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/data/plain/knownResults.txt | 775 +++++++++++++++++++++++++++++++ 1 file changed, 775 insertions(+) create mode 100644 java/joelib2/data/plain/knownResults.txt (limited to 'java/joelib2/data/plain/knownResults.txt') diff --git a/java/joelib2/data/plain/knownResults.txt b/java/joelib2/data/plain/knownResults.txt new file mode 100644 index 0000000..33805fc --- /dev/null +++ b/java/joelib2/data/plain/knownResults.txt @@ -0,0 +1,775 @@ +VENDOR: http://joelib.sf.net +RELEASE_VERSION: $Revision: 1.5 $ +RELEASE_DATE: $Date: 2006/02/22 02:18:22 $ + +######################################################################### +# Here are the results stored which are known in JOELib. +# +# With the joelib2.feature.ResultFactory you can have a look at known +# results and the class which can parse this result type. +# +######################################################################### +# 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. +######################################################################## + +################################################################################# +$JOELIB_RESULT$ joelib2.feature.result.AtomDynamicResult +A_AROMATIC +A_CHARGECENTER +A_ENLP +A_ENPI +A_ENSIG +A_FORMCHARGE +A_FREEEL +A_HASH +A_HGROUP +A_ISMETAL +A_IUPAC_GROUP +A_LPSTAB +A_NEIGHBOR +A_NEL +A_NONHNEIGHBOR +A_PERIPH +A_PICENTER +A_PISYS +A_POLARIZABILITY +A_QPI +A_QSIG +A_QTOT +A_RADICCENTER +A_RINGSIZE +################################################################################# +#$JOELIB_RESULT$ joelib2.feature.result.BondDynamicResult +# +# now me must use the ASYM_BOND_PROPERTY_INDEX property +# to access this descriptor data correctly +# It's necessary to define a +# joelib2.feature.result.AsymBondDynamicResult class !!! +# the BondDynamicResult is DEPRECATED !!! +# +#B_BDE +#B_BOORD +#B_DENPI +#B_DENSIG +#B_DQPI +#B_DQSIG +#B_DQTOT +#B_NDELOC +#B_NSTAB +#B_PDELOC +#B_POLARIZABILITY +#B_PSTAB +#B_RINGSIZE +#B_SDELOC +#B_SQIT +#B_STABRS +#B_TBDE +################################################################################# +## When normalizing the data, the integers will be stored as double values AND +## can be also loaded as double values !!! +## +$JOELIB_RESULT$ joelib2.feature.result.IntResult +## +$REGEXP$ SMARTS_c_.