From e77cc376aaff8ca481fdace6d5795c5b5feb0e87 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Mon, 20 Feb 2012 14:45:20 +0100 Subject: Added pc descriptor calc service --- java/joelib2.properties | 502 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 502 insertions(+) create mode 100644 java/joelib2.properties (limited to 'java/joelib2.properties') diff --git a/java/joelib2.properties b/java/joelib2.properties new file mode 100644 index 0000000..fdad7ff --- /dev/null +++ b/java/joelib2.properties @@ -0,0 +1,502 @@ +############################################################################## +############################################################################## +############################################################################## +# +# JOELib2 properties +# +# \ slashes should be written as \\ +# spaces can be written as \ \, but white spaces are removed at the end of +# lines !!! +# Please use the Unicode expression \u0020 to encode white spaces !!! +# +############################################################################## +# +# Version: $Revision: 1.15 $ +# $Date: 2006/07/24 22:29:15 $ +# $Author: wegner $ +# +############################################################################## +# Copyright OELIB: OpenEye Scientific Software, Santa Fe, +# U.S.A., 1999,2000,2001 +# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of +# Tuebingen, Germany, 2001,2002,2003,2004,2005 +# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, +# 2003,2004,2005 +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation version 2 of the License. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +############################################################################## +############################################################################## + +############################################################################## +# resource locations of data files +############################################################################## +joelib2.data.BasicHybridisationTyper.resourceFile=joelib2/data/plain/hybridisation.txt +joelib2.data.BasicAromaticityTyper.resourceFile=joelib2/data/plain/aromatic.txt +joelib2.data.BasicAromaticityTyper.useAromaticityModel=true +joelib2.data.BasicImplicitValenceTyper.resourceFile=joelib2/data/plain/implicitValence.txt +joelib2.data.BasicAtomTyper.resourceFile=joelib2/data/plain/atomtype.txt +joelib2.data.BasicElementHolder.resourceFile=joelib2/data/plain/element.txt +joelib2.data.BasicIsotopeHolder.resourceFile=joelib2/data/plain/isotope.txt +joelib2.data.BasicProtonationModel.resourceFile=joelib2/data/plain/phmodel.txt + +joelib2.data.BasicGroupContributionHolder.resourceDir=joelib2/data/plain +joelib2.data.BasicGroupContributionHolder.contributionExtension=.contributions +joelib2.data.BasicGroupContributionHolder.models=LogP MR PSA + +joelib2.feature.ResultFactory.resourceFile=joelib2/data/plain/knownResults.txt +joelib2.process.types.DescriptorStatistic.descriptors2ignore=joelib2/data/plain/desc2ignore.txt +joelib2.process.types.DescriptorBinning.descriptors2ignore=joelib2/data/plain/desc2ignore.txt + +############################################################################## +# Database +############################################################################## +wsi.ra.database.DatabaseConnection.location=jdbc:mysql://localhost/test +wsi.ra.database.DatabaseConnection.password= +wsi.ra.database.DatabaseConnection.username= +wsi.ra.database.DatabaseConnection.driver=org.gjt.mm.mysql.Driver + +############################################################################## +# 2D rendering options +############################################################################## +joelib2.gui.render2D.Renderer2DModel.bond.length=30.0 +joelib2.gui.render2D.Renderer2DModel.bond.distance=6.0 +joelib2.gui.render2D.Renderer2DModel.bond.width=2.0 +joelib2.gui.render2D.Renderer2DModel.drawNumbers=true +joelib2.gui.render2D.Renderer2DModel.useKekuleStructure=true +joelib2.gui.render2D.Renderer2DModel.showEndCarbons=true +joelib2.gui.render2D.Renderer2DModel.atomColoring=false +joelib2.gui.render2D.Renderer2DModel.drawCarbonAtoms=false +joelib2.gui.render2D.Renderer2DModel.orthoLineOffset=20 +joelib2.gui.render2D.Renderer2DModel.arrowOffset=10 +joelib2.gui.render2D.Renderer2DModel.arrowSize=5 + +joelib2.gui.render2D.Renderer2DModel.background.color.r=255 +joelib2.gui.render2D.Renderer2DModel.background.color.g=255 +joelib2.gui.render2D.Renderer2DModel.background.color.b=255 + +joelib2.gui.render2D.Renderer2DModel.foreground.color.r=0 +joelib2.gui.render2D.Renderer2DModel.foreground.color.g=0 +joelib2.gui.render2D.Renderer2DModel.foreground.color.b=0 + +joelib2.gui.render2D.Renderer2DModel.highlight.color.r=255 +joelib2.gui.render2D.Renderer2DModel.highlight.color.g=0 +joelib2.gui.render2D.Renderer2DModel.highlight.color.b=0 + +joelib2.gui.render2D.Renderer2DModel.number.color.r=0 +joelib2.gui.render2D.Renderer2DModel.number.color.g=0 +joelib2.gui.render2D.Renderer2DModel.number.color.b=255 + +joelib2.gui.render2D.Renderer2DModel.conjugatedRing.color.r=0 +joelib2.gui.render2D.Renderer2DModel.conjugatedRing.color.g=0 +joelib2.gui.render2D.Renderer2DModel.conjugatedRing.color.b=0 + +joelib2.gui.render2D.Renderer2DModel.arrow.color.r=0 +joelib2.gui.render2D.Renderer2DModel.arrow.color.g=255 +joelib2.gui.render2D.Renderer2DModel.arrow.color.b=0 + +joelib2.gui.render2D.Renderer2DModel.orthogonalLine.color.r=0 +joelib2.gui.render2D.Renderer2DModel.orthogonalLine.color.g=0 +joelib2.gui.render2D.Renderer2DModel.orthogonalLine.color.b=255 + +############################################################################## +# Smiles ARbitrary Target Specification (SMARTS) matcher parameters +############################################################################## +# '*' matches also explicite hydrogens when 'true' +# '*' matches only non-hydrogen (heavy weight) atoms when 'false' +joelib2.smarts.SMARTSParser.anyRecognizesExpliciteHydrogens=false + +############################################################################## +# Supported file types +############################################################################## +joelib2.filetypes.1.name = SDF +joelib2.filetypes.2.name = XYZ +joelib2.filetypes.3.name = SMILES +joelib2.filetypes.4.name = TINKER +joelib2.filetypes.5.name = CTX +joelib2.filetypes.6.name = CML +joelib2.filetypes.7.name = POV +joelib2.filetypes.8.name = MOL2 +joelib2.filetypes.9.name = PDB +joelib2.filetypes.10.name = MATLAB +joelib2.filetypes.11.name = FLAT +joelib2.filetypes.11.representation = joelib2.io.types.Flat +joelib2.filetypes.12.name = MOLCONNZ +joelib2.filetypes.12.representation = joelib2.io.types.MolconnZ +joelib2.filetypes.13.name = HIN +joelib2.filetypes.14.name = GAUSSIANCART +joelib2.filetypes.15.name = JPEG +joelib2.filetypes.16.name = GIF +joelib2.filetypes.17.name = PPM +# PNG requires another implementation or Marvin +#joelib2.filetypes.18.name = PNG +joelib2.filetypes.18.name = BMP +joelib2.filetypes.19.name = PDF +joelib2.filetypes.20.name = ZIP +joelib2.filetypes.21.name = PREP +joelib2.filetypes.22.name = MOPACOUT + +#joelib2.filetypes.16.name = GHEMICAL + +# if you want another loader/writer define one +#joelib2.filetypes.1.representation = joelib2.io.types.MDLSD +#joelib2.filetypes.2.representation = joelib2.io.types.XYZ +#joelib2.filetypes.3.representation = joelib2.io.types.Smiles + +############################################################################## +# filters +############################################################################## +joelib2.filter.1.name =NOTFilter +joelib2.filter.1.representation =joelib2.process.filter.NOTFilter +joelib2.filter.1.descriptionFile =docs/process/notFilter +joelib2.filter.2.name =ORFilter +joelib2.filter.2.representation =joelib2.process.filter.ORFilter +joelib2.filter.2.descriptionFile =docs/process/orFilter +joelib2.filter.3.name =ANDFilter +joelib2.filter.3.representation =joelib2.process.filter.ANDFilter +joelib2.filter.3.descriptionFile =docs/process/andFilter +joelib2.filter.4.name =HasDataFilter +joelib2.filter.4.representation =joelib2.process.filter.HasDataFilter +joelib2.filter.4.descriptionFile =docs/process/hasDataFilter +joelib2.filter.5.name =DescriptorFilter +joelib2.filter.5.representation =joelib2.process.filter.DescriptorFilter +joelib2.filter.5.descriptionFile =docs/process/descriptorFilter +joelib2.filter.6.name =NativeValueFilter +joelib2.filter.6.representation =joelib2.process.filter.NativeValueFilter +joelib2.filter.6.descriptionFile =docs/process/nativeValueFilter + +############################################################################## +# processes +############################################################################## +joelib2.process.1.name =ProcessPipe +joelib2.process.1.representation =joelib2.process.ProcessPipe +joelib2.process.1.descriptionFile =docs/process/processPipe +joelib2.process.2.name =FeatureSelectionWriter +joelib2.process.2.representation =joelib2.process.types.FeatureSelectionWriter +joelib2.process.2.descriptionFile =docs/process/featureSelectionWriter +joelib2.process.3.name =DescriptorStatistic +joelib2.process.3.representation =joelib2.process.types.DescStatistic +joelib2.process.3.descriptionFile =docs/process/descriptorStatistic +################ +joelib2.process.4.name =DescriptorBinning +joelib2.process.4.representation =joelib2.process.types.DescBinning +joelib2.process.4.descriptionFile =docs/process/descriptorBinning +joelib2.process.types.DescBinning.numberOfBins=20 +################ +joelib2.process.5.name =DistanceCalculation +joelib2.process.5.representation =joelib2.process.types.DistanceCalculation +joelib2.process.5.descriptionFile =docs/process/distanceCalculation + +############################################################################## +# miscellaneous +############################################################################## + +#SD Files +# if set to false aromatic bonds are stored, so this structure can be used +# as QUERY structure. That's only an export feature, internally you can have +# both types by using the kekule bonds or the 'normal/aromatic' bonds. +joelib2.io.types.MDLSD.writeAromaticityAsKekuleSystem=true + +#SMILES +joelib2.smiles.SMILESGenerator.assignCisTransInformations=true +joelib2.smiles.SMILESGenerator.assignChiralityInformations=true +joelib2.io.types.Smiles.canonical=false +joelib2.io.types.Smiles.lineStructure=SMILES|TITLE +joelib2.io.types.Smiles.lineStructure.delimiter=| +joelib2.io.types.Smiles.lineStructure.input.delimiter=\u0020\t\n\r +joelib2.io.types.Smiles.lineStructure.output.delimiter=\u0020 + +# MolconnZ +joelib2.io.types.MolconnZ.parserDefinition=joelib2/data/plain/molconnz350.txt + +# Flat +joelib2.io.types.Flat.lineStructure.input.delimiter=\u0020\t\n\r +joelib2.io.types.Flat.lineStructure.output.delimiter=\t +joelib2.io.types.Flat.lineStructure.delimiter=\u0020\t +joelib2.io.types.Flat.lineStructure=TITLE + +########### +# CML +# version: 1.0 and 2.0 +# ouput: attributearray, array, large, huge +# delimiter: if you comment this line, standard white space will be used +# force.formalCharge: formal charges will be always written, even when they are zero +# partialCharge: write partial atom charge +# hydrogen=joelib2.feature.types.count: write number of implicite+explicite hydrogens +########### +## use slower memory saving preparser for avoiding to load the complete data set into memory +## This flag will be automatically switched 'ON' for CML files in compressed ZIP files ! +## The basic convert does not need it, because it uses already another sequential +## SAX reader (forced by a callback) +joelib2.io.types.ChemicalMarkupLanguage.useSlowerMemorySavingPreparser=false +########### +joelib2.io.types.ChemicalMarkupLanguage.output.defaultVersion=2.0 +joelib2.io.types.ChemicalMarkupLanguage.defaultDelimiter=\u0020 +#joelib2.io.types.ChemicalMarkupLanguage.defaultDelimiter=| +joelib2.io.types.ChemicalMarkupLanguage.output=huge +joelib2.io.types.ChemicalMarkupLanguage.output.force.formalCharge=false +joelib2.io.types.ChemicalMarkupLanguage.output.partialCharge=true +joelib2.io.types.ChemicalMarkupLanguage.output.hydrogenCount=true +joelib2.io.types.ChemicalMarkupLanguage.output.useNamespace=true +joelib2.io.types.ChemicalMarkupLanguage.output.namespace=cml +joelib2.io.types.ChemicalMarkupLanguage.output.xmlDeclaration=http://www.xml-cml.org/schema/cml2/core +joelib2.io.types.ChemicalMarkupLanguage.DTD.resourceDir=joelib2/io/types/cml/data/ +########### +## a first step to 'reproducable' descriptor calculation algorithms +joelib2.io.types.ChemicalMarkupLanguage.output.storeChemistryKernelInfo=true +## these informations are not really a CML standard +########### +joelib2.io.types.ChemicalMarkupLanguage.output.symmetryInformations=false +########### + +# PovRay +# ouput type can be: stick, sphere, ball_and_stick +joelib2.io.types.POVRay.output=ball_and_stick +joelib2.io.types.POVRay.atomPropertyColoring=false +joelib2.io.types.POVRay.atomProperty=Gasteiger_Marsili + +# Image writer +joelib2.gui.render2D.Mol2Image.defaultWidth=500 +joelib2.gui.render2D.Mol2Image.defaultHeight=400 + +# PDF writer +joelib2.io.types.PDF.fontSize=10 +joelib2.io.types.PDF.fontOffset=2 +joelib2.io.types.PDF.pageBorder=20 + +joelib2.temporary.directory.windows=C:\\temp +joelib2.temporary.directory.linux=/tmp + +joelib2.process.types.DescBinning.descriptors2ignore=joelib2/data/plain/desc2ignore.txt +joelib2.process.types.DescStatistic.descriptors2ignore=joelib2/data/plain/desc2ignore.txt +joelib2.process.types.DescVarianceNorm.descriptors2ignore=joelib2/data/plain/desc2ignore.txt +joelib2.feature.data.MolDesc=joelib2.feature.types.counter.descriptors2ignore=joelib2/data/plain/desc2ignore.txt +joelib2.feature.data.MoleculesDescriptorMatrix.descriptors2ignore=joelib2/data/plain/desc2ignore.txt + +joelib2.feature.data.MoleculesDescriptorMatrix.normalizeOnLoad=true +#joelib2.feature.data.MoleculesDescriptorMatrix.normalizeStatFile=../../datasets/test.sdf + +############################################################################## +# number output (!!!) format +# import not implemented for locale!=en and/or groupingUsed!=false +############################################################################## + +# initialize the number ouput format ! +# number of '0' means the minimum number of digits to use +# number of '#' means the maximum number of digits to use +# in the property file you must use \# to quote the #'s +# If not used all digits will be used. +# deviant to the Java standard the exponential terms with E0 are removed. + +#wsi.ra.text.DecimalFormatHelper.double.format=0.