Mercurial > repos > bgruening > ctb_rdkit_descriptors
diff rdkit_descriptors.xml @ 8:a1c53f0533b0 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 4d0bfcf37bfbedafc7ff0672dfe452766ca8a606"
| author | bgruening |
|---|---|
| date | Wed, 17 Feb 2021 12:59:43 +0000 |
| parents | cf725c82c865 |
| children |
line wrap: on
line diff
--- a/rdkit_descriptors.xml Tue Jul 28 08:43:19 2020 -0400 +++ b/rdkit_descriptors.xml Wed Feb 17 12:59:43 2021 +0000 @@ -1,9 +1,9 @@ <tool id="ctb_rdkit_descriptors" name="Descriptors" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> + <description>calculated with RDKit</description> <macros> <token name="@TOOL_VERSION@">2020.03.4</token> - <token name="@GALAXY_VERSION@">0</token> + <token name="@GALAXY_VERSION@">1</token> </macros> - <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> <requirement type="package" version="@TOOL_VERSION@">rdkit</requirement> @@ -14,14 +14,222 @@ -i '${infile}' --iformat '${infile.ext}' -o '${outfile}' + #if $select_multiple: + -s '${select_multiple}' + #end if $header ]]> </command> <inputs> - <param name="infile" format="smi,sdf,mol2" type="data" label="Molecule data" - help="In SDF or SMILES format"/> + <param name="infile" format="smi,sdf,mol2,pdb,inchi" type="data" label="Molecule data" + help="In SDF, SMILES, MOL2, PDB or InChI format"/> <param name="header" type="boolean" label="Include the descriptor name as header" truevalue="--header" falsevalue="" checked="false" /> + <param name="select_multiple" type="select" label="Calculate only a subset of the descriptors" + multiple="true" help="If left blank, all descriptors will be calculated"> + <option value="BalabanJ">BalabanJ</option> + <option value="BertzCT">BertzCT</option> + <option value="Chi0">Chi0</option> + <option value="Chi0n">Chi0n</option> + <option value="Chi0v">Chi0v</option> + <option value="Chi1">Chi1</option> + <option value="Chi1n">Chi1n</option> + <option value="Chi1v">Chi1v</option> + <option value="Chi2n">Chi2n</option> + <option value="Chi2v">Chi2v</option> + <option value="Chi3n">Chi3n</option> + <option value="Chi3v">Chi3v</option> + <option value="Chi4n">Chi4n</option> + <option value="Chi4v">Chi4v</option> + <option value="EState_VSA1">EState_VSA1</option> + <option value="EState_VSA10">EState_VSA10</option> + <option value="EState_VSA11">EState_VSA11</option> + <option value="EState_VSA2">EState_VSA2</option> + <option value="EState_VSA3">EState_VSA3</option> + <option value="EState_VSA4">EState_VSA4</option> + <option value="EState_VSA5">EState_VSA5</option> + <option value="EState_VSA6">EState_VSA6</option> + <option value="EState_VSA7">EState_VSA7</option> + <option value="EState_VSA8">EState_VSA8</option> + <option value="EState_VSA9">EState_VSA9</option> + <option value="ExactMolWt">ExactMolWt</option> + <option value="FormalCharge">FormalCharge</option> + <option value="FpDensityMorgan1">FpDensityMorgan1</option> + <option value="FpDensityMorgan2">FpDensityMorgan2</option> + <option value="FpDensityMorgan3">FpDensityMorgan3</option> + <option value="FractionCSP3">FractionCSP3</option> + <option value="HallKierAlpha">HallKierAlpha</option> + <option value="HeavyAtomCount">HeavyAtomCount</option> + <option value="HeavyAtomMolWt">HeavyAtomMolWt</option> + <option value="Ipc">Ipc</option> + <option value="Kappa1">Kappa1</option> + <option value="Kappa2">Kappa2</option> + <option value="Kappa3">Kappa3</option> + <option value="LabuteASA">LabuteASA</option> + <option value="MaxAbsEStateIndex">MaxAbsEStateIndex</option> + <option value="MaxAbsPartialCharge">MaxAbsPartialCharge</option> + <option value="MaxEStateIndex">MaxEStateIndex</option> + <option value="MaxPartialCharge">MaxPartialCharge</option> + <option value="MinAbsEStateIndex">MinAbsEStateIndex</option> + <option value="MinAbsPartialCharge">MinAbsPartialCharge</option> + <option value="MinEStateIndex">MinEStateIndex</option> + <option value="MinPartialCharge">MinPartialCharge</option> + <option value="MolLogP">MolLogP</option> + <option value="MolMR">MolMR</option> + <option value="MolWt">MolWt</option> + <option value="NHOHCount">NHOHCount</option> + <option value="NOCount">NOCount</option> + <option