| Next changeset 1:2f212f34b80c (2017-05-24) |
|
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807 |
|
added:
rdkit_descriptors.py rdkit_descriptors.xml test-data/CID_3037.sdf test-data/rdkit_descriptors_result1.tab |
| b |
| diff -r 000000000000 -r d7ea4e8cb1f3 rdkit_descriptors.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rdkit_descriptors.py Sat May 20 12:41:19 2017 -0400 |
| [ |
| @@ -0,0 +1,77 @@ +#!/usr/bin/env python + +from rdkit.Chem import Descriptors +from rdkit import Chem +import sys, os, re +import argparse +import inspect + +def get_supplier( infile, format = 'smiles' ): + """ + Returns a generator over a SMILES or InChI file. Every element is of RDKit + molecule and has its original string as _Name property. + """ + with open(infile) as handle: + for line in handle: + line = line.strip() + if format == 'smiles': + mol = Chem.MolFromSmiles( line, sanitize=True ) + elif format == 'inchi': + mol = Chem.inchi.MolFromInchi( line, sanitize=True, removeHs=True, logLevel=None, treatWarningAsError=False ) + if mol is None: + yield False + else: + mol.SetProp( '_Name', line.split('\t')[0] ) + yield mol + + +def get_rdkit_descriptor_functions(): + """ + Returns all descriptor functions under the Chem.Descriptors Module as tuple of (name, function) + """ + ret = [ (name, f) for name, f in inspect.getmembers( Descriptors ) if inspect.isfunction( f ) and not name.startswith( '_' ) ] + ret.sort() + return ret + + +def descriptors( mol, functions ): + """ + Calculates the descriptors of a given molecule. + """ + for name, function in functions: + yield (name, function( mol )) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument('-i', '--infile', required=True, help='Path to the input file.') + parser.add_argument("--iformat", help="Specify the input file format.") + + parser.add_argument('-o', '--outfile', type=argparse.FileType('w+'), + default=sys.stdout, help="path to the result file, default it sdtout") + + parser.add_argument("--header", dest="header", action="store_true", + default=False, + help="Write header line.") + + args = parser.parse_args() + + if args.iformat == 'sdf': + supplier = Chem.SDMolSupplier( args.infile ) + elif args.iformat =='smi': + supplier = get_supplier( args.infile, format = 'smiles' ) + elif args.iformat == 'inchi': + supplier = get_supplier( args.infile, format = 'inchi' ) + + functions = get_rdkit_descriptor_functions() + + if args.header: + args.outfile.write( '%s\n' % '\t'.join( [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] ) ) + |
| b |
| diff -r 000000000000 -r d7ea4e8cb1f3 rdkit_descriptors.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rdkit_descriptors.xml Sat May 20 12:41:19 2017 -0400 |
| [ |
| @@ -0,0 +1,155 @@ +<tool id="ctb_rdkit_describtors" name="Descriptors" version="0.3"> + <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="2016.03.3">rdkit</requirement> + </requirements> + <command> +<![CDATA[ + python '$__tool_directory__/rdkit_descriptors.py' + -i '${infile}' + --iformat '${infile.ext}' + -o '${outfile}' + $header +]]> + </command> + <inputs> + <param name="infile" format="smi,sdf,mol2" type="data" label="Molecule data" + help="In SD- or SMILES-format"/> + <param name="header" type="boolean" label="Include the descriptor name as header" + truevalue="--header" falsevalue="" checked="false" /> + </inputs> + <outputs> + <data format="tabular" name="outfile" /> + </outputs> + <tests> + <test> + <param name="infile" ftype='sdf' value="CID_3037.sdf" /> + <param name="header" value="True" /> + <output name="outfile" ftype='tabular' file="rdkit_descriptors_result1.tab" /> + </test> + </tests> + <help> +<![CDATA[ + +.. class:: infomark + +**What this tool does** + +| RDKit is an open source toolkit for cheminformatics