diff options
Diffstat (limited to 'pubchem.rb')
| -rw-r--r-- | pubchem.rb | 28 |
1 files changed, 20 insertions, 8 deletions
@@ -1,6 +1,13 @@ require '../opentox-client/lib/opentox-client.rb' require 'json' require 'base64' +require 'restclient/components' +require 'rack/cache' +#RestClient.enable Rack::Cache, :verbose => true#, :allow_reload => true, :allow_revalidate => true +RestClient.enable Rack::Cache, + :verbose => true, + :metastore => 'file:/tmp/cache/meta', + :entitystore => 'file:/tmp/cache/body' def Math.gauss(x, sigma = 0.3) d = 1.0 - x.to_f @@ -15,10 +22,11 @@ module OpenTox attr_accessor :similarity, :p, :assays def initialize cid=nil - @pug_uri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/" + #@pug_uri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/" + @pug_uri = "http://localhost:8081/" @cid = cid @assays = nil - @similarity_threshold = 85 + @similarity_threshold = 90 @neighbors = nil @predicted_assays = nil #@predicted_targets = nil @@ -42,7 +50,7 @@ module OpenTox 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")) + cid = RestClient.get(File.join(pug_uri,URI.escape(name),"cids","TXT")) #puts response #response.split("\n") do |cid| puts cid @@ -53,6 +61,10 @@ module OpenTox compounds end + def name + RestClient.get File.join(@pug_uri, "compound", "cid", cid.to_s, "property", "IUPACName","TXT").chomp + end + def neighbors unless @neighbors @neighbors = [] @@ -63,11 +75,11 @@ module OpenTox 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 - puts "Neighbor CIDs received" + puts "#{result["IdentifierList"]["CID"].size} Neighbor CIDs received" result["IdentifierList"]["CID"].each do |cid| unless cid.to_s == @cid.to_s c = PubChemCompound.new cid.to_s - @neighbors << c if c.assays #and !(c.targets + c.non_targets).empty? + @neighbors << c if c.assays and !c.assays.empty? end end if result and result["IdentifierList"] =begin @@ -122,7 +134,7 @@ module OpenTox neighbors.collect{|n| n.assays.collect{|a| a["AID"]}}.flatten.compact.uniq.each do |aid| predicted_assay = {"AID" => aid} neighbors.each do |neighbor| - if similarity(neighbor) > 0.5 # avoid downweighting + if similarity(neighbor) and similarity(neighbor) > 0.5 # avoid downweighting search = neighbor.assays.select{|a| a["AID"] == aid} search.each do |assay| predicted_assay["Target GI"] ||= assay["Target GI"] @@ -168,11 +180,11 @@ module OpenTox end def predicted_targets - predicted_active_assays.select{|a| a[:target_gi]} if predicted_assays + 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 + predicted_inactive_assays.select{|a| a["Target GI"]} if predicted_assays end def to_smiles |