| Previous changeset 1:13c6f797f1c3 (2019-05-21) Next changeset 3:617d4555d8d3 (2019-10-16) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 3372cca3d07562b643b8152d489dcbd2325acf4a |
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modified:
rdkit_descriptors.py rdkit_descriptors.xml test-data/rdkit_descriptors_result1.tab |
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| diff -r 13c6f797f1c3 -r 6674260c1459 rdkit_descriptors.py --- a/rdkit_descriptors.py Tue May 21 09:08:54 2019 -0400 +++ b/rdkit_descriptors.py Thu May 23 18:57:30 2019 -0400 |
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| @@ -65,12 +65,12 @@ functions = get_rdkit_descriptor_functions() if args.header: - args.outfile.write( '%s\n' % '\t'.join( [name for name, f in functions] ) ) + args.outfile.write( '%s\n' % '\t'.join( ['MoleculeID'] + [name for name, f in functions] ) ) for mol in supplier: if not mol: continue descs = descriptors( mol, functions ) molecule_id = mol.GetProp("_Name") - args.outfile.write( "%s\n" % '\t'.join( [molecule_id]+ [str(res) for name, res in descs] ) ) + args.outfile.write( "%s\n" % '\t'.join( [molecule_id]+ [str(round(res, 6)) for name, res in descs] ) ) |
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| diff -r 13c6f797f1c3 -r 6674260c1459 rdkit_descriptors.xml --- a/rdkit_descriptors.xml Tue May 21 09:08:54 2019 -0400 +++ b/rdkit_descriptors.xml Thu May 23 18:57:30 2019 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ctb_rdkit_descriptors" name="Descriptors" version="0.5"> +<tool id="ctb_rdkit_descriptors" name="Descriptors" version="0.6"> <description>calculated with RDKit</description> <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism--> <requirements> |
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| diff -r 13c6f797f1c3 -r 6674260c1459 test-data/rdkit_descriptors_result1.tab --- a/test-data/rdkit_descriptors_result1.tab Tue May 21 09:08:54 2019 -0400 +++ b/test-data/rdkit_descriptors_result1.tab Thu May 23 18:57:30 2019 -0400 |
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| @@ -1,2 +1,2 @@ -BalabanJ BertzCT Chi0 Chi0n Chi0v Chi1 Chi1n Chi1v Chi2n Chi2v Chi3n Chi3v Chi4n Chi4v EState_VSA1 EState_VSA10 EState_VSA11 EState_VSA2 EState_VSA3 EState_VSA4 EState_VSA5 EState_VSA6 EState_VSA7 EState_VSA8 EState_VSA9 ExactMolWt FpDensityMorgan1 FpDensityMorgan2 FpDensityMorgan3 FractionCSP3 HallKierAlpha HeavyAtomCount HeavyAtomMolWt Ipc Kappa1 Kappa2 Kappa3 LabuteASA MaxAbsEStateIndex MaxAbsPartialCharge MaxEStateIndex MaxPartialCharge MinAbsEStateIndex MinAbsPartialCharge MinEStateIndex MinPartialCharge MolLogP MolMR MolWt NHOHCount NOCount NumAliphaticCarbocycles NumAliphaticHeterocycles NumAliphaticRings NumAromaticCarbocycles NumAromaticHeterocycles NumAromaticRings NumHAcceptors NumHDonors NumHeteroatoms NumRadicalElectrons NumRotatableBonds NumSaturatedCarbocycles NumSaturatedHeterocycles NumSaturatedRings NumValenceElectrons PEOE_VSA1 PEOE_VSA10 PEOE_VSA11 PEOE_VSA12 PEOE_VSA13 PEOE_VSA14 PEOE_VSA2 PEOE_VSA3 