Rm pc_descriptors from installer. Already stored in compound repo.

2 files changed, 0 insertions, 434 deletions

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"