Mercurial > repos > bgruening > ctb_rdkit_descriptors

changeset 2:6674260c1459 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 3372cca3d07562b643b8152d489dcbd2325acf4a
author bgruening
date Thu, 23 May 2019 18:57:30 -0400
parents 13c6f797f1c3
children 617d4555d8d3
files rdkit_descriptors.py rdkit_descriptors.xml test-data/rdkit_descriptors_result1.tab
diffstat 3 files changed, 5 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/rdkit_descriptors.py	Tue May 21 09:08:54 2019 -0400
+++ b/rdkit_descriptors.py	Thu May 23 18:57:30 2019 -0400
@@ -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] ) )
 
--- a/rdkit_descriptors.xml	Tue May 21 09:08:54 2019 -0400
+++ b/rdkit_descriptors.xml	Thu May 23 18:57:30 2019 -0400
@@ -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>
--- 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
@@ -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