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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e |
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modified:
qed.py silicos_qed.xml |
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removed:
errors.pyc |
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| diff -r 5ccd3a432785 -r ab73abead7fa errors.pyc |
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| Binary file errors.pyc has changed |
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| diff -r 5ccd3a432785 -r ab73abead7fa qed.py --- a/qed.py Tue May 23 03:57:14 2017 -0400 +++ b/qed.py Tue May 07 13:41:23 2019 -0400 |
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| @@ -330,18 +330,18 @@ # Elucidate filetype and open supplier ifile = os.path.abspath(args.input) if not os.path.isfile(ifile): - print "Error: ", ifile, " is not a file or cannot be found." + print("Error: ", ifile, " is not a file or cannot be found.") sys.exit(1) if not os.path.exists(ifile): - print "Error: ", ifile, " does not exist or cannot be found." + print("Error: ", ifile, " does not exist or cannot be found.") sys.exit(1) if not os.access(ifile, os.R_OK): - print "Error: ", ifile, " is not readable." + print("Error: ", ifile, " is not readable.") sys.exit(1) if not args.iformat: # try to guess the filetype - filetype = check_filetype( ifile ) + filetype = check_filetype(ifile) else: filetype = args.iformat # sdf or smi @@ -350,7 +350,7 @@ We want to store the original SMILES in the output. So in case of a SMILES file iterate over the file and convert each line separate. """ if filetype == 'sdf': - supplier = Chem.SDMolSupplier( ifile ) + supplier = Chem.SDMolSupplier(ifile) # Process file if args.header: args.outfile.write("MW\tALOGP\tHBA\tHBD\tPSA\tROTB\tAROM\tALERTS\tLRo5\tQED\tNAME\n") @@ -358,7 +358,7 @@ for mol in supplier: count += 1 if mol is None: - print "Warning: skipping molecule ", count, " and continuing with next." + print("Warning: skipping molecule ", count, " and continuing with next.") continue props = properties(mol) @@ -399,7 +399,7 @@ mol = Chem.MolFromSmiles(smiles) count += 1 if mol is None: - print "Warning: skipping molecule ", count, " and continuing with next." + print("Warning: skipping molecule ", count, " and continuing with next.") continue props = properties(mol) |
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| diff -r 5ccd3a432785 -r ab73abead7fa silicos_qed.xml --- a/silicos_qed.xml Tue May 23 03:57:14 2017 -0400 +++ b/silicos_qed.xml Tue May 07 13:41:23 2019 -0400 |
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| @@ -1,8 +1,8 @@ -<tool id="ctb_silicos_qed" name="Drug-likeness" version="0.1"> +<tool id="ctb_silicos_qed" name="Drug-likeness" version="0.2"> <description>quantitative estimation (QED)</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="2015.09.2">rdkit</requirement> + <requirement type="package" version="2019.03.1">rdkit</requirement> </requirements> <command detect_errors="aggressive"> <![CDATA[ @@ -15,13 +15,13 @@ ]]> </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="method" type="select" label="Method"> + <param format="smi,sdf" name="infile" type="data" label="Molecule data in SDF or SMILES format" help="Dataset missing? See TIP below"/> + <param name="method" type="select" label="Method" help="Method for weighting features"> <option value="max">Max weight (QEDw,max)</option> <option value="mean">Mean weight (QEDw,mo)</option> - <option value="unweighted">unweighted (QEDw,u)</option> + <option value="unweighted">Unweighted (QEDw,u)</option> </param> - <param name="header" type="boolean" label="Include the descriptor name as header" truevalue="--header" falsevalue="" checked="false" /> + <param name="header" type="boolean" label="Include the descriptor names as header" truevalue="--header" falsevalue="" checked="false" /> </inputs> <outputs> <data format="tabular" name="outfile" /> @@ -56,21 +56,37 @@ **What this tool does** -Estimates the drug-likeness of molecules and reports a score. Comes with three applicable varieties (QED\ :sub:`w,mo`\ , QED\ :sub:`w,max`\ , QED\ :sub:`w,u` ). +Estimates the drug-likeness of molecules, based on eight commonly used molecular +properties, and reports a score between 0 (all properties unfavourable) to 1 (all +properties favourable). Two possible methods to weight the features are available +(QED\ :sub:`w,mo`\ , QED\ :sub:`w,max`\), as well as an option to leave features +unweighted (QED\ :sub:`w,u`). + +The eight properties used are: molecular weight (MW), octanol–water partition +coefficient (ALOGP), number of hydrogen bond donors (HBDs), number of hydrogen +bond acceptors (HBAs), molecular polar surface area (PSA), number of rotatable +bonds (ROTBs), number of aromatic rings (AROMs) and number of structural alerts +(ALERTS). ----- .. class:: warningmark -**HINT** +**Hint** -- All invalid, blank and comment lines are skipped when performing computations. The number of skipped lines is displayed in the resulting history item. +All invalid, blank and comment lines are skipped when performing computations. The +number of skipped lines is displayed in the resulting history item. The method refers +to a set of weights that can be applied to the features. These are derived in the +`original paper`_ describing QED. + - QED\ :sub:`w,max` using the set of weights that give maximal information content - QED\ :sub:`w,mo` using the mean weights of the optimal 1,000 weight combinations that give the highest information content -- QED\ :sub:`w,u` with all weights as unity, hence unweighted. +- QED\ :sub:`w,u` with all weights as unity i.e. unweighted. + +.. _original paper: https://www.nature.com/articles/nchem.1243 ----- @@ -79,11 +95,11 @@ **Input** -| - `SD-Format`_ -| - `SMILES Format`_ +| - `SDF format`_ +| - `SMILES format`_ -.. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file -.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification +.. _SDF format: http://en.wikipedia.org/wiki/Chemical_table_file +.. _SMILES format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification ----- @@ -91,6 +107,9 @@ **Output** +A table listing the values of the eight features, the QED score, the name of the +molecule, and the number of Lipinski rules which the molecule obeys. + +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+ | MW | ALOGP | HBA | HBD | PSA | ROTB | AROM | ALERTS | QED | NAME | Ro5 | +========+=======+=====+=====+========+======+======+========+=======+================+=====+ |