Hacking NMRShiftDB

Rich Apodaca — Mon, 04 Sep 2006 13:28:00 +0000

NMRShiftDB is an open web database of peer-reviewed NMR chemical shifts compiled by volunteers. As of this writing, it contains 22,429 measured spectra from 18,986 structures, and reports 927 registered users. The database code itself is open source.

Although NMRShiftDB has a web interface, its architecture is designed to simplify writing programs that use it. A previous article showed how a working PubChem API could be written with just a few lines of Ruby. This time, I'll show how the same thing can be done for NMRShiftDB.

Ingredients

This tutorial uses Arton's excellent Ruby Java Bridge, the installation and use of which has been previously discussed. Also used is Ruby's InChI interface, Rino, for which installation instructions are here.

Create a working directory called nmr. Into this directory, copy cdk-20060714.jar, which can be downloaded here.

Code

Create a file called nmr.rb containing the following Ruby code:

require 'net/http'
require 'smi2inchi'

# A very simple NMRShiftDB Web API.
class NMRFetcher

  # Creates a <tt>Translator</tt> instance.
  def initialize
    @translator = Translator.new
  end

  # Returns an XML record, as a string, for the molecule
  # with SMILES matching <tt>smiles</tt> and spectrum type
  # matching <tt>spectrumtype</tt> (13C, 1H, 15N and 31P).
  def get_record(smiles, spectrumtype)
    body = nil
    inchi = (smi2inchi(smiles)).gsub('InChI=', 'inchi=')
    path = '/NmrshiftdbServlet?nmrshiftdbaction=exportcmlbyinchi&' + inchi + '&spectrumtype=' + spectrumtype

    Net::HTTP.start('nmrshiftdb.ice.mpg.de') do |http|
      response = http.get(path)
      body = response.body
    end

    if !valid_record?(body)
      return nil
    end

    body
  end

private

  def valid_record?(body)
    !body.eql?('No such molecule or spectrum')
  end

  def smi2inchi(smiles)
    @translator.translate(smiles)
  end
end

The magic in the above code is nothing more than a simple HTTP request sent to nmrshiftdb.ice.mpg.de, contained in the get_record method. This request encodes an InChI identifier, which is generated from the SMILES string passed as an argument. We also specify a spectrum type.

Now create a file called smi2inchi.rb, containing the following Ruby code:

ENV['CLASSPATH'] = './cdk-20060714.jar'
require 'rubygems'
require_gem 'rjb'
require_gem 'rino'
require 'rjb'

StringWriter = Rjb::import 'java.io.StringWriter'

SmilesParser = Rjb::import 'org.openscience.cdk.smiles.SmilesParser'
MDLWriter = Rjb::import 'org.openscience.cdk.io.MDLWriter'

# Converts a SMILES string into an InChI identifier using
# the CDK Library (Java) and the Rino Library (Ruby/C).
class Translator

  def initialize
    @smiles_parser = SmilesParser.new
    @mdl_writer = MDLWriter.new
    @mol2inchi = Rino::MolfileReader.new
  end

  # Returns an InChI identifier from the specified SMILES string.
  # Uses the CDK classes SmilesParser and MDLWriter to generate
  # a molfile from a SMILES string. Then this molfile is
  # parsed by Rino::MolfileReader.
  def translate(smiles)
    mol = @smiles_parser.parseSmiles(smiles)

    sw = StringWriter.new

    @mdl_writer.setWriter(sw)
    @mdl_writer.write(mol)

    @mol2inchi.read(sw.toString)
  end
end

The description and use of this code was discussed in a recent article on generating InChI identifiers from SMILES strings.

Before using the code we've just created you'll need to set the LD_LIBRARY_PATH (or equivalent) to point to the native Java libraries. On Linux with Sun's JDK, this is done from the command line with:

$ export LD_LIBRARY_PATH=$JAVA_HOME/jre/lib/i386:$LD_LIBRARY_PATH

Using the NMRFetcher class is just a matter of creating an instance, and invoking get_record with the desired SMILES string and spectrum type (1H, 13C). Doing so returns a CML document containing the structure of the compound and its spectrum. If no record matches, the method returns nil. The code below give an example in which the CML output is pretty-printed using the wonderful Ruby API for XML, REXML:

require "rexml/document"
require 'nmr'

nmr = NMRFetcher.new
smiles = 'c1ccccc1' #benzene, to keep things simple
type = '13C'
record = nmr.get_record(smiles, type)

if record #pretty-print the CML record using REXML
  file = File.new('result.xml', 'w')

