diff options
Diffstat (limited to 'pubchem.rb')
| -rw-r--r-- | pubchem.rb | 295 |
1 files changed, 200 insertions, 95 deletions
@@ -1,154 +1,221 @@ require '../opentox-client/lib/opentox-client.rb' require 'json' +require 'base64' def Math.gauss(x, sigma = 0.3) d = 1.0 - x.to_f Math.exp(-(d*d)/(2*sigma*sigma)) end -module PubChem - - attr_accessor :result - - def initialize - @pug_uri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/" - end - - def pubchem_search url - json = RestClient.get url#, :accept => "application/json", :timeout => 90000000 - @result = JSON.parse json - rescue - puts url - puts $!.message - @result = nil - end - -end - module OpenTox + # doc @ http://pubchem.ncbi.nlm.nih.gov/pug_rest/ class PubChemCompound < Compound - include PubChem - # doc @ http://pubchem.ncbi.nlm.nih.gov/pug_rest/ attr_writer :cid attr_accessor :similarity, :p, :assays - def initialize - super - @summary = [] - @similarity_threshold = 75 - @neighbors = [] - @predicted_targets = [] + def initialize cid=nil + @pug_uri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/" + @cid = cid + @assays = nil + @similarity_threshold = 85 + @neighbors = nil + @predicted_assays = nil + #@predicted_targets = nil + #@priors = {} + #@priors = JSON.parse(File.read("priors.json")) end - def from_name name - @inchi = RestClientWrapper.get File.join(CACTUS_URI,URI.escape(name),"stdinchi") + def fingerprint + unless @fingerprint + begin + # ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.txt + base64key = `curl http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/#{cid}/SDF|grep -A1 PUBCHEM_CACTVS_SUBSKEYS|sed '1d'`.chomp + @fingerprint = Base64.decode64(base64key)[4..-1].unpack("B*").first[0..-8].split(//).collect{|c| c == "1"} + rescue + end + end + @fingerprint + end + + def self.from_name name + pug_uri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name" + compounds = [] + session[:name] = name + cid = RestClientWrapper.get(File.join(pug_uri,URI.escape(name),"cids","TXT")) + #puts response + #response.split("\n") do |cid| + puts cid + compound = OpenTox::PubChemCompound.new + compound.cid = cid.chomp + compounds << compound + #end + compounds end def neighbors - if @neighbors.empty? - pubchem_search File.join(@pug_uri, "compound", "similarity", "cid", cid.to_s, "JSON")+"?Threshold=#{@similarity_threshold}&MaxRecords=100" - listkey = @result["Waiting"]["ListKey"] - while @result["Waiting"] do - sleep 1 - pubchem_search File.join(@pug_uri, "compound", "listkey", listkey, "assaysummary", "JSON") + unless @neighbors + @neighbors = [] + result = pubchem_search File.join(@pug_uri, "compound", "similarity", "cid", cid.to_s, "JSON")+"?Threshold=#{@similarity_threshold}&MaxRecords=100" + while result["Waiting"] do + sleep 2 + listkey = result["Waiting"]["ListKey"] + result = pubchem_search File.join(@pug_uri, "compound", "listkey", listkey, "cids", "JSON") + #result = pubchem_search File.join(@pug_uri, "compound", "listkey", listkey, "assaysummary", "JSON") end - columns = @result["Table"]["Columns"]["Column"] - table = @result["Table"]["Row"].collect{|cell| cell.values.flatten} - cid_idx = columns.index("CID") - cids = table.collect{|r| r[cid_idx]}.uniq - cids.each do |cid| + puts "Neighbor CIDs received" + result["IdentifierList"]["CID"].each do |cid| unless cid.to_s == @cid.to_s - tab = table.collect{|r| r if r[cid_idx] == cid}.compact - c = PubChemCompound.new - c.extract_result columns, tab - c.similarity = tanimoto c - @neighbors << c unless (c.targets + c.non_targets).empty? + c = PubChemCompound.new cid.to_s + @neighbors << c if c.assays #and !(c.targets + c.non_targets).empty? + end + end if result and result["IdentifierList"] +=begin + if result and result["Table"] + columns = result["Table"]["Columns"]["Column"] + table = result["Table"]["Row"].collect{|cell| cell.values.flatten} + cid_idx = columns.index("CID") + cids = table.collect{|r| r[cid_idx]}.uniq + cids.each do |cid| + unless cid.to_s == @cid.to_s + tab = table.collect{|r| r if r[cid_idx] == cid}.compact + c = PubChemCompound.new + c.extract_result columns, tab + c.similarity = tanimoto c + @neighbors << c unless (c.targets + c.non_targets).empty? + end end end - @neighbors.sort!{|a,b| b.similarity <=> a.similarity} +=end + #@neighbors.sort!