From 1fcb22e875c45fa4a1aba5afa70397bcb4621e06 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Thu, 23 Aug 2012 14:51:34 +0300 Subject: Simplified notification --- utils.sh | 15 ++++----------- 1 file changed, 4 insertions(+), 11 deletions(-) diff --git a/utils.sh b/utils.sh index b4cceab..384f57d 100755 --- a/utils.sh +++ b/utils.sh @@ -120,20 +120,13 @@ notify() { echo if ps -o stat= -p $PPID | grep "s" >/dev/null 2>&1; then echo "IMPORTANT: How to configure your system if everything went fine:" - echo "IMPORTANT: ot-tools are supported for bash shell." - echo "IMPORTANT: a) Include '$OT_TOOLS_CONF' in shell startup (e.g. ~/.bashrc)." - echo "IMPORTANT: b) Manually source '$OT_TOOLS_CONF' every time." - echo "IMPORTANT: The command in both cases: '. $OT_TOOLS_CONF'" - echo "IMPORTANT: If you are using another shell please source '$OT_UI_CONF'" - echo "IMPORTANT: NOW would be the best time to configure!" - echo "Visit 'http://opentox.github.com/General/2012/08/09/install-opentox-development-environment/' for further information (e.g. the usage of ot-tools)." - echo - echo "Thank you for your attention." - echo + echo "IMPORTANT: bash shell only: '. $OT_TOOLS_CONF'" (convenient ot-tools) + echo "IMPORTANT: other shells: '. $OT_UI_CONF' (no ot-tools available)" + echo "IMPORTANT: More information: 'http://opentox.github.com/General/2012/08/09/install-opentox-development-environment'" + echo "IMPORTANT: Thank you for your attention." fi } - # Force loading configuration from local, if we are installing for the first time if [ -z "$OT_PREFIX" ]; then . ./config.sh -- cgit v1.2.3 From 3d94e02bffc42e79269ca20e9460a147e52807d3 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Thu, 23 Aug 2012 14:52:46 +0300 Subject: Syntax error fixed --- utils.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/utils.sh b/utils.sh index 384f57d..bf08681 100755 --- a/utils.sh +++ b/utils.sh @@ -120,7 +120,7 @@ notify() { echo if ps -o stat= -p $PPID | grep "s" >/dev/null 2>&1; then echo "IMPORTANT: How to configure your system if everything went fine:" - echo "IMPORTANT: bash shell only: '. $OT_TOOLS_CONF'" (convenient ot-tools) + echo "IMPORTANT: bash shell only: '. $OT_TOOLS_CONF' (convenient ot-tools)" echo "IMPORTANT: other shells: '. $OT_UI_CONF' (no ot-tools available)" echo "IMPORTANT: More information: 'http://opentox.github.com/General/2012/08/09/install-opentox-development-environment'" echo "IMPORTANT: Thank you for your attention." -- cgit v1.2.3 From 3bbe02ee0cfa0a99a4c3fb31735e1235fda72123 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Thu, 23 Aug 2012 14:56:08 +0300 Subject: Added call to otconfig --- utils.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/utils.sh b/utils.sh index bf08681..0e0335c 100755 --- a/utils.sh +++ b/utils.sh @@ -120,7 +120,7 @@ notify() { echo if ps -o stat= -p $PPID | grep "s" >/dev/null 2>&1; then echo "IMPORTANT: How to configure your system if everything went fine:" - echo "IMPORTANT: bash shell only: '. $OT_TOOLS_CONF' (convenient ot-tools)" + echo "IMPORTANT: bash shell only: '. $OT_TOOLS_CONF; otconfig' (convenient ot-tools)" echo "IMPORTANT: other shells: '. $OT_UI_CONF' (no ot-tools available)" echo "IMPORTANT: More information: 'http://opentox.github.com/General/2012/08/09/install-opentox-development-environment'" echo "IMPORTANT: Thank you for your attention." -- cgit v1.2.3 From aec61467e2344d36b56be3570559b8fa79e12188 