From b47303f0d0f7effc0c410b7ba13c3d7e616e38c7 Mon Sep 17 00:00:00 2001 From: davor Date: Thu, 24 Jan 2013 11:57:57 +0100 Subject: Rm pc_descriptors from installer. Already stored in compound repo. --- install | 2 - pc_descriptors.yaml | 432 ---------------------------------------------------- 2 files changed, 434 deletions(-) delete mode 100644 pc_descriptors.yaml diff --git a/install b/install index 9057b3a..1dea679 100755 --- a/install +++ b/install @@ -71,10 +71,8 @@ if ! grep "rbenv" $OT_UI_CONF >/dev/null 2>&1 ; then echo 'if ! echo "$PATH" | grep "$HOME/.rbenv/bin">/dev/null 2>&1; then export PATH="$HOME/.rbenv/bin:$PATH"; eval "$(rbenv init -)"; fi' >> $OT_UI_CONF fi -[ -f $HOME/.opentox/config/pc_descriptors.yaml ] || (cmd="cp pc_descriptors.yaml $HOME/.opentox/config/" && run_cmd "$cmd" "Pc descriptor file") [ -f $OT_TOOLS_CONF ] || (cmd="cp ot-tools-user.sh $OT_TOOLS_CONF" && run_cmd "$cmd" "ot-tools.sh => $HOME/.opentox") - # Install global ruby version . ./utils.sh install_ruby global diff --git a/pc_descriptors.yaml b/pc_descriptors.yaml deleted file mode 100644 index ba32800..0000000 --- a/pc_descriptors.yaml +++ /dev/null @@ -1,432 +0,0 @@ ---- - -# cdk - -LengthOverBreadthDescriptor: - :pc_type: "geometrical" - :lib: "cdk" - :name: "Length Over Breadth" - -KierHallSmartsDescriptor: - :pc_type: "topological" - :lib: "cdk" - :name: "Kier & Hall SMARTS" - -FragmentComplexityDescriptor: - :pc_type: "topological" - :lib: "cdk" - :name: "Fragment Complexity" - -APolDescriptor: - :pc_type: "electronic" - :lib: "cdk" - :name: "Atomic Polarizabilities" - -LargestChainDescriptor: - :pc_type: "constitutional" - :lib: "cdk" - :name: "Largest Chain" - -ChiPathDescriptor: - :pc_type: "topological" - :lib: "cdk" - :name: "Chi Path Indices" - -PetitjeanNumberDescriptor: - :pc_type: "topological" - :lib: "cdk" - :name: "Petitjean Number" - -LongestAliphaticChainDescriptor: - :pc_type: "constitutional" - :lib: "cdk" - :name: "Longest Aliphatic Chain" - -KappaShapeIndicesDescriptor: - :pc_type: "topological" - :lib: "cdk" - :name: "Kier and Hall kappa molecular shape indices" - -AromaticBondsCountDescriptor: - :pc_type: "constitutional" - :lib: "cdk" - :name: "Aromatic Bonds Count" - -CPSADescriptor: - :pc_type: "cpsa" - :lib: "cdk" - :name: "Charged Partial Surface Areas" - -VAdjMaDescriptor: - :pc_type: "topological" - :lib: "cdk" - :name: "Vertex adjacency information magnitude" - -AutocorrelationDescriptorMass: - :pc_type: "topological" - :lib: "cdk" - :name: "Moreau-Broto Autocorrelation (mass) descriptors" - -RuleOfFiveDescriptor: - :pc_type: "constitutional" - :lib: "cdk" - :name: "Lipinski's Rule of Five" - -GravitationalIndexDescriptor: - :pc_type: "geometrical" - :lib: "cdk" - :name: "Gravitational Index" - -WienerNumbersDescriptor: - :pc_type: "topological" - :lib: "cdk" - :name: "Wiener Numbers" - -ChiPathClusterDescriptor: - :pc_type: "topological" - :lib: "cdk" - :name: "Chi Path-Cluster Indices" - -AtomCountDescriptor: - :pc_type: "constitutional" - :lib: "cdk" - :name: "Atoms Count" - -MomentOfInertiaDescriptor: - :pc_type: "geometrical" - :lib: "cdk" - :name: "Moments of Inertia" - -CarbonTypesDescriptor: - :pc_type: "topological" - :lib: "cdk" - :name: "Carbon Types" - -AutocorrelationDescriptorPolarizability: - :pc_type: "topological" - :lib: "cdk" - :name: "Moreau-Broto Autocorrelation (polarizability) descriptors" - -EccentricConnectivityIndexDescriptor: - :pc_type: "topological" - :lib: "cdk" - :name: "Eccentric Connectivity Index" - -BCUTDescriptor: - :pc_type: "hybrid" - :lib: "cdk" - :name: "BCUT" - -AromaticAtomsCountDescriptor: - :pc_type: "constitutional" - :lib: "cdk" - :name: "Aromatic Atoms Count" - -WHIMDescriptor: - :pc_type: "hybrid" - :lib: "cdk" - :name: "WHIM" - -ALOGPDescriptor: - :pc_type: "constitutional" - :lib: "cdk" - :name: "ALogP" - -XLogPDescriptor: - :pc_type: "constitutional" - :lib: "cdk" - :name: "XLogP" - -PetitjeanShapeIndexDescriptor: - :pc_type: "topological" - :lib: "cdk" - :name: "Petitjean Number" - -MDEDescriptor: - :pc_type: "topological" - :lib: "cdk" - :name: "Molecular Distance Edge" - -ChiChainDescriptor: - :pc_type: "topological" - :lib: "cdk" - :name: "Chi Chain Indices" - -BondCountDescriptor: - :pc_type: "constitutional" - :lib: "cdk" - :name: "Bonds Count" - -MannholdLogPDescriptor: - :pc_type: "constitutional" - :lib: "cdk" - :name: "Mannhold LogP" - -BPolDescriptor: - :pc_type: "electronic" - :lib: "cdk" - :name: "Bond Polarizabilities" - -AutocorrelationDescriptorCharge: - :pc_type: "topological" - :lib: "cdk" - :name: "Moreau-Broto Autocorrelation (charge) descriptors" - -ZagrebIndexDescriptor: - :pc_type: "topological" - :lib: "cdk" - :name: "Zagreb Index" - -ChiClusterDescriptor: - :pc_type: "topological" - :lib: "cdk" - :name: "Chi Cluster Indices" - -RotatableBondsCountDescriptor: - :pc_type: "constitutional" - :lib: "cdk" - :name: "Rotatable Bonds Count" - -TPSADescriptor: - :pc_type: "topological" - :lib: "cdk" - :name: "Topological Polar Surface Area" - -HBondDonorCountDescriptor: - :pc_type: "electronic" - :lib: "cdk" - :name: "Hydrogen Bond Donors" - -HBondAcceptorCountDescriptor: - :pc_type: "electronic" - :lib: "cdk" - :name: "Hydrogen Bond Acceptors" - -LargestPiSystemDescriptor: - :pc_type: "constitutional" - :lib: "cdk" - :name: "Largest Pi Chain" - - -# joelib - - -HBA2: - :pc_type: "electronic" - :lib: "joelib" - :name: "Hydrogen Bond Acceptors 2" -MolarRefractivity: - :pc_type: "constitutional" - :lib: "joelib" - :name: "Molar Refractivity" -KierShape3: - :pc_type: "topological" - :lib: "joelib" - :name: "Kier Shape 3" -SO2Groups: - :pc_type: "constitutional" - :lib: "joelib" - :name: "SO2 Groups" -MolecularWeight: - :pc_type: "constitutional" - :lib: "joelib" - :name: "Molecular Weight" -LogP: - :pc_type: "constitutional" - :lib: "joelib" - :name: "Log P" -OSOGroups: - :pc_type: "constitutional" - :lib: "joelib" - :name: "OSO Groups" -AromaticOHGroups: - :pc_type: "constitutional" - :lib: "joelib" - :name: "Aromatic OH Groups" -AromaticBonds: - :pc_type: "constitutional" - :lib: "joelib" - :name: "Aromatic Bonds" -AcidicGroups: - :pc_type: "constitutional" - :lib: "joelib" - :name: "Acidic Groups" -GraphShapeCoefficient: - :pc_type: "topological" - :lib: "joelib" - :name: "Graph Shape Coefficient" -GeometricalShapeCoefficient: - :pc_type: "topological" - :lib: "joelib" - :name: "Geometrical Shape Coefficient" -ZagrebIndex1: - :pc_type: "topological" - :lib: "joelib" - :name: "Zagreb Index1" -TopologicalRadius: - :pc_type: "topological" - :lib: "joelib" - :name: "Topological Radius" -GeometricalDiameter: - :pc_type: "geometrical" - :lib: "joelib" - :name: "Geometrical Diameter" -FractionRotatableBonds: - :pc_type: "constitutional" - :lib: "joelib" - :name: "Fraction Rotatable Bonds" -NumberOfAtoms: - :pc_type: "constitutional" - :lib: "joelib" - :name: "Number Of Atoms" -HeteroCycles: - :pc_type: "constitutional" - :lib: "joelib" - :name: "Hetero Cycles" -RotatableBonds: - :pc_type: "constitutional" - :lib: "joelib" - :name: "Rotatable Bonds" -BasicGroups: - :pc_type: "constitutional" - :lib: "joelib" - :name: "Basic Groups" -TopologicalDiameter: - :pc_type: "topological" - :lib: "joelib" - :name: "Topological Diameter" -NumberOfBonds: - :pc_type: "constitutional" - :lib: "joelib" - :name: "Number Of Bonds" -NO2Groups: - :pc_type: "constitutional" - :lib: "joelib" - :name: "NO2 Groups" -HBD1: - :pc_type: "electronic" - :lib: "joelib" - :name: "Hydrogen Bond Donors 1" -AliphaticOHGroups: - :pc_type: "constitutional" - :lib: "joelib" - :name: "Aliphatic OH Groups" -HBD2: - :pc_type: "electronic" - :lib: "joelib" - :name: "Hydrogen Bond Donors 2" -HydrophobicGroups: - :pc_type: "constitutional" - :lib: "joelib" - :name: "Hydrophobic Groups" -HeavyBonds: - :pc_type: "constitutional" - :lib: "joelib" - :name: "Heavy Bonds" -KierShape1: - :pc_type: "topological" - :lib: "joelib" - :name: "Kier Shape1" -NumberOfHal: - :pc_type: "constitutional" - :lib: "joelib" - :name: "Number Of Halogens" -HBA1: - :pc_type: "electronic" - :lib: "joelib" - :name: "Hydrogen Bond Acceptors 1" -PolarSurfaceArea: - :pc_type: "topological" - :lib: "joelib" - :name: "Polar Surface Area" -KierShape2: - :pc_type: "topological" - :lib: "joelib" - :name: "Kier Shape 2" -GeometricalRadius: - :pc_type: "geometrical" - :lib: "joelib" - :name: "Geometrical Radius" - - -# openbabel -NumAtoms: - :pc_type: "constitutional" - :lib: "openbabel" - :name: "Number of atoms" -NumBonds: - :pc_type: "constitutional" - :lib: "openbabel" - :name: "Number of bonds" -NumHvyAtoms: - :pc_type: "constitutional" - :lib: "openbabel" - :name: "Number of heavy atoms" -NumResidues: - :pc_type: "constitutional" - :lib: "openbabel" - :name: "Number of residues" -NumRotors: - :pc_type: "constitutional" - :lib: "openbabel" - :name: "Number of rotatable bonds" -GetEnergy: - :pc_type: "constitutional" - :lib: "openbabel" - :name: "Heat of formation for this molecule (in kcal/mol)" -GetMolWt: - :pc_type: "constitutional" - :lib: "openbabel" - :name: "Standard molar mass given by IUPAC atomic masses (amu)" -GetExactMass: - :pc_type: "constitutional" - :lib: "openbabel" - :name: "Mass given by isotopes (or most abundant isotope if not specified)" -GetTotalCharge: - :pc_type: "topological" - :lib: "openbabel" - :name: "Total charge" -HBA1: - :pc_type: "electronic" - :lib: "openbabel" - :name: "Number of hydrogen bond acceptors 1 (JoelLib)" -HBA2: - :pc_type: "electronic" - :lib: "openbabel" - :name: "Number of hydrogen bond acceptors 2 (JoelLib)" -HBD: - :pc_type: "electronic" - :lib: "openbabel" - :name: "Number of hydrogen bond donors (JoelLib)" -L5: - :pc_type: "constitutional" - :lib: "openbabel" - :name: "Lipinski rule of five" -logP: - :pc_type: "constitutional" - :lib: "openbabel" - :name: "Octanol/water partition coefficient" -MR: - :pc_type: "constitutional" - :lib: "openbabel" - :name: "Molar refractivity" -MW: - :pc_type: "constitutional" - :lib: "openbabel" - :name: "Molecular weight" -nF: - :pc_type: "constitutional" - :lib: "openbabel" - :name: "Number of fluorine atoms" -#nHal: -# :pc_type: "constitutional" -# :lib: "openbabel" -# :name: "Number of halogen atoms" -#spinMult: -# :pc_type: "electronic" -# :lib: "openbabel" -# :name: "Total spin multiplicity" -TPSA: - :pc_type: "topological" - :lib: "openbabel" - :name: "Topological polar surface area" -- cgit v1.2.3