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University of Toronto St. George

Copyright c 19982013 ChemAxon Ltd All Rights Reserved This software is the confidential and proprietary information ofChemAxon You shall not disclose such Confidential Informationand shall use it only in accordance with the terms of the agreementsyou entered into with ChemAxonimport chemaxonmarvinpluginCalculatorPlugin import chemaxonmarvinpluginPluginException import chemaxonstrucMolAtom import chemaxonstrucMolBond import chemaxonstrucMolecule import chemaxonlicenseLicenseHandler import javautilProperties import javautilStringTokenizer Plugin class to calculate BemisMurcko framework of input molecules author Gabor Imreauthor Zsolt Mohacsipublic class BemisMurckoPlugin extends CalculatorPluginstatic private String TYPERANGEnew Stringstructure atomcount bondcountprivate Object typesnew Objectstructure The input moleculeprivate Molecule molnullThe output formatprivate String formatnull Structural framework will produce single atom instead of empty structureprivate boolean keepSingleForAcyclictrue if structure contains multiple fragments then process only the largestone after removing explicit H atomsprivate boolean processOnlyLargestInputFragmentfalse if result contains multiple fragments then keep only the largest oneprivate boolean keepOnlyLargestResultFragmentfalse Returns the name of the plugin to be used by the License Managerreturn identifier of the productpublic String getProductNamereturn LicenseHandlerFREEPLUGINSets the input moleculeparam mol is the input moleculethrows PluginException on errorprotected void setInputMoleculeMolecule mol throws PluginExceptionthismolmolSets the input parameters for the pluginAccepted parameters keepsingleatom truefalse if set true then a single atomwill be assigned to acyclic fragments if false then acyclic fragmentswill be projected to empty structureslfin truefalse if set true then the calculation will runonly on the largest input fragment Note that this necessarily yields thelargest scaffoldlfout truefalse if set true then only the largest calculatedscaffold will be returned Note that the returne
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