diff options
Diffstat (limited to 'lib/compound.rb')
| -rw-r--r-- | lib/compound.rb | 31 |
1 files changed, 28 insertions, 3 deletions
diff --git a/lib/compound.rb b/lib/compound.rb index 7c7c3d8..49c166f 100644 --- a/lib/compound.rb +++ b/lib/compound.rb @@ -1,3 +1,6 @@ +@@cactus_uri="http://cactus.nci.nih.gov/chemical/structure/" +@@ambit_uri="http://ambit.uni-plovdiv.bg:8080/ambit2/depict/cdk?search=" + module OpenTox class Compound #< OpenTox @@ -6,7 +9,6 @@ module OpenTox # Initialize with <tt>:uri => uri</tt>, <tt>:smiles => smiles</tt> or <tt>:name => name</tt> (name can be also an InChI/InChiKey, CAS number, etc) def initialize(params) - @@cactus_uri="http://cactus.nci.nih.gov/chemical/structure/" if params[:smiles] @inchi = smiles2inchi(params[:smiles]) @uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi)) @@ -45,12 +47,35 @@ module OpenTox obconversion(@inchi,'inchi','sdf') end - def image + def gif RestClientWrapper.get("#{@@cactus_uri}#{@inchi}/image") end + def png + RestClientWrapper.get(File.join @uri, "image") + end + + def names + begin + RestClientWrapper.get("#{@@cactus_uri}#{@inchi}/names") + rescue + "not available" + end + end + + def display_smarts_uri(activating, deactivating, highlight = nil) + LOGGER.debug activating.to_yaml unless activating.nil? + activating_smarts = URI.encode "\"#{activating.join("\"/\"")}\"" + deactivating_smarts = URI.encode "\"#{deactivating.join("\"/\"")}\"" + if highlight.nil? + File.join @@config[:services]["opentox-compound"], "smiles", URI.encode(smiles), "smarts/activating", URI.encode(activating_smarts),"deactivating", URI.encode(deactivating_smarts) + else + File.join @@config[:services]["opentox-compound"], "smiles", URI.encode(smiles), "smarts/activating", URI.encode(activating_smarts),"deactivating", URI.encode(deactivating_smarts), "highlight", URI.encode(highlight) + end + end + def image_uri - "#{@@cactus_uri}#{@inchi}/image" + File.join @uri, "image" end # Matchs a smarts string |