{|a,b| b.similarity <=> a.similarity} end @neighbors end - def summary - if @summary.empty? - pubchem_search File.join(@pug_uri, "compound", "cid", cid.to_s, "assaysummary", "JSON") - extract_result @result["Table"]["Columns"]["Column"], @result["Table"]["Row"].collect{|cell| cell.values.flatten} + def assays + unless @assays + result = pubchem_search File.join(@pug_uri, "compound", "cid", cid.to_s, "assaysummary", "JSON") + extract_result result["Table"]["Columns"]["Column"], result["Table"]["Row"].collect{|cell| cell.values.flatten} if result and result["Table"] end - @summary + @assays end def active_assays - summary.select{|a| a["Activity Outcome"] == "active"} + assays.select{|a| a["Activity Outcome"] == "active"} if assays end def inactive_assays - summary.select{|a| a["Activity Outcome"] == "inactive"} + assays.select{|a| a["Activity Outcome"] == "inactive"} if assays end def targets - active_assays.select{|a| a["Target GI"]} + active_assays.select{|a| a["Target GI"]} if assays end def non_targets - inactive_assays.select{|a| a["Target GI"]} + inactive_assays.select{|a| a["Target GI"]} if assays end - def predicted_targets - if @predicted_targets.empty? - target_gis = neighbors.collect{|n| n.summary.collect{|a| a["Target GI"]}}.flatten.compact.uniq - target_gis.each do |gid| - target = {:target_gi => gid} + def predicted_assays + unless @predicted_assays + @predicted_assays = [] + neighbors.collect{|n| n.assays.collect{|a| a["AID"]}}.flatten.compact.uniq.each do |aid| + predicted_assay = {"AID" => aid} neighbors.each do |neighbor| - if neighbor.similarity > 0.5 # avoid downweighting - search = neighbor.summary.select{|a| a["Target GI"] == gid} - unless search.empty? or search.size == 1 - print "+++ (" - print search.size - puts ")" - puts search.inspect - end + if similarity(neighbor) > 0.5 # avoid downweighting + search = neighbor.assays.select{|a| a["AID"] == aid} search.each do |assay| - target[:aid] ||= assay["AID"] - target[:name] ||= assay["Target Name"] - target[:assay_name] ||= assay["Assay Name"] - target[:active_similarities] ||= [] - target[:inactive_similarities] ||= [] + predicted_assay["Target GI"] ||= assay["Target GI"] + predicted_assay["Target Name"] ||= assay["Target Name"] + predicted_assay["Assay Name"] ||= assay["Assay Name"] + predicted_assay[:active_similarities] ||= [] + predicted_assay[:inactive_similarities] ||= [] if assay["Activity Outcome"] == "active" - target[:p_active] ? target[:p_active] = target[:p_active]*neighbor.similarity : target[:p_active] = neighbor.similarity - target[:p_inactive] ? target[:p_inactive] = target[:p_inactive]*(1-neighbor.similarity) : target[:p_inactive] = 1-neighbor.similarity - target[:active_similarities] << neighbor.similarity + predicted_assay[:p_active] ? predicted_assay[:p_active] = predicted_assay[:p_active]*similarity(neighbor) : predicted_assay[:p_active] = similarity(neighbor) + predicted_assay[:p_inactive] ? predicted_assay[:p_inactive] = predicted_assay[:p_inactive]*(1-similarity(neighbor)) : predicted_assay[:p_inactive] = 1-similarity(neighbor) + predicted_assay[:active_similarities] << similarity(neighbor) elsif assay["Activity Outcome"] == "inactive" - target[:p_active] ? target[:p_active] = target[:p_active]*(1-neighbor.similarity) : target[:p_active] = 1-neighbor.similarity - target[:p_inactive] ? target[:p_inactive] = target[:p_inactive]*neighbor.similarity : target[:p_inactive] = neighbor.similarity - target[:inactive_similarities] << neighbor.similarity + predicted_assay[:p_active] ? predicted_assay[:p_active] = predicted_assay[:p_active]*(1-similarity(neighbor)) : predicted_assay[:p_active] = 1-similarity(neighbor) + predicted_assay[:p_inactive] ? predicted_assay[:p_inactive] = predicted_assay[:p_inactive]*similarity(neighbor) : predicted_assay[:p_inactive] = similarity(neighbor) + predicted_assay[:inactive_similarities] << similarity(neighbor) end end end end - if target[:p_active] and target[:p_inactive] and target[:p_active] + target[:p_inactive] != 0 - target[:p_active] = target[:p_active]/(target[:p_active]+target[:p_inactive]) - target[:p_inactive] = target[:p_inactive]/(target[:p_active]+target[:p_inactive]) - if target[:p_active] > target[:p_inactive] - target[:prediction] = "active" - elsif