Mon Sep 17 00:00:00 2001 From: davor Date: Thu, 23 Aug 2012 18:08:32 +0300 Subject: Added libcairo2-dev -> png support. --- debian.list | 1 + 1 file changed, 1 insertion(+) diff --git a/debian.list b/debian.list index 73be6d9..e26c1b0 100644 --- a/debian.list +++ b/debian.list @@ -6,6 +6,7 @@ cmake install curl install libavahi-glib-dev install libavahi-client-dev install +libcairo2-dev install libglib2.0-dev install libgsl0-dev install libopenbabel4 install -- cgit v1.2.3 From fb88184886869f8563fde69ca4e5ed30c46b6c86 Mon Sep 17 00:00:00 2001 From: davor Date: Mon, 27 Aug 2012 13:10:58 +0200 Subject: Replaced ambit_descriptors with pc_descriptors. --- ambit_descriptors.yaml | 124 -------------- install | 2 +- pc_descriptors.yaml | 432 +++++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 433 insertions(+), 125 deletions(-) delete mode 100644 ambit_descriptors.yaml create mode 100644 pc_descriptors.yaml diff --git a/ambit_descriptors.yaml b/ambit_descriptors.yaml deleted file mode 100644 index 1e2c347..0000000 --- a/ambit_descriptors.yaml +++ /dev/null @@ -1,124 +0,0 @@ ---- -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor: - :category: "geometrical" - :name: "Length Over Breadth" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor: - :category: "topological" - :name: "Kier & Hall SMARTS" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor: - :category: "topological" - :name: "Fragment Complexity" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor: - :category: "electronic" - :name: "Atomic Polarizabilities" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor: - :category: "constitutional" - :name: "Largest Chain" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor: - :category: "topological" - :name: "Chi Path Indices" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor: - :category: "topological" - :name: "Petitjean Number" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor: - :category: "constitutional" - :name: "Longest Aliphatic Chain" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor: - :category: "topological" - :name: "Kier and Hall kappa molecular shape indices" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor: - :category: "constitutional" - :name: "Aromatic Bonds Count" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor: - :category: "cpsa" - :name: "Charged Partial Surface Areas" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor: - :category: "topological" - :name: "Vertex adjacency information magnitude" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass: - :category: "topological" - :name: "Moreau-Broto Autocorrelation (mass) descriptors" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor: - :category: "constitutional" - :name: "Lipinski's Rule of Five" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor: - :category: "geometrical" - :name: "Gravitational Index" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor: - :category: "topological" - :name: "Wiener Numbers" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor: - :category: "topological" - :name: "Chi Path-Cluster Indices" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor: - :category: "constitutional" - :name: "Atoms Count" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor: - :category: "geometrical" - :name: "Moments of Inertia" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor: - :category: "topological" - :name: "Carbon Types" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability: - :category: "topological" - :name: "Moreau-Broto Autocorrelation (polarizability) descriptors" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor: - :category: "topological" - :name: "Eccentric Connectivity Index" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor: - :category: "hybrid" - :name: "BCUT" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor: - :category: "constitutional" - :name: "Aromatic Atoms Count" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor: - :category: "hybrid" - :name: "WHIM" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor: - :category: "constitutional" - :name: "ALogP" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor: - :category: "constitutional" - :name: "XLogP" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor: - :category: "topological" - :name: "Petitjean Number" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor: - :category: "topological" - :name: "Molecular Distance Edge" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor: - :category: "topological" - :name: "Chi Chain Indices" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor: - :category: "constitutional" - :name: "Bonds Count" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor: - :category: "constitutional" - :name: "Mannhold LogP" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor: - :category: "electronic" - :name: "Bond Polarizabilities" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge: - :category: "topological" - :name: "Moreau-Broto Autocorrelation (charge) descriptors" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor: - :category: "topological" - :name: "Zagreb Index" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor: - :category: "topological" - :name: "Chi Cluster Indices" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor: - :category: "constitutional" - :name: "Rotatable Bonds Count" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor: - :category: "topological" - :name: "Topological Polar Surface Area" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor: - :category: "electronic" - :name: "Hydrogen Bond Donors" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor: - :category: "electronic" - :name: "Hydrogen Bond Acceptors" -http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor: - :category: "constitutional" - :name: "Largest Pi Chain" diff --git a/install b/install index 7561732..00355a7 100755 --- a/install +++ b/install @@ -56,7 +56,7 @@ 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/ambit_descriptors.yaml ] || (cmd="cp ambit_descriptors.yaml $HOME/.opentox/config/" && run_cmd "$cmd" "Ambit keys file") +[ -f $HOME/.opentox/config/pc_descriptors.yaml ] || (cmd="cp pc_descriptors.yaml $HOME/.opentox/config/" && run_cmd "$cmd" "Pc descriptor file") [ -f $HOME/.opentox/config/jl_keys.yaml ] || (cmd="cp jl_keys.yaml $HOME/.opentox/config/" && run_cmd "$cmd" "Joelib keys file") [ -f $OT_TOOLS_CONF ] || (cmd="cp ot-tools-user.sh $OT_TOOLS_CONF" && run_cmd "$cmd" "ot-tools.sh => $HOME/.opentox)") diff --git a/pc_descriptors.yaml b/pc_descriptors.yaml new file mode 100644 index 0000000..e6fd7df --- /dev/null +++ b/pc_descriptors.yaml @@ -0,0 +1,432 @@ +--- + +# 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 From