mspire-lipid 0.2.0
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- checksums.yaml +7 -0
- data/.document +5 -0
- data/.gitignore +53 -0
- data/.rspec +1 -0
- data/Gemfile +4 -0
- data/LICENSE +21 -0
- data/README.md +11 -0
- data/Rakefile +24 -0
- data/bin/lipidomic-search.rb +203 -0
- data/lib/mspire/lipid.rb +19 -0
- data/lib/mspire/lipid/ion.rb +71 -0
- data/lib/mspire/lipid/ion/fragment.rb +68 -0
- data/lib/mspire/lipid/modification.rb +120 -0
- data/lib/mspire/lipid/search.rb +205 -0
- data/lib/mspire/lipid/search/bin.rb +79 -0
- data/lib/mspire/lipid/search/db_isobar_group.rb +20 -0
- data/lib/mspire/lipid/search/hit.rb +79 -0
- data/lib/mspire/lipid/search/probability_distribution.rb +50 -0
- data/lib/mspire/lipid/search/query.rb +23 -0
- data/lib/mspire/lipid/version.rb +6 -0
- data/lib/mspire/lipid_maps.rb +110 -0
- data/mspire-lipid.gemspec +38 -0
- data/scratch/OBConversion_methods.txt +47 -0
- data/scratch/atom_methods.txt +145 -0
- data/scratch/bond_methods.txt +867 -0
- data/scratch/mol_methods.txt +183 -0
- data/scratch/split_molecules.rb +93 -0
- data/script/find_nearest_lipid.rb +134 -0
- data/spec/mspire/lipid/ion_spec.rb +96 -0
- data/spec/mspire/lipid/modification_spec.rb +70 -0
- data/spec/mspire/lipid/search_spec.rb +82 -0
- data/spec/mspire/lipid_maps_spec.rb +64 -0
- data/spec/mspire/lipid_spec.rb +16 -0
- data/spec/spec_helper.rb +13 -0
- data/spec/testfiles/lipidmaps_download.tsv +11 -0
- data/spec/testfiles/lipidmaps_programmatic_short.tsv +32 -0
- data/spec/testfiles/lipidmaps_sd_download.tsv +11 -0
- metadata +202 -0
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module Mspire
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class Lipid
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class Search
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class ProbabilityDistribution
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DEFAULT_TYPE = :ppm
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R = Rserve::Simpler.new
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# takes location, scale and shape parameters
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attr_accessor :location, :scale, :shape
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# type is :ppm or :delta_abs
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attr_accessor :type
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def initialize(location, scale, shape, type=DEFAULT_TYPE)
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@location, @scale, @shape = location, scale, shape
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@type = type
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end
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# takes a deviation and returns the pvalue
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def pvalue(hit)
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R.converse "pgev(log(#{hit.send(type)}), #{@location}, #{@scale}, #{@shape})"
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end
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# same as pvalue, just tries to limit the number of calls to R to
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# speed things up!
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def pvalues(hits)
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deltas = hits.map {|v| v.send(type).abs }
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reply = R.converse("sapply(r_devs, function(elt) pgev(log(elt), #{@location}, #{@scale}, #{@shape}))", :r_devs => deltas)
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reply.is_a?(Array) ? reply : [reply]
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end
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def self.require_r_library(lib)
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reply = R.converse "library(#{lib})"
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unless reply.size > 4 # ~roughly
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$stderr.puts "The libraries ismev and evd must be installed in your R env!"
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$stderr.puts "From within R (works best if R is started with sudo or root for installing):"
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$stderr.puts %Q{install.packages("ismev") ; install.packages("evd")}
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raise "must have R (rserve) and ismev and evd installed!"
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end
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end
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# returns an EVD object
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def self.deviations_to_probability_distribution(type, devs)
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%w(ismev evd).each {|lib| require_r_library(lib) }
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params = R.converse("m <- gev.fit(log(devs_r))\n c(m$mle[1], m$mle[2], m$mle[3])", :devs_r => devs )
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self.new(*params, type)
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end
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end
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end
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end
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end
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module Mspire
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class Lipid
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class Search
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class Query
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# the experimentally observed lowest mz
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attr_accessor :mz
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# the index of search spectrum that the m/z was derived from
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# this allows for the creation of an isotope envelope starting from a
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# particular m/z value.
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attr_accessor :index
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def initialize(mz, index)
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@mz, @index = mz, index
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end
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end
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end
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end
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end
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require 'mspire/lipid'
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require 'mspire/mass'
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module Mspire
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module LipidMaps
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DEFAULTS = {
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:high_res_mass => true,
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:rubabel_molecules => false,
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:molecular_formula_objects => true,
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}
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# returns an array of Lipids
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# if high_res_mass is true (default), then the formula is used to calculate a higher
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# resolution mass than what is in lipidmaps
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#
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# :high_res_mass => true (ensures that a high res mass is present or calculated)
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def self.parse_file(lipidmaps_tsv, opts={})
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require 'rubabel' if opts[:rubabel_molecules]
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opts = DEFAULTS.merge(opts)
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io = File.open(lipidmaps_tsv)
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header = io.readline.split("\t")
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# the lipidmaps_filetype
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lm_ft = case header.size
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when 8
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:programmatic
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when 20
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:download
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when 21
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:download_sd
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when 22
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:download_2013
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when 23
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:download_sd_2013 # <- have not test this yet
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end
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index_mapping =
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case lm_ft
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when :programmatic
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(0...(Mspire::Lipid.members.size)).to_a
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when :download, :download_sd
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indices = {
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:lm_id => 0,
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:systematic_name => 1,
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:category => 3,
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:main_class => 4,
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:mass => 5,
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:formula => 6,
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:pubchem_id => 7,
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:inchi_key => 8,
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:common_name => 11,
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:kegg_id => 12,
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:chebi_id => 13,
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:sub_class => 14,
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:structure => 20,
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}
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Mspire::Lipid.members.map {|key| indices[key] }
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when :download_2013, :download_sd_2013
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indices = {
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:lm_id => 2,
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:systematic_name => 3,
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:category => 5,
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:main_class => 6,
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:mass => 7,
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:formula => 8,
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:pubchem_id => 9,
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# add in future->?
