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require 'java'
require 'jchem_connection'

require 'lib/jchem/lib/jchem.jar'

java_package 'search.db'

java_import 'chemaxon.jchem.db.JChemSearch'
java_import 'chemaxon.sss.SearchConstants'
java_import 'chemaxon.sss.search.JChemSearchOptions'

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    def self.apply!(features, ca, oxy, hy, halo, s, ni, total_atom_nr, morphology, amino_acid_derivative, bile_acid_or_alcohol)
      # TODO: ca + oxy + hy == total_atom_nr does not always hold
      # for fatty acids, exple given CCCCCCCC(=O)O.NN.
      # Deal with this!

      if features.include?('fatty-ester-head') &&
          features.include_any?('pregnane-skeleton',
                                 'cholestane-skeleton',
                                 'androstane-skeleton',
                                 'estrane-skeleton',

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require 'rubygems'
require 'bio'

module PubMed

  # Download and annotate the given pubmed_id and return a citation in textile format.
  # Example Citation: 
  # Smythe MA, Stephens JL, Koerber JM, Mattson JC: A comparison of lepirudin and argatroban outcomes. 
  # Clin Appl Thromb Hemost. 2005 Oct;11(4):371-4. "Pubmed":http://www.ncbi.nlm.nih.gov/pubmed/16244762
  def PubMed.annotate(pubmed_id)

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require 'zip/zip'

# Interface to the mutfinder library 
class ReadAnalysis  
  
  @@nml_dir = File.join(Rails.root, 'lib', 'mutfinder')
  @@result_dir = File.join(@@nml_dir, '/var/results/')
  
  # Main entry point for analysis. Just pass an analysis ID
  # (An object is not passed because this doesnt work with delayed_job)

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def check_cas_number
  # Check the CAS number for validity (the last number in a CAS number is a checksum)
  if cas_number.present?
    matches = cas_number.scan(/^(\d{1,7})-(\d{1,2})-(\d)$/)
    
    if matches.first.blank? || matches.first.size != 3
      self.errors.add(:cas_number, "format invalid")
    else
      match = matches.first

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# Note that this action responds to fracked up datatable parameters.
  # If you need to use this for some other reason (HTML, etc), you
  # might want to consider moving it into it's own method 
  # (datatable or something).
  def index
    # These are the columns, in the correct order, used by datatables
    cols = [:gene_name, :gene_symbol, :gene_id, :interaction, :chromosome]

    @gene_regulations = 
      if params[:kind] == 'up_regulated'

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json.key_format! camelize: :lower
json.draw params[:draw].to_i + 1
json.records_total @total_count
json.records_filtered @filter_count
json.data do
  json.array! @gene_regulations.each do |gene_regulation|
    json.array! [ gene_regulation.gene_name,
                  bio_link_out(:genecard, gene_regulation.gene_symbol), 
                  bio_link_out(:ncbi_gene, gene_regulation.gene_id), 
                  gene_regulation.interaction,

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$ ->
  $('.gene-regulations').each ->
    table = $(this)
    source = table.data('source')
    table.dataTable
      processing: true
      serverSide: true
      ajax: source
      aoColumnDefs: [
        # Don't sort columns with class 'no-sort'

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Drug Groups

Vitamin D - Several individual compounds is_a vitamin D Often referred to as a single compound, even by DPD/FDA

Prodrug

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require 'zip/zipfilesystem'
require 'builder'
namespace :hmdb do
  namespace :export do
    DOWNLOAD_PATH = 'public/downloads'

    desc "Run all export tasks"
    task :all => [ :xml, :structures, :sequences ]

    # desc 'Export all compounds to json format'