Mercurial > repos > bgruening > openbabel
diff filter/ob_filter.xml @ 0:527ecd2fc500 draft
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| author | bgruening |
|---|---|
| date | Thu, 15 Aug 2013 03:25:06 -0400 |
| parents | |
| children | 125da3a296ca |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter/ob_filter.xml Thu Aug 15 03:25:06 2013 -0400 @@ -0,0 +1,240 @@ +<tool id="ctb_filter" name="Filter" version="1.0"> + <description> a set of molecules from a file</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="2.3.2">openbabel</requirement> + <requirement type="package" version="0.1">cheminfolib</requirement> + </requirements> + <command interpreter="python"> + ob_filter.py + -i "${infile}" + -o "${outfile}" + -iformat "${infile.ext}" + -oformat "${infile.ext}" + --filters '{ + #if $filter_methods.filter_methods_opts == "ruleof5": + "hbd" : [0, 5], + "hba" : [0, 10], + "molwt" : [0, 500], + "logp" : [-5, 5], + #elif $filter_methods.filter_methods_opts == "LeadLike": + "rotbonds" : [0, 7], + "molwt" : [0, 350], + "logp" : [-5, 3.5], + #elif $filter_methods.filter_methods_opts == "DrugLike": + "hba" : [0, 10], + "rotbonds" : [0, 8], + "molwt" : [150, 500], + "logp" : [-5, 5], + "psa" : [0, 150], + #elif $filter_methods.filter_methods_opts == "FragmentLike": + "rotbonds" : [0, 5], + "molwt" : [0, 250], + "logp" : [-5, 2.5], + #else: + #for $filter in $filter_methods.filter_set: + #set $filter_selected = $filter.filter_sel.filter_sel_opts + #set $filter_min = $filter_selected + "_min" + #set $filter_max = $filter_selected + "_max" + "$filter_selected" : [$filter.filter_sel[$filter_min], $filter.filter_sel[$filter_max] ], + #end for + #end if + }' + </command> + <inputs> + <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" label="Select input file previously created with the 'Compute physico-chemical properties' tool"/> + <conditional name="filter_methods"> + <param name="filter_methods_opts" type="select" label="Select a pre-defined filtering set"> + <option value="user">User-defined properties</option> + <option value="ruleof5">Lipinski's Rule-of-Five</option> + <option value="LeadLike">Lead-like properties</option> + <option value="DrugLike">Drug-like properties</option> + <option value="FragmentLike">Fragment-like properties</option> + </param> + <when value="ruleof5" /> + <when value="LeadLike" /> + <when value="DrugLike" /> + <when value="FragmentLike" /> + <when value="user"> + <repeat name="filter_set" title="Filters selection"> + <conditional name="filter_sel"> + <param name="filter_sel_opts" type="select" label="Select properties to filter"> + <option value="hbd">Number of Hydrogen-bond donor groups</option> + <option value="hba">Number of Hydrogen-bond acceptor groups</option> + <option value="psa">Total polar Surface Area</option> + <option value="rotbonds">Number of rotatable bonds</option> + <option value="molwt">Molecular weight</option> + <option value="logp">Predicted value of LogP</option> + <option value="mr">Predicted value for the Molecular Refractivity</option> + <option value="atoms">Number of atoms</option> + <!-- Add later, we need to add a new smarts pattern to plugindefines.txt + <option value="hatoms">Number of heavy atoms</option>--> + <!-- We skip that options, for further information please read: http://www.dalkescientific.com/writings/diary/archive/2011/06/04/dealing_with_sssr.html --> + <!--<option value="rings">Number of rings</option>--> + </param> + <when value="hbd"> + <param name="hbd_min" size="3" type="integer" value="" label="Minimum number of HB donors"/> + <param name="hbd_max" size="3" type="integer" value="" label="Maximum number of HB donors"/> + </when> + <when value="hba"> + <param name="hba_min" size="3" type="integer" value="" label="Minimum number of HB acceptors"/> + <param name="hba_max" size="3" type="integer" value="" label="Maximum number of HB acceptors"/> + </when> + <when value="psa"> + <param name="psa_min" size="5" type="integer" value="" label="Minimum threshold for the Total Polar Surface Area"/> + <param name="psa_max" size="5" type="integer" value="" label="Maximum threshold for the Total Polar Surface Area"/> + </when> + <when value="rotbonds"> + <param name="rotbonds_min" size="3" type="integer" value="" label="Minimum number of rotatable bonds"/> + <param name="rotbonds_max" size="3" type="integer" value="" label="Maximum number of rotatable bonds"/> + </when> + <when value="molwt"> + <param name="molwt_min" size="5" type="integer" value="" label="Minimum threshold value for the Molecular Weight"/> + <param name="molwt_max" size="5" type="integer" value="" label="Maximum threshold value for the Molecular Weight"/> + </when> + <when