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#:pubchem_cid => 10,
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:inchi_key => 11,
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:common_name => 13,
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:kegg_id => 14,
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:chebi_id => 15,
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:sub_class => 16,
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:structure => 22,
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}
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Mspire::Lipid.members.map {|key| indices[key] }
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end
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formula_i = index_mapping[Mspire::Lipid.members.index(:formula)]
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lipids = io.each_line.map do |line|
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line.chomp!
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data = line.split("\t")
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if data[formula_i] =~ /[A-Z]/ # <- there is a formula!
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lipid = Mspire::Lipid.new( *index_mapping.map {|i| data[i] } )
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lipid.mass = lipid.mass.to_f
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lipid
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end
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end.compact
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if opts.values_at(:molecular_formula_objects, :rubabel_molecules).any? || (opts[:high_res_mass] && lm_ft == :programmatic)
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lipids.each do |lipid|
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if opts[:molecular_formula_objects]
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lipid.formula = Mspire::MolecularFormula.from_string(lipid.formula)
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end
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if lm_ft == :programmatic && opts[:high_res_mass]
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lipid.mass = lipid.formula.mass
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end
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if opts[:rubabel_molecules]
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lipid.structure = Rubabel::Molecule.from_string(lipid.structure.gsub('|', "\n"), :sdf)
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end
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end
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end
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lipids
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end
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end
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end
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# coding: utf-8
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lib = File.expand_path('../lib', __FILE__)
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$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
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require 'mspire/lipid/version'
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Gem::Specification.new do |spec|
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spec.name = "mspire-lipid"
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spec.version = Mspire::Lipid::VERSION
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spec.authors = ["John T. Prince"]
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spec.email = ["jtprince@gmail.com"]
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spec.summary = %q{mass spectrometry based lipidomics - especially shotgun lipidomics}
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spec.description = %q{mass spectrometry based lipidomics - especially shotgun lipidomics.}
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spec.homepage = ""
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spec.license = "MIT"
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spec.files = `git ls-files -z`.split("\x0")
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spec.executables = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
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spec.test_files = spec.files.grep(%r{^(test|spec|features)/})
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spec.require_paths = ["lib"]
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[
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["mspire-molecular_formula", "~> 0.1.0"],
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["rubabel", ">= 0.1.6"],
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].each do |args|
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spec.add_dependency(*args)
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end
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[
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["bundler", "~> 1.6.2"],
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["rake"],
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["rspec", "~> 2.14.1"],
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["rdoc", "~> 4.1.1"],
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["simplecov", "~> 0.8.2"],
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["fftw3"], # just until not needed in mspire-molform
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].each do |args|
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spec.add_development_dependency(*args)
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end
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end
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get_in_stream
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get_out_stream
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set_in_stream
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set_out_stream
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set_in_and_out_formats
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set_in_format
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set_out_format
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get_in_format
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get_out_format
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get_in_filename
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get_in_pos
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get_in_len
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get_title
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get_aux_conv
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set_aux_conv
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is_option
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get_options
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add_option
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remove_option
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set_options
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copy_options
