2C8 +CYP2C9 +CYP2C19 +CYP2D6 +CYP2E1 +CYP3A4" HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +6 CC(C)C1=CC=C(C)C=C1O "Cc1ccc(C(C)CO)c(c1)O +" InChI=1S/C10H14O2/c1-7-3-4-9(8(2)6-11)10(12)5-7/h3-5,8,11-12H,6H2,1-2H3 CLJPRXFHCRIUKW-UHFFFAOYSA-N C(C(C)C1=CC=C(C)C=C1O)O "9-Hydroxythymol +61955-76-8 +2-(1-hydroxypropan-2-yl)-5-methylphenol +p-cymene-3,8-diol +HY-N10925 +p-Mentha-1,3,5-triene-3,9-diol +CS-0637580" 14432748 C10H14O2 166.099379688 2.0848000000000004 0 0 0 BTM00007 BTM00007 Hydroxylation of terminal methyl BTMR1061 "CYP1A2 +CYP2A6 +CYP2B6 +CYP2C8 +CYP2C9 +CYP2C19 +CYP2D6 +CYP2E1 +CYP3A4" HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +7 CC(C)C1=CC=C(C)C=C1O "C=C(C)c1ccc(C)cc1O +" InChI=1S/C10H12O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-6,11H,1H2,2-3H3 IHWFPRKZRRGTTI-UHFFFAOYSA-N CC(=C)C1=CC=C(C)C=C1O "8,9-Dehydrothymol +2-isopropenyl-5-methylphenol +18612-99-2 +5-methyl-2-prop-1-en-2-ylphenol +Phenol, 5-methyl-2-(1-methylethenyl)- +m-Cresol, 6-isopropenyl- +SCHEMBL686122 +2-Isopropenyl-5-methyl-phenol +DTXSID60423892 +5-Methyl-2-(1-methylethenyl)phenol +5-Methyl-2-(prop-1-en-2-yl)phenol" 6429037 C10H12O 148.088815004 3.0469000000000004 0 0 0 BTM00008 BTM00008 Terminal desaturation BTMR1190 "CYP1A2 +CYP2A6 +CYP2C9 +CYP2D6 +CYP3A4" HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +8 CC(C)C1=CC=C(C)C=C1O "CC(C)c1ccc(C)c(c1O)O +" InChI=1S/C10H14O2/c1-6(2)8-5-4-7(3)9(11)10(8)12/h4-6,11-12H,1-3H3 LYUBXLHGANLIMX-UHFFFAOYSA-N CC(C)C1=CC=C(C)C(=C1O)O "Cymopyrocatechol +490-06-2 +3-Isopropyl-6-methylpyrocatechol +p-cymene-2,3-diol +3-isopropyl-6-methylbenzene-1,2-diol +3-isopropyl-6-methylcatechol +Pyrocatechol, 2-isopropyl-6-methyl- +93XFQ715UL +3-methyl-6-(propan-2-yl)benzene-1,2-diol +1,2-Benzenediol, 3-methyl-6-(1-methylethyl)- +NSC-40567 +NSC 40567 +BRN 2248022 +3-methyl-6-propan-2-ylbenzene-1,2-diol +NSC40567 +UNII-93XFQ715UL +SCHEMBL1494556 +2,3-DIHYDROXY-P-CYMENE +DTXSID10197652 +AKOS006275160 +3-isopropyl-6-methyl-1,2-benzenediol +3-methyl-6-propan-2-yl-benzene-1,2-diol +CS-0353716 +EN300-1599484 +2,3-DIHYDROXY-4-ISOPROPYL-1-METHYLBENZENE +A828568 +3-METHYL-6-(1-METHYLETHYL)-1,2-BENZENEDIOL" 95873 C10H14O2 166.099379688 2.9756 0 0 0 BTM00009 BTM00009 O-Hydroxylation of phenol BTMR1037 "CYP1A2 +CYP2A6 +CYP2B6 +CYP2C8 +CYP2C9 +CYP2C19 +CYP2D6 +CYP2E1 +CYP3A4" HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output2.tsv Tue Jun 06 11:23:51 2023 +0000 @@ -0,0 +1,215 @@ + SMILES query SMILES target InChI InChIKey SMILES Synonyms