* +Entry_Number +TRUE_CLASS +#activity_class +# +# PETRA descriptors +# +E_CHARGE +E_DELTAHF +E_HASH +E_POLARIZABILITY +E_RADICAL +E_STABIL +E_STRAIN +M_CHARGE +M_DELTAHF +M_HASH +M_HGROUP +M_NAME +M_POLARIZABILITY +M_RADICAL +M_STABIL +M_STRAIN +# +# Molconn Z 350 +# +id +nvx +nrings +ncirc +nelem +#aname +$REGEXP$ nas\p{Upper}\p{Lower}* +$REGEXP$ nd\d +$REGEXP$ ne\d+ +tg +tg3 +tm +tm3 +$REGEXP$ n\dpe\d+ +$REGEXP$ ec\d+ +$REGEXP$ NHBint\d+ +$REGEXP$ count\d +# +# MOE descriptors +# +a_acc +a_acid +a_base +a_don +a_hyd +a_aro +a_count +a_nH +a_heavy +a_nB +a_nBr +a_nC +a_nCl +a_nF +a_nI +a_nN +a_nO +a_nP +a_nS +b_heavy +b_1rotN +b_ar +b_count +b_double +b_rotN +b_single +b_triple +################################################################################# +$JOELIB_RESULT$ joelib2.feature.result.APropDoubleArrResult +Auto_correlation +$REGEXP$ .*Burden_modified_eigenvalues:[^:]+ +$REGEXP$ .*Auto_correlation:[^:]+ +$REGEXP$ .*RDF:[^:]+ +$REGEXP$ .*BurdenModifiedEigenvalues:[^:]+ +$REGEXP$ .*Autocorrelation:[^:]+ +$REGEXP$ .*RadialDistributionFunction:[^:]+ +################################################################################# +$JOELIB_RESULT$ joelib2.feature.result.APropDoubleResult +$REGEXP$ NONE:s\d+:.*:F\d+:\d+ +$REGEXP$ APkPCA:s\d+:.*:F\d+:\d+ +$REGEXP$ APskPCA:s\d+:.*:F\d+:\d+ +$REGEXP$ APPCA:s\d+:.*:F\d+:\d+ +$REGEXP$ :*Global_topological_charge_index:.+ +#$REGEXP$ .*Burden_modified_eigenvalues:.+:\d+ +################################################################################# +$JOELIB_RESULT$ joelib2.feature.result.DoubleResult +## +TRUE +### +LOGBB +IC50 +activity_class +hia_measured +logS_expected +residue_huuskonen +XlogP +Number_of_HBA_2 +predicted_logP +pIC50 +Moriguchi_logP +Rekker_logP +Hansch_Leo_logP +Suzuki_Kudo_logP +####Achim's sensors +$REGEXP$ S1_W\d+.* +$REGEXP$ S2_W\d+.* +$REGEXP$ S3_W\d+.* +$REGEXP$ S1_STD\d+.* +$REGEXP$ S2_STD\d+.* +$REGEXP$ S3_STD\d+.* +#melting_point:::contains also 'liq' entries ! +#melting_point +# pca, kpca extracted eigenvalue projection and inner product features +$REGEXP$ feature\d+ +# +# Molconn Z 350 +# +$REGEXP$ SHBint\d+ +Qv +SHCsats +SHCsatu +SHvin +SHtvin +SHavin +SHarom +SHHBD +SHWHBD +SHHBA +petitjeanSC +fw +x0 +x1 +x2 +xp3 +xp4 +xp5 +xp6 +xp7 +xp8 +xp9 +xp10 +xv0 +xv1 +xv2 +xvp3 +xvp4 +xvp5 +xvp6 +xvp7 +xvp8 +xvp9 +xvp10 +xc3 +xc4 +xpc4 +xch3 +xch4 +xch5 +xch6 +xch7 +xch8 +xch9 +xch10 +xvc3 +xvc4 +xvpc4 +xvch3 +xvch4 +xvch5 +xvch6 +xvch7 +xvch8 +xvch9 +xvch10 +dx0 +dx1 +dx2 +dxp3 +dxp4 +dxp5 +dxp6 +dxp7 +dxp8 +dxp9 +dxp10 +dxv0 +dxv1 +dxv2 +dxvp3 +dxvp4 +dxvp5 +dxvp6 +dxvp7 +dxvp8 +dxvp9 +dxvp10 +k0 +k1 +k2 +k3 +ka1 +ka2 +ka3 +si +totop +sumI +sumDELI +tets2 +phia +$REGEXP$ s\d+ +SHsOH +SHdNH +SHsSH +SHsNH2 +SHssNH +SHtCH +SHother +SHCHnX +Hmax +Gmax +Hmin +Gmin +Hmaxpos +Hminneg +SsLi +SssBe +SssssBem +SssBH +SsssB +SssssBm +SsCH3 +SdCH2 +SssCH2 +StCH +SdsCH +SaaCH +SsssCH +SddC +StsC +SdssC +SaasC +SaaaC +SssssC +SsNH3p +SsNH2 +SssNH2p +SdNH +SssNH +SaaNH +StN +SsssNHp +SdsN +SaaN +SsssN +SddsN +SaasN +SssssNp +SsOH +SdO +SssO +SaaO +SsF +SsSiH3 +SssSiH2 +SsssSiH +SssssSi +SsPH2 +SssPH +SsssP +SdsssP +SsssssP +SsSH +SdS +SssS +SaaS +SdssS +SddssS +SssssssS +SsCl +SsGeH3 +SssGeH2 +SsssGeH +SssssGe +SsAsH2 +SssAsH +SsssAs +SdsssAs +SsssssAs +SsSeH +SdSe +SssSe +SaaSe +SdssSe +SddssSe +SsBr +SsSnH3 +SssSnH2 +SsssSnH +SssssSn +SsI +SsPbH3 +SssPbH2 +SsssPbH +SssssPb +CHsOH +CHdNH +CHsSH +CHsNH2 +CHssNH +CHtCH +CHother +CHCHnX +CHmax +CGmax +CHmin +CGmin +CHmaxpos +CHminneg +CsLi +CssBe +CssssBe +CssBH +CsssB +CssssB +CsCH3 +CdCH2 +CssCH2 +CtCH +CdsCH +CaaCH +CsssCH +CddC +CtsC +CdssC +CaasC +CaaaC +CssssC +CsNH3 +CsNH2 +CssNH2 +CdNH +CssNH +CaaNH +CtN +CsssNH +CdsN +CaaN +CsssN +CddsN +CaasN +CssssNp +CsOH +CdO +CssO +CaaO +CsF +CsSiH3 +CssSiH2 +CsssSiH +CssssSi +CsPH2 +CssPH +CsssP +CdsssP +CsssssP +CsSH +CdS +CssS +CaaS +CdssS +CddssS +CssssssS +CsCl +CsGeH3 +CssGeH2 +CsssGeH +CssssGe +CsAsH2 +CssAsH +CsssAs +CdsssAs +CsssssAs +CsSeH +CdSe +CssSe +CaaSe +CdssSe +CddssSe +CsBr +CsSnH3 +CssSnH2 +CsssSnH +CssssSn +CsI +CsPbH3 +CssPbH2 +CsssPbH +CssssPb +$REGEXP$ Hs\d+ +idw +idwbar +idc +idcbar +W +Wp +pf +Wt +knotp +knotpv +nclass +numHBd +numwHBd +numHBa +$REGEXP$ nxp\d+ +nxc3 +nxc4 +nxpc4 +$REGEXP$ nxch\d+ +ntpath +diam +muldiam +rad +mulrad +ishape +# +# MOE descriptors +# +a_IC +a_ICM +b_rotR +b_1rotR +diameter +petitjean +radius +VDistEq +VDistMa +weinerPath +weinerPol +chi0v +chi0v_C +chi1v +chi1v_C +reactive +Weight +chi0 +chi0_C +chi1 +chi1_C +FCharge +VAdjEq +VAdjMa +zagreb +balabanJ +PEOE_PC+ +PEOE_PC- +PEOE_RPC+ +PEOE_RPC- +$REGEXP$ PEOE_VSA[-+]\d +PEOE_VSA_FHYD +PEOE_VSA_FNEG +PEOE_VSA_FPNEG +PEOE_VSA_FPOL +PEOE_VSA_FPOS +PEOE_VSA_FPPOS +PEOE_VSA_HYD +PEOE_VSA_NEG +PEOE_VSA_PNEG +PEOE_VSA_POL +PEOE_VSA_POS +PEOE_VSA_PPOS +PC+ +PC- +Q_PC+ +Q_PC- +Q_RPC+ +Q_RPC- +Q_VSA_FHYD +Q_VSA_FNEG +Q_VSA_FPNEG +Q_VSA_FPOL +Q_VSA_FPOS +Q_VSA_FPPOS +Q_VSA_HYD +Q_VSA_NEG +Q_VSA_PNEG +Q_VSA_POL +Q_VSA_POS +Q_VSA_PPOS +RPC+ +RPC- +E +E_ang +E_ele +E_nb +E_oop +E_sol +E_stb +E_str +E_strain +E_tor +E_vdw +E_rele +E_rnb +E_rsol +E_rvdw +Kier1 +Kier2 +Kier3 +KierA1 +KierA2 +KierA3 +KierFlex +apol +bpol +mr +dipole +dipoleX +dipoleY +dipoleZ +pmi +pmiX +pmiY +pmiZ +rgyr +vsa_acc +vsa_acid +vsa_base +vsa_don +vsa_hyd +vsa_other +vsa_pol +SlogP +$REGEXP$ SlogP_VSA\d+ +SMR +$REGEXP$ SMR_VSA\d+ +ASA +ASA+ +ASA- +ASA_H +ASA_P +CASA+ +CASA- +DASA +DCASA +FASA+ +FASA- +FASA_H +FASA_P +FCASA+ +FCASA- +VSA +TPSA +density +vdw_area +vdw_vol +dens +glob +std_dim1 +std_dim2 +std_dim3 +vol +logP(o/w) +# +# Human Intestinal Absorption (HIA) +# +connolly_surface_polar +connolly_surf_hydrophob +rotatable_bonds +hydrogen_donors +eccentricity +std_dim1 +hia_measured +molecular_weight +connolly_surf_pol_percent +logP +hydrogen_acceptors +dipol +# +# JOELib resolved atom property transformation descriptors +# +$REGEXP$ Global_topological_charge_index_\d+ +$REGEXP$ .*Auto_correlation:.+:\d+ +$REGEXP$ .*Atom_mass:\d+ +$REGEXP$ [^:]+Atom_valence:\d+ +$REGEXP$ .*Atom_valence:\d+ +$REGEXP$ .*Atom_van_der_waals_volume:\d+ +$REGEXP$ .*Atom_in_conjugated_environment:\d+ +$REGEXP$ .*Burden_modified_eigenvalues:.+:\d+ +$REGEXP$ .*Conjugated_electrotopological_state_index:\d+ +$REGEXP$ .*Conjugated_topological_distance:\d+ +$REGEXP$ .*Electronegativity_pauling:\d+ +$REGEXP$ .*Electrotopological_state_index:\d+ +$REGEXP$ .*Electrogeometrical_state_index:\d+ +$REGEXP$ .*Electron_affinity:\d+ +$REGEXP$ .*Gasteiger_Marsili:\d+ +$REGEXP$ .*Graph_potentials:\d+ +$REGEXP$ .*Intrinsic_state:\d+ +$REGEXP$ .*Atom_is_negative:\d+ +$REGEXP$ .*Atom_in_acceptor:\d+ +$REGEXP$ .*Atom_in_donor_or_acceptor:\d+ +$REGEXP$ .*Atom_in_donor:\d+ +$REGEXP$ .*Atom_in_ring:\d+ +$REGEXP$ .*Atom_is_positive:\d+ +$REGEXP$ .*Atom_in_terminal_carbon:\d+ +$REGEXP$ .*AtomENAllredRochow:\d+ +$REGEXP$ .*AtomENPauling:\d+ +$REGEXP$ .*AtomElectronAffinity:\d+ +$REGEXP$ .*AtomExplicitHydrogenCount:\d+ +$REGEXP$ .*AtomFreeElectronsCount:\d+ +$REGEXP$ .*AtomFreeOxygenCount:\d+ +$REGEXP$ .*AtomHeavyValence:\d+ +$REGEXP$ .*AtomHeteroValence:\d+ +$REGEXP$ .*AtomImplicitHydrogenCount:\d+ +$REGEXP$ .*AtomImplicitValence:\d+ +$REGEXP$ .*AtomInAcceptor:\d+ +$REGEXP$ .*AtomInAromaticSystem:\d+ +$REGEXP$ .*AtomInConjEnvironment:\d+ +$REGEXP$ .*AtomInDonor:\d+ +$REGEXP$ .