value="logp"> + <param name="logp_min" size="4" type="float" value="" label="Minimum threshold value for the log-P"/> + <param name="logp_max" size="4" type="float" value="" label="Maximum threshold value for the log-P"/> + </when> + <when value="mr"> + <param name="mr_min" size="4" type="float" value="" label="Minimum threshold value for the Molecular Refractivity"/> + <param name="mr_max" size="4" type="float" value="" label="Maximum threshold value for the Molecular Refractivity"/> + </when> + <when value="atoms"> + <param name="atoms_min" size="3" type="integer" value="" label="Minimum number of atoms"/> + <param name="atoms_max" size="3" type="integer" value="" label="Maximum number of atoms"/> + </when> + <!--<when value="rings"> + <param name="rings_min" size="3" type="integer" value="" label="Minimum number of rings"/> + <param name="rings_max" size="3" type="integer" value="" label="Maximum number of rings"/> + </when>--> + </conditional> + </repeat> + </when> + </conditional> + </inputs> + <outputs> + <data format_source="infile" name="outfile" /> + </outputs> + <tests> + <test> + <param name="infile" ftype="smi" value="CID_2244.smi"/> + <param name="filter_methods_opts" value="ruleof5" /> + <output name="outfile" ftype="smi" file="ob_filter_on_CID2244.smi" /> + </test> + <!-- + Limitation of the test framework: + https://trello.com/card/disambiguated-conditional-parameters-not-supported-in-unit-tests/506338ce32ae458f6d15e4b3/820 + <test> + <param name="infile" ftype="smi" value="CID_2244.smi"/> + <param name="filter_methods_opts" value="user" /> + <param name="filter_sel_opts" value="hba" /> + <param name="hbd_min" value="0" /> + <param name="hbd_max" value="5" /> + <output name="outfile" ftype="smi" file="ob_filter_on_CID2244_2.smi" /> + </test> + --> + </tests> + <help> + + +.. class:: infomark + +**What this tool does** + +Filters a library of compounds based on user-defined physico-chemical parameters or predefined options (e.g. Ro5, lead-like properties, etc.). Multiple parameters can be selected for more specific queries. + +----- + +.. class:: warningmark + +**Hint** + +| If your input file is in SDF format you can use the *Compute physico-chemical properties* tool to precalulate the properties and use the filter on that precomputed dataset. It should be faster and can be reused but it's bigger than a SMILES file. +| +| For exact matches please use the target value for both minimum and maximum parameters (e.g. a selection of exactly 4 rotatable bonds can be performed by selecting 4 as minimum and maximum value). +| +| Selecting the same property multiple times with different parameters will result in querying the largest overlapping subset of values for the parameter (e.g. a selection of between 0 and 3 rotatable bonds plus a selection between 2 and 4 will result in a query for compounds between 2 and 3 rotatable bonds). + +----- + +.. class:: infomark + +**Definition of the pre-defined filtering rules** + + **# Lipinski's Rule of Five:** + =< 5 Hydrogen-bond donor groups + + =< 10 Hydrogen-bond acceptor groups + + =< 500 Molecular weight + + =< 5 octanol/water partition coefficient (log P) + + **# Lead Like properties** (Teague, Davis, Leeson, Oprea, Angew Chem Int Ed Engl. 1999 Dec 16;38(24):3743-3748): + =< 7 rotatable bonds + + =< 350 Molecular weight + + =< 3.5 octanol/water partition coefficient (log P) + + **# Drug Like properties** (Lipinski, J Pharmacol Toxicol Methods. 2000 Jul-Aug;44(1):235-49): + =< 10 Hydrogen-bond acceptor groups + + =< 8 rotatable bonds + + 150 =< Molecular weight =< 500 + + =< 150 Polar Surface Area + + =< 5 octanol/water partition coefficient (log P) + + **# Fragment Like properties** (Carr RA, Congreve M, Murray CW, Rees DC, Drug Discov Today. 2005 Jul 15;10(14):987): + =< 5 rotatable bonds + + =< 250 Molecular weight + + =< 2.5 octanol/water partition coefficient (log P) + +----- + +.. class:: infomark + +**Input** + +| - `SD-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 + +----- + +.. class:: infomark + +**Output** + +| SDF formatted coordinates of the molecules, with selected properties stored as meta-data for each compound. +| +| SMILES, InChI or mol2 formatted files containing the 1D strings or 3D coordinates of each compound. + +----- + +.. class:: infomark + +**Cite** + +N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_ + +.. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://journal.chemistrycentral.com/content/2/1/5 + +N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_ + +.. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33 + +`Open Babel`_ + +.. _`Open Babel`: http://openbabel.org/wiki/Main_Page + + </help> +</tool>