# HG changeset patch
# User recetox
# Date 1686050631 0
# Node ID 0b86600b715e826928768e59c4721b8794b364b8

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7

diff -r 000000000000 -r 0b86600b715e biotransformer.xml
--- /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>
diff -r 000000000000 -r 0b86600b715e macros.xml
--- /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>
diff -r 000000000000 -r 0b86600b715e test-data/output1.tsv
--- /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
diff -r 000000000000 -r 0b86600b715e test-data/output2.tsv
--- /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
diff -r 000000000000 -r 0b86600b715e test-data/output3.tsv
--- /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
diff -r 000000000000 -r 0b86600b715e test-data/smiles.csv
--- /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
diff -r 000000000000 -r 0b86600b715e wrapper_biotransformer.py
--- /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')