Class: OpenTox::PhysChem

Inherits:
NumericSubstanceProperty show all
Defined in:
lib/physchem.rb

Overview

Feature for physico-chemical descriptors

Constant Summary collapse

JAVA_DIR = 
File.join(File.dirname(__FILE__),"..","java")
CDK_JAR = 
Dir[File.join(JAVA_DIR,"cdk-*jar")].last
JOELIB_JAR = 
File.join(JAVA_DIR,"joelib2.jar")
LOG4J_JAR = 
File.join(JAVA_DIR,"log4j.jar")
JMOL_JAR = 
File.join(JAVA_DIR,"Jmol.jar")
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]
CDK_DESCRIPTIONS = 
YAML.load(`java -classpath #{CDK_JAR}:#{JAVA_DIR}  CdkDescriptorInfo`)
CDK = 
cdkdescriptors
JOELIB =

strip Joelib messages from stdout



DESCRIPTORS =



OPENBABEL.merge(CDK.merge(JOELIB))





Class Method Summary
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Instance Method Summary
collapse






Class Method Details





.cdk_descriptors ⇒ Array<OpenTox::PhysChem>







Get CDK descriptor features








Returns:










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# File 'lib/physchem.rb', line 80

def self.cdk_descriptors
  descriptors CDK
end












.descriptors(desc = DESCRIPTORS) ⇒ Array<OpenTox::PhysChem>







Get descriptor features








Parameters:


    

  • 

(Hash)

    • 



Returns:










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# File 'lib/physchem.rb', line 45

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)
  end
end












.joelib_descriptors ⇒ Array<OpenTox::PhysChem>







Get JOELIB descriptor features








Returns:










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# File 'lib/physchem.rb', line 86

def self.joelib_descriptors
  descriptors JOELIB
end












.openbabel_descriptors ⇒ Array<OpenTox::PhysChem>







Get OpenBabel descriptor features








Returns:










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# File 'lib/physchem.rb', line 74

def self.openbabel_descriptors
  descriptors OPENBABEL
end












.unique_descriptors ⇒ Array<OpenTox::PhysChem>







Get unique descriptor features








Returns:










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# File 'lib/physchem.rb', line 54

def self.unique_descriptors
  udesc = []
  UNIQUEDESCRIPTORS.each do |name|
    lib,desc = name.split('.',2)
    if lib == "Cdk"
      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)
      end
    else
      description = DESCRIPTORS[name]
      udesc << self.find_or_create_by(:name => name, :library => lib, :descriptor => desc, :description => description)
    end
  end
  udesc
end













Instance Method Details





#cdk(descriptor, compound) ⇒ Hash







Calculate CDK descriptors








Parameters:



Returns:


    

  • 
(Hash)

    • 










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# File 'lib/physchem.rb', line 107

def cdk descriptor, compound
  java_descriptor "cdk", descriptor, compound
end












#joelib(descriptor, compound) ⇒ Hash







Calculate JOELIB descriptors








Parameters:



Returns:


    

  • 
(Hash)

    • 










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# File 'lib/physchem.rb', line 115

def joelib descriptor, compound
  java_descriptor "joelib", descriptor, compound
end












#openbabel(descriptor, compound) ⇒ Hash







Calculate OpenBabel descriptors








Parameters:



Returns:


    

  • 
(Hash)

    • 










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# File 'lib/physchem.rb', line 94

def openbabel descriptor, compound
  obdescriptor = OpenBabel::OBDescriptor.find_type descriptor
  obmol = OpenBabel::OBMol.new
  obconversion = OpenBabel::OBConversion.new
  obconversion.set_in_format 'smi'
  obconversion.read_string obmol, compound.smiles
  {"#{library.capitalize}.#{descriptor}" => fix_value(obdescriptor.predict(obmol))}
end