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get_supported_input_format
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get_supported_output_format
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convert
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full_convert
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add_chem_object
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get_chem_object
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is_last
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is_first_input
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set_first_input
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get_output_index
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set_output_index
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set_more_files_to_come
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set_one_object_only
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set_last
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is_last_file
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get_count
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write
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write_string
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write_file
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close_out_file
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read
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read_string
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read_file
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open_in_and_out_files
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report_number_converted
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num_input_objects
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Visit=
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Visit
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duplicate
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set_idx
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set_id
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set_hyb
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set_atomic_num
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set_isotope
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set_implicit_valence
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increment_implicit_valence
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decrement_implicit_valence
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set_formal_charge
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set_spin_multiplicity
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set_type
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set_partial_charge
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set_coord_ptr
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set_vector
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set_residue
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set_parent
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set_aromatic
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unset_aromatic
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set_clockwise_stereo
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set_anti_clockwise_stereo
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set_positive_stereo
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set_negative_stereo
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unset_stereo
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set_in_ring
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set_chiral
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clear_coord_ptr
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get_formal_charge
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get_atomic_num
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get_isotope
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get_spin_multiplicity
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get_atomic_mass
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get_exact_mass
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get_idx
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get_index
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get_id
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get_coordinate_idx
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get_cidx
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get_valence
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get_hyb
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get_implicit_valence
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get_hvy_valence
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get_hetero_valence
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get_type
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get_x
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get_y
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get_z
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x
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y
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z
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get_coordinate
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get_vector
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get_partial_charge
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get_residue
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get_parent
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get_new_bond_vector
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get_bond
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get_next_atom
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begin_bonds
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end_bonds
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begin_bond
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next_bond
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begin_nbr_atom
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next_nbr_atom
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get_distance
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get_angle
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new_residue
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add_residue
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delete_residue
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add_bond
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insert_bond
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delete_bond
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clear_bond
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hto_methyl
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set_hyb_and_geom
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force_no_h
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has_no_hforced
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force_impl_h
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has_impl_hforced
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count_free_oxygens
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implicit_hydrogen_count