  (REXML::Document.new(record)).write(file, 0)

  file.close
else #write an error
  File.open('result.error', 'w') do |file|
    file << 'No record of SMILES: ' + smiles
  end
end

The above code can be put into a file (test.rb) and run:

$ ruby test.rb

Alternatively, it can be entered interactively and played with using irb:

$ irb
irb(main):001:0>

Output

The program produces the following Chemical Markup Language output in a file called result.xml:

<cml>
  <molecule title='Benzene' id='nmrshiftdb7901' xmlns='http://www.xml-cml.org/schema/cml2/core'>
    <atomArray xmlns='http://www.xml-cml.org/schema'>
      <atom elementType='C' y2='0.7625' x2='-1.4063' id='a1' formalCharge='0' hydrogenCount='0'/>
      <atom elementType='C' y2='0.35' x2='-2.1207' id='a2' formalCharge='0' hydrogenCount='0'/>
      <atom elementType='C' y2='-0.475' x2='-2.1207' id='a3' formalCharge='0' hydrogenCount='0'/>
      <atom elementType='C' y2='-0.8875' x2='-1.4063' id='a4' formalCharge='0' hydrogenCount='0'/>
      <atom elementType='C' y2='-0.475' x2='-0.6918' id='a5' formalCharge='0' hydrogenCount='0'/>
      <atom elementType='C' y2='0.35' x2='-0.6918' id='a6' formalCharge='0' hydrogenCount='0'/>
    </atomArray>
    <bondArray xmlns='http://www.xml-cml.org/schema'>
      <bond atomRefs2='a1 a2' order='S' id='b1'/>
      <bond atomRefs2='a2 a3' order='D' id='b2'/>
      <bond atomRefs2='a3 a4' order='S' id='b3'/>
      <bond atomRefs2='a4 a5' order='D' id='b4'/>
      <bond atomRefs2='a5 a6' order='S' id='b5'/>
      <bond atomRefs2='a1 a6' order='D' id='b6'/>
    </bondArray>
  </molecule>
  <spectrum moleculeRef='nmrshiftdb7901' xmlns:cml='http://www.xml-cml.org/dict/cml' xmlns:cmlDict='http://www.xml-cml.org/dict/cmlDict' xmlns:siUnits='http://www.xml-cml.org/units/siUnits' type='NMR' xmlns:macie='http://www.xml-cml.org/dict/macie' xmlns:units='http://www.xml-cml.org/units/units' id='nmrshiftdb15502' xmlns:subst='http://www.xml-cml.org/dict/substDict' xmlns:nmr='http://www.nmrshiftdb.org/dict' xmlns='http://www.xml-cml.org/schema/cml2/spect'>
    <conditionList xmlns='http://www.xml-cml.org/schema'>
      <scalar dataType='xsd:string' units='siUnits:k' dictRef='cml:temp'>298</scalar>
      <scalar dataType='xsd:string' units='siUnits:hertz' dictRef='cml:field'>Unreported</scalar>
    </conditionList>
    <metadataList xmlns='http://www.xml-cml.org/schema'>
      <metadata name='nmr:OBSERVENUCLEUS' content='13C'/>
    </metadataList>
    <peakList xmlns='http://www.xml-cml.org/schema'>
      <peak xUnits='units:ppm' peakShape='sharp' xValue='128.5' id='p0' atomRefs='a1 a2 a3 a4 a5 a6'/>
    </peakList>
  </spectrum>
</cml>

The kind of output produced by NMRFetcher and NMRShiftDB could be used in a variety of ways. Notice, near the bottom of the document, how peak assignments are made relative the the atom labels in the molecule declaration. It should be possible, for example, to create interactive 2-D structure diagrams from this document in which a user mouses over an atom and gets a C-13 chemical shift.

NMRShiftDB is a valuable and free online resource for NMR spectroscopy. Programatically mixing its capabilities with free software and other online services offers numerous opportunities to build innovative chemical informatics systems.

Depth-First: Hacking NMRShiftDB

Hacking NMRShiftDB

Ingredients

Code

Output