value="NumAliphaticCarbocycles">NumAliphaticCarbocycles</option> + <option value="NumAliphaticHeterocycles">NumAliphaticHeterocycles</option> + <option value="NumAliphaticRings">NumAliphaticRings</option> + <option value="NumAromaticCarbocycles">NumAromaticCarbocycles</option> + <option value="NumAromaticHeterocycles">NumAromaticHeterocycles</option> + <option value="NumAromaticRings">NumAromaticRings</option> + <option value="NumHAcceptors">NumHAcceptors</option> + <option value="NumHDonors">NumHDonors</option> + <option value="NumHeteroatoms">NumHeteroatoms</option> + <option value="NumRadicalElectrons">NumRadicalElectrons</option> + <option value="NumRotatableBonds">NumRotatableBonds</option> + <option value="NumSaturatedCarbocycles">NumSaturatedCarbocycles</option> + <option value="NumSaturatedHeterocycles">NumSaturatedHeterocycles</option> + <option value="NumSaturatedRings">NumSaturatedRings</option> + <option value="NumValenceElectrons">NumValenceElectrons</option> + <option value="PEOE_VSA1">PEOE_VSA1</option> + <option value="PEOE_VSA10">PEOE_VSA10</option> + <option value="PEOE_VSA11">PEOE_VSA11</option> + <option value="PEOE_VSA12">PEOE_VSA12</option> + <option value="PEOE_VSA13">PEOE_VSA13</option> + <option value="PEOE_VSA14">PEOE_VSA14</option> + <option value="PEOE_VSA2">PEOE_VSA2</option> + <option value="PEOE_VSA3">PEOE_VSA3</option> + <option value="PEOE_VSA4">PEOE_VSA4</option> + <option value="PEOE_VSA5">PEOE_VSA5</option> + <option value="PEOE_VSA6">PEOE_VSA6</option> + <option value="PEOE_VSA7">PEOE_VSA7</option> + <option value="PEOE_VSA8">PEOE_VSA8</option> + <option value="PEOE_VSA9">PEOE_VSA9</option> + <option value="RingCount">RingCount</option> + <option value="SMR_VSA1">SMR_VSA1</option> + <option value="SMR_VSA10">SMR_VSA10</option> + <option value="SMR_VSA2">SMR_VSA2</option> + <option value="SMR_VSA3">SMR_VSA3</option> + <option value="SMR_VSA4">SMR_VSA4</option> + <option value="SMR_VSA5">SMR_VSA5</option> + <option value="SMR_VSA6">SMR_VSA6</option> + <option value="SMR_VSA7">SMR_VSA7</option> + <option value="SMR_VSA8">SMR_VSA8</option> + <option value="SMR_VSA9">SMR_VSA9</option> + <option value="SSSR">SSSR</option> + <option value="SlogP_VSA1">SlogP_VSA1</option> + <option value="SlogP_VSA10">SlogP_VSA10</option> + <option value="SlogP_VSA11">SlogP_VSA11</option> + <option value="SlogP_VSA12">SlogP_VSA12</option> + <option value="SlogP_VSA2">SlogP_VSA2</option> + <option value="SlogP_VSA3">SlogP_VSA3</option> + <option value="SlogP_VSA4">SlogP_VSA4</option> + <option value="SlogP_VSA5">SlogP_VSA5</option> + <option value="SlogP_VSA6">SlogP_VSA6</option> + <option value="SlogP_VSA7">SlogP_VSA7</option> + <option value="SlogP_VSA8">SlogP_VSA8</option> + <option value="SlogP_VSA9">SlogP_VSA9</option> + <option value="TPSA">TPSA</option> + <option value="VSA_EState1">VSA_EState1</option> + <option value="VSA_EState10">VSA_EState10</option> + <option value="VSA_EState2">VSA_EState2</option> + <option value="VSA_EState3">VSA_EState3</option> + <option value="VSA_EState4">VSA_EState4</option> + <option value="VSA_EState5">VSA_EState5</option> + <option value="VSA_EState6">VSA_EState6</option> + <option value="VSA_EState7">VSA_EState7</option> + <option value="VSA_EState8">VSA_EState8</option> + <option value="VSA_EState9">VSA_EState9</option> + <option value="fr_Al_COO">fr_Al_COO</option> + <option value="fr_Al_OH">fr_Al_OH</option> + <option value="fr_Al_OH_noTert">fr_Al_OH_noTert</option> + <option value="fr_ArN">fr_ArN</option> + <option value="fr_Ar_COO">fr_Ar_COO</option> + <option value="fr_Ar_N">fr_Ar_N</option> + <option value="fr_Ar_NH">fr_Ar_NH</option> + <option value="fr_Ar_OH">fr_Ar_OH</option> + <option value="fr_COO">fr_COO</option> + <option value="fr_COO2">fr_COO2</option> + <option value="fr_C_O">fr_C_O</option> + <option value="fr_C_O_noCOO">fr_C_O_noCOO</option> + <option value="fr_C_S">fr_C_S</option> + <option value="fr_HOCCN">fr_HOCCN</option> + <option value="fr_Imine">fr_Imine</option> + <option value="fr_NH0">fr_NH0</option> + <option value="fr_NH1">fr_NH1</option> + <option value="fr_NH2">fr_NH2</option> + <option value="fr_N_O">fr_N_O</option> + <option