*AtomInTerminalCarbon:\d+ +$REGEXP$ .*AtomIsAmideNitrogen:\d+ +$REGEXP$ .*AtomIsAmideNitrogen:\d+ +$REGEXP$ .*AtomIsAromaticNOxide:\d+ +$REGEXP$ .*AtomIsAxial:\d+ +$REGEXP$ .*AtomIsCarbon:\d+ +$REGEXP$ .*AtomIsCarboxylOxygen:\d+ +$REGEXP$ .*AtomIsChiral:\d+ +$REGEXP$ .*AtomIsClockwise:\d+ +$REGEXP$ .*AtomIsClockwise:\d+ +$REGEXP$ .*AtomIsElectronegative:\d+ +$REGEXP$ .*AtomIsHalogen:\d+ +$REGEXP$ .*AtomIsHeteroatom:\d+ +$REGEXP$ .*AtomIsNegative:\d+ +$REGEXP$ .*AtomIsNitrogen:\d+ +$REGEXP$ .*AtomIsNonPolarHydrogen:\d+ +$REGEXP$ .*AtomIsOxygen:\d+ +$REGEXP$ .*AtomIsPhosphateOxygen:\d+ +$REGEXP$ .*AtomIsPhosphorus:\d+ +$REGEXP$ .*AtomIsPolarHydrogen:\d+ +$REGEXP$ .*AtomIsPositive:\d+ +$REGEXP$ .*AtomIsUnsaturated:\d+ +$REGEXP$ .*AtomIsUnsaturated:\d+ +$REGEXP$ .*AtomKekuleBondOrderSum:\d+ +$REGEXP$ .*AtomMass:\d+ +$REGEXP$ .*AtomVanDerWaalsVolume:\d+ +$REGEXP$ .*CharacteristicPolynomialCoefficients:\d+ +$REGEXP$ .*ConjElectroTopolState:\d+ +$REGEXP$ .*ElectrotopologicalState:\d+ +$REGEXP$ .*GraphPotentials:\d+ +$REGEXP$ .*IntrinsicState:\d+ +$REGEXP$ .*AtomIsAlphaBetaUnsaturated:\d+ +$REGEXP$ .*AtomIsSulfateOxygen:\d+ +$REGEXP$ .*AtomInDonAcc:\d+ +$REGEXP$ .*ConjugatedTopologicalDistance:\d+ +$REGEXP$ .*AtomBondOrderSum:\d+ +$REGEXP$ .*ElectrogeometricalState:\d+ +$REGEXP$ .*AtomIsSulfur:\d+ +$REGEXP$ .*AtomPartialCharge:\d+ +$REGEXP$ .*AtomIsHydrogen:\d+ +$REGEXP$ .*AtomValence:\d+ +$REGEXP$ .*AtomHybridisation:\d+ +$REGEXP$ .*AtomIsNitroOxygen:\d+ +$REGEXP$ .*AtomIsAntiClockwise:\d+ +$REGEXP$ .*AtomInRingsCount:\d+ +$REGEXP$ .*AtomENSanderson:\d+ +$REGEXP$ .*AtomInRing:\d+ +$REGEXP$ .*CharacteristicPolynomial:\d+ +$REGEXP$ .*AtomValenceSum:\d+ +################################################################################# +$JOELIB_RESULT$ joelib2.feature.result.BooleanResult +$REGEXP$ SMARTS_b_.* +$REGEXP$ SMARTS_MACCS_.* +$REGEXP$ SMARTS_SSKey_.* +################################################################################# +# +# MOE special descriptors +# +$JOELIB_RESULT$ joelib2.feature.result.IntBitArrayResult +FP:MACCS +################################################################################# +$JOELIB_RESULT$ joelib2.feature.result.BitArrayResult +dy_fp +################################################################################# +################################################################################# -- cgit v1.2.3