From dc4ab1f4e64d738d6c0b70f0b690a2359685080f Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Wed, 12 Oct 2016 21:32:27 +0200 Subject: physchem regression, correlation_filter for fingerprints --- lib/physchem.rb | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) (limited to 'lib/physchem.rb') diff --git a/lib/physchem.rb b/lib/physchem.rb index c32e382..327acd8 100644 --- a/lib/physchem.rb +++ b/lib/physchem.rb @@ -14,7 +14,7 @@ module OpenTox JMOL_JAR = File.join(JAVA_DIR,"Jmol.jar") obexclude = ["cansmi","cansmiNS","formula","InChI","InChIKey","s","smarts","title","L5"] - OBDESCRIPTORS = Hash[OpenBabel::OBDescriptor.list_as_string("descriptors").split("\n").collect do |d| + OPENBABEL = Hash[OpenBabel::OBDescriptor.list_as_string("descriptors").split("\n").collect do |d| name,description = d.split(/\s+/,2) ["Openbabel."+name,description] unless obexclude.include? name end.compact.sort{|a,b| a[0] <=> b[0]}] @@ -25,17 +25,17 @@ module OpenTox prefix="Cdk."+d[:java_class].split('.').last.sub(/Descriptor/,'') d[:names].each { |name| cdkdescriptors[prefix+"."+name] = d[:description] } end - CDKDESCRIPTORS = cdkdescriptors + CDK = cdkdescriptors # exclude Hashcode (not a physchem property) and GlobalTopologicalChargeIndex (Joelib bug) joelibexclude = ["MoleculeHashcode","GlobalTopologicalChargeIndex"] # strip Joelib messages from stdout - JOELIBDESCRIPTORS = Hash[YAML.load(`java -classpath #{JOELIB_JAR}:#{LOG4J_JAR}:#{JAVA_DIR} JoelibDescriptorInfo | sed '0,/---/d'`).collect do |d| + JOELIB = Hash[YAML.load(`java -classpath #{JOELIB_JAR}:#{LOG4J_JAR}:#{JAVA_DIR} JoelibDescriptorInfo | sed '0,/---/d'`).collect do |d| name = d[:java_class].sub(/^joelib2.feature.types./,'') ["Joelib."+name, "JOELIb does not provide meaningful descriptions, see java/JoelibDescriptors.java for details."] unless joelibexclude.include? name end.compact.sort{|a,b| a[0] <=> b[0]}] - DESCRIPTORS = OBDESCRIPTORS.merge(CDKDESCRIPTORS.merge(JOELIBDESCRIPTORS)) + DESCRIPTORS = OPENBABEL.merge(CDK.merge(JOELIB)) require_relative "unique_descriptors.rb" @@ -65,15 +65,15 @@ module OpenTox end def self.openbabel_descriptors - descriptors OBDESCRIPTORS + descriptors OPENBABEL end def self.cdk_descriptors - descriptors CDKDESCRIPTORS + descriptors CDK end def self.joelib_descriptors - descriptors JOELIBDESCRIPTORS + descriptors JOELIB end def calculate compound -- cgit v1.2.3