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module OpenTox
# Feature for physico-chemical descriptors
class PhysChem < NumericFeature
field :library, type: String
field :descriptor, type: String
field :description, type: String
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")
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
end.compact.sort{|a,b| a[0] <=> b[0]}]
cdkdescriptors = {}
CDK_DESCRIPTIONS = YAML.load(`java -classpath #{CDK_JAR}:#{JAVA_DIR} CdkDescriptorInfo`)
CDK_DESCRIPTIONS.each do |d|
prefix="Cdk."+d[:java_class].split('.').last.sub(/Descriptor/,'')
d[:names].each { |name| cdkdescriptors[prefix+"."+name] = d[:description] }
end
CDKDESCRIPTORS = 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|
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))
require_relative "unique_descriptors.rb"
def self.descriptors
DESCRIPTORS.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
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
# Description of available descriptors
def self.description descriptor
lib = descriptor.split('_').first
case lib
when "Openbabel"
OBDESCRIPTORS[descriptor]
when "Cdk"
name = descriptor.split('_')[0..-2].join('_')
CDKDESCRIPTORS[name]
when "Joelib"
JOELIBDESCRIPTORS[descriptor]
when "lookup"
"Read feature values from a dataset"
end
end
def calculate compound
result = send library.downcase,descriptor,compound
p result
result[self.name]
end
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
def cdk descriptor, compound
java_descriptor "cdk", descriptor, compound
end
def joelib descriptor, compound
java_descriptor "joelib", descriptor, compound
end
private
def java_descriptor lib, descriptor, compound
sdf_3d = "/tmp/#{SecureRandom.uuid}.sdf"
File.open(sdf_3d,"w+"){|f| f.print compound.sdf}
# use java system call (rjb blocks within tasks)
# use Tempfiles to avoid "Argument list too long" error
case lib
when "cdk"
`java -classpath #{CDK_JAR}:#{JAVA_DIR} CdkDescriptors #{sdf_3d} #{descriptor}`
when "joelib"
`java -classpath #{JOELIB_JAR}:#{JMOL_JAR}:#{LOG4J_JAR}:#{JAVA_DIR} JoelibDescriptors #{sdf_3d} #{descriptor}`
end
result = YAML.load_file("#{sdf_3d}#{lib}.yaml").first
result.keys.each{|k| result[k] = result.delete(k)}
result
end
def fix_value val
val = val.first if val.is_a? Array and val.size == 1
val = nil if val == "NaN"
if val.numeric?
val = Float(val)
val = nil if val.nan? or val.infinite?
end
val
end
end
end
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