and machine learning. +| This implementation focuses on descriptor calculation, though, RDKit offers a vast number of other functions. +| +| The table below shows a brief overview of the descriptors. +| + ++-----------------------------------+------------+ +| 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 | ++-----------------------------------+------------+ + +| +| A full list of the descriptors can be obtained here_. + +.. _here: https://rdkit.readthedocs.org/en/latest/GettingStartedInPython.html#list-of-available-descriptors + +----- + +.. class:: warningmark + +**HINT** + +Use the **cut columns from a table** tool to select just the desired descriptors. + +----- + +.. class:: infomark + +**Input** + +| - `SD-Format`_ +| - `SMILES Format`_ +| - `Corina MOL2`_ + +.. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file +.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification +.. _Corina MOL2: http://www.molecular-networks.com/products/corina + +----- + +.. class:: infomark + + **Output** + +Tabularfile, where each descriptor (value) is shown in a seperate column. + + +]]> + </help> + <citations> + <citation type="bibtex"> + @article{rdkit, + author = {Greg Landrum}, + title = {RDKit: Open-source cheminformatics}, + url ={http://www.rdkit.org} + }</citation> + </citations> +</tool> |
| b |
| diff -r 000000000000 -r d7ea4e8cb1f3 test-data/CID_3037.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CID_3037.sdf Sat May 20 12:41:19 2017 -0400 |
| b |
| @@ -0,0 +1,220 @@ +3037 + -OEChem-08231108593D + + 27 28 0 0 0 0 0 0 0999 V2000 + -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1809 -2.1668 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1788 2.1664 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0011 -0.0002 1.4744 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2222 -0.2738 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2377 0.2772 0.6480 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2586 -1.3462 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2565 1.3457 -0.2314 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3343 0.5568 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3322 -0.5574 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4069 -1.5879 -0.9855 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4048 1.5875 -0.9852 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.4827 0.3152 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.4807 -0.3156 0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.5190 -0.7571 -0.8481 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5170 0.7568 -0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1548 0.8649 2.1342 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1601 -0.8435 2.1593 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3089 1.3938 1.4913 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3053 -1.3909 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4415 -2.4213 -1.6818 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4469 2.4191 -1.6835 H 0 0 0 0 0 0 0 0 0 0 0 0 + -4.4070 -0.9574 -1.4422 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.4050 0.9570 -1.4418 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2961 -2.2262 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.3872 2.8487 -1.0397 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 14 1 0 0 0 0 + 2 15 1 0 0 0 0 + 3 8 1 0 0 0 0 + 3 26 1 0 0 0 0 + 4 9 1 0 0 0 0 + 4 27 1 0 0 0 0 + 5 6 1 0 0 0 0 + 5 7 1 0 0 0 0 + 5 18 1 0 0 0 0 + 5 19 1 0 0 0 0 + 6 8 2 0 0 0 0 + 6 10 1 0 0 0 0 + 7 9 2 0 0 0 0 + 7 11 1 0 0 0 0 + 8 12 1 0 0 0 0 + 9 13 1 0 0 0 0 + 10 14 2 0 0 0 0 + 10 20 1 0 0 0 0 + 11 15 2 0 0 0 0 + 11 21 1 0 0 0 0 + 12 16 2 0 0 0 0 + 12 22 1 0 0 0 0 + 13 17 2 0 0 0 0 + 13 23 1 0 0 0 0 + 