value="fr_Ndealkylation1">fr_Ndealkylation1</option> + <option value="fr_Ndealkylation2">fr_Ndealkylation2</option> + <option value="fr_Nhpyrrole">fr_Nhpyrrole</option> + <option value="fr_SH">fr_SH</option> + <option value="fr_aldehyde">fr_aldehyde</option> + <option value="fr_alkyl_carbamate">fr_alkyl_carbamate</option> + <option value="fr_alkyl_halide">fr_alkyl_halide</option> + <option value="fr_allylic_oxid">fr_allylic_oxid</option> + <option value="fr_amide">fr_amide</option> + <option value="fr_amidine">fr_amidine</option> + <option value="fr_aniline">fr_aniline</option> + <option value="fr_aryl_methyl">fr_aryl_methyl</option> + <option value="fr_azide">fr_azide</option> + <option value="fr_azo">fr_azo</option> + <option value="fr_barbitur">fr_barbitur</option> + <option value="fr_benzene">fr_benzene</option> + <option value="fr_benzodiazepine">fr_benzodiazepine</option> + <option value="fr_bicyclic">fr_bicyclic</option> + <option value="fr_diazo">fr_diazo</option> + <option value="fr_dihydropyridine">fr_dihydropyridine</option> + <option value="fr_epoxide">fr_epoxide</option> + <option value="fr_ester">fr_ester</option> + <option value="fr_ether">fr_ether</option> + <option value="fr_furan">fr_furan</option> + <option value="fr_guanido">fr_guanido</option> + <option value="fr_halogen">fr_halogen</option> + <option value="fr_hdrzine">fr_hdrzine</option> + <option value="fr_hdrzone">fr_hdrzone</option> + <option value="fr_imidazole">fr_imidazole</option> + <option value="fr_imide">fr_imide</option> + <option value="fr_isocyan">fr_isocyan</option> + <option value="fr_isothiocyan">fr_isothiocyan</option> + <option value="fr_ketone">fr_ketone</option> + <option value="fr_ketone_Topliss">fr_ketone_Topliss</option> + <option value="fr_lactam">fr_lactam</option> + <option value="fr_lactone">fr_lactone</option> + <option value="fr_methoxy">fr_methoxy</option> + <option value="fr_morpholine">fr_morpholine</option> + <option value="fr_nitrile">fr_nitrile</option> + <option value="fr_nitro">fr_nitro</option> + <option value="fr_nitro_arom">fr_nitro_arom</option> + <option value="fr_nitro_arom_nonortho">fr_nitro_arom_nonortho</option> + <option value="fr_nitroso">fr_nitroso</option> + <option value="fr_oxazole">fr_oxazole</option> + <option value="fr_oxime">fr_oxime</option> + <option value="fr_para_hydroxylation">fr_para_hydroxylation</option> + <option value="fr_phenol">fr_phenol</option> + <option value="fr_phenol_noOrthoHbond">fr_phenol_noOrthoHbond</option> + <option value="fr_phos_acid">fr_phos_acid</option> + <option value="fr_phos_ester">fr_phos_ester</option> + <option value="fr_piperdine">fr_piperdine</option> + <option value="fr_piperzine">fr_piperzine</option> + <option value="fr_priamide">fr_priamide</option> + <option value="fr_prisulfonamd">fr_prisulfonamd</option> + <option value="fr_pyridine">fr_pyridine</option> + <option value="fr_quatN">fr_quatN</option> + <option value="fr_sulfide">fr_sulfide</option> + <option value="fr_sulfonamd">fr_sulfonamd</option> + <option value="fr_sulfone">fr_sulfone</option> + <option value="fr_term_acetylene">fr_term_acetylene</option> + <option value="fr_tetrazole">fr_tetrazole</option> + <option value="fr_thiazole">fr_thiazole</option> + <option value="fr_thiocyan">fr_thiocyan</option> + <option value="fr_thiophene">fr_thiophene</option> + <option value="fr_unbrch_alkane">fr_unbrch_alkane</option> + <option value="fr_urea">fr_urea</option> + <option value="qed">qed</option> + </param> </inputs> <outputs> <data format="tabular" name="outfile" /> @@ -32,6 +240,18 @@ <param name="header" value="True" /> <output name="outfile" ftype='tabular' file="rdkit_descriptors_result1.tab" /> </test> + <test> + <param name="infile" ftype='sdf' value="CID_3037.sdf" /> + <param name="header" value="True" /> + <param name="select_multiple" value="qed,FormalCharge,MolWt" /> + <output name="outfile" ftype='tabular' file="rdkit_descriptors_subset.tab" /> + </test> + <test> + <param name="infile" ftype='pdb' value="mol.pdb" /> + <param name="header" value="False" /> + <param name="select_multiple" value="FormalCharge" /> + <output