From 3cd136861c68b8c24cc653c903c620d55be4b294 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Mon, 2 Apr 2012 09:18:14 +0200 Subject: Remove PC descriptor --- java/joelib2/data/plain/knownResults.txt | 775 ------------------------------- 1 file changed, 775 deletions(-) delete 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 deleted file mode 100644 index 33805fc..0000000 --- a/java/joelib2/data/plain/knownResults.txt +++ /dev/null @@ -1,775 +0,0 @@ -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