\#\#\#\#\#E0 + +# the both following parameters should be used carefully, because +# the import is not implemented correctly !!! +# e.g.: en, de + +#wsi.ra.text.DecimalFormatHelper.double.locale=en +#wsi.ra.text.DecimalFormatHelper.double.groupingUsed=false + +############################################################################## +# external processes +############################################################################## +joelib2.external.1.name =Title2Data +joelib2.external.1.representation =joelib2.ext.Title2Data +joelib2.external.1.descriptionFile =docs/ext/title2Data +joelib2.external.1.linux =../lib/linux/title2data +joelib2.external.1.windows =..\lib\windows\title2data.exe +joelib2.external.1.argument.1 =MOL_TITLE + +############################################################################## +# Features and feature properties +############################################################################## +joelib2.feature.addIfNotExist=true +############################################## +joelib2.feature.0.representation =joelib2.ring.RingFinderSSSR +joelib2.feature.1.representation =joelib2.algo.BFS +joelib2.feature.2.representation =joelib2.algo.DFS +joelib2.feature.3.representation =joelib2.algo.APropertyBFS +joelib2.feature.4.representation =joelib2.feature.types.atomlabel.AtomBondOrderSum +joelib2.feature.5.representation =joelib2.feature.types.atomlabel.AtomElectronAffinity +joelib2.feature.6.representation =joelib2.feature.types.atomlabel.AtomENAllredRochow +joelib2.feature.7.representation =joelib2.feature.types.atomlabel.AtomENPauling +joelib2.feature.8.representation =joelib2.feature.types.atomlabel.AtomENSanderson +joelib2.feature.9.representation =joelib2.feature.types.atomlabel.AtomExplicitHydrogenCount +joelib2.feature.10.representation =joelib2.feature.types.atomlabel.AtomFreeElectronsCount +joelib2.feature.11.representation =joelib2.feature.types.atomlabel.AtomFreeOxygenCount +joelib2.feature.12.representation =joelib2.feature.types.atomlabel.AtomHeavyValence +joelib2.feature.13.representation =joelib2.feature.types.atomlabel.AtomHeteroValence +joelib2.feature.14.representation =joelib2.feature.types.atomlabel.AtomHybridisation +joelib2.feature.15.representation =joelib2.feature.types.atomlabel.AtomImplicitHydrogenCount +joelib2.feature.16.representation =joelib2.feature.types.atomlabel.AtomImplicitValence +joelib2.feature.17.representation =joelib2.feature.types.atomlabel.AtomInAcceptor +joelib2.feature.18.representation =joelib2.feature.types.atomlabel.AtomInAromaticSystem +joelib2.feature.19.representation =joelib2.feature.types.atomlabel.AtomInConjEnvironment +joelib2.feature.20.representation =joelib2.feature.types.atomlabel.AtomInDonAcc +joelib2.feature.21.representation =joelib2.feature.types.atomlabel.AtomInDonor +joelib2.feature.22.representation =joelib2.feature.types.atomlabel.AtomInRing +joelib2.feature.23.representation =joelib2.feature.types.atomlabel.AtomInRingsCount +joelib2.feature.24.representation =joelib2.feature.types.atomlabel.AtomInTerminalCarbon +joelib2.feature.25.representation =joelib2.feature.types.atomlabel.AtomIsAlphaBetaUnsaturated +joelib2.feature.26.representation =joelib2.feature.types.atomlabel.AtomIsAmideNitrogen +joelib2.feature.27.representation =joelib2.feature.types.atomlabel.AtomIsAntiClockwise +joelib2.feature.28.representation =joelib2.feature.types.atomlabel.AtomIsAromaticNOxide +joelib2.feature.29.representation =joelib2.feature.types.atomlabel.AtomIsAxial +joelib2.feature.30.representation =joelib2.feature.types.atomlabel.AtomIsCarbon +joelib2.feature.31.representation =joelib2.feature.types.atomlabel.AtomIsCarboxylOxygen +joelib2.feature.32.representation =joelib2.feature.types.atomlabel.AtomIsChiral +joelib2.feature.33.representation =joelib2.feature.types.atomlabel.AtomIsClockwise +joelib2.feature.34.representation =joelib2.feature.types.atomlabel.AtomIsElectronegative +joelib2.feature.35.representation =joelib2.feature.types.atomlabel.AtomIsHalogen +joelib2.feature.36.representation =joelib2.feature.types.atomlabel.AtomIsHeteroatom +joelib2.feature.37.representation =joelib2.feature.types.atomlabel.AtomIsHydrogen +joelib2.feature.38.representation =joelib2.feature.types.atomlabel.AtomIsNegative +joelib2.feature.39.representation =joelib2.feature.types.atomlabel.AtomIsNitrogen +joelib2.feature.40.representation =joelib2.feature.types.atomlabel.AtomIsNitroOxygen +joelib2.feature.41.representation =joelib2.feature.types.atomlabel.AtomIsNonPolarHydrogen +joelib2.feature.42.representation =joelib2.feature.types.atomlabel.AtomIsOxygen +joelib2.feature.43.representation =joelib2.feature.types.atomlabel.AtomIsPhosphateOxygen +joelib2.feature.44.representation =joelib2.feature.types.atomlabel.AtomIsPhosphorus +joelib2.feature.45.representation =joelib2.feature.types.atomlabel.AtomIsPolarHydrogen +joelib2.feature.46.representation =joelib2.feature.types.atomlabel.AtomIsPositive +joelib2.feature.47.representation =joelib2.feature.types.atomlabel.AtomIsSulfateOxygen +joelib2.feature.48.representation =joelib2.feature.types.atomlabel.AtomIsSulfur +joelib2.feature.49.representation =joelib2.feature.types.atomlabel.AtomIsUnsaturated +joelib2.feature.50.representation =joelib2.feature.types.atomlabel.AtomKekuleBondOrderSum +joelib2.feature.51.representation =joelib2.feature.types.atomlabel.AtomMass +joelib2.feature.52.representation =joelib2.feature.types.atomlabel.AtomPartialCharge +joelib2.feature.53.representation =joelib2.feature.types.atomlabel.AtomType +joelib2.feature.54.representation =joelib2.feature.types.atomlabel.AtomValence +joelib2.feature.55.representation =joelib2.feature.types.atomlabel.AtomValenceSum +joelib2.feature.56.representation =joelib2.feature.types.atomlabel.AtomVanDerWaalsVolume +joelib2.feature.57.representation =joelib2.feature.types.atompair.TopologicalAtomPair +joelib2.feature.58.representation =joelib2.feature.types.bondlabel.BondInAromaticSystem +joelib2.feature.59.representation =joelib2.feature.types.bondlabel.BondInRing +joelib2.feature.60.representation =joelib2.feature.types.bondlabel.BondIsAmide +joelib2.feature.61.representation =joelib2.feature.types.bondlabel.BondIsCarbonyl +joelib2.feature.62.representation =joelib2.feature.types.bondlabel.BondIsClosure +joelib2.feature.63.representation =joelib2.feature.types.bondlabel.BondIsEster +joelib2.feature.64.representation =joelib2.feature.types.bondlabel.BondIsPrimaryAmide +joelib2.feature.65.representation =joelib2.feature.types.bondlabel.BondIsRotor +joelib2.feature.66.representation =joelib2.feature.types.bondlabel.BondKekuleType +joelib2.feature.67.representation =joelib2.feature.types.count.AcidicGroups +joelib2.feature.68.representation =joelib2.feature.types.count.AliphaticOHGroups +joelib2.feature.69.representation =joelib2.feature.types.count.AromaticBonds +joelib2.feature.70.representation =joelib2.feature.types.count.AromaticOHGroups +joelib2.feature.71.representation =joelib2.feature.types.count.BasicGroups +joelib2.feature.72.representation =joelib2.feature.types.count.HBA1 +joelib2.feature.73.representation =joelib2.feature.types.count.HBA2 +joelib2.feature.74.representation =joelib2.feature.types.count.HBD1 +joelib2.feature.75.representation =joelib2.feature.types.count.HBD2 +joelib2.feature.76.representation =joelib2.feature.types.count.HeavyBonds +joelib2.feature.77.representation =joelib2.feature.types.count.HeteroCycles +joelib2.feature.78.representation =joelib2.feature.types.count.HydrophobicGroups +joelib2.feature.79.representation =joelib2.feature.types.count.NO2Groups +joelib2.feature.80.representation =joelib2.feature.types.count.NumberOfAtoms +joelib2.feature.81.representation =joelib2.feature.types.count.NumberOfB +joelib2.feature.82.representation =joelib2.feature.types.count.NumberOfBonds +joelib2.feature.83.representation =joelib2.feature.types.count.NumberOfBr +joelib2.feature.84.representation =joelib2.feature.types.count.NumberOfC +joelib2.feature.85.representation =joelib2.feature.types.count.NumberOfCl +joelib2.feature.86.representation =joelib2.feature.types.count.NumberOfF +joelib2.feature.87.representation =joelib2.feature.types.count.NumberOfHal +joelib2.feature.88.representation =joelib2.feature.types.count.NumberOfI +joelib2.feature.89.representation =joelib2.feature.types.count.NumberOfN +joelib2.feature.90.representation =joelib2.feature.types.count.NumberOfO +joelib2.feature.91.representation =joelib2.feature.types.count.NumberOfP +joelib2.feature.92.representation =joelib2.feature.types.count.NumberOfS +joelib2.feature.93.representation =joelib2.feature.types.count.OSOGroups +joelib2.feature.94.representation =joelib2.feature.types.count.SO2Groups +joelib2.feature.95.representation =joelib2.feature.types.count.SOGroups +joelib2.feature.96.representation =joelib2.feature.types.APropertyDistanceMatrix +joelib2.feature.97.representation =joelib2.feature.types.Autocorrelation +joelib2.feature.98.representation =joelib2.feature.types.BCUT +joelib2.feature.99.representation =joelib2.feature.types.BurdenEigenvalues +joelib2.feature.100.representation =joelib2.feature.types.BurdenModifiedEigenvalues +joelib2.feature.101.representation =joelib2.feature.types.ConjElectroTopolState +joelib2.feature.102.representation =joelib2.feature.types.ConjugatedTopologicalDistance +joelib2.feature.103.representation =joelib2.feature.types.DistanceDistanceMatrix +joelib2.feature.104.representation =joelib2.feature.types.DistanceMatrix +joelib2.feature.105.representation =joelib2.feature.types.ElectrogeometricalState +joelib2.feature.106.representation =joelib2.feature.types.ElectrotopologicalState +joelib2.feature.107.representation =joelib2.feature.types.FractionRotatableBonds +joelib2.feature.108.representation =joelib2.feature.types.GeomDistanceMatrix +joelib2.feature.109.representation =joelib2.feature.types.GeometricalDiameter +joelib2.feature.110.representation =joelib2.feature.types.GeometricalRadius +joelib2.feature.111.representation =joelib2.feature.types.GeometricalShapeCoefficient +joelib2.feature.112.representation =joelib2.feature.types.GlobalTopologicalChargeIndex +joelib2.feature.113.representation =joelib2.feature.types.GraphPotentials +joelib2.feature.114.representation =joelib2.feature.types.GraphShapeCoefficient +joelib2.feature.115.representation =joelib2.feature.types.IntrinsicState +joelib2.feature.116.representation =joelib2.feature.types.KierShape1 +joelib2.feature.117.representation =joelib2.feature.types.KierShape2 +joelib2.feature.118.representation =joelib2.feature.types.KierShape3 +joelib2.feature.119.representation =joelib2.feature.types.LogP +joelib2.feature.120.representation =joelib2.feature.types.MolarRefractivity +joelib2.feature.121.representation =joelib2.feature.types.MolecularWeight +joelib2.feature.122.representation =joelib2.feature.types.PolarSurfaceArea +j############################################## +joelib2.feature.123.representation =joelib2.feature.types.RadialDistributionFunction +joelib2.feature.types.RadialDistributionFunction.minSphericalVolume = 0.2 +joelib2.feature.types.RadialDistributionFunction.maxSphericalVolume = 10.0 +joelib2.feature.types.RadialDistributionFunction.sphericalVolumeResolution = 0.05 +joelib2.feature.types.RadialDistributionFunction.smoothingFactor = 25 +############################################## +joelib2.feature.124.representation =joelib2.feature.types.RotatableBonds +joelib2.feature.125.representation =joelib2.feature.types.SMILESMolecule +joelib2.feature.126.representation =joelib2.feature.types.SSKey3DS +joelib2.feature.127.representation =joelib2.feature.types.TopologicalDiameter +joelib2.feature.128.representation =joelib2.feature.types.TopologicalRadius +joelib2.feature.129.representation =joelib2.feature.types.WeightedBurdenEigenvalues +joelib2.feature.130.representation =joelib2.feature.types.WeightedBurdenModifiedEigenvalues +joelib2.feature.131.representation =joelib2.feature.types.ZagrebIndex1 +joelib2.feature.132.representation =joelib2.feature.types.MoleculeHashcode +joelib2.feature.133.representation =joelib2.feature.types.CharacteristicPolynomialCoefficients +joelib2.feature.134.representation =joelib2.feature.types.CharacteristicPolynomial +#joelib2.feature.135.representation =joelib2.feature.types.cfm.CompressedFeatureMatrix +#joelib2.feature.136.representation = +#joelib2.feature.137.representation = +#joelib2.feature.138.representation = +#joelib2.feature.139.representation = +#joelib2.feature.140.representation = +#joelib2.feature.141.representation = + +############################################################################## +# End of JOELib2 properties definitions +############################################################################## + +############################################################################## +# Start of JTextTools definitions +############################################################################## +jtt.docbook.DocBookEquations.latex=/usr/bin/latex +jtt.docbook.DocBookEquations.dvips=/usr/bin/dvips +jtt.docbook.DocBookEquations.convert=/usr/bin/convert +#jtt.docbook.DocBookEquations.latex=C:/Programme/latex/texmf/miktex/bin/latex.exe +#jtt.docbook.DocBookEquations.dvips=C:/Programme/latex/texmf/miktex/bin/dvips.exe +#jtt.docbook.DocBookEquations.convert=C:/Programme/ImageMagick/convert.exe +jtt.docbook.DocBookEquations.fontSize=12 +jtt.docbook.DocBookEquations.bold=true +jtt.docbook.DocBookEquations.large=true +jtt.docbook.DocBookEquations.fileExtension=sgml + +jtt.docbook.DocBookMolecules.fileExtension=sgml + +jtt.docbook.Jade.jade=/usr/bin/jade +#jtt.docbook.Jade.jade=C:/cygwin/usr/share/sgml/docbook/jade121/jade +jtt.docbook.Jade.DSSSL.rtf=/usr/share/sgml/docbook/dsssl-stylesheets-1.77/print/docbook.dsl +jtt.docbook.Jade.DSSSL.html=/usr/share/sgml/docbook/dsssl-stylesheets-1.77/html/docbook.dsl +jtt.docbook.Jade.SGML.catalg.files=/usr/share/sgml/docbook_4.2/docbook.cat:/usr/share/sgml/jade_dsl/catalog +jtt.docbook.Jade.index=true + +jtt.docbook.DocBookArticles.version=XML V4.2 +jtt.docbook.DocBookArticles.fileExtension=sgml +jtt.docbook.DocBookArticles.DTD=/usr/share/sgml/docbook_4.2/docbook.dtd +############################################################################## +# End of JTextTools definitions +############################################################################## -- cgit v1.2.3