target[:p_active] < target[:p_inactive] - target[:prediction] = "inactive" + if predicted_assay[:p_active] and predicted_assay[:p_inactive] and predicted_assay[:p_active] != 0 and predicted_assay[:p_inactive] != 0 + predicted_assay[:p_active] = predicted_assay[:p_active]/(predicted_assay[:p_active]+predicted_assay[:p_inactive]) + predicted_assay[:p_inactive] = predicted_assay[:p_inactive]/(predicted_assay[:p_active]+predicted_assay[:p_inactive]) + if predicted_assay[:p_active] > predicted_assay[:p_inactive] + predicted_assay[:prediction] = "active" + elsif predicted_assay[:p_active] < predicted_assay[:p_inactive] + predicted_assay[:prediction] = "inactive" end - @predicted_targets << target + @predicted_assays << predicted_assay end end - @predicted_targets.sort{|a,b| b[:p_active] <=> a[:p_active]} + #@predicted_targets.sort{|a,b| b[:p_active] <=> a[:p_active]} end - @predicted_targets + @predicted_assays + end + + def predicted_active_assays + predicted_assays.select{|a| a[:prediction] == "active"} if predicted_assays + end + + def predicted_inactive_assays + predicted_assays.select{|a| a[:prediction] == "inactive"} if predicted_assays + end + + def predicted_targets + predicted_active_assays.select{|a| a[:target_gi]} if predicted_assays + end + + def predicted_non_targets + inactive_assays.select{|a| a[:target_gi]} if predicted_assays end def to_smiles RestClient.get(File.join(@pug_uri, "compound", "cid", cid.to_s, "property", "CanonicalSMILES", "TXT")).strip end + def image_uri + File.join @pug_uri, "compound", "cid", @cid, "PNG"#?record_type=3d&image_size=small" + end + + def similarity compound + cosine compound + end + def tanimoto compound + if fingerprint and compound.fingerprint + m11 = 0.0 + m1 = 0.0 + fingerprint.each_index do |i| + m11 += 1 if (@fingerprint[i] and compound.fingerprint[i]) + m1 += 1 if (@fingerprint[i] or compound.fingerprint[i]) + end + m11/m1 + end + end + + def cosine compound + if fingerprint and compound.fingerprint + m11 = 0.0 + m01 = 0.0 + m10 = 0.0 + m00 = 0.0 + fingerprint.each_index do |i| + m11 += 1 if (@fingerprint[i] and compound.fingerprint[i]) + m01 += 1 if (!@fingerprint[i] and compound.fingerprint[i]) + m10 += 1 if (@fingerprint[i] and !compound.fingerprint[i]) + m00 += 1 if (!@fingerprint[i] and !compound.fingerprint[i]) + end + m11/((m01+m11)*(m10+m11))**0.5 + end + end + +=begin f1 = File.open(File.join(".","tmp",SecureRandom.uuid+".smi"),"w+") f1.puts to_smiles f1.close @@ -160,20 +227,62 @@ module OpenTox File.delete(f2.path) sim end +=end + + def pubchem_search url + attempts = 0 + begin + attempts += 1 + json = RestClient.get url, :timeout => 90000000 + puts url + JSON.parse json + rescue + if $!.message =~ /Timeout/i and attempts < 4 + sleep 2 + retry + elsif $!.message =~ /Timeout/i and attempts >= 4 + File.open("timeouts","a+"){|f| f.puts url} + puts url + puts $!.message + nil + elsif $!.message.match /404/ + nil + else + puts url + puts $!.message + nil + end + end + end def extract_result columns, table + @assays = [] table.each do |row| - @summary << {} + @assays << {} row.each_with_index do |cell,i| if columns[i] == "CID" @cid = cell if @cid.nil? else - cell.blank? ? @summary.last[columns[i]] = nil : @summary.last[columns[i]] = cell + cell.blank? ? @assays.last[columns[i]] = nil : @assays.last[columns[i]] = cell end end end end + def priors aid + unless @priors[aid] + @priors[aid] = {"nr_active" => 0, "nr_inactive" => 0} + result = nil + result = pubchem_search File.join(@pug_uri, "assay", "aid", aid.to_s, "cids", "JSON?cids_type=active&list_return=listkey") + @priors[aid]["nr_active"] = result["IdentifierList"]["Size"].to_i if result + result = nil + result = pubchem_search File.join(@pug_uri, "assay", "aid", aid.to_s, "cids", "JSON?cids_type=inactive&list_return=listkey") + @priors[aid]["nr_inactive"] = result["IdentifierList"]["Size"].to_i if result + File.open("priors.json","w+"){|f| f.puts @priors.to_json} + end + @priors[aid] + end + =begin def assay_summary assay if assay["Target GI"] and !@assays[assay["AID"]] @@ -262,10 +371,6 @@ module OpenTox def to_name RestClient.get(File.join(@pug_uri, "compound", "cid", @cid, "property", "IUPACName", "TXT")).strip end - - def to_image_uri - File.join @pug_uri, "compound", "cid", @cid, "PNG?record_type=3d&image_size=small" - end =end end |