From 48234554ea99b972a01718ac36c4e8332dd9159b Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Sat, 7 May 2016 10:34:03 +0200 Subject: -log10 for regression datasets, test cleanups --- lib/physchem.rb | 1 + 1 file changed, 1 insertion(+) (limited to 'lib/physchem.rb') diff --git a/lib/physchem.rb b/lib/physchem.rb index f7b880f..86300ba 100644 --- a/lib/physchem.rb +++ b/lib/physchem.rb @@ -131,3 +131,4 @@ module OpenTox end end +OpenTox::PhysChem.descriptors # load descriptor features -- cgit v1.2.3 From 91787edb3682900bc5a2feeca66e5142f387fcc6 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Fri, 7 Oct 2016 10:25:58 +0200 Subject: unified interface for prediction algorithms --- lib/physchem.rb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'lib/physchem.rb') diff --git a/lib/physchem.rb b/lib/physchem.rb index 86300ba..c32e382 100644 --- a/lib/physchem.rb +++ b/lib/physchem.rb @@ -42,7 +42,7 @@ module OpenTox def self.descriptors desc=DESCRIPTORS desc.collect do |name,description| lib,desc = name.split('.',2) - self.find_or_create_by(:name => name, :library => lib, :descriptor => desc, :description => description, :measured => false, :calculated => true, :numeric => true, :nominal => false) + self.find_or_create_by(:name => name, :library => lib, :descriptor => desc, :description => description, :measured => false, :calculated => true) end end @@ -54,11 +54,11 @@ module OpenTox CDK_DESCRIPTIONS.select{|d| desc == d[:java_class].split('.').last.sub('Descriptor','') }.first[:names].each do |n| dname = "#{name}.#{n}" description = DESCRIPTORS[dname] - udesc << self.find_or_create_by(:name => dname, :library => lib, :descriptor => desc, :description => description, :measured => false, :calculated => true, :numeric => true, :nominal => false) + udesc << self.find_or_create_by(:name => dname, :library => lib, :descriptor => desc, :description => description, :measured => false, :calculated => true) end else description = DESCRIPTORS[name] - udesc << self.find_or_create_by(:name => name, :library => lib, :descriptor => desc, :description => description, :measured => false, :calculated => true, :numeric => true, :nominal => false) + udesc << self.find_or_create_by(:name => name, :library => lib, :descriptor => desc, :description => description, :measured => false, :calculated => true) end end udesc -- cgit v1.2.3 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