Class: OpenTox::PhysChem

Inherits:
NumericFeature 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")
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
end.compact.sort{|a,b| a[0]
CDK_DESCRIPTIONS = 
YAML.load(`java -classpath #{CDK_JAR}:#{JAVA_DIR}  CdkDescriptorInfo`)
CDKDESCRIPTORS = 
cdkdescriptors
JOELIBDESCRIPTORS =

strip Joelib messages from stdout


      
        
DESCRIPTORS =
          
        

        
OBDESCRIPTORS.merge(CDKDESCRIPTORS.merge(JOELIBDESCRIPTORS))


      
    

  







  
    

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Methods inherited from NumericFeature

  
#initialize


  
  
  
  
  
  

  
Constructor Details

  
    
This class inherits a constructor from OpenTox::NumericFeature

  




  

    
Class Method Details


    
      

  

  
    .cdk_descriptors  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/physchem.rb', line 71

def self.cdk_descriptors
  descriptors CDKDESCRIPTORS
end


    		
  





    
      

  

  
    .descriptors(desc = DESCRIPTORS)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/physchem.rb', line 42

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)
  end
end


    		
  





    
      

  

  
    .joelib_descriptors  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/physchem.rb', line 75

def self.joelib_descriptors
  descriptors JOELIBDESCRIPTORS
end


    		
  





    
      

  

  
    .openbabel_descriptors  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/physchem.rb', line 67

def self.openbabel_descriptors
  descriptors OBDESCRIPTORS
end


    		
  





    
      

  

  
    .unique_descriptors  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/physchem.rb', line 49

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, :measured => false, :calculated => true, :numeric => true, :nominal => false)
      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)
    end
  end
  udesc
end


    		
  





    
  


  

    
Instance Method Details


    
      

  

  
    #calculate(compound)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/physchem.rb', line 79

def calculate compound
  result = send library.downcase,descriptor,compound
  result[self.name]
end


    		
  





    
      

  

  
    #cdk(descriptor, compound)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/physchem.rb', line 93

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


    		
  





    
      

  

  
    #joelib(descriptor, compound)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/physchem.rb', line 97

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


    		
  





    
      

  

  
    #openbabel(descriptor, compound)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/physchem.rb', line 84

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