diff options
author | Christoph Helma <helma@in-silico.ch> | 2015-11-04 17:50:32 +0100 |
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committer | Christoph Helma <helma@in-silico.ch> | 2015-11-04 17:50:32 +0100 |
commit | c23f4b8a915c0df4f34b6c3787829e1f513df571 (patch) | |
tree | 298faed0b20077615357a6bc0a4b6d7e61bd8a16 | |
parent | ca2bb0f90335b1f2c4ecc28ee423e85b281ffcf0 (diff) | |
parent | 2081bda2b72f34758847fe699fecf890dae1e3df (diff) |
Merge branch 'development' of github.com:opentox/lazar into development
-rw-r--r-- | lib/compound.rb | 32 | ||||
-rw-r--r-- | lib/dataset.rb | 2 | ||||
-rw-r--r-- | lib/rest-client-wrapper.rb | 8 | ||||
-rw-r--r-- | test/compound.rb | 14 |
4 files changed, 51 insertions, 5 deletions
diff --git a/lib/compound.rb b/lib/compound.rb index c5e7f02..ad0eaba 100644 --- a/lib/compound.rb +++ b/lib/compound.rb @@ -21,6 +21,7 @@ module OpenTox field :png_id, type: BSON::ObjectId field :svg_id, type: BSON::ObjectId field :sdf_id, type: BSON::ObjectId + field :molecular_weight, type: Float field :fingerprints, type: Hash, default: {} field :default_fingerprint_size, type: Integer field :dataset_ids, type: Array, default: [] @@ -335,6 +336,37 @@ module OpenTox #$mongo["compounds"].aggregate(aggregate).collect{ |r| [r["_id"], r["tanimoto"]] } end + + # Get mg from logmmol (for nch LOAEL/pTD50 data) + # @return [Float] value in mg + def logmmol_to_mg(value, mw) + mg = (10**(-1.0*value.to_f)*(mw.to_f*1000)) + return mg + end + + # Get mg from mmol + # @return [Float] value in mg + def mmol_to_mg(value, mw) + mg = (value.to_f)*(mw.to_f) + return mg + end + + # Get mg from logmg + # @return [Float] value in mg + def logmg_to_mg(value) + mg = 10**value.to_f + return mg + end + + # Calculate molecular weight of Compound with OB and store it in object + # @return [Float] molecular weight + def molecular_weight + if self["molecular_weight"]==0.0 || self["molecular_weight"].nil? + update(:molecular_weight => OpenTox::Algorithm::Descriptor.physchem(self, ["Openbabel.MW"]).first) + end + self["molecular_weight"] + end + private diff --git a/lib/dataset.rb b/lib/dataset.rb index af116a9..366c79f 100644 --- a/lib/dataset.rb +++ b/lib/dataset.rb @@ -173,7 +173,7 @@ module OpenTox $logger.debug "Skipping import of #{file}, it is already in the database (id: #{dataset.id})." else $logger.debug "Parsing #{file}." - table = CSV.read file, :skip_blanks => true + table = CSV.read file, :skip_blanks => true, :encoding => 'windows-1251:utf-8' dataset = self.new(:source => source, :name => name) dataset.parse_table table, bioassay end diff --git a/lib/rest-client-wrapper.rb b/lib/rest-client-wrapper.rb index de1b74f..6b5d602 100644 --- a/lib/rest-client-wrapper.rb +++ b/lib/rest-client-wrapper.rb @@ -26,15 +26,15 @@ module OpenTox define_singleton_method method do |uri,payload={},headers={},waiting_task=nil| # check input - bad_request_error "Headers are not a hash: #{headers.inspect}", uri unless headers==nil or headers.is_a?(Hash) + bad_request_error "Headers are not a hash: #{headers.inspect} for #{uri}." unless headers==nil or headers.is_a?(Hash) headers[:subjectid] ||= @@subjectid - bad_request_error "Invalid URI: '#{uri}'", uri unless URI.valid? uri + bad_request_error "Invalid URI: '#{uri}'" unless URI.valid? uri #resource_not_found_error "URI '#{uri}' not found.", uri unless URI.accessible?(uri, @subjectid) unless URI.ssl?(uri) # make sure that no header parameters are set in the payload [:accept,:content_type,:subjectid].each do |header| if defined? $aa || URI(uri).host == URI($aa[:uri]).host else - bad_request_error "#{header} should be submitted in the headers", uri if payload and payload.is_a?(Hash) and payload[header] + bad_request_error "#{header} should be submitted in the headers of URI: #{uri}" if payload and payload.is_a?(Hash) and payload[header] end end @@ -72,7 +72,7 @@ module OpenTox msg = "Could not parse error response from rest call '#{method}' to '#{uri}':\n#{response}" cause = nil end - Object.method(error[:method]).call msg, uri, cause # call error method + Object.method(error[:method]).call "#{msg}, #{uri}, #{cause}" # call error method else response end diff --git a/test/compound.rb b/test/compound.rb index ff20c1c..50cc5aa 100644 --- a/test/compound.rb +++ b/test/compound.rb @@ -184,4 +184,18 @@ print c.sdf #assert_equal neighbors, neighbors2 end end + + def test_molecular_weight + c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C" + assert_equal 100.15888, c.molecular_weight + end + + def test_mg_conversions + c = OpenTox::Compound.from_smiles "O" + mw = c.molecular_weight + assert_equal 18.01528, mw + assert_equal 0.8105107141417474, c.logmmol_to_mg(4.34688225631145, mw) + assert_equal 9007.64, c.mmol_to_mg(500, mw) + assert_equal 2437.9999984148976, c.logmg_to_mg(3.387033701) + end end |