diff options
Diffstat (limited to 'lib/descriptor.rb')
| -rw-r--r-- | lib/descriptor.rb | 35 |
1 files changed, 20 insertions, 15 deletions
diff --git a/lib/descriptor.rb b/lib/descriptor.rb index 93ce591..d6b2e85 100644 --- a/lib/descriptor.rb +++ b/lib/descriptor.rb @@ -4,10 +4,10 @@ ENV["JAVA_HOME"] ||= "/usr/lib/jvm/java-7-openjdk" module OpenTox - module Algorithm + #module Algorithm # Class for descriptor calculations - class Descriptor + module Descriptor include OpenTox JAVA_DIR = File.join(File.dirname(__FILE__),"..","java") @@ -19,20 +19,19 @@ module OpenTox obexclude = ["cansmi","cansmiNS","formula","InChI","InChIKey","s","smarts","title","L5"] OBDESCRIPTORS = 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 + ["Openbabel_"+name,description] unless obexclude.include? name end.compact.sort{|a,b| a[0] <=> b[0]}] cdk_desc = YAML.load(`java -classpath #{CDK_JAR}:#{JAVA_DIR} CdkDescriptorInfo`) - CDKDESCRIPTORS = Hash[cdk_desc.collect { |d| ["Cdk."+d[:java_class].split('.').last.sub(/Descriptor/,''), d[:description]] }.sort{|a,b| a[0] <=> b[0]}] - CDKDESCRIPTOR_VALUES = cdk_desc.collect { |d| prefix="Cdk."+d[:java_class].split('.').last.sub(/Descriptor/,''); d[:names].collect{ |name| prefix+"."+name } }.flatten + CDKDESCRIPTORS = Hash[cdk_desc.collect { |d| ["Cdk_"+d[:java_class].split('.').last.sub(/Descriptor/,''), d[:description]] }.sort{|a,b| a[0] <=> b[0]}] + CDKDESCRIPTOR_VALUES = cdk_desc.collect { |d| prefix="Cdk_"+d[:java_class].split('.').last.sub(/Descriptor/,''); d[:names].collect{ |name| prefix+"_"+name } }.flatten # 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| - name = d[:java_class].sub(/^joelib2.feature.types./,'') - # impossible to obtain meaningful descriptions from JOELIb, see java/JoelibDescriptors.java - ["Joelib."+name, "no description available"] unless joelibexclude.include? name + name = d[:java_class].sub(/^joelib2.feature.types./,'').gsub(/\./,"_") + ["Joelib_"+name, "impossible to obtain meaningful descriptions from JOELIb, see java/JoelibDescriptors.java"] unless joelibexclude.include? name end.compact.sort{|a,b| a[0] <=> b[0]}] DESCRIPTORS = OBDESCRIPTORS.merge(CDKDESCRIPTORS.merge(JOELIBDESCRIPTORS)) @@ -42,12 +41,12 @@ module OpenTox # Description of available descriptors def self.description descriptor - lib = descriptor.split('.').first + lib = descriptor.split('_').first case lib when "Openbabel" OBDESCRIPTORS[descriptor] when "Cdk" - name = descriptor.split('.')[0..-2].join('.') + name = descriptor.split('_')[0..-2].join('_') CDKDESCRIPTORS[name] when "Joelib" JOELIBDESCRIPTORS[descriptor] @@ -101,7 +100,7 @@ module OpenTox @physchem_descriptors = [] # CDK may return more than one result per descriptor, they are stored as separate features des = {} @descriptors.each do |d| - lib, descriptor = d.split(".",2) + lib, descriptor = d.split("_",2) lib = lib.downcase.to_sym des[lib] ||= [] des[lib] << descriptor @@ -125,7 +124,7 @@ module OpenTox @data_entries[c][d+last_feature_idx] = fix_value(descriptor.predict(obmol)) end end - @physchem_descriptors += descriptors.collect{|d| "Openbabel.#{d}"} + @physchem_descriptors += descriptors.collect{|d| "Openbabel_#{d}"} end def self.java_descriptors descriptors, lib @@ -208,10 +207,16 @@ module OpenTox end def self.serialize - @data_entries.collect!{|de| de.collect{|v| v.round(5) unless v.nil?}} + #@data_entries.collect!{|de| de.collect{|v| v.round(5) unless v.nil?}} case @input_class + # TODO beautify and fix for other objects when "OpenTox::Compound" - @data_entries.first + r = {} + @data_entries.first.each_with_index do |d,i| + # TODO fix @ source + r[@physchem_descriptors[i].gsub(/\./,'_')] = d + end + r when "Array" @data_entries when "OpenTox::Dataset" @@ -243,5 +248,5 @@ module OpenTox end private_class_method :sdf_3d, :fix_value, :parse, :run_cmd, :serialize end - end + #end end |