diff options
author | Christoph Helma <helma@in-silico.ch> | 2013-06-19 16:29:43 +0200 |
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committer | Christoph Helma <helma@in-silico.ch> | 2013-06-19 16:29:43 +0200 |
commit | bc9d5b9266e18d39ab5fd83db272bffde98c4161 (patch) | |
tree | e30a2a96d77b2f010c8b10316b2163d112613355 /lib | |
parent | 4dba36635f5d214c4453d2d0d67426d6f14f5b6b (diff) |
openbabel requirement removed. initial descriptor classes.
Diffstat (limited to 'lib')
-rw-r--r-- | lib/algorithm.rb | 29 | ||||
-rw-r--r-- | lib/compound.rb | 23 | ||||
-rw-r--r-- | lib/overwrite.rb | 8 |
3 files changed, 58 insertions, 2 deletions
diff --git a/lib/algorithm.rb b/lib/algorithm.rb index 8576681..1ffc883 100644 --- a/lib/algorithm.rb +++ b/lib/algorithm.rb @@ -5,11 +5,38 @@ module OpenTox # Execute algorithm with parameters, please consult the OpenTox API and the webservice documentation for acceptable parameters # @param [optional,Hash] params Algorithm parameters - # @param [optional,Boolean] wait set to true if method should wait for task result + # @param [optional,Boolean] wait set to false if method should return a task uri instead of the algorithm result # @return [String] URI of new resource (dataset, model, ...) def run params=nil, wait=true uri = RestClientWrapper.post @uri, params, { :content_type => "text/uri-list", :subjectid => @subjectid} wait_for_task uri if wait end end + + module Descriptor + + class Smarts + + def self.fingerprint compounds, smarts, count=false + matcher = Algorithm.new File.join($algorithm[:uri],"descriptor","smarts","fingerprint") + smarts = [smarts] unless smarts.is_a? Array + if compounds.is_a? OpenTox::Compound + json = matcher.run :compound_uri => compounds.uri, :smarts => smarts, :count => count + elsif compounds.is_a? OpenTox::Dataset + # TODO: add task and return dataset instead of result + json = matcher.run :dataset_uri => compounds.uri, :smarts => smarts, :count => count + else + bad_request_error "Cannot match smarts on #{compounds.class} objects." + end + + JSON.parse json + end + + def self.count compounds, smarts + fingerprint compounds,smarts,true + end + end + + + end end diff --git a/lib/compound.rb b/lib/compound.rb index 89bf840..daeabb9 100644 --- a/lib/compound.rb +++ b/lib/compound.rb @@ -1,4 +1,4 @@ -require "openbabel" +#require "openbabel" CACTUS_URI="http://cactus.nci.nih.gov/chemical/structure/" module OpenTox @@ -116,6 +116,27 @@ module OpenTox # compound.match?("cN") # returns false # @param [String] smarts Smarts string def match?(smarts) + matcher = Algorithm.new File.join($algorithm[:uri],"descriptor","smarts") + matcher.run :compound_uri => @uri, :smarts => smarts, :count => false + end + + # Match an array of smarts strings, returns array with matching smarts + # @example + # compound = OpenTox::Compound.from_name("Benzene") + # compound.match(['cc','cN']) # returns ['cc'] + # @param [Array] smarts_array Array with Smarts strings + # @return [Array] Array with matching Smarts strings + def match(smarts_array) + matcher = Algorithm.new File.join($algorithm[:uri],"descriptor","smarts") + matcher.run :compound_uri => @uri, :smarts => smarts_array, :count => false + end + + # Match a smarts string + # @example + # compound = OpenTox::Compound.from_name("Benzene") + # compound.match?("cN") # returns false + # @param [String] smarts Smarts string + def match?(smarts) obconversion = OpenBabel::OBConversion.new obmol = OpenBabel::OBMol.new obconversion.set_in_format('inchi') diff --git a/lib/overwrite.rb b/lib/overwrite.rb index 04de58d..b2382e0 100644 --- a/lib/overwrite.rb +++ b/lib/overwrite.rb @@ -28,6 +28,14 @@ class String downcase end + # convert strings to boolean values + # @return [TrueClass,FalseClass] true or false + def to_boolean + return true if self == true || self =~ (/(true|t|yes|y|1)$/i) + return false if self == false || self.nil? || self =~ (/(false|f|no|n|0)$/i) + bad_request_error "invalid value for Boolean: \"#{self}\"" + end + # encloses URI in text with with link tag # @return [String] new text with marked links def link_urls |