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explicit_hydrogen_count
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member_of_ring_count
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member_of_ring_size
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count_ring_bonds
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smallest_bond_angle
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average_bond_angle
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bosum
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kbosum
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has_residue
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is_carbon
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is_heteroatom
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is_carboxyl_oxygen
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is_amide_nitrogen
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is_polar_hydrogen
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is_non_polar_hydrogen
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is_aromatic_noxide
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is_chiral
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is_axial
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is_clockwise
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is_positive_stereo
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has_chirality_specified
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has_chiral_volume
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is_hbond_acceptor
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is_hbond_donor
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is_hbond_donor_h
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has_alpha_beta_unsat
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has_bond_of_order
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count_bonds_of_order
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has_non_single_bond
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has_aromatic_bond
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matches_smarts
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clear
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do_transformations
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get_title
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set_title
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has_data
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delete_data
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clone_data
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data_size
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get_all_data
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get_data
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begin_data
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end_data
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@@ -0,0 +1,867 @@
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Visit=
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Visit
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set_idx
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set_id
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set_bo
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set_bond_order
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set_begin
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set_end
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set_parent
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set_length
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set
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set_ksingle
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set_kdouble
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set_ktriple
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set_aromatic
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set_wedge
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set_hash
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set_wedge_or_hash
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set_up
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set_down
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set_in_ring
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set_closure
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unset_hash
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unset_wedge
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unset_up
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unset_down
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unset_aromatic
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unset_kekule
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get_idx
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get_id
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get_bo
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get_bond_order
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get_flags
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get_begin_atom_idx
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get_end_atom_idx
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get_begin_atom
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get_end_atom
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get_nbr_atom
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+
get_parent
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40
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+
get_equib_length
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+
get_length
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42
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+
get_nbr_atom_idx
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+
find_smallest_ring
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44
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+
is_aromatic
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45
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+
is_in_ring
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46
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+
is_rotor
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is_amide
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is_primary_amide
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is_secondary_amide
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is_tertiary_amide
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is_ester
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is_carbonyl
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is_single
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is_double
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is_triple
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is_ksingle
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is_kdouble
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is_ktriple
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is_closure
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is_up
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is_down