PUBCHEM_CID Molecular formula Major Isotope Mass ALogP Lipinski_Violations Insecticide_Likeness_Violations Post_Em_Herbicide_Likeness_Violations Metabolite ID cdk:Title Reaction Reaction ID Enzyme(s) Biosystem Precursor ID Precursor SMILES Precursor InChI Precursor InChIKey Precursor ALogP Precursor Major Isotope Mass +0 CC(C)C1=CC=C(C)C=C1O "CC(C)c1ccc(C)cc1OC1C(C(C(C(C(=O)O)O1)O)O)O +" InChI=1S/C16H22O7/c1-7(2)9-5-4-8(3)6-10(9)22-16-13(19)11(17)12(18)14(23-16)15(20)21/h4-7,11-14,16-19H,1-3H3,(H,20,21) ADQJSAVCKZSGMK-UHFFFAOYSA-N CC(C)C1=CC=C(C)C=C1OC2OC(C(O)=O)C(C(C2O)O)O "NSC404789 +NSC-404789 +(2S,3S,4S,5R)-3,4,5-trihydroxy-6-(5-methyl-2-propan-2-ylphenoxy)oxane-2-carboxylic acid +3,5-trihydroxy-6-(2-isopropyl-5-methyl-phenoxy)tetrahydro-2H-pyran-2-carboxylic acid" 346530 C16H22O7 326.13655304400004 1.5474999999999992 0 1 1 BTM00001 BTM00001 Aromatic OH-glucuronidation BTMR0166 EC 2.4.1.17 HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +1 CC(C)C1=CC=C(C)C=C1O "CC(C)c1ccc(C)cc1OS(=O)(=O)O +" InChI=1S/C10H14O4S/c1-7(2)9-5-4-8(3)6-10(9)14-15(11,12)13/h4-7H,1-3H3,(H,11,12,13) NODSEPOUFZPJEQ-UHFFFAOYSA-N CC(C)C1=CC=C(C)C=C1OS(O)(=O)=O "thymol sulfate +Thymol sulphate +Thymol sulfuric acid +Thymol sulphuric acid +SCHEMBL235717 +CHEBI:82911 +(5-methyl-2-propan-2-ylphenyl) hydrogen sulfate +5-methyl-2-(propan-2-yl)phenyl hydrogen sulfate +Q27156452" 12456386 C10H14O4S 230.061279928 2.5061999999999993 0 0 0 BTM00002 BTM00002 Sulfonation of phenolic compound BTMR1376 EC 2.8.2.1 HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +2 CC(C)C1=CC=C(C)C=C1O "CC(C)c1ccc(C)cc1OC +" InChI=1S/C11H16O/c1-8(2)10-6-5-9(3)7-11(10)12-4/h5-8H,1-4H3 LSQXNMXDFRRDSJ-UHFFFAOYSA-N CC(C)C1=CC=C(C)C=C1OC "Thymol methyl ether +2-Isopropyl-5-methylanisole +1076-56-8 +O-Methylthymol +Thymyl methyl ether +Methyl thymyl ether +3-Methoxy-p-cymene +4-Isopropyl-3-methoxytoluene +1-Isopropyl-2-methoxy-4-methylbenzene +Methyl thymol ether +Benzene, 2-methoxy-4-methyl-1-(1-methylethyl)- +ANISOLE, 2-ISOPROPYL-5-METHYL- +2-methoxy-4-methyl-1-propan-2-ylbenzene +1-Methyl-3-methoxy-4-isopropylbenzene +Benzene,2-methoxy-4-methyl-1-(1-methylethyl)- +methylthymol +FEMA No. 3436 +Thymol methyl +thymol Me ether +2-Methoxy-4-methyl-1-(1-methylethyl)benzene +2-methoxy-4-methyl-1-(propan-2-yl)benzene +Fema3436 +VTE0C4390U +DTXSID5047617 +NSC-404221 +Methylthymol, o- +EINECS 214-063-9 +NSC 404221 +BRN 2042889 +UNII-VTE0C4390U +AI3-03431 +thymyl methyl oxide +Methyl THYMYL oxide +starbld0009587 +Thymol