PEOE_VSA4 PEOE_VSA5 PEOE_VSA6 PEOE_VSA7 PEOE_VSA8 PEOE_VSA9 RingCount SMR_VSA1 SMR_VSA10 SMR_VSA2 SMR_VSA3 SMR_VSA4 SMR_VSA5 SMR_VSA6 SMR_VSA7 SMR_VSA8 SMR_VSA9 SlogP_VSA1 SlogP_VSA10 SlogP_VSA11 SlogP_VSA12 SlogP_VSA2 SlogP_VSA3 SlogP_VSA4 SlogP_VSA5 SlogP_VSA6 SlogP_VSA7 SlogP_VSA8 SlogP_VSA9 TPSA VSA_EState1 VSA_EState10 VSA_EState2 VSA_EState3 VSA_EState4 VSA_EState5 VSA_EState6 VSA_EState7 VSA_EState8 VSA_EState9 fr_Al_COO fr_Al_OH fr_Al_OH_noTert fr_ArN fr_Ar_COO fr_Ar_N fr_Ar_NH fr_Ar_OH fr_COO fr_COO2 fr_C_O fr_C_O_noCOO fr_C_S fr_HOCCN fr_Imine fr_NH0 fr_NH1 fr_NH2 fr_N_O fr_Ndealkylation1 fr_Ndealkylation2 fr_Nhpyrrole fr_SH fr_aldehyde fr_alkyl_carbamate fr_alkyl_halide fr_allylic_oxid fr_amide fr_amidine fr_aniline fr_aryl_methyl fr_azide fr_azo fr_barbitur fr_benzene fr_benzodiazepine fr_bicyclic fr_diazo fr_dihydropyridine fr_epoxide fr_ester fr_ether fr_furan fr_guanido fr_halogen fr_hdrzine fr_hdrzone fr_imidazole fr_imide fr_isocyan fr_isothiocyan fr_ketone fr_ketone_Topliss fr_lactam fr_lactone fr_methoxy fr_morpholine fr_nitrile fr_nitro fr_nitro_arom fr_nitro_arom_nonortho fr_nitroso fr_oxazole fr_oxime fr_para_hydroxylation fr_phenol fr_phenol_noOrthoHbond fr_phos_acid fr_phos_ester fr_piperdine fr_piperzine fr_priamide fr_prisulfonamd fr_pyridine fr_quatN fr_sulfide fr_sulfonamd fr_sulfone fr_term_acetylene fr_tetrazole fr_thiazole fr_thiocyan fr_thiophene fr_unbrch_alkane fr_urea qed -3037 2.370227579270102 503.6108804181844 12.413849083443592 8.821564533342674 10.333422425379583 8.0585506480638 5.008352593120903 5.764281539139358 3.7228452481073373 4.595716809051308 2.463985083856104 2.934179289431582 1.5965258413271721 1.9859262940770028 0.0 10.213054789681411 0.0 11.49902366656781 27.592991233802653 0.0 12.13273413692322 24.26546827384644 0.0 0.0 23.20187978046503 268.00578492 0.7647058823529411 1.1764705882352942 1.588235294117647 0.07692307692307693 -1.38 17 259.04699999999997 6943.445199590422 12.08686679380967 4.861181105580097 2.8426724700782957 109.048439398113 9.68320845930965 0.5076617533400031 9.68320845930965 0.11870889965789788 0.14701436130007584 0.11870889965789788 0.14701436130007584 -0.5076617533400031 3.9954000000000027 69.03960000000004 269.127 2 2 0 0 0 2 0 2 2 2 4 0 2 0 0 0 88 10.213054789681411 11.49902366656781 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 23.20187978046503 47.52510539416365 16.466088250408664 0.0 2 10.213054789681411 23.20187978046503 0.0 0.0 0.0 6.4208216229260096 0.0 57.5703720216463 0.0 11.49902366656781 0.0 0.0 11.49902366656781 23.20187978046503 10.213054789681411 6.4208216229260096 0.0 11.126902983393991 36.39820241076966 10.045266627482652 0.0 0.0 40.46 0.0 11.70886971249405 0.0 0.0 0.0 0.0 0.0 0.0 0.0 32.01335250972817 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.8647127178367139 +MoleculeID BalabanJ BertzCT Chi0 Chi0n Chi0v Chi1 Chi1n Chi1v Chi2n Chi2v Chi3n Chi3v Chi4n Chi4v EState_VSA1 EState_VSA10 EState_VSA11 EState_VSA2 EState_VSA3 EState_VSA4 EState_VSA5 EState_VSA6 