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is_wedge
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is_hash
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is_wedge_or_hash
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is_cis_or_trans
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+
is_double_bond_geometry
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+
clear
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+
do_transformations
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+
get_title
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set_title
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+
has_data
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+
delete_data
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+
clone_data
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+
data_size
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+
get_all_data
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+
get_data
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begin_data
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end_data
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Visit=
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Visit
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set_idx
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set_id
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set_bo
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set_bond_order
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set_begin
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set_end
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set_parent
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set_length
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set
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set_ksingle
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set_kdouble
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set_ktriple
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set_aromatic
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set_wedge
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set_hash
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set_wedge_or_hash
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set_up
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set_down
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set_in_ring
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set_closure
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+
unset_hash
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unset_wedge
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unset_up
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unset_down
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+
unset_aromatic
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unset_kekule
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+
get_idx
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get_id
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get_bo
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get_bond_order
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+
get_flags
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+
get_begin_atom_idx
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+
get_end_atom_idx
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114
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+
get_begin_atom
|
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115
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+
get_end_atom
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116
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+
get_nbr_atom
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+
get_parent
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118
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+
get_equib_length
|
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119
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+
get_length
|
|
120
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+
get_nbr_atom_idx
|
|
121
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+
find_smallest_ring
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122
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+
is_aromatic
|
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123
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+
is_in_ring
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124
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is_rotor
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is_amide
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126
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is_primary_amide
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is_secondary_amide
|
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is_tertiary_amide
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is_ester
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is_carbonyl
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is_single
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is_double
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is_triple
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is_ksingle
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is_kdouble
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is_ktriple
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is_closure
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is_up
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is_down
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is_wedge
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is_hash
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is_wedge_or_hash
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+
is_cis_or_trans
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144
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+
is_double_bond_geometry
|
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145
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+
clear
|
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146
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+
do_transformations
|
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147
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+
get_title
|
|
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+
set_title
|
|
149
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+
has_data
|
|
150
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+
delete_data
|
|
151
|
+
clone_data
|
|
152
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+
data_size
|
|
153
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+
get_all_data
|
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154
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+
get_data
|
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155
|
+
begin_data
|
|
156
|
+
end_data
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157
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+
Visit=
|
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+
Visit
|
|
159
