diff options
Diffstat (limited to 'fminer.rb')
| -rw-r--r-- | fminer.rb | 31 |
1 files changed, 19 insertions, 12 deletions
@@ -102,10 +102,9 @@ post '/fminer/:method/match?' do res_dataset.add_feature(f,m) end - step_width = 100 / c_dataset.compounds.size.to_f - count = 0 - if params[:nr_hits] == "true" + step_width = 100 / c_dataset.compounds.size.to_f + count = 0 c_dataset.compounds.each do |c| res_dataset.add_compound(c) comp = OpenTox::Compound.new(c) @@ -118,21 +117,29 @@ post '/fminer/:method/match?' do end else LOGGER.debug "match #{c_dataset.compounds.size} compounds with #{f_dataset.features.keys.size} features" - + step_width = 100 / f_dataset.features.size.to_f + count = 0 + obconversion = OpenBabel::OBConversion.new - obmol = OpenBabel::OBMol.new - obconversion.set_in_format('inchi') + obconversion.set_in_format('inchi') smarts_pattern = OpenBabel::OBSmartsPattern.new + + obmols = {} c_dataset.compounds.each do |c| res_dataset.add_compound(c) - comp = OpenTox::Compound.new(c) - obconversion.read_string(obmol,comp.inchi) - f_dataset.features.each do |f,m| - smarts_pattern.init(m[OT.smarts]) - res_dataset.add(c,f,1) if smarts_pattern.match(obmol) + inchi = OpenTox::Compound.new(c).inchi + obmol = OpenBabel::OBMol.new + obconversion.read_string(obmol,inchi) + obmols[c] = obmol + end + + f_dataset.features.each do |f,m| + smarts_pattern.init(m[OT.smarts]) + c_dataset.compounds.each do |c| + res_dataset.add(c,f,1) if smarts_pattern.match(obmols[c]) end count += 1 - task.progress step_width*count if count%100==0 + task.progress step_width*count if count%10==0 end end res_dataset.save @subjectid |