14 16 1 0 0 0 0 + 15 17 1 0 0 0 0 + 16 24 1 0 0 0 0 + 17 25 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +3037 + +> <PUBCHEM_CONFORMER_RMSD> +0.6 + +> <PUBCHEM_CONFORMER_DIVERSEORDER> +8 +10 +12 +1 +7 +5 +11 +3 +6 +9 +4 +2 + +> <PUBCHEM_MMFF94_PARTIAL_CHARGES> +25 +1 -0.18 +10 -0.15 +11 -0.15 +12 -0.15 +13 -0.15 +14 0.18 +15 0.18 +16 -0.15 +17 -0.15 +2 -0.18 +20 0.15 +21 0.15 +22 0.15 +23 0.15 +24 0.15 +25 0.15 +26 0.45 +27 0.45 +3 -0.53 +4 -0.53 +5 0.29 +6 -0.14 +7 -0.14 +8 0.08 +9 0.08 + +> <PUBCHEM_EFFECTIVE_ROTOR_COUNT> +2 + +> <PUBCHEM_PHARMACOPHORE_FEATURES> +4 +1 3 donor +1 4 donor +6 6 8 10 12 14 16 rings +6 7 9 11 13 15 17 rings + +> <PUBCHEM_HEAVY_ATOM_COUNT> +17 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +5 + +> <PUBCHEM_CONFORMER_ID> +00000BDD00000008 + +> <PUBCHEM_MMFF94_ENERGY> +44.6858 + +> <PUBCHEM_FEATURE_SELFOVERLAP> +20.297 + +> <PUBCHEM_SHAPE_FINGERPRINT> +10062212 137 18261117369936506423 +104564 63 17986963035811110412 +11458722 120 18339359768245870841 +11471102 22 5472872458301843344 +11578080 2 18190204380446433792 +116883 192 18265608969609498196 +12236239 1 18410856576819659107 +12592029 89 18338223951597366363 +13549 16 18410575084668353682 +13693222 15 6555421915516066822 +13764800 53 14189033175566991199 +14115302 16 18186237320680093898 +14341114 328 10087642619424135543 +14787075 74 9511159855286719151 +14993402 34 18410855451538227223 +15099037 51 18340768233908588503 +15207287 21 15719111361650760302 +15375358 24 15647053767618106914 +15775835 57 18272650117329930317 +16945 1 17906452130063974618 +17834072 14 15936410035134206066 +18186145 218 17132117918276567720 +19422 9 18271525295227750719 +20279233 1 15719389529571237654 +20645476 183 18339080393619327415 +23402539 116 18186809105365620101 +23402655 69 18342736308283284156 +23559900 14 17603590712323212176 +25 1 17561083592297532664 +26918003 58 6266902359448424189 +296302 2 15213020427345972082 +3082319 5 18338798905472319583 +34934 24 18341891845236497020 +633830 44 17703790310130762689 +74978 22 18266740181857992718 +7832392 63 18340206284835898173 +81228 2 15720767252053392762 +9981440 41 17403743242177431832 + +> <PUBCHEM_SHAPE_MULTIPOLES> +341.85 +8.38 +1.9 +1.1 +0.02 +0 +-1.15 +1.94 +-0.01 +0 +-0.39 +-4.15 +0.01 +0 + +> <PUBCHEM_SHAPE_SELFOVERLAP> +722.787 + +> <PUBCHEM_SHAPE_VOLUME> +193 + +> <PUBCHEM_COORDINATE_TYPE> +2 +5 +255 + +$$$$ + |
| b |
| diff -r 000000000000 -r d7ea4e8cb1f3 test-data/rdkit_descriptors_result1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rdkit_descriptors_result1.tab Sat May 20 12:41:19 2017 -0400 |
| b |
| @@ -0,0 +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 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 +3037 2.37022757927 503.610880418 12.4138490834 8.82156453334 10.3334224254 8.05855064806 5.00835259312 5.76428153914 3.72284524811 4.59571680905 2.46398508386 2.93417928943 1.59652584133 1.98592629408 0.0 10.2130547897 0.0 11.4990236666 27.5929912338 0.0 12.1327341369 24.2654682738 0.0 0.0 23.2018797805 268.00578492 0.0769230769231 -1.38 17 259.047 6943.44519959 12.0868667938 4.86118110558 2.84267247008 109.048439398 9.68320845931 0.50766175334 9.68320845931 0.118708899658 0.1470143613 0.118708899658 0.1470143613 -0.50766175334 3.9954 69.0396 269.127 2 2 0 0 0 2 0 2 2 2 4 0 2 0 0 0 88 10.2130547897 11.4990236666 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 23.2018797805 47.5251053942 16.4660882504 0.0 2 10.2130547897 23.2018797805 0.0 0.0 0.0 6.42082162293 0.0 57.5703720216 0.0 11.4990236666 0.0 0.0 11.4990236666 23.2018797805 10.2130547897 6.42082162293 0.0 11.1269029834 36.3982024108 10.0452666275 0.0 0.0 40.46 0.0 11.7088697125 0.0 0.0 0.0 0.0 0.0 0.0 0.0 32.0133525097 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 |