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require 'digest/md5'
ENV["JAVA_HOME"] ||= "/usr/lib/jvm/java-7-openjdk"
module OpenTox
module Algorithm
class Descriptor
include OpenTox
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"]
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 = Hash[YAML.load(`java -classpath #{CDK_JAR}:#{JAVA_DIR} CdkDescriptorInfo`).collect { |d| ["Cdk."+d[:java_class].split('.').last.sub(/Descriptor/,''), d[:description]] }.sort{|a,b| a[0] <=> b[0]}]
# 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
end.compact.sort{|a,b| a[0] <=> b[0]}]
DESCRIPTORS = OBDESCRIPTORS.merge(CDKDESCRIPTORS.merge(JOELIBDESCRIPTORS))
require_relative "unique_descriptors.rb"
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 self.smarts_match compounds, smarts, count=false
obconversion = OpenBabel::OBConversion.new
obmol = OpenBabel::OBMol.new
obconversion.set_in_format('inchi')
smarts_pattern = OpenBabel::OBSmartsPattern.new
fingerprint = {}
compounds = [compounds] unless compounds.is_a? Array
smarts = [smarts] unless smarts.is_a? Array
compounds.each do |compound|
obconversion.read_string(obmol,compound.inchi)
fingerprint[compound] = {}
smarts.each do |smart|
smarts_pattern.init(smart)
if smarts_pattern.match(obmol)
count ? value = smarts_pattern.get_map_list.to_a.size : value = 1
else
value = 0
end
fingerprint[compound][smart] = value
end
end
fingerprint
end
def self.smarts_count compounds, smarts
smarts_match compounds,smarts,true
end
def self.physchem compounds, descriptors
des = {}
descriptors.each do |d|
lib, descriptor = d.split(".",2)
lib = lib.downcase.to_sym
des[lib] ||= []
des[lib] << descriptor
end
result = {}
des.each do |lib,d|
send(lib, compounds, d).each do |compound,values|
result[compound] ||= {}
result[compound].merge! values
end
end
result
end
def self.openbabel compounds, descriptors
$logger.debug "compute #{descriptors.size} openbabel descriptors for #{compounds.size} compounds"
obdescriptors = descriptors.collect{|d| OpenBabel::OBDescriptor.find_type d}
obmol = OpenBabel::OBMol.new
obconversion = OpenBabel::OBConversion.new
obconversion.set_in_format 'inchi'
fingerprint = {}
compounds.each do |compound|
obconversion.read_string obmol, compound.inchi
fingerprint[compound] = {}
obdescriptors.each_with_index do |descriptor,i|
fingerprint[compound]["Openbabel."+descriptors[i]] = fix_value(descriptor.predict(obmol))
end
end
fingerprint
end
def self.run_cmd cmd
$logger.debug "running '#{cmd}'"
IO.popen(cmd).each{|line| $logger.debug line.chomp}
end
def self.cdk compounds, descriptors
$logger.debug "compute #{descriptors.size} cdk descriptors for #{compounds.size} compounds"
sdf = sdf_3d compounds
# use java system call (rjb blocks within tasks)
# use Tempfiles to avoid "Argument list too long" error
run_cmd "java -classpath #{CDK_JAR}:#{JAVA_DIR} CdkDescriptors #{sdf} #{descriptors.join(" ")}"
fingerprint = {}
YAML.load_file(sdf+"cdk.yaml").each_with_index do |calculation,i|
$logger.error "Descriptor calculation failed for compound #{compounds[i].uri}." if calculation.empty?
descriptors.each do |descriptor|
fingerprint[compounds[i]] = calculation
end
end
FileUtils.rm sdf+"cdk.yaml"
fingerprint
end
def self.joelib compounds, descriptors
$logger.debug "compute #{descriptors.size} joelib descriptors for #{compounds.size} compounds"
# use java system call (rjb blocks within tasks)
# use Tempfiles to avoid "Argument list too long" error
sdf = sdf_3d compounds
run_cmd "java -classpath #{JOELIB_JAR}:#{JMOL_JAR}:#{LOG4J_JAR}:#{JAVA_DIR} JoelibDescriptors #{sdf} #{descriptors.join(' ')}"
fingerprint = {}
YAML.load_file(sdf+"joelib.yaml").each_with_index do |calculation,i|
$logger.error "Descriptor calculation failed for compound #{compounds[i].uri}." if calculation.empty?
descriptors.each do |descriptor|
fingerprint[compounds[i]] = calculation
end
end
FileUtils.rm sdf+"joelib.yaml"
fingerprint
end
def self.lookup compounds, features, dataset
fingerprint = []
compounds.each do |compound|
fingerprint << []
features.each do |feature|
end
end
end
def self.sdf_3d compounds
obconversion = OpenBabel::OBConversion.new
obmol = OpenBabel::OBMol.new
obconversion.set_in_format 'inchi'
obconversion.set_out_format 'sdf'
digest = Digest::MD5.hexdigest compounds.collect{|c| c.uri}.inspect
sdf_file = "/tmp/#{digest}.sdf"
if File.exists? sdf_file # do not recreate existing 3d sdfs
$logger.debug "re-using cached 3d structures from #{sdf_file}"
else
tmp_file = Tempfile.new('sdf')
$logger.debug "3d structures will be cached in #{sdf_file} (tmp in #{tmp_file})"
# create 3d sdf file (faster in Openbabel than in CDK)
# MG: moreover, CDK 3d generation is faulty
# MG: WARNING: Openbabel 3d generation is not deterministic
# MG: WARNING: Openbabel 3D generation does not work for mixtures
c = 0
compounds.each do |compound|
c += 1
$logger.debug "compute 3d structures for compound #{c}/#{compounds.size}"
obconversion.read_string obmol, compound.inchi
sdf_2d = obconversion.write_string(obmol)
OpenBabel::OBOp.find_type("Gen3D").do(obmol)
sdf_3d = obconversion.write_string(obmol)
if sdf_3d.match(/.nan/)
warning = "3D generation failed for compound #{compound.uri}, trying to calculate descriptors from 2D structure."
$logger.warn warning
# TODO
#@feature_dataset[RDF::OT.Warnings] ? @feature_dataset[RDF::OT.Warnings] << warning : @feature_dataset[RDF::OT.Warnings] = warning
tmp_file.write sdf_2d
else
tmp_file.write sdf_3d
end
end
tmp_file.close
File.rename(tmp_file, sdf_file)
end
sdf_file
end
def self.fix_value val
val = val.first if val.is_a? Array and val.size == 1
if val.numeric?
val = Float(val)
val = nil if val.nan? or val.infinite?
else
val = nil if val == "NaN"
end
val
end
private_class_method :sdf_3d, :fix_value
end
end
end
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