derivative, 21 +4-06-00-03335 (Beilstein Handbook Reference) +3-METHOXY-PARA-CYMENE +SCHEMBL196752 +2-Isopropyl-5-methyl-Anisole +CHEMBL2424841 +DTXCID3027617 +CHEBI:167336 +BDBM248170 +Tox21_302575 +MFCD01674973 +NSC404221 +2-ISO PROPYL-5-METHYLANISOLE +AKOS015914183 +Thymol methyl ether (= methyl thymol) +NCGC00256877-01 +LS-13985 +CAS-1076-56-8 +CS-0335474 +FT-0754651 +I0996 +1-Methyl-3-methoxy-4-isopropylbenzene, 98% +D91215 +Q27292012 +1-METHYL-3-METHOXY-4-ISOPROPYL BENZENE [FHFI] +1-Isopropyl-2-methoxy-4-methylbenzene, analytical standard" 14104 C11H16O 164.120115132 3.493999999999998 0 0 0 BTM00003 BTM00003 Methylation of phenolic compound BTMR1377 EC 2.1.1.25 HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +3 CC(C)C1=CC=C(C)C=C1O "Cc1ccc(c(c1)O)C(C)(C)O +" InChI=1S/C10H14O2/c1-7-4-5-8(9(11)6-7)10(2,3)12/h4-6,11-12H,1-3H3 UWRRYLNXMGBJKK-UHFFFAOYSA-N CC(C)(C1=CC=C(C)C=C1O)O "SCHEMBL22652590 +2-(2-hydroxypropan-2-yl)-5-methylphenol +EN300-1838871 +4478-33-5" 11332674 C10H14O2 166.099379688 2.0267999999999997 0 0 0 BTM00004 BTM00004 Hydroxylation of non-terminal aliphatic carbon adjacent to aromatic ring BTMR1077 "CYP1A2 +CYP2C8 +CYP2C9 +CYP2D6 +CYP3A4" HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +4 CC(C)C1=CC=C(C)C=C1O "CC(C)c1cc(c(C)cc1O)O +" InChI=1S/C10H14O2/c1-6(2)8-5-9(11)7(3)4-10(8)12/h4-6,11-12H,1-3H3 OQIOHYHRGZNZCW-UHFFFAOYSA-N CC(C)C1=CC(=C(C)C=C1O)O "Thymohydroquinone +2217-60-9 +Hydrothymoquinone +Thymoquinol +p-Cymene-2,5-diol +1,4-Benzenediol, 2-methyl-5-(1-methylethyl)- +2-Methyl-5-isopropylhydroquinone +Hydroquinone, 5-isopropyl-2-methyl- +2-methyl-5-(propan-2-yl)benzene-1,4-diol +NSC 34803 +2-ISOPROPYL-5-METHYLBENZENE-1,4-DIOL +1C2ICM1R8V +2-methyl-5-(1-methylethyl)-1,4-benzenediol +NSC-34803 +BRN 2084452 +Thymohydrochinon +2-methyl-5-propan-2-ylbenzene-1,4-diol +2-hydroxythymol +2,5-DIHYDROXY-P-CYMENE +Thymohydroquinone (I) +UNII-1C2ICM1R8V +SCHEMBL69082 +CHEMBL4204349 +2-isopropyl-5-methylhydroquinone +DTXSID70176706 +WLN: QR DQ B1 EY1&1 +NSC34803 +1, 2-methyl-5-(1-methylethyl)- +AKOS006274324 +2-isopropyl-5-methyl-benzene-1,4-diol +CS-0259073 +FT-0700031 +4-HYDROXY-5-ISOPROPYL-2-METHYLPHENOL +EN300-722422 +Z1198148655 +2-Methyl-5-(1-Methylethyl)cyclohexa-2,5-Diene-1,4-Dione +9J9 +IMW" 95779 C10H14O2 166.099379688 2.9756 0 0 0 BTM00005 BTM00005 p-Hydroxylation of phenol BTMR1038 "CYP1A2 +CYP2A6 +CYP2B6 +CYP2C8 +CYP2C9 +CYP2C19 +CYP2D6 +CYP2E1 +CYP3A4" HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +5 CC(C)C1=CC=C(C)C=C1O "CC(C)c1ccc(cc1O)CO +" InChI=1S/C10H14O2/c1-7(2)9-4-3-8(6-11)5-10(9)12/h3-5,7,11-12H,6H2,1-2H3 UNNQYEJIPIBHFS-UHFFFAOYSA-N CC(C)C1=CC=C(CO)C=C1O "77311-68-3 +5-(Hydroxymethyl)-2-(propan-2-yl)phenol +5-hydroxymethyl-2-isopropylphenol +DTXSID70554040 +2-Isopropyl-5-(hydroxymethyl)phenol" 14002478 C10H14O2 166.099379688 2.1523000000000003 0 0 0 BTM00006 BTM00006 Aliphatic hydroxylation of methyl carbon adjacent to aromatic ring BTMR1058 "CYP1A2 +CYP2A6 +CYP2B6 +CYP2C8 +CYP2C9 +CYP2C19 +CYP2D6 +CYP2E1 +CYP3A4" HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +6 CC(C)C1=CC=C(C)C=C1O "Cc1ccc(C(C)CO)c(c1)O +" InChI=1S/C10H14O2/c1-7-3-4-9(8(2)6-11)10(12)5-7/h3-5,8,11-12H,6H2,1-2H3 CLJPRXFHCRIUKW-UHFFFAOYSA-N C(C(C)C1=CC=C(C)C=C1O)O "9-Hydroxythymol +61955-76-8 +2-(1-hydroxypropan-2-yl)-5-methylphenol +p-cymene-3,8-diol +HY-N10925 +p-Mentha-1,3,5-triene-3,9-diol +CS-0637580" 14432748 C10H14O2 166.099379688 2.0848000000000004 0 0 0 BTM00007 BTM00007 Hydroxylation of terminal methyl BTMR1061 "CYP1A2 +CYP2A6 +CYP2B6 +CYP2C8 +CYP2C9 +CYP2C19 +CYP2D6 +CYP2E1 +CYP3A4" HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +7 CC(C)C1=CC=C(C)C=C1O "C=C(C)c1ccc(C)cc1O +" InChI=1S/C10H12O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-6,11H,1H2,2-3H3 IHWFPRKZRRGTTI-UHFFFAOYSA-N CC(=C)C1=CC=C(C)C=C1O "8,9-Dehydrothymol +2-isopropenyl-5-methylphenol +18612-99-2 +5-methyl-2-prop-1-en-2-ylphenol +Phenol, 5-methyl-2-(1-methylethenyl)- +m-Cresol, 6-isopropenyl- +SCHEMBL686122 +2-Isopropenyl-5-methyl-phenol +DTXSID60423892 +5-Methyl-2-(1-methylethenyl)phenol +5-Methyl-2-(prop-1-en-2-yl)phenol" 6429037 C10H12O 148.088815004 3.0469000000000004 0 0 0 BTM00008 BTM00008 Terminal desaturation BTMR1190 "CYP1A2 +CYP2A6 +CYP2C9 +CYP2D6 +CYP3A4" HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +8 CC(C)C1=CC=C(C)C=C1O "CC(C)c1ccc(C)c(c1O)O +" InChI=1S/C10H14O2/c1-6(2)8-5-4-7(3)9(11)10(8)12/h4-6,11-12H,1-3H3 LYUBXLHGANLIMX-UHFFFAOYSA-N CC(C)C1=CC=C(C)C(=C1O)O "Cymopyrocatechol +490-06-2 +3-Isopropyl-6-methylpyrocatechol +p-cymene-2,3-diol +3-isopropyl-6-methylbenzene-1,2-diol +3-isopropyl-6-methylcatechol +Pyrocatechol, 2-isopropyl-6-methyl- +93XFQ715UL +3-methyl-6-(propan-2-yl)benzene-1,2-diol +1,2-Benzenediol, 3-methyl-6-(1-methylethyl)- +NSC-40567 +NSC 40567 +BRN 2248022 +3-methyl-6-propan-2-ylbenzene-1,2-diol +NSC40567 +UNII-93XFQ715UL +SCHEMBL1494556 +2,3-DIHYDROXY-P-CYMENE +DTXSID10197652 +AKOS006275160 +3-isopropyl-6-methyl-1,2-benzenediol +3-methyl-6-propan-2-yl-benzene-1,2-diol +CS-0353716 +EN300-1599484 +2,3-DIHYDROXY-4-ISOPROPYL-1-METHYLBENZENE +A828568 +3-METHYL-6-(1-METHYLETHYL)-1,2-BENZENEDIOL" 95873 C10H14O2 166.099379688 2.9756 0 0 0 BTM00009 BTM00009 O-Hydroxylation of phenol BTMR1037 "CYP1A2 +CYP2A6 +CYP2B6 +CYP2C8 +CYP2C9 +CYP2C19 +CYP2D6 +CYP2E1 +CYP3A4" HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output3.tsv Tue Jun 06 11:23:51 2023 +0000 @@ -0,0 +1,179 @@ + SMILES query SMILES target InChI InChIKey SMILES Synonyms PUBCHEM_CID Molecular formula Major Isotope Mass ALogP Lipinski_Violations Insecticide_Likeness_Violations Post_Em_Herbicide_Likeness_Violations Metabolite ID cdk:Title Reaction Reaction ID Enzyme(s) Biosystem Precursor ID Precursor SMILES Precursor InChI Precursor InChIKey Precursor ALogP Precursor Major Isotope Mass +0 CC(C)C1=CC=C(C)C=C1O "CC(C)c1ccc(C)cc1OC1C(C(C(C(C(=O)O)O1)O)O)O +" InChI=1S/C16H22O7/c1-7(2)9-5-4-8(3)6-10(9)22-16-13(19)11(17)12(18)14(23-16)15(20)21/h4-7,11-14,16-19H,1-3H3,(H,20,21) ADQJSAVCKZSGMK-UHFFFAOYSA-N CC(C)C1=CC=C(C)C=C1OC2OC(C(O)=O)C(C(C2O)O)O "NSC404789 +NSC-404789 +(2S,3S,4S,5R)-3,4,5-trihydroxy-6-(5-methyl-2-propan-2-ylphenoxy)oxane-2-carboxylic acid +3,5-trihydroxy-6-(2-isopropyl-5-methyl-phenoxy)tetrahydro-2H-pyran-2-carboxylic acid" 346530 C16H22O7 326.13655304400004 1.5474999999999992 0 1 1 BTM00001 BTM00001 Aromatic OH-glucuronidation BTMR0166 EC 2.4.1.17 HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +1 CC(C)C1=CC=C(C)C=C1O "CC(C)c1ccc(C)cc1OS(=O)(=O)O +" InChI=1S/C10H14O4S/c1-7(2)9-5-4-8(3)6-10(9)14-15(11,12)13/h4-7H,1-3H3,(H,11,12,13) NODSEPOUFZPJEQ-UHFFFAOYSA-N CC(C)C1=CC=C(C)C=C1OS(O)(=O)=O "thymol sulfate +Thymol sulphate +Thymol sulfuric acid +Thymol sulphuric acid +SCHEMBL235717 +CHEBI:82911 +(5-methyl-2-propan-2-ylphenyl) hydrogen sulfate +5-methyl-2-(propan-2-yl)phenyl hydrogen sulfate +Q27156452" 12456386 C10H14O4S 230.061279928 2.5061999999999993 0 0 0 BTM00002 BTM00002 Sulfonation of phenolic compound BTMR1376 EC 2.8.2.1 HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +2 CC(C)C1=CC=C(C)C=C1O "CC(C)c1ccc(C)cc1OC +" InChI=1S/C11H16O/c1-8(2)10-6-5-9(3)7-11(10)12-4/h5-8H,1-4H3 LSQXNMXDFRRDSJ-UHFFFAOYSA-N CC(C)C1=CC=C(C)C=C1OC "Thymol methyl ether +2-Isopropyl-5-methylanisole +1076-56-8 +O-Methylthymol +Thymyl methyl ether +Methyl thymyl ether +3-Methoxy-p-cymene +4-Isopropyl-3-methoxytoluene +1-Isopropyl-2-methoxy-4-methylbenzene +Methyl thymol ether +Benzene, 2-methoxy-4-methyl-1-(1-methylethyl)- +ANISOLE, 2-ISOPROPYL-5-METHYL- +2-methoxy-4-methyl-1-propan-2-ylbenzene +1-Methyl-3-methoxy-4-isopropylbenzene +Benzene,2-methoxy-4-methyl-1-(1-methylethyl)- +methylthymol +FEMA No. 3436 +Thymol methyl +thymol Me ether +2-Methoxy-4-methyl-1-(1-methylethyl)benzene +2-methoxy-4-methyl-1-(propan-2-yl)benzene +Fema3436 +VTE0C4390U +DTXSID5047617 +NSC-404221 +Methylthymol, o- +EINECS 214-063-9 +NSC 404221 +BRN 2042889 +UNII-VTE0C4390U +AI3-03431 +thymyl methyl oxide +Methyl THYMYL oxide +starbld0009587 +Thymol derivative, 21 +4-06-00-03335 (Beilstein Handbook Reference) +3-METHOXY-PARA-CYMENE +SCHEMBL196752 +2-Isopropyl-5-methyl-Anisole +CHEMBL2424841 +DTXCID3027617 +CHEBI:167336 +BDBM248170 +Tox21_302575 +MFCD01674973 +NSC404221 +2-ISO PROPYL-5-METHYLANISOLE +AKOS015914183 +Thymol methyl ether (= methyl thymol) +NCGC00256877-01 +LS-13985 +CAS-1076-56-8 +CS-0335474 +FT-0754651 +I0996 +1-Methyl-3-methoxy-4-isopropylbenzene, 98% +D91215 +Q27292012 +1-METHYL-3-METHOXY-4-ISOPROPYL BENZENE [FHFI] +1-Isopropyl-2-methoxy-4-methylbenzene, analytical standard" 14104 C11H16O 164.120115132 3.493999999999998 0 0 0 BTM00003 BTM00003 Methylation of phenolic compound BTMR1377 EC 2.1.1.25 HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +3 CC(C)C1=CC=C(C)C=C1O "Cc1ccc(c(c1)O)C(C)(C)O +" InChI=1S/C10H14O2/c1-7-4-5-8(9(11)6-7)10(2,3)12/h4-6,11-12H,1-3H3 UWRRYLNXMGBJKK-UHFFFAOYSA-N CC(C)(C1=CC=C(C)C=C1O)O "SCHEMBL22652590 +2-(2-hydroxypropan-2-yl)-5-methylphenol +EN300-1838871 +4478-33-5" 11332674 C10H14O2 166.099379688 2.0267999999999997 0 0 0 BTM00004 BTM00004 Hydroxylation of non-terminal aliphatic carbon adjacent to aromatic ring BTMR1077 "CYP1A2 +CYP2C8 +CYP2C9 +CYP2D6 +CYP3A4" HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +4 CC(C)C1=CC=C(C)C=C1O "CC(C)c1cc(c(C)cc1O)O +" InChI=1S/C10H14O2/c1-6(2)8-5-9(11)7(3)4-10(8)12/h4-6,11-12H,1-3H3 OQIOHYHRGZNZCW-UHFFFAOYSA-N CC(C)C1=CC(=C(C)C=C1O)O "Thymohydroquinone +2217-60-9 +Hydrothymoquinone +Thymoquinol +p-Cymene-2,5-diol +1,4-Benzenediol, 2-methyl-5-(1-methylethyl)- +2-Methyl-5-isopropylhydroquinone +Hydroquinone, 5-isopropyl-2-methyl- +2-methyl-5-(propan-2-yl)benzene-1,4-diol +NSC 34803 +2-ISOPROPYL-5-METHYLBENZENE-1,4-DIOL +1C2ICM1R8V +2-methyl-5-(1-methylethyl)-1,4-benzenediol +NSC-34803 +BRN 2084452 +Thymohydrochinon +2-methyl-5-propan-2-ylbenzene-1,4-diol +2-hydroxythymol +2,5-DIHYDROXY-P-CYMENE +Thymohydroquinone (I) +UNII-1C2ICM1R8V +SCHEMBL69082 +CHEMBL4204349 +2-isopropyl-5-methylhydroquinone +DTXSID70176706 +WLN: QR DQ B1 EY1&1 +NSC34803 +1, 2-methyl-5-(1-methylethyl)- +AKOS006274324 +2-isopropyl-5-methyl-benzene-1,4-diol +CS-0259073 +FT-0700031 +4-HYDROXY-5-ISOPROPYL-2-METHYLPHENOL +EN300-722422 +Z1198148655 +2-Methyl-5-(1-Methylethyl)cyclohexa-2,5-Diene-1,4-Dione +9J9 +IMW" 95779 C10H14O2 166.099379688 2.9756 0 0 0 BTM00005 BTM00005 p-Hydroxylation of phenol BTMR1038 "CYP1A2 +CYP2A6 +CYP2B6 +CYP2C8 +CYP2C9 +CYP2C19 +CYP2D6 +CYP2E1 +CYP3A4" HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +5 CC(C)C1=CC=C(C)C=C1O "CC(C)c1ccc(cc1O)CO +" InChI=1S/C10H14O2/c1-7(2)9-4-3-8(6-11)5-10(9)12/h3-5,7,11-12H,6H2,1-2H3 UNNQYEJIPIBHFS-UHFFFAOYSA-N CC(C)C1=CC=C(CO)C=C1O "77311-68-3 +5-(Hydroxymethyl)-2-(propan-2-yl)phenol +5-hydroxymethyl-2-isopropylphenol +DTXSID70554040 +2-Isopropyl-5-(hydroxymethyl)phenol" 14002478 C10H14O2 166.099379688 2.1523000000000003 0 0 0 BTM00006 BTM00006 Aliphatic hydroxylation of methyl carbon adjacent to aromatic ring BTMR1058 "CYP1A2 +CYP2A6 +CYP2B6 +CYP2C8 +CYP2C9 +CYP2C19 +CYP2D6 +CYP2E1 +CYP3A4" HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +6 CC(C)C1=CC=C(C)C=C1O "Cc1ccc(C(C)CO)c(c1)O +" InChI=1S/C10H14O2/c1-7-3-4-9(8(2)6-11)10(12)5-7/h3-5,8,11-12H,6H2,1-2H3 CLJPRXFHCRIUKW-UHFFFAOYSA-N C(C(C)C1=CC=C(C)C=C1O)O "9-Hydroxythymol +61955-76-8 +2-(1-hydroxypropan-2-yl)-5-methylphenol +p-cymene-3,8-diol +HY-N10925 +p-Mentha-1,3,5-triene-3,9-diol +CS-0637580" 14432748 C10H14O2 166.099379688 2.0848000000000004 0 0 0 BTM00007 BTM00007 Hydroxylation of terminal methyl BTMR1061 "CYP1A2 +CYP2A6 +CYP2B6 +CYP2C8 +CYP2C9 +CYP2C19 +CYP2D6 +CYP2E1 +CYP3A4" HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044 +7 CC(C)C1=CC=C(C)C=C1O "C=C(C)c1ccc(C)cc1O +" InChI=1S/C10H12O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-6,11H,1H2,2-3H3 IHWFPRKZRRGTTI-UHFFFAOYSA-N CC(=C)C1=CC=C(C)C=C1O "8,9-Dehydrothymol +2-isopropenyl-5-methylphenol +18612-99-2 +5-methyl-2-prop-1-en-2-ylphenol +Phenol, 5-methyl-2-(1-methylethenyl)- +m-Cresol, 6-isopropenyl- +SCHEMBL686122 +2-Isopropenyl-5-methyl-phenol +DTXSID60423892 +5-Methyl-2-(1-methylethenyl)phenol +5-Methyl-2-(prop-1-en-2-yl)phenol" 6429037 C10H12O 148.088815004 3.0469000000000004 0 0 0 BTM00008 BTM00008 Terminal desaturation BTMR1190 "CYP1A2 +CYP2A6 +CYP2C9 +CYP2D6 +CYP3A4" HUMAN NSC404789 CC(C)C1=CC=C(C)C=C1O InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)6-10(9)11/h4-7,11H,1-3H3 MGSRCZKZVOBKFT-UHFFFAOYSA-N 150.1044
