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Updated docs
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Brian Kelley
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Code/JavaWrappers/FilterCatalogParams_doc.i
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76
Code/JavaWrappers/FilterCatalogParams_doc.i
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/*
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*
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* Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
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* All rights reserved.
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*
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are
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* met:
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*
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* * Redistributions of source code must retain the above copyright
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* notice, this list of conditions and the following disclaimer.
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* * Redistributions in binary form must reproduce the above
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* copyright notice, this list of conditions and the following
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* disclaimer in the documentation and/or other materials provided
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* with the distribution.
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* * Neither the name of Novartis Institutes for BioMedical Research Inc.
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* nor the names of its contributors may be used to endorse or promote
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* products derived from this software without specific prior written permission.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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%typemap(javaimports) RDKit::FilterCatalogParams "
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/**
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<p>
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Paramter Class for initializing a FilterCatalog with the specified set of FilterCatalogs. Current
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catalogs include:
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<pre><code>
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FilterCatalogParams.FilterCatalogs.ALL
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FilterCatalogParams.FilterCatalogs.BRENK
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FilterCatalogParams.FilterCatalogs.PAINS_A
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FilterCatalogParams.FilterCatalogs.PAINS_B
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FilterCatalogParams.FilterCatalogs.PAINS_C
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FilterCatalogParams.FilterCatalogs.PAINS
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FilterCatalogParams.FilterCatalogs.ZINC
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</pre></code>
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Details:
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<h4>Brenk</h4>
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<ul>
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<li>Reference: <a href=\"http://www.ncbi.nlm.nih.gov/pubmed/18064617\">Brenk</a> Lessons Learnt from Assembling Screening Libraries for Drug Discovery for Neglected Diseases</li>
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<li>Scope: unwanted functionality due to potential tox reasons or unfavourable pharmacokinetic properties</li>
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</ul>
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<h4>NIH</h4>
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<ul>
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<li>Reference: <a href=\"http://pubs.rsc.org/en/Content/ArticleLanding/2015/OB/c4ob02287d#!divAbstract\">NIH</a> A Unified Lead-oriented Synthesis of over Fifty Molecular Scaffolds. </li>
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<li>Reference: <a href=\"http://pubs.acs.org/doi/abs/10.1021/jm901070c\">NIH</a> Quantitative Analyses of Aggregation, Autofluorescence, and Reactivity Artifacts in a Screen for Inhibitors of a Thiol Protease</li>
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<li>Scope: uannotate compounds with problematic functional groups </li>
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</ul>
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<h4>PAINS</h4>
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<ul>
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<li>Reference: <a href=\"http://pubs.rsc.org/en/Content/ArticleLanding/2015/OB/c4ob02287d#!divAbstract\">NIH</a> New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays </li>
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<li>Scope: PAINS filters </li>
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</ul>
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<h4>ZINC</h4>
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<ul>
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<li>Reference: <a href=\"http://blaster.docking.org/filtering/\">ZINC</a></li>
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<li>Scope: drug-likeness and unwanted functional group filters </li>
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</ul>
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**/"
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63
Code/JavaWrappers/FilterCatalog_doc.i
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63
Code/JavaWrappers/FilterCatalog_doc.i
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@@ -0,0 +1,63 @@
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/*
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*
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* Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
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* All rights reserved.
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*
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are
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* met:
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*
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* * Redistributions of source code must retain the above copyright
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* notice, this list of conditions and the following disclaimer.
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* * Redistributions in binary form must reproduce the above
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* copyright notice, this list of conditions and the following
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* disclaimer in the documentation and/or other materials provided
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* with the distribution.
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* * Neither the name of Novartis Institutes for BioMedical Research Inc.
|
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* nor the names of its contributors may be used to endorse or promote
|
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* products derived from this software without specific prior written permission.
|
||||
*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
|
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* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
|
||||
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
|
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* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
|
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* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
|
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* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
|
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* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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%typemap(javaimports) RDKit::FilterCatalog "
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/** FilterCatalog Class used to filter out undesireable molecules
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<br>
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Basic usage:
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<pre><code>
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FilterCatalog catalog = new FilterCatalog(
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FilterCatalogParams.FilterCatalogs.PAINS_A);
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// go through a mol supplier
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while (!molSupplier.atEnd()) {
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ROMol m = suppl.next();
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FilterCatalogEntry_Vect matches = catalog.getMatches(mol);
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if( matches.size() ) {
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// reject -- get descriptions of rejection
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for (int entryIdx = 0; entryIdx < matches.size(); ++entryIdx) {
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entry = matches.get(entryIdx);
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String description = entry.getDescription(); // why
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// optional properties
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String reference = entry.getProp(\"Reference\");
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String scope = entry.getProp(\"Scope\");
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}
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}
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else {
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// accept
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}
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}
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</code></pre>
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**/
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"
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57
Code/JavaWrappers/FilterCatalogs_doc.i
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57
Code/JavaWrappers/FilterCatalogs_doc.i
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@@ -0,0 +1,57 @@
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/*
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*
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* Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
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* All rights reserved.
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*
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are
|
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* met:
|
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*
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* * Redistributions of source code must retain the above copyright
|
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* notice, this list of conditions and the following disclaimer.
|
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* * Redistributions in binary form must reproduce the above
|
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* copyright notice, this list of conditions and the following
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* disclaimer in the documentation and/or other materials provided
|
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* with the distribution.
|
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* * Neither the name of Novartis Institutes for BioMedical Research Inc.
|
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* nor the names of its contributors may be used to endorse or promote
|
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* products derived from this software without specific prior written permission.
|
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
|
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* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
|
||||
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
|
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* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
|
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* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
|
||||
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
|
||||
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
|
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* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
|
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* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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%typemap(javaimports) RDKit::FilterCatalogParams::FilterCatalog "
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/**
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<p>
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Initialize a FilterCatalog with the specified set of FilterCatalogs. Current
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catalogs include:
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<pre><code>
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FilterCatalogParams.FilterCatalogs.ALL
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FilterCatalogParams.FilterCatalogs.BRENK
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FilterCatalogParams.FilterCatalogs.PAINS_A
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FilterCatalogParams.FilterCatalogs.PAINS_B
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FilterCatalogParams.FilterCatalogs.PAINS_C
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FilterCatalogParams.FilterCatalogs.PAINS
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FilterCatalogParams.FilterCatalogs.ZINC
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</pre></code>
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Details:
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<h4>Brenk</h4>
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<ul>
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<li><pre># Reference: Brenk R et al. Lessons Learnt from Assembling Screening Libraries for Drug Discovery for Neglected Diseases. ChemMedChem 3 (2008) 435-444. doi:10.1002/cmdc.200700139.</pre></li>
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<li><Scope: unwanted functionality due to potential tox reasons or unfavourable pharmacokinetic properties</li>
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</ul>
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**/"
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@@ -141,6 +141,9 @@ typedef unsigned long long int uintmax_t;
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%include "../TDTWriter_doc.i"
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%include "../Transform2D_doc.i"
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%include "../Transform3D_doc.i"
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%include "../FilterCatalog_doc.i"
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%include "../FilterCatalogParams_doc.i"
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%include "../FilterCatalogs_doc.i"
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// DO THIS BEFORE ANY OF THE OTHER INCLUDES
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%include "../RDKitExceptions.i"
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