diff options
Diffstat (limited to 'lib/descriptor.rb')
| -rw-r--r-- | lib/descriptor.rb | 63 |
1 files changed, 43 insertions, 20 deletions
diff --git a/lib/descriptor.rb b/lib/descriptor.rb index a8f5123..9a93b32 100644 --- a/lib/descriptor.rb +++ b/lib/descriptor.rb @@ -1,6 +1,8 @@ require 'digest/md5' ENV["JAVA_HOME"] ||= "/usr/lib/jvm/java-7-openjdk" -BABEL_3D_CACHE_DIR = File.join(Dir.pwd,'/babel_3d_cache') +BABEL_3D_CACHE_DIR = File.join(File.dirname(__FILE__),"..",'/babel_3d_cache') +# TODO store 3D structures in mongodb +# TODO store descriptors in mongodb module OpenTox @@ -35,6 +37,7 @@ module OpenTox DESCRIPTORS = OBDESCRIPTORS.merge(CDKDESCRIPTORS.merge(JOELIBDESCRIPTORS)) DESCRIPTOR_VALUES = OBDESCRIPTORS.keys + CDKDESCRIPTOR_VALUES + JOELIBDESCRIPTORS.keys + require_relative "unique_descriptors.rb" def self.description descriptor @@ -53,6 +56,7 @@ module OpenTox end def self.smarts_match compounds, smarts, count=false + compounds = parse compounds obconversion = OpenBabel::OBConversion.new obmol = OpenBabel::OBMol.new obconversion.set_in_format('inchi') @@ -80,7 +84,8 @@ module OpenTox smarts_match compounds,smarts,true end - def self.physchem compounds, descriptors + def self.physchem compounds, descriptors=UNIQUEDESCRIPTORS + compounds = parse compounds des = {} descriptors.each do |d| lib, descriptor = d.split(".",2) @@ -99,6 +104,7 @@ module OpenTox end def self.openbabel compounds, descriptors + compounds = parse compounds $logger.debug "compute #{descriptors.size} openbabel descriptors for #{compounds.size} compounds" obdescriptors = descriptors.collect{|d| OpenBabel::OBDescriptor.find_type d} obmol = OpenBabel::OBMol.new @@ -115,19 +121,8 @@ module OpenTox fingerprint end - def self.run_cmd cmd - cmd = "#{cmd} 2>&1" - $logger.debug "running external cmd: '#{cmd}'" - p = IO.popen(cmd) do |io| - while line = io.gets - $logger.debug "> #{line.chomp}" - end - io.close - raise "external cmd failed '#{cmd}' (see log file for error msg)" unless $?.to_i == 0 - end - end - def self.cdk compounds, descriptors + compounds = parse compounds $logger.debug "compute #{descriptors.size} cdk descriptors for #{compounds.size} compounds" sdf = sdf_3d compounds # use java system call (rjb blocks within tasks) @@ -135,7 +130,7 @@ module OpenTox 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? + $logger.error "Descriptor calculation failed for compound #{compounds[i].inchi}." if calculation.empty? descriptors.each do |descriptor| fingerprint[compounds[i]] = calculation end @@ -145,6 +140,7 @@ module OpenTox end def self.joelib compounds, descriptors + compounds = parse compounds $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 @@ -152,7 +148,7 @@ module OpenTox 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? + $logger.error "Descriptor calculation failed for compound #{compounds[i].inchi}." if calculation.empty? descriptors.each do |descriptor| fingerprint[compounds[i]] = calculation end @@ -162,6 +158,7 @@ module OpenTox end def self.lookup compounds, features, dataset + compounds = parse compounds fingerprint = [] compounds.each do |compound| fingerprint << [] @@ -170,13 +167,26 @@ module OpenTox end end + def self.run_cmd cmd + cmd = "#{cmd} 2>&1" + $logger.debug "running external cmd: '#{cmd}'" + p = IO.popen(cmd) do |io| + while line = io.gets + $logger.debug "> #{line.chomp}" + end + io.close + raise "external cmd failed '#{cmd}' (see log file for error msg)" unless $?.to_i == 0 + end + end + def self.sdf_3d compounds + compounds = parse 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 + digest = Digest::MD5.hexdigest compounds.collect{|c| c.inchi}.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}" @@ -200,11 +210,11 @@ module OpenTox sdf_2d = obconversion.write_string(obmol) error = nil if compound.inchi.include?(";") # component includes multiple compounds (; in inchi, . in smiles) - error = "OpenBabel 3D generation failes for multi-compound #{compound.uri}, trying to calculate descriptors from 2D structure." + error = "OpenBabel 3D generation failes for multi-compound #{compound.inchi}, trying to calculate descriptors from 2D structure." else OpenBabel::OBOp.find_type("Gen3D").do(obmol) sdf_3d = obconversion.write_string(obmol) - error = "3D generation failed for compound #{compound.uri}, trying to calculate descriptors from 2D structure." if sdf_3d.match(/.nan/) + error = "3D generation failed for compound #{compound.inchi}, trying to calculate descriptors from 2D structure." if sdf_3d.match(/.nan/) end if error $logger.warn error @@ -226,6 +236,19 @@ module OpenTox sdf_file end + def self.parse compounds + case compounds.class.to_s + when "OpenTox::Compound" + compounds = [compounds] + when "Array" + compounds + when "OpenTox::Dataset" + compounds = compounds.compounds + else + bad_request_error "Cannot calculate descriptors for #{compounds.class} objects." + end + end + def self.fix_value val val = val.first if val.is_a? Array and val.size == 1 if val.numeric? @@ -236,7 +259,7 @@ module OpenTox end val end - private_class_method :sdf_3d, :fix_value + private_class_method :sdf_3d, :fix_value, :parse, :run_cmd end end end |