c92587c43f2c9b5b1538259073a8ac2e03980efb Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Mon, 3 Sep 2012 17:13:43 +0200 Subject: Removed RUBY_DIR --- config.sh | 1 - utils.sh | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/config.sh b/config.sh index 8ca0d2e..3d062af 100755 --- a/config.sh +++ b/config.sh @@ -41,7 +41,6 @@ RASQAL_VER="rasqal-$RASQAL_NUM_VER" OB_DEST="$OT_PREFIX/$OB_VER" OB_DEST_BINDINGS="$OT_PREFIX/openbabel-ruby-install" RUBY_DWL="http://ftp.ruby-lang.org/pub/ruby/1.9" -RUBY_DIR="$HOME/.rbenv/versions/$RUBY_NUM_VER" RAPTOR2_DWL="$REDLAND_DWL/source/$RAPTOR2_VER.tar.gz" RASQAL_DWL="$REDLAND_DWL/source/$RASQAL_VER.tar.gz" REDLAND_DEB="$REDLAND_DWL/binaries/$OT_DIST/unstable" diff --git a/utils.sh b/utils.sh index 0e0335c..5c34539 100755 --- a/utils.sh +++ b/utils.sh @@ -79,7 +79,7 @@ install_ruby() { if ! $RBENV versions $RUBY_NUM_VER | grep $RUBY_NUM_VER>/dev/null 2>&1; then [ -d $OT_PREFIX/tmp ] || mkdir -p $OT_PREFIX/tmp && cd $OT_PREFIX/tmp ([ -d $OT_PREFIX/tmp/ruby-$RUBY_NUM_VER ] || $CURL $RUBY_DWL/ruby-$RUBY_NUM_VER.tar.gz 2>/dev/null | $TAR xz) && cd ruby-$RUBY_NUM_VER - cmd="./configure --prefix=$RUBY_DIR" && run_cmd "$cmd" "Configure" + cmd="./configure --prefix=$HOME/.rbenv/versions/$RUBY_NUM_VER" && run_cmd "$cmd" "Configure" cmd="$MAKE -j2" && run_cmd "$cmd" "Make" cmd="$MAKE install" && run_cmd "$cmd" "Install" fi -- cgit v1.2.3 From f20e16cc5287bbda04725dded30ea3eb1c19c77e Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Tue, 4 Sep 2012 08:36:55 +0200 Subject: Support for manual OB install --- debian.list | 2 -- install | 1 + openbabel-install | 45 +++++++++++++++++++++++++++++++++++++++++++++ ubuntu.list | 2 -- 4 files changed, 46 insertions(+), 4 deletions(-) create mode 100755 openbabel-install diff --git a/debian.list b/debian.list index e26c1b0..b10234d 100644 --- a/debian.list +++ b/debian.list @@ -9,8 +9,6 @@ libavahi-client-dev install libcairo2-dev install libglib2.0-dev install libgsl0-dev install -libopenbabel4 install -libopenbabel-dev install libopenssl-ruby install libpcre3-dev install libraptor1-dev install diff --git a/install b/install index 00355a7..c8f335f 100755 --- a/install +++ b/install @@ -41,6 +41,7 @@ echo [ -f $OT_DEFAULT_CONF ] || (cmd="echo '\$aa = { :uri => nil }' > $OT_DEFAULT_CONF" && run_cmd "$cmd" "default.rb => $HOME/.opentox/config") . ./base-install # Debian specific; disable this for others. +./openbabel-install # Download, compile and build openbabel. Install to OT_PREFIX ./raptor2-install # Download, compile and build raptor2. Install to OT_PREFIX. ./rasqal-install # Download, compile and build rasqal. Install to OT_PREFIX. ./4store-install # Download, compile and build 4store. Install to OT_PREFIX. diff --git a/openbabel-install b/openbabel-install new file mode 100755 index 0000000..8656a4e --- /dev/null +++ b/openbabel-install @@ -0,0 +1,45 @@ +#!/bin/sh + +# Installs 4store on Debian and compatible systems. +# Author: Andreas Maunz + +DIR=`pwd` + +# Boot +. ./utils.sh || (echo "Utils could not be loaded, check opentox-ui.sh." 1>&2 && exit 1) +SELF=$(basename $0 -install) +check_log $SELF +[ "`id -u`" = "0" ] && echo "This script must not be run as root" 1>&2 && exit 1 +check_utils "wget cmake tar" + +# Build +cd $OT_PREFIX/tmp/ +mkdir $SELF 2>/dev/null +cd $SELF +cmd="$WGET http://downloads.sourceforge.net/project/openbabel/openbabel/$OB_NUM_VER/openbabel-$OB_NUM_VER.tar.gz" && run_cmd "$cmd" "Download" +cmd="$TAR zxf $OB_VER.tar.gz $OB_VER" && run_cmd "$cmd" "Unpack" +mkdir build 2>/dev/null +cd build +cmd="$CMAKE ../$OB_VER -DCMAKE_INSTALL_PREFIX=$OB_DEST" && run_cmd "$cmd" "Cmake" +cmd="make -j2" && run_cmd "$cmd" "Make" +cmd="make install" && run_cmd "$cmd" "Make Install" + +# Config +if [ ! -f "$OB_CONF" ]; then + echo "if echo \"\$PATH\" | grep -v \"$OB_DEST\">/dev/null 2>&1; then export PATH=\"$OB_DEST/bin:\$PATH\"; fi" >> "$OB_CONF" + echo "if echo \"\$LD_LIBRARY_PATH\" | grep -v \"$OB_DEST\">/dev/null 2>&1; then export LD_LIBRARY_PATH=\"$OB_DEST/lib:\$LD_LIBRARY_PATH\"; fi" >> "$OB_CONF" + echo "if ! [ -d \"$OB_DEST\" ]; then echo \"\$0: '$OB_DEST' is not a directory!\"; fi" >> "$OB_CONF" + echo "if [ -z \"\$BABEL_LIBDIR\" ]; then export BABEL_LIBDIR=\"$OB_DEST/lib/openbabel/$OB_NUM_VER\"; fi" >> "$OB_CONF" + echo "if ! [ -d \"\$BABEL_LIBDIR\" ]; then echo \"\$0: '\$BABEL_LIBDIR' is not a directory!\"; fi" >> "$OB_CONF" + echo "if [ -z \"\$BABEL_DATADIR\" ]; then export BABEL_DATADIR=\"$OB_DEST/share/openbabel/$OB_NUM_VER\"; fi" >> "$OB_CONF" + echo "if ! [ -d \"\$BABEL_DATADIR\" ]; then echo \"\$0: '\$BABEL_DATADIR' is not a directory!\"; fi" >> "$OB_CONF" + echo "Openbabel configuration has been stored in '$OB_CONF'." + if ! grep "$OB_CONF" $OT_UI_CONF >/dev/null 2>&1 ; then + echo ". \"$OB_CONF\"" >> $OT_UI_CONF + fi +fi + +notify + +# return to wd +cd $DIR diff --git a/ubuntu.list b/ubuntu.list index 73be6d9..923759d 100644 --- a/ubuntu.list +++ b/ubuntu.list @@ -8,8 +8,6 @@ libavahi-glib-dev install libavahi-client-dev install libglib2.0-dev install libgsl0-dev install -libopenbabel4 install -libopenbabel-dev install libopenssl-ruby install libpcre3-dev install libraptor1-dev install -- cgit v1.2.3 From 39f5502f3b38e7f26fedce427a89681eee21651c Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Tue, 4 Sep 2012 08:59:44 +0200 Subject: Added pkg-config --- openbabel-install | 2 ++ 1 file changed, 2 insertions(+) diff --git a/openbabel-install b/openbabel-install index 8656a4e..5f183c5 100755 --- a/openbabel-install +++ b/openbabel-install @@ -27,12 +27,14 @@ cmd="make install" && run_cmd "$cmd" "Make Install" # Config if [ ! -f "$OB_CONF" ]; then echo "if echo \"\$PATH\" | grep -v \"$OB_DEST\">/dev/null 2>&1; then export PATH=\"$OB_DEST/bin:\$PATH\"; fi" >> "$OB_CONF" + echo "if echo \"\$PKG_CONFIG_PATH\" | grep -v \"$OB_DEST/lib/pkgconfig\">/dev/null 2>&1; then export PKG_CONFIG_PATH=\"$OB_DEST/lib/pkgconfig:\$PKG_CONFIG_PATH\"; fi" >> "$OB_CONF" echo "if echo \"\$LD_LIBRARY_PATH\" | grep -v \"$OB_DEST\">/dev/null 2>&1; then export LD_LIBRARY_PATH=\"$OB_DEST/lib:\$LD_LIBRARY_PATH\"; fi" >> "$OB_CONF" echo "if ! [ -d \"$OB_DEST\" ]; then echo \"\$0: '$OB_DEST' is not a directory!\"; fi" >> "$OB_CONF" echo "if [ -z \"\$BABEL_LIBDIR\" ]; then export BABEL_LIBDIR=\"$OB_DEST/lib/openbabel/$OB_NUM_VER\"; fi" >> "$OB_CONF" echo "if ! [ -d \"\$BABEL_LIBDIR\" ]; then echo \"\$0: '\$BABEL_LIBDIR' is not a directory!\"; fi" >> "$OB_CONF" echo "if [ -z \"\$BABEL_DATADIR\" ]; then export BABEL_DATADIR=\"$OB_DEST/share/openbabel/$OB_NUM_VER\"; fi" >> "$OB_CONF" echo "if ! [ -d \"\$BABEL_DATADIR\" ]; then echo \"\$0: '\$BABEL_DATADIR' is not a directory!\"; fi" >> "$OB_CONF" + echo "Openbabel configuration has been stored in '$OB_CONF'." if ! grep "$OB_CONF" $OT_UI_CONF >/dev/null 2>&1 ; then echo ". \"$OB_CONF\"" >> $OT_UI_CONF -- cgit v1.2.3