Mercurial > repos > bgruening > rdkit
diff rdkit_descriptors.xml @ 0:6bb56f3a8de0 draft default tip
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author | bgruening |
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date | Thu, 15 Aug 2013 03:35:10 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rdkit_descriptors.xml Thu Aug 15 03:35:10 2013 -0400 @@ -0,0 +1,143 @@ +<tool id="ctb_rdkit_describtors" name="Descriptors" version="0.1"> + <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="2012_12_1">rdkit</requirement> + </requirements> + <command interpreter="python">rdkit_descriptors.py -i "${infile}" --iformat "${infile.ext}" -o "${outfile}" $header 2>&1</command> + <inputs> + <param format="smi,sdf" name="infile" type="data" label="Molecule data in SD- or SMILES-format" help="Dataset missing? See TIP below"/> + <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> + </tests> + <help> + +.. 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://code.google.com/p/rdkit/wiki/DescriptorsInTheRDKit + +----- + +.. class:: warningmark + +**HINT** + +Use the **cut columns from a table** tool to select just the desired descriptors. + +----- + +.. class:: infomark + +**Input** + +| - `SD-Format`_ +| - `SMILES Format`_ +| - TDT_ +| - SLN +| - `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 +.. _TDT: https://earray.chem.agilent.com/earray/helppages/index.htm#tdt_format_files.htm +.. _Corina MOL2: http://www.molecular-networks.com/products/corina + +----- + +.. class:: infomark + + **Output** + +Tabularfile, where each descriptor (value) is shown in a seperate column. + +----- + +.. class:: informark + +**Cite** + +Greg Landrum - RDKit_: Open-source cheminformatics + +.. _RDKit: http://www.rdkit.org + + + </help> +</tool>