name="outfile" ftype='tabular' file="mol_pdb_charges.tab" /> + </test> </tests> <help> <![CDATA[ @@ -41,73 +261,40 @@ **What this tool does** | RDKit is an open source toolkit for cheminformatics and machine learning. -| This tool calculates various molecular descriptors for the input data. The table below shows a brief overview of the descriptors. +| This tool calculates various molecular descriptors for the input data. The table below shows a brief overview of the descriptors (or families of related descriptors) which are calculated. | - -+-----------------------------------+------------+ -| Descriptor/Descriptor Family | Language | -+===================================+============+ -| Gasteiger/Marsili Partial Charges | C++ | -+-----------------------------------+------------+ -| BalabanJ | Python | -+-----------------------------------+------------+ -| BertzCT | Python | -+-----------------------------------+------------+ -| Ipc | Python | -+-----------------------------------+------------+ -| HallKierAlpha | Python | -+-----------------------------------+------------+ -| Kappa1 - Kappa3 | Python | -+-----------------------------------+------------+ -| Chi0, Chi1 | Python | -+-----------------------------------+------------+ -| Chi0n - Chi4n | Python | -+-----------------------------------+------------+ -| Chi0v - Chi4v | Python | -+-----------------------------------+------------+ -| MolLogP | C++ | -+-----------------------------------+------------+ -| MolMR | C++ | -+-----------------------------------+------------+ -| MolWt | C++ | -+-----------------------------------+------------+ -| HeavyAtomCount | Python | -+-----------------------------------+------------+ -| HeavyAtomMolWt | Python | -+-----------------------------------+------------+ -| NHOHCount | C++ | -+-----------------------------------+------------+ -| NOCount | C++ | -+-----------------------------------+------------+ -| NumHAcceptors | C++ | -+-----------------------------------+------------+ -| NumHDonors | C++ | -+-----------------------------------+------------+ -| NumHeteroatoms | C++ | -+-----------------------------------+------------+ -| NumRotatableBonds | C++ | -+-----------------------------------+------------+ -| NumValenceElectrons | Python | -+-----------------------------------+------------+ -| RingCount | C++ | -+-----------------------------------+------------+ -| TPSA | C++ | -+-----------------------------------+------------+ -| LabuteASA | C++ | -+-----------------------------------+------------+ -| PEOE_VSA1 - PEOE_VSA14 | Python/C++ | -+-----------------------------------+------------+ -| SMR_VSA1 - SMR_VSA10 | Python/C++ | -+-----------------------------------+------------+ -| SlogP_VSA1 - SlogP_VSA12 | Python/C++ | -+-----------------------------------+------------+ -| EState_VSA1 - EState_VSA11 | Python | -+-----------------------------------+------------+ -| VSA_EState1 - VSA_EState10 | Python | -+-----------------------------------+------------+ -| Topliss fragments | Python | -+-----------------------------------+------------+ - +| - Gasteiger/Marsili Partial Charges +| - BalabanJ +| - BertzCT +| - Ipc +| - HallKierAlpha +| - Kappa1 - Kappa3 +| - Chi0, Chi1 +| - Chi0n - Chi4n +| - Chi0v - Chi4v +| - FormalCharge +| - MolLogP +| - MolMR +| - MolWt +| - HeavyAtomCount +| - HeavyAtomMolWt +| - NHOHCount +| - NOCount +| - NumHAcceptors +| - NumHDonors +| - NumHeteroatoms +| - NumRotatableBonds +| - NumValenceElectrons +| - RingCount +| - SSSR +| - TPSA +| - LabuteASA +| - PEOE_VSA1 - PEOE_VSA14 +| - SMR_VSA1 - SMR_VSA10 +| - SlogP_VSA1 - SlogP_VSA12 +| - EState_VSA1 - EState_VSA11 +| - VSA_EState1 - VSA_EState10 +| - Topliss fragments | | A full list of the descriptors can be obtained here_. @@ -119,7 +306,7 @@ **Hint** -Use the **cut columns from a table** tool to select just the desired descriptors. +Use the **cut columns from a table** tool to select just the desired descriptors. Alternatively, if you just want to calculate a subset of the descriptors, there is an option available to do so. ----- @@ -130,6 +317,8 @@ | - `SDF Format`_ | - `SMILES Format`_ | - `Corina MOL2`_ +| - PDB +| - InChi .. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification