From 1c8a1c2c96cc348faa96495244276455587ab775 Mon Sep 17 00:00:00 2001 From: popenc Date: Mon, 16 Sep 2024 14:13:26 -0400 Subject: [PATCH] updated biotransformerjar --- biotransformerjar/biotransformer.bat | 1 + biotransformerjar/biotransformer.jar | 4 +- .../bayesian_model_parameters.csv | 66 +++++++++++++++++++ .../mnd_model_parameters.csv | 7 ++ biotransformerjar/test.csv | 26 ++++++++ 5 files changed, 102 insertions(+), 2 deletions(-) create mode 100644 biotransformerjar/biotransformer.bat create mode 100644 biotransformerjar/supportfiles/LiverModelParameters/bayesian_model_parameters.csv create mode 100644 biotransformerjar/supportfiles/LiverModelParameters/mnd_model_parameters.csv create mode 100644 biotransformerjar/test.csv diff --git a/biotransformerjar/biotransformer.bat b/biotransformerjar/biotransformer.bat new file mode 100644 index 0000000..5035bd8 --- /dev/null +++ b/biotransformerjar/biotransformer.bat @@ -0,0 +1 @@ +java -jar biotransformer.jar -k pred -b cyp450 -ismi OC1=CC=CC=C1 -ocsv "test.csv" -nsteps 1 \ No newline at end of file diff --git a/biotransformerjar/biotransformer.jar b/biotransformerjar/biotransformer.jar index 6bf3fca..5de0190 100644 --- a/biotransformerjar/biotransformer.jar +++ b/biotransformerjar/biotransformer.jar @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:f8fa51a5b70b80220c5e7d4866dfe13ab4262f655704fd3acd42d58e7b2cdb6f -size 108890210 +oid sha256:d99487ea54982d73a0772f2034c74d0e22d14e55be01b024bd9ece9c70d16ebf +size 86946161 diff --git a/biotransformerjar/supportfiles/LiverModelParameters/bayesian_model_parameters.csv b/biotransformerjar/supportfiles/LiverModelParameters/bayesian_model_parameters.csv new file mode 100644 index 0000000..9ab0463 --- /dev/null +++ b/biotransformerjar/supportfiles/LiverModelParameters/bayesian_model_parameters.csv @@ -0,0 +1,66 @@ +tertiary amines,0.0;0.8333333333333334,1.0;0.10808926080892609,2.0;0.02789400278940028,4.0;0.012552301255230125,3.0;0.017433751743375175 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+S.O2,0.0;0.9721059972105998,1.0;0.026499302649930265,2.0;6.97350069735007E-4 +sulfone groups,0.0;0.997907949790795,4.0;0.001394700139470014 +ether oxygens,0.0;0.7238493723849372,2.0;0.17642956764295675,4.0;0.08647140864714087,8.0;0.0020920502092050207,10.0;0.0020920502092050207,6.0;0.007670850767085077,12.0;6.97350069735007E-4 +C.ar,0.0;0.7078103207810321,8.0;0.022315202231520222,9.0;0.001394700139470014,10.0;0.0041841004184100415,3.0;0.028591352859135284,12.0;0.03277545327754533,14.0;6.97350069735007E-4,15.0;6.97350069735007E-4,4.0;0.010460251046025104,16.0;0.0020920502092050207,5.0;0.029288702928870293,6.0;0.15760111576011157,7.0;0.001394700139470014 +phenolic OH with exclusion,0.0;0.8751743375174338,1.0;0.07531380753138076,2.0;0.03138075313807531,4.0;0.005578800557880056,5.0;0.001394700139470014,3.0;0.010460251046025104 +anilines,0.0;0.9567642956764296,1.0;0.03347280334728033,2.0;0.0041841004184100415,4.0;0.002789400278940028,3.0;0.0020920502092050207 +para-hydroxylation sites,0.0;0.9707112970711297,1.0;0.027196652719665274,2.0;0.001394700139470014 +branched alkanes,0.0;0.698744769874477,2.0;0.05299860529986053,32.0;0.00697350069735007,34.0;0.0048814504881450485,36.0;0.007670850767085077,38.0;0.007670850767085077,40.0;0.0041841004184100415,42.0;0.010460251046025104,44.0;0.002789400278940028,46.0;6.97350069735007E-4,48.0;0.003486750348675035,50.0;6.97350069735007E-4,52.0;6.97350069735007E-4,4.0;0.04881450488145049,6.0;0.02580195258019526,8.0;0.013249651324965132,10.0;0.01882845188284519,12.0;0.017433751743375175,14.0;0.011157601115760111,16.0;0.00697350069735007,18.0;0.006276150627615063,20.0;0.013249651324965132,22.0;0.005578800557880056,24.0;0.007670850767085077,26.0;0.009762900976290097,28.0;0.0041841004184100415,30.0;0.008368200836820083 +carbonyl,1.0;0.43375174337517436,0.0;0.2503486750348675,2.0;0.26638772663877264,4.0;0.008368200836820083,5.0;0.002789400278940028,3.0;0.03765690376569038 +methoxy groups,0.0;0.9504881450488145,1.0;0.038354253835425386,2.0;0.008368200836820083,3.0;0.0020920502092050207 +piperzine rings,0.0;0.997907949790795,4.0;0.001394700139470014 +benzene rings,0.0;0.7796373779637378,36.0;6.97350069735007E-4,12.0;0.18131101813110181,24.0;0.03626220362622036,48.0;0.001394700139470014 +N functional groups attched to aromatics,0.0;0.9651324965132496,1.0;0.03277545327754533,2.0;0.001394700139470014 +tert-alicyclic amines,0.0;0.9909344490934449,1.0;0.007670850767085077,2.0;6.97350069735007E-4 +esters,0.0;0.8640167364016736,1.0;0.07670850767085077,2.0;0.058577405857740586 +primary amines,0.0;0.8131101813110181,1.0;0.14644351464435146,2.0;0.03486750348675035,4.0;0.0020920502092050207,3.0;0.002789400278940028 +C.2,0.0;0.15550906555090654,2.0;0.18898186889818688,8.0;0.020223152022315203,9.0;0.02301255230125523,10.0;0.016736401673640166,11.0;0.013249651324965132,3.0;0.09414225941422594,12.0;0.0020920502092050207,13.0;0.003486750348675035,1.0;0.2914923291492329,4.0;0.08158995815899582,16.0;6.97350069735007E-4,18.0;6.97350069735007E-4,5.0;0.040446304044630406,20.0;6.97350069735007E-4,22.0;0.0041841004184100415,6.0;0.03765690376569038,24.0;0.001394700139470014,26.0;6.97350069735007E-4,7.0;0.022315202231520222 +C.1,0.0;0.99581589958159,1.0;0.0020920502092050207,2.0;0.001394700139470014 +O.co2,0.0;0.9700139470013946,2.0;0.029288702928870293 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amides,0.0;0.9804741980474198,1.0;0.01813110181311018,2.0;6.97350069735007E-4 +thiazole rings,0.0;0.997907949790795,1.0;0.001394700139470014 +H-pyrrole nitrogen,0.0;0.9246861924686193,1.0;0.056485355648535567,2.0;0.01394700139470014,4.0;6.97350069735007E-4,3.0;0.003486750348675035 +allylic oxidation sites with exclusion,0.0;0.7273361227336123,2.0;0.06694560669456066,8.0;0.023709902370990237,9.0;0.007670850767085077,10.0;0.003486750348675035,3.0;0.02301255230125523,12.0;0.0020920502092050207,1.0;0.05369595536959554,4.0;0.03277545327754533,18.0;6.97350069735007E-4,5.0;0.01603905160390516,20.0;0.002789400278940028,21.0;0.001394700139470014,22.0;0.0020920502092050207,6.0;0.026499302649930265,26.0;6.97350069735007E-4,7.0;0.008368200836820083 +aromatic hydroxyl gorups,0.0;0.8626220362622036,1.0;0.08368200836820083,2.0;0.03556485355648536,4.0;0.006276150627615063,5.0;0.001394700139470014,3.0;0.00906555090655509,6.0;6.97350069735007E-4 +O.2,1.0;0.4595536959553696,0.0;0.1910739191073919,2.0;0.2810320781032078,4.0;0.01394700139470014,5.0;0.0048814504881450485,3.0;0.04881450488145049 +terminal acetylenes,0.0;0.997907949790795,1.0;0.001394700139470014 +aliphatic hydroxyl groups with exclusion,0.0;0.5585774058577406,1.0;0.24546722454672246,2.0;0.09065550906555091,4.0;0.023709902370990237,8.0;0.0041841004184100415,5.0;0.007670850767085077,10.0;0.001394700139470014,11.0;6.97350069735007E-4,3.0;0.061366806136680614,6.0;0.003486750348675035,7.0;0.0020920502092050207 +O.3,0.0;0.11436541143654114,2.0;0.26359832635983266,8.0;0.001394700139470014,9.0;0.001394700139470014,10.0;0.0020920502092050207,11.0;0.003486750348675035,3.0;0.18340306834030684,12.0;6.97350069735007E-4,14.0;6.97350069735007E-4,15.0;6.97350069735007E-4,1.0;0.2914923291492329,4.0;0.07043235704323571,16.0;6.97350069735007E-4,5.0;0.027196652719665274,6.0;0.0299860529986053,7.0;0.007670850767085077 +pyridine rings,0.0;0.9748953974895398,2.0;0.024407252440725245 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O2,0.0;0.4909344490934449,1.0;0.4211994421199442,2.0;0.07810320781032078,4.0;0.001394700139470014,3.0;0.007670850767085077 +aliphatic carboxlic acids,0.0;0.5223152022315202,1.0;0.3926080892608089,2.0;0.07531380753138076,4.0;0.001394700139470014,3.0;0.007670850767085077 +XCCNR groups,0.0;0.9428172942817294,1.0;0.056485355648535567 +imide groups,0.0;0.995118549511855,2.0;0.0041841004184100415 +morpholine rings,0.0;0.99860529986053,2.0;6.97350069735007E-4 +N.am,0.0;0.8389121338912134,1.0;0.11366806136680614,2.0;0.03695955369595537,4.0;0.006276150627615063,3.0;0.003486750348675035 +furan rings,0.0;0.99302649930265,2.0;0.006276150627615063 +guanidine groups,0.0;0.9818688981868898,2.0;0.016736401673640166,4.0;6.97350069735007E-4 +aromatic amines,0.0;0.9246861924686193,1.0;0.056485355648535567,2.0;0.01394700139470014,4.0;6.97350069735007E-4,3.0;0.003486750348675035 +Number of aliphatic hydroxyl groups,0.0;0.5509065550906556,1.0;0.24476987447698745,2.0;0.09274755927475593,4.0;0.027196652719665274,8.0;0.0048814504881450485,5.0;0.011854951185495118,10.0;0.001394700139470014,11.0;6.97350069735007E-4,3.0;0.0599721059972106,6.0;0.003486750348675035,7.0;0.001394700139470014 +amidine groups,0.0;0.997907949790795,1.0;0.001394700139470014 +N.ar,0.0;0.9079497907949791,2.0;0.03277545327754533,1.0;0.045327754532775454,4.0;0.011157601115760111,3.0;0.0020920502092050207 +S.O,0.0;0.9937238493723849,1.0;0.005578800557880056 +N.pl3,0.0;0.9846582984658299,1.0;0.014644351464435146 +secondary