EState_VSA7 EState_VSA8 EState_VSA9 ExactMolWt FpDensityMorgan1 FpDensityMorgan2 FpDensityMorgan3 FractionCSP3 HallKierAlpha HeavyAtomCount HeavyAtomMolWt Ipc Kappa1 Kappa2 Kappa3 LabuteASA MaxAbsEStateIndex MaxAbsPartialCharge MaxEStateIndex MaxPartialCharge MinAbsEStateIndex MinAbsPartialCharge MinEStateIndex MinPartialCharge MolLogP MolMR MolWt NHOHCount NOCount NumAliphaticCarbocycles NumAliphaticHeterocycles NumAliphaticRings NumAromaticCarbocycles NumAromaticHeterocycles NumAromaticRings NumHAcceptors NumHDonors NumHeteroatoms NumRadicalElectrons NumRotatableBonds NumSaturatedCarbocycles NumSaturatedHeterocycles NumSaturatedRings NumValenceElectrons PEOE_VSA1 PEOE_VSA10 PEOE_VSA11 PEOE_VSA12 PEOE_VSA13 PEOE_VSA14 PEOE_VSA2 PEOE_VSA3 PEOE_VSA4 PEOE_VSA5 PEOE_VSA6 PEOE_VSA7 PEOE_VSA8 PEOE_VSA9 RingCount SMR_VSA1 SMR_VSA10 SMR_VSA2 SMR_VSA3 SMR_VSA4 SMR_VSA5 SMR_VSA6 SMR_VSA7 SMR_VSA8 SMR_VSA9 SlogP_VSA1 SlogP_VSA10 SlogP_VSA11 SlogP_VSA12 SlogP_VSA2 SlogP_VSA3 SlogP_VSA4 SlogP_VSA5 SlogP_VSA6 SlogP_VSA7 SlogP_VSA8 SlogP_VSA9 TPSA VSA_EState1 VSA_EState10 VSA_EState2 VSA_EState3 VSA_EState4 VSA_EState5 VSA_EState6 VSA_EState7 VSA_EState8 VSA_EState9 fr_Al_COO fr_Al_OH fr_Al_OH_noTert fr_ArN fr_Ar_COO fr_Ar_N fr_Ar_NH fr_Ar_OH fr_COO fr_COO2 fr_C_O fr_C_O_noCOO fr_C_S fr_HOCCN fr_Imine fr_NH0 fr_NH1 fr_NH2 fr_N_O fr_Ndealkylation1 fr_Ndealkylation2 fr_Nhpyrrole fr_SH fr_aldehyde fr_alkyl_carbamate fr_alkyl_halide fr_allylic_oxid fr_amide fr_amidine fr_aniline fr_aryl_methyl fr_azide fr_azo fr_barbitur fr_benzene fr_benzodiazepine fr_bicyclic fr_diazo fr_dihydropyridine fr_epoxide fr_ester fr_ether fr_furan fr_guanido fr_halogen fr_hdrzine fr_hdrzone fr_imidazole fr_imide fr_isocyan fr_isothiocyan fr_ketone fr_ketone_Topliss fr_lactam fr_lactone fr_methoxy fr_morpholine fr_nitrile fr_nitro fr_nitro_arom fr_nitro_arom_nonortho fr_nitroso fr_oxazole fr_oxime fr_para_hydroxylation fr_phenol fr_phenol_noOrthoHbond fr_phos_acid fr_phos_ester fr_piperdine fr_piperzine fr_priamide fr_prisulfonamd fr_pyridine fr_quatN fr_sulfide fr_sulfonamd fr_sulfone fr_term_acetylene fr_tetrazole fr_thiazole fr_thiocyan fr_thiophene fr_unbrch_alkane fr_urea qed +3037 2.370228 503.61088 12.413849 8.821565 10.333422 8.058551 5.008353 5.764282 3.722845 4.595717 2.463985 2.934179 1.596526 1.985926 0.0 10.213055 0.0 11.499024 27.592991 0.0 12.132734 24.265468 0.0 0.0 23.20188 268.005785 0.764706 1.176471 1.588235 0.076923 -1.38 17 259.047 6943.4452 12.086867 4.861181 2.842672 109.048439 9.683208 0.507662 9.683208 0.118709 0.147014 0.118709 0.147014 -0.507662 3.9954 69.0396 269.127 2 2 0 0 0 2 0 2 2 2 4 0 2 0 0 0 88 10.213055 11.499024 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 23.20188 47.525105 16.466088 0.0 2 10.213055 23.20188 0.0 0.0 0.0 6.420822 0.0 57.570372 0.0 11.499024 0.0 0.0 11.499024 23.20188 10.213055 6.420822 0.0 11.126903 36.398202 10.045267 0.0 0.0 40.46 0.0 11.70887 0.0 0.0 0.0 0.0 0.0 0.0 0.0 32.013353 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.864713 |