diff options
Diffstat (limited to 'lib/compound.rb')
| -rw-r--r-- | lib/compound.rb | 40 |
1 files changed, 40 insertions, 0 deletions
diff --git a/lib/compound.rb b/lib/compound.rb index f631ca9..e7b4da0 100644 --- a/lib/compound.rb +++ b/lib/compound.rb @@ -21,6 +21,17 @@ module OpenTox else @inchi = RestClientWrapper.get(@uri, :accept => 'chemical/x-inchi').to_s.chomp if @uri end + + if @uri and @inchi.to_s.size==0 + LOGGER.warn "REMOVE ABMIT HACK: no inchi for compound "+@uri.to_s+", load via smiles" + @inchi = Compound.smiles2inchi(Compound.smiles(@uri)) + end + end + + # request smiles from compound service via accept header + # @return smiles as string + def self.smiles(uri) + RestClientWrapper.get(uri, :accept => 'chemical/x-daylight-smiles').to_s.chomp end # Create a compound from smiles string @@ -153,6 +164,35 @@ module OpenTox #smarts_array.collect { |s| s if match?(s)}.compact end + # Match_hits an array of smarts strings, returns hash with matching smarts as key and number of non-unique hits as value + # @example + # compound = OpenTox::Compound.from_name("Benzene") + # compound.match(['cc','cN']) # returns ['cc'] + # @param [Array] smarts_array Array with Smarts strings + # @return [Hash] Hash with matching smarts as key and number of non-unique hits as value + def match_hits(smarts_array) + # avoid recreation of OpenBabel objects + obconversion = OpenBabel::OBConversion.new + obmol = OpenBabel::OBMol.new + obconversion.set_in_format('inchi') + obconversion.read_string(obmol,@inchi) + smarts_pattern = OpenBabel::OBSmartsPattern.new + smarts_hits = {} + #LOGGER.debug "dv ----------- obmol #{Compound.new(@inchi).to_smiles}" + smarts_array.collect do |smarts| + #LOGGER.debug "dv ----------- all smarts #{smarts}" + smarts_pattern.init(smarts) + if smarts_pattern.match(obmol) + hits = smarts_pattern.get_map_list + smarts_hits[smarts] = hits.size + end + end + #LOGGER.debug "dv ----------- smarts => hits #{smarts_hits}" + return smarts_hits + #smarts_array.collect { |s| s if match?(s)}.compact + end + + # Get URI of compound image with highlighted fragments # # @param [Array] activating Array with activating Smarts strings |