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/smiles.csv Tue Jun 06 11:23:51 2023 +0000 @@ -0,0 +1,1 @@ +CC(C)C1=CC=C(C)C=C1O \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/wrapper_biotransformer.py Tue Jun 06 11:23:51 2023 +0000 @@ -0,0 +1,75 @@ +import re +import subprocess +import sys +import tempfile + +import pandas +from openbabel import openbabel, pybel +openbabel.obErrorLog.StopLogging() + + +def InchiToSmiles(df): + '''Translate inchi to smiles''' + sm = [] + for item in df['InChI']: + tmp = pybel.readstring("inchi", item) + sm.append(tmp.write("smi")) + return sm + + +executable = ["biotransformer"] + +argv = sys.argv[1:] +icsv = argv.pop(argv.index("-icsv") + 1) +argv.remove("-icsv") +ocsv = argv.pop(argv.index("-ocsv") + 1) +argv.remove("-ocsv") +ocsv_dup = argv.pop(argv.index("-ocsvDup") + 1) +argv.remove("-ocsvDup") +ocsv_dup2 = argv.pop(argv.index("-ocsvDup2") + 1) +argv.remove("-ocsvDup2") + +in_df = pandas.read_csv(icsv, header=None) +out_df1 = pandas.DataFrame() # all results +out_df2 = pandas.DataFrame() # filtered results based on 6 columns +out_df3 = pandas.DataFrame() # filtered results based on 3 columns + +smList1 = [] # list with smiles string +smList2 = [] +smList3 = [] +for _, (smiles,) in in_df.iterrows(): + with tempfile.NamedTemporaryFile() as out: + print("Working on compound: " + smiles) + if not re.search(r'\.', smiles): + subprocess.run(executable + argv + ["-ismi", smiles] + ["-ocsv", out.name]) + try: + bio_out = pandas.read_csv(out.name) + tmp2 = bio_out.drop_duplicates(subset=["InChI", "InChIKey", "Synonyms", "Molecular formula", "Major Isotope Mass", "ALogP"]) + tmp3 = bio_out.drop_duplicates(subset=["Molecular formula", "Major Isotope Mass", "ALogP"]) + + smList1.append([smiles] * bio_out.shape[0]) + smList2.append([smiles] * tmp2.shape[0]) + smList3.append([smiles] * tmp3.shape[0]) + + out_df1 = pandas.concat([out_df1, bio_out]) + out_df2 = pandas.concat([out_df2, tmp2]) + out_df3 = pandas.concat([out_df3, tmp3]) + except pandas.errors.EmptyDataError: + continue + else: + print("ERROR: Input compound cannot be a mixture.") +smList1 = sum(smList1, []) # merge sublists into one list +smList2 = sum(smList2, []) +smList3 = sum(smList3, []) + +out_df1.insert(0, "SMILES query", smList1) +out_df1.insert(1, "SMILES target", InchiToSmiles(out_df1)) +out_df1.to_csv(ocsv, sep='\t') + +out_df2.insert(0, "SMILES query", smList2) +out_df2.insert(1, "SMILES target", InchiToSmiles(out_df2)) +out_df2.to_csv(ocsv_dup, sep='\t') + +out_df3.insert(0, "SMILES query", smList3) +out_df3.insert(1, "SMILES target", InchiToSmiles(out_df3)) +out_df3.to_csv(ocsv_dup2, sep='\t')