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+
set_idx
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+
set_id
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+
set_bo
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+
set_bond_order
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163
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+
set_begin
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164
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+
set_end
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165
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+
set_parent
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166
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+
set_length
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167
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+
set
|
|
168
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+
set_ksingle
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169
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+
set_kdouble
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|
170
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+
set_ktriple
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171
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+
set_aromatic
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172
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+
set_wedge
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173
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+
set_hash
|
|
174
|
+
set_wedge_or_hash
|
|
175
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+
set_up
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176
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+
set_down
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177
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+
set_in_ring
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+
set_closure
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179
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+
unset_hash
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|
180
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+
unset_wedge
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181
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+
unset_up
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|
182
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+
unset_down
|
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183
|
+
unset_aromatic
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|
184
|
+
unset_kekule
|
|
185
|
+
get_idx
|
|
186
|
+
get_id
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|
187
|
+
get_bo
|
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188
|
+
get_bond_order
|
|
189
|
+
get_flags
|
|
190
|
+
get_begin_atom_idx
|
|
191
|
+
get_end_atom_idx
|
|
192
|
+
get_begin_atom
|
|
193
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+
get_end_atom
|
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194
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+
get_nbr_atom
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195
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+
get_parent
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|
196
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+
get_equib_length
|
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197
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+
get_length
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|
198
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+
get_nbr_atom_idx
|
|
199
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+
find_smallest_ring
|
|
200
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+
is_aromatic
|
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201
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+
is_in_ring
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is_rotor
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is_amide
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is_primary_amide
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is_secondary_amide
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206
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is_tertiary_amide
|
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207
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is_ester
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is_carbonyl
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is_single
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|
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is_double
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|
211
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is_triple
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212
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+
is_ksingle
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213
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is_kdouble
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|
214
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+
is_ktriple
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|
215
|
+
is_closure
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|
216
|
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is_up
|
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217
|
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is_down
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218
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+
is_wedge
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219
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+
is_hash
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220
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+
is_wedge_or_hash
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|
221
|
+
is_cis_or_trans
|
|
222
|
+
is_double_bond_geometry
|
|
223
|
+
clear
|
|
224
|
+
do_transformations
|
|
225
|
+
get_title
|
|
226
|
+
set_title
|
|
227
|
+
has_data
|
|
228
|
+
delete_data
|
|
229
|
+
clone_data
|
|
230
|
+
data_size
|
|
231
|
+
get_all_data
|
|
232
|
+
get_data
|
|
233
|
+
begin_data
|
|
234
|
+
end_data
|
|
235
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+
Visit=
|
|
236
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+
Visit
|
|
237
|
+
set_idx
|
|
238
|
+
set_id
|
|
239
|
+
set_bo
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|
240
|
+
set_bond_order
|
|
241
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+
set_begin
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|
242
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+
set_end
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|
243
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+
set_parent
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|
244
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+
set_length
|
|
245
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+
set
|
|
246
|
+
set_ksingle
|
|
247
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+
set_kdouble
|
|
248
|
+
set_ktriple
|
|
249
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+
set_aromatic
|
|
250
|
+
set_wedge
|
|
251