amines,0.0;0.7894002789400278,1.0;0.1492329149232915,2.0;0.04184100418410042,4.0;0.006276150627615063,5.0;0.001394700139470014,3.0;0.011157601115760111 +thiophene rings,0.0;0.99860529986053,2.0;6.97350069735007E-4 +carbonyl with exclusion,1.0;0.28451882845188287,0.0;0.5857740585774058,2.0;0.12203626220362622,4.0;0.001394700139470014,3.0;0.005578800557880056 +aryl methyl sites,0.0;0.9316596931659693,1.0;0.05788005578800558,2.0;0.007670850767085077,3.0;0.0020920502092050207 diff --git a/biotransformerjar/supportfiles/LiverModelParameters/mnd_model_parameters.csv b/biotransformerjar/supportfiles/LiverModelParameters/mnd_model_parameters.csv new file mode 100644 index 0000000..d807b54 --- /dev/null +++ b/biotransformerjar/supportfiles/LiverModelParameters/mnd_model_parameters.csv @@ -0,0 +1,7 @@ +262.17754820532497,7.397489539748954,4.177824267782427,2.230822873082287,0.9262366836362249,74.45941422594156 +19121.197938678764,900.6142573776134,106.59186959285508,24.243791391020498,116.31836309427729,1418.3413527525402 +900.6142573776134,72.42638142422823,2.1127197819832833,-1.6984442382544676,5.68563588698854,15.63010034254774 +106.59186959285508,2.1127197819832833,5.501851333134951,3.05658310136961,-0.9917102527832794,91.17104558743699 +24.243791391020498,-1.6984442382544676,3.05658310136961,2.64197882078787,-0.779415517432717,57.56277119331504 +116.31836309427729,5.68563588698854,-0.9917102527832794,-0.779415517432717,1.5572660318860245,-20.291127876488083 +1418.3413527525402,15.63010034254774,91.17104558743699,57.56277119331504,-20.291127876488083,1696.9906071882438 diff --git a/biotransformerjar/test.csv b/biotransformerjar/test.csv new file mode 100644 index 0000000..fb03f7b --- /dev/null +++ b/biotransformerjar/test.csv @@ -0,0 +1,26 @@ +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 +"InChI=1S/C6H6O2/c7-5-1-2-6(8)4-3-5/h1-4,7-8H",QIGBRXMKCJKVMJ-UHFFFAOYSA-N,OC1=CC=C(C=C1)O,,,C6H6O2,110.036779432,1.4225999999999996,0,0,0,BTM00001,BTM00001,p-Hydroxylation of phenol,BTMR1038,"CYP1A2 +CYP2A6 +CYP2B6 +CYP2C8 +CYP2C9 +CYP2C19 +CYP2D6 +CYP2E1 +CYP3A4",HUMAN,,OC1=CC=CC=C1,"InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H",ISWSIDIOOBJBQZ-UHFFFAOYSA-N,,94.04186 +"InChI=1S/C6H6O2/c7-5-3-1-2-4-6(5)8/h1-4,7-8H",YCIMNLLNPGFGHC-UHFFFAOYSA-N,OC1=CC=CC=C1O,,,C6H6O2,110.036779432,1.4225999999999996,0,0,0,BTM00002,BTM00002,O-Hydroxylation of phenol,BTMR1037,"CYP1A2 +CYP2A6 +CYP2B6 +CYP2C8 +CYP2C9 +CYP2C19 +CYP2D6 +CYP2E1 +CYP3A4",HUMAN,,OC1=CC=CC=C1,"InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H",ISWSIDIOOBJBQZ-UHFFFAOYSA-N,,94.04186 +"InChI=1S/C6H6O2/c7-4-1-2-5-6(3-4)8-5/h1-3,5-7H",FVHTWPRXVHEBCJ-UHFFFAOYSA-N,OC1=CC2C(C=C1)O2,,,C6H6O2,110.036779432,0.11760000000000034,0,0,0,BTM00003,BTM00003,Epoxidation of arene,BTMR1028,"CYP1A2 +CYP2B6 +CYP2C8 +CYP2C9 +CYP2C19 +CYP2E1 +CYP3A4",HUMAN,,OC1=CC=CC=C1,"InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H",ISWSIDIOOBJBQZ-UHFFFAOYSA-N,,94.04186