|
+
set_hash
|
|
252
|
+
set_wedge_or_hash
|
|
253
|
+
set_up
|
|
254
|
+
set_down
|
|
255
|
+
set_in_ring
|
|
256
|
+
set_closure
|
|
257
|
+
unset_hash
|
|
258
|
+
unset_wedge
|
|
259
|
+
unset_up
|
|
260
|
+
unset_down
|
|
261
|
+
unset_aromatic
|
|
262
|
+
unset_kekule
|
|
263
|
+
get_idx
|
|
264
|
+
get_id
|
|
265
|
+
get_bo
|
|
266
|
+
get_bond_order
|
|
267
|
+
get_flags
|
|
268
|
+
get_begin_atom_idx
|
|
269
|
+
get_end_atom_idx
|
|
270
|
+
get_begin_atom
|
|
271
|
+
get_end_atom
|
|
272
|
+
get_nbr_atom
|
|
273
|
+
get_parent
|
|
274
|
+
get_equib_length
|
|
275
|
+
get_length
|
|
276
|
+
get_nbr_atom_idx
|
|
277
|
+
find_smallest_ring
|
|
278
|
+
is_aromatic
|
|
279
|
+
is_in_ring
|
|
280
|
+
is_rotor
|
|
281
|
+
is_amide
|
|
282
|
+
is_primary_amide
|
|
283
|
+
is_secondary_amide
|
|
284
|
+
is_tertiary_amide
|
|
285
|
+
is_ester
|
|
286
|
+
is_carbonyl
|
|
287
|
+
is_single
|
|
288
|
+
is_double
|
|
289
|
+
is_triple
|
|
290
|
+
is_ksingle
|
|
291
|
+
is_kdouble
|
|
292
|
+
is_ktriple
|
|
293
|
+
is_closure
|
|
294
|
+
is_up
|
|
295
|
+
is_down
|
|
296
|
+
is_wedge
|
|
297
|
+
is_hash
|
|
298
|
+
is_wedge_or_hash
|
|
299
|
+
is_cis_or_trans
|
|
300
|
+
is_double_bond_geometry
|
|
301
|
+
clear
|
|
302
|
+
do_transformations
|
|
303
|
+
get_title
|
|
304
|
+
set_title
|
|
305
|
+
has_data
|
|
306
|
+
delete_data
|
|
307
|
+
clone_data
|
|
308
|
+
data_size
|
|
309
|
+
get_all_data
|
|
310
|
+
get_data
|
|
311
|
+
begin_data
|
|
312
|
+
end_data
|
|
313
|
+
Visit=
|
|
314
|
+
Visit
|
|
315
|
+
set_idx
|
|
316
|
+
set_id
|
|
317
|
+
set_bo
|
|
318
|
+
set_bond_order
|
|
319
|
+
set_begin
|
|
320
|
+
set_end
|
|
321
|
+
set_parent
|
|
322
|
+
set_length
|
|
323
|
+
set
|
|
324
|
+
set_ksingle
|
|
325
|
+
set_kdouble
|
|
326
|
+
set_ktriple
|
|
327
|
+
set_aromatic
|
|
328
|
+
set_wedge
|
|
329
|
+
set_hash
|
|
330
|
+
set_wedge_or_hash
|
|
331
|
+
set_up
|
|
332
|
+
set_down
|
|
333
|
+
set_in_ring
|
|
334
|
+
set_closure
|
|
335
|
+
unset_hash
|
|
336
|
+
unset_wedge
|
|
337
|
+
unset_up
|
|
338
|
+
unset_down
|
|
339
|
+
unset_aromatic
|
|
340
|
+
unset_kekule
|
|
341
|
+
get_idx
|
|
342
|
+
get_id
|
|
343
|
+
get_bo
|
|
344
|
+
get_bond_order
|
|
345
|
+
get_flags
|
|
346
|
+
get_begin_atom_idx
|
|
347
|
+
get_end_atom_idx
|
|
348
|
+
get_begin_atom
|
|
349
|
+
get_end_atom
|
|
350
|
+
get_nbr_atom
|
|
351
|
+
get_parent
|
|
352
|
+
get_equib_length
|
|
353
|
+
get_length
|
|
354
|
+
get_nbr_atom_idx
|
|
355
|
+
find_smallest_ring
|
|
356
|
+
is_aromatic
|
|
357
|
+
is_in_ring
|
|
358
|
+
is_rotor
|
|
359
|
+
is_amide
|
|
360
|
+
is_primary_amide
|
|
361
|
+
is_secondary_amide
|
|
362
|
+
is_tertiary_amide
|
|
363
|
+
is_ester
|
|
364
|
+
is_carbonyl
|
|
365
|
+
is_single
|
|
366
|
+
is_double
|
|
367
|
+
is_triple
|
|
368
|
+
is_ksingle
|
|
369
|
+
is_kdouble
|
|
370
|
+
is_ktriple
|
|
371
|
+
is_closure
|
|
372
|
+
is_up
|
|
373
|
+
is_down
|
|
374
|
+
is_wedge
|
|
375
|
+
is_hash
|
|
376
|
+
is_wedge_or_hash
|
|
377
|
+
is_cis_or_trans
|
|
378
|
+
is_double_bond_geometry
|
|
379
|
+
clear
|
|
380
|
+
do_transformations
|
|
381
|
+
get_title
|
|
382
|
+
set_title
|
|
383
|
+
has_data
|
|
384
|
+
delete_data
|
|
385
|
+
clone_data
|
|
386
|
+
data_size
|
|
387
|
+
get_all_data
|
|
388
|
+
get_data
|
|
389
|
+
begin_data
|
|
390
|
+
end_data
|
|
391
|
+
Visit=
|
|
392
|
+
Visit
|
|
393
|
+
set_idx
|
|
394
|
+
set_id
|
|
395
|
+
set_bo
|
|
396
|
+
set_bond_order
|
|
397
|
+
set_begin
|
|
398
|
+
set_end
|
|
399
|
+
set_parent
|
|
400
|
+
set_length
|
|
401
|
+
set
|
|
402
|
+
set_ksingle
|
|
403
|
+
set_kdouble
|
|
404
|
+
set_ktriple
|
|
405
|
+
set_aromatic
|
|
406
|
+
set_wedge
|
|
407
|
+
set_hash
|
|
408
|
+
set_wedge_or_hash
|
|
409
|
+
set_up
|
|
410
|
+
set_down
|
|
411
|
+
set_in_ring
|
|
412
|
+
set_closure
|
|
413
|
+
unset_hash
|
|
414
|
+
unset_wedge
|
|
415
|
+
unset_up
|
|
416
|
+
unset_down
|
|
417
|
+
unset_aromatic
|
|
418
|
+
unset_kekule
|
|
419
|
+
get_idx
|
|
420
|
+
get_id
|
|
421
|
+
get_bo
|
|
422
|
+
get_bond_order
|
|
423
|
+
get_flags
|
|
424
|
+
get_begin_atom_idx
|
|
425
|
+
get_end_atom_idx
|
|
426
|
+
get_begin_atom
|
|
427
|
+
get_end_atom
|
|
428
|
+
get_nbr_atom
|
|
429
|
+
get_parent
|
|
430
|
+
get_equib_length
|
|
431
|
+
get_length
|
|
432
|
+
get_nbr_atom_idx
|
|
433
|
+
find_smallest_ring
|
|
434
|
+
is_aromatic
|
|
435
|
+
is_in_ring
|
|
436
|
+
is_rotor
|
|
437
|
+
is_amide
|
|
438
|
+
is_primary_amide
|
|
439
|
+
is_secondary_amide
|
|
440
|
+
is_tertiary_amide
|
|
441
|
+
is_ester
|
|
442
|
+
is_carbonyl
|
|
443
|
+
is_single
|
|
444
|
+
is_double
|
|
445
|
+
is_triple
|
|
446
|
+
is_ksingle
|
|
447
|
+
is_kdouble
|
|
448
|
+
is_ktriple
|
|
449
|
+
is_closure
|
|
450
|
+
is_up
|
|
451
|
+
is_down
|
|
452
|
+
is_wedge
|
|
453
|
+
is_hash
|
|
454
|
+
is_wedge_or_hash
|
|
455
|
+
is_cis_or_trans
|
|
456
|
+
is_double_bond_geometry
|
|
457
|
+
clear
|
|
458
|
+
do_transformations
|
|
459
|
+
get_title
|
|
460
|
+
set_title
|
|
461
|
+
has_data
|
|
462
|
+
delete_data
|
|
463
|
+
clone_data
|
|
464
|
+
data_size
|
|
465
|
+
get_all_data
|
|
466
|
+
get_data
|
|
467
|
+
begin_data
|
|
468
|
+
end_data
|
|
469
|
+
Visit=
|
|
470
|
+
Visit
|
|
471
|
+
set_idx
|
|
472
|
+
set_id
|
|
473
|
+
set_bo
|
|
474
|
+
set_bond_order
|
|
475
|
+
set_begin
|
|
476
|
+
set_end
|
|
477
|
+
set_parent
|
|
478
|
+
set_length
|
|
479
|
+
set
|
|
480
|
+
set_ksingle
|
|
481
|
+
set_kdouble
|
|
482
|
+
set_ktriple
|
|
483
|
+
set_aromatic
|
|
484
|
+
set_wedge
|
|
485
|
+
set_hash
|
|
486
|
+
set_wedge_or_hash
|
|
487
|
+
set_up
|
|
488
|
+
set_down
|
|
489
|
+
set_in_ring
|
|
490
|
+
set_closure
|
|
491
|
+
unset_hash
|
|
492
|
+
unset_wedge
|
|
493
|
+
unset_up
|
|
494
|
+
unset_down
|
|
495
|
+
unset_aromatic
|
|
496
|
+
unset_kekule
|
|
497
|
+
get_idx
|
|
498
|
+
get_id
|
|
499
|
+
get_bo
|
|
500
|
+
get_bond_order
|
|
501
|
+
get_flags
|
|
502
|
+
get_begin_atom_idx
|
|
503
|
+
get_end_atom_idx
|
|
504
|
+
get_begin_atom
|
|
505
|
+
get_end_atom
|
|
506
|
+
get_nbr_atom
|
|
507
|
+
get_parent
|
|
508
|
+
get_equib_length
|
|
509
|
+
get_length
|
|
510
|
+
get_nbr_atom_idx
|
|
511
|
+
find_smallest_ring
|
|
512
|
+
is_aromatic
|
|
513
|
+
is_in_ring
|
|
514
|
+
is_rotor
|
|
515
|
+
is_amide
|
|
516
|
+
is_primary_amide
|
|
517
|
+
is_secondary_amide
|
|
518
|
+
is_tertiary_amide
|
|
519
|
+
is_ester
|
|
520
|
+
is_carbonyl
|
|
521
|
+
is_single
|
|
522
|
+
is_double
|
|
523
|
+
is_triple
|
|
524
|
+
is_ksingle
|
|
525
|
+
is_kdouble
|
|
526
|
+
is_ktriple
|
|
527
|
+
is_closure
|
|
528
|
+
is_up
|
|
529
|
+
is_down
|
|
530
|
+
is_wedge
|
|
531
|
+
is_hash
|
|
532
|
+
is_wedge_or_hash
|
|
533
|
+
is_cis_or_trans
|
|
534
|
+
is_double_bond_geometry
|
|
535
|
+
clear
|
|
536
|
+
do_transformations
|
|
537
|
+
get_title
|
|
538
|
+
set_title
|
|
539
|
+
has_data
|
|
540
|
+
delete_data
|
|
541
|
+
clone_data
|
|
542
|
+
data_size
|
|
543
|
+
get_all_data
|
|
544
|
+
get_data
|
|
545
|
+
begin_data
|
|
546
|
+
end_data
|
|
547
|
+
Visit=
|
|
548
|
+
Visit
|
|
549
|
+
set_idx
|
|
550
|
+
set_id
|
|
551
|
+
set_bo
|
|
552
|
+
set_bond_order
|
|
553
|
+
set_begin
|
|
554
|
+
set_end
|
|
555
|
+
set_parent
|
|
556
|
+
set_length
|
|
557
|
+
set
|
|
558
|
+
set_ksingle
|
|
559
|
+
set_kdouble
|
|
560
|
+
set_ktriple
|
|
561
|
+
set_aromatic
|
|
562
|
+
set_wedge
|
|
563
|
+
set_hash
|
|
564
|
+
set_wedge_or_hash
|
|
565
|
+
set_up
|
|
566
|
+
set_down
|
|
567
|
+
set_in_ring
|
|
568
|
+
set_closure
|
|
569
|
+
unset_hash
|
|
570
|
+
unset_wedge
|
|
571
|
+
unset_up
|
|
572
|
+
unset_down
|
|
573
|
+
unset_aromatic
|
|
574
|
+
unset_kekule
|
|
575
|
+
get_idx
|
|
576
|
+
get_id
|
|
577
|
+
get_bo
|
|
578
|
+
get_bond_order
|
|
579
|
+
get_flags
|
|
580
|
+
get_begin_atom_idx
|
|
581
|
+
get_end_atom_idx
|
|
582
|
+
get_begin_atom
|
|
583
|
+
get_end_atom
|
|
584
|
+
get_nbr_atom
|
|
585
|
+
get_parent
|
|
586
|
+
get_equib_length
|
|
587
|
+
get_length
|
|
588
|
+
get_nbr_atom_idx
|
|
589
|
+
find_smallest_ring
|
|
590
|
+
is_aromatic
|
|
591
|
+
is_in_ring
|
|
592
|
+
is_rotor
|
|
593
|
+
is_amide
|
|
594
|
+
is_primary_amide
|
|
595
|
+
is_secondary_amide
|
|
596
|
+
is_tertiary_amide
|
|
597
|
+
is_ester
|
|
598
|
+
is_carbonyl
|
|
599
|
+
is_single
|
|
600
|
+
is_double
|
|
601
|
+
is_triple
|
|
602
|
+
is_ksingle
|
|
603
|
+
is_kdouble
|
|
604
|
+
is_ktriple
|
|
605
|
+
is_closure
|
|
606
|
+
is_up
|
|
607
|
+
is_down
|
|
608
|
+
is_wedge
|
|
609
|
+
is_hash
|
|
610
|
+
is_wedge_or_hash
|
|
611
|
+
is_cis_or_trans
|
|
612
|
+
is_double_bond_geometry
|
|
613
|
+
clear
|
|
614
|
+
do_transformations
|
|
615
|
+
get_title
|
|
616
|
+
set_title
|
|
617
|
+
has_data
|
|
618
|
+
delete_data
|
|
619
|
+
clone_data
|
|
620
|
+
data_size
|
|
621
|
+
get_all_data
|
|
622
|
+
get_data
|
|
623
|
+
begin_data
|
|
624
|
+
end_data
|
|
625
|
+
Visit=
|
|
626
|
+
Visit
|
|
627
|
+
set_idx
|
|
628
|
+
set_id
|
|
629
|
+
set_bo
|
|
630
|
+
set_bond_order
|
|
631
|
+
set_begin
|
|
632
|
+
set_end
|
|
633
|
+
set_parent
|
|
634
|
+
set_length
|
|
635
|
+
set
|
|
636
|
+
set_ksingle
|
|
637
|
+
set_kdouble
|
|
638
|
+
set_ktriple
|
|
639
|
+
set_aromatic
|
|
640
|
+
set_wedge
|
|
641
|
+
set_hash
|
|
642
|
+
set_wedge_or_hash
|
|
643
|
+
set_up
|
|
644
|
+
set_down
|
|
645
|
+
set_in_ring
|
|
646
|
+
set_closure
|
|
647
|
+
unset_hash
|
|
648
|
+
unset_wedge
|
|
649
|
+
unset_up
|
|
650
|
+
unset_down
|
|
651
|
+
unset_aromatic
|
|
652
|
+
unset_kekule
|
|
653
|
+
get_idx
|
|
654
|
+
get_id
|
|
655
|
+
get_bo
|
|
656
|
+
get_bond_order
|
|
657
|
+
get_flags
|
|
658
|
+
get_begin_atom_idx
|
|
659
|
+
get_end_atom_idx
|
|
660
|
+
get_begin_atom
|
|
661
|
+
get_end_atom
|
|
662
|
+
get_nbr_atom
|
|
663
|
+
get_parent
|
|
664
|
+
get_equib_length
|
|
665
|
+
get_length
|
|
666
|
+
get_nbr_atom_idx
|
|
667
|
+
find_smallest_ring
|
|
668
|
+
is_aromatic
|
|
669
|
+
is_in_ring
|
|
670
|
+
is_rotor
|
|
671
|
+
is_amide
|
|
672
|
+
is_primary_amide
|
|
673
|
+
is_secondary_amide
|
|
674
|
+
is_tertiary_amide
|
|
675
|
+
is_ester
|
|
676
|
+
is_carbonyl
|
|
677
|
+
is_single
|
|
678
|
+
is_double
|
|
679
|
+
is_triple
|
|
680
|
+
is_ksingle
|
|
681
|
+
is_kdouble
|
|
682
|
+
is_ktriple
|
|
683
|
+
is_closure
|
|
684
|
+
is_up
|
|
685
|
+
is_down
|
|
686
|
+
is_wedge
|
|
687
|
+
is_hash
|
|
688
|
+
is_wedge_or_hash
|
|
689
|
+
is_cis_or_trans
|
|
690
|
+
is_double_bond_geometry
|
|
691
|
+
clear
|
|
692
|
+
do_transformations
|
|
693
|
+
get_title
|
|
694
|
+
set_title
|
|
695
|
+
has_data
|
|
696
|
+
delete_data
|
|
697
|
+
clone_data
|
|
698
|
+
data_size
|
|
699
|
+
get_all_data
|
|
700
|
+
get_data
|
|
701
|
+
begin_data
|
|
702
|
+
end_data
|
|
703
|
+
Visit=
|
|
704
|
+
Visit
|
|
705
|
+
set_idx
|
|
706
|
+
set_id
|
|
707
|
+
set_bo
|
|
708
|
+
set_bond_order
|
|
709
|
+
set_begin
|
|
710
|
+
set_end
|
|
711
|
+
set_parent
|
|
712
|
+
set_length
|
|
713
|
+
set
|
|
714
|
+
set_ksingle
|
|
715
|
+
set_kdouble
|
|
716
|
+
set_ktriple
|
|
717
|
+
set_aromatic
|
|
718
|
+
set_wedge
|
|
719
|
+
set_hash
|
|
720
|
+
set_wedge_or_hash
|
|
721
|
+
set_up
|
|
722
|
+
set_down
|
|
723
|
+
set_in_ring
|
|
724
|
+
set_closure
|
|
725
|
+
unset_hash
|
|
726
|
+
unset_wedge
|
|
727
|
+
unset_up
|
|
728
|
+
unset_down
|
|
729
|
+
unset_aromatic
|
|
730
|
+
unset_kekule
|
|
731
|
+
get_idx
|
|
732
|
+
get_id
|
|
733
|
+
get_bo
|
|
734
|
+
get_bond_order
|
|
735
|
+
get_flags
|
|
736
|
+
get_begin_atom_idx
|
|
737
|
+
get_end_atom_idx
|
|
738
|
+
get_begin_atom
|
|
739
|
+
get_end_atom
|
|
740
|
+
get_nbr_atom
|
|
741
|
+
get_parent
|
|
742
|
+
get_equib_length
|
|
743
|
+
get_length
|
|
744
|
+
get_nbr_atom_idx
|
|
745
|
+
find_smallest_ring
|
|
746
|
+
is_aromatic
|
|
747
|
+
is_in_ring
|
|
748
|
+
is_rotor
|
|
749
|
+
is_amide
|
|
750
|
+
is_primary_amide
|
|
751
|
+
is_secondary_amide
|
|
752
|
+
is_tertiary_amide
|
|
753
|
+
is_ester
|
|
754
|
+
is_carbonyl
|
|
755
|
+
is_single
|
|
756
|
+
is_double
|
|
757
|
+
is_triple
|
|
758
|
+
is_ksingle
|
|
759
|
+
is_kdouble
|
|
760
|
+
is_ktriple
|
|
761
|
+
is_closure
|
|
762
|
+
is_up
|
|
763
|
+
is_down
|
|
764
|
+
is_wedge
|
|
765
|
+
is_hash
|
|
766
|
+
is_wedge_or_hash
|
|
767
|
+
is_cis_or_trans
|
|
768
|
+
is_double_bond_geometry
|
|
769
|
+
clear
|
|
770
|
+
do_transformations
|
|
771
|
+
get_title
|
|
772
|
+
set_title
|
|
773
|
+
has_data
|
|
774
|
+
delete_data
|
|
775
|
+
clone_data
|
|
776
|
+
data_size
|
|
777
|
+
get_all_data
|
|
778
|
+
get_data
|
|
779
|
+
begin_data
|
|
780
|
+
end_data
|
|
781
|
+
Visit=
|
|
782
|
+
Visit
|
|
783
|
+
set_idx
|
|
784
|
+
set_id
|
|
785
|
+
set_bo
|
|
786
|
+
set_bond_order
|
|
787
|
+
set_begin
|
|
788
|
+
set_end
|
|
789
|
+
set_parent
|
|
790
|
+
set_length
|
|
791
|
+
set
|
|
792
|
+
set_ksingle
|
|
793
|
+
set_kdouble
|
|
794
|
+
set_ktriple
|
|
795
|
+
set_aromatic
|
|
796
|
+
set_wedge
|
|
797
|
+
set_hash
|
|
798
|
+
set_wedge_or_hash
|
|
799
|
+
set_up
|
|
800
|
+
set_down
|
|
801
|
+
set_in_ring
|
|
802
|
+
set_closure
|
|
803
|
+
unset_hash
|
|
804
|
+
unset_wedge
|
|
805
|
+
unset_up
|
|
806
|
+
unset_down
|
|
807
|
+
unset_aromatic
|
|
808
|
+
unset_kekule
|
|
809
|
+
get_idx
|
|
810
|
+
get_id
|
|
811
|
+
get_bo
|
|
812
|
+
get_bond_order
|
|
813
|
+
get_flags
|
|
814
|
+
get_begin_atom_idx
|
|
815
|
+
get_end_atom_idx
|
|
816
|
+
get_begin_atom
|
|
817
|
+
get_end_atom
|
|
818
|
+
get_nbr_atom
|
|
819
|
+
get_parent
|
|
820
|
+
get_equib_length
|
|
821
|
+
get_length
|
|
822
|
+
get_nbr_atom_idx
|
|
823
|
+
find_smallest_ring
|
|
824
|
+
is_aromatic
|
|
825
|
+
is_in_ring
|
|
826
|
+
is_rotor
|
|
827
|
+
is_amide
|
|
828
|
+
is_primary_amide
|
|
829
|
+
is_secondary_amide
|
|
830
|
+
is_tertiary_amide
|
|
831
|
+
is_ester
|
|
832
|
+
is_carbonyl
|
|
833
|
+
is_single
|
|
834
|
+
is_double
|
|
835
|
+
is_triple
|
|
836
|
+
is_ksingle
|
|
837
|
+
is_kdouble
|
|
838
|
+
is_ktriple
|
|
839
|
+
is_closure
|
|
840
|
+
is_up
|
|
841
|
+
is_down
|
|
842
|
+
is_wedge
|
|
843
|
+
is_hash
|
|
844
|
+
is_wedge_or_hash
|
|
845
|
+
is_cis_or_trans
|
|
846
|
+
is_double_bond_geometry
|
|
847
|
+
clear
|
|
848
|
+
do_transformations
|
|
849
|
+
get_title
|
|
850
|
+
set_title
|
|
851
|
+
has_data
|
|
852
|
+
delete_data
|
|
853
|
+
clone_data
|
|
854
|
+
data_size
|
|
855
|
+
get_all_data
|
|
856
|
+
get_data
|
|
857
|
+
begin_data
|
|
858
|
+
end_data
|
|
859
|
+
to_i
|
|
860
|
+
to_f
|
|
861
|
+
to_a
|
|
862
|
+
&
|
|
863
|
+
|
|
|
864
|
+
^
|
|
865
|
+
to_r
|
|
866
|
+
rationalize
|
|
867
|
+
to_c
|