Which open source tools can calculate canonical tautomers? Code? Command line?

Asked by [ Editor ] about 1 year ago

Which open source tools can calculate canonical tautomers?
I am specifically interested in source code?
or
Executable command line methods?

NN comments

Mark Rijnbeek used the InChI approach published by Thalheim in 2010, allowing you to do in Groovy:

import org.openscience.cdk.interfaces.;

import org.openscience.cdk.smiles.;

import org.openscience.cdk.tautomers.;

import org.openscience.cdk.tools.manipulator.;

import org.openscience.cdk.*;

IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();

IMolecule adenine = builder.newInstance(IMolecule.class);

IAtom a1 = builder.newInstance(IAtom.class,“N”);

adenine.addAtom(a1);

IAtom a2 = builder.newInstance(IAtom.class,“N”);

adenine.addAtom(a2);

IAtom a3 = builder.newInstance(IAtom.class,“N”);

adenine.addAtom(a3);

IAtom a4 = builder.newInstance(IAtom.class,“N”);

adenine.addAtom(a4);

IAtom a5 = builder.newInstance(IAtom.class,“N”);

adenine.addAtom(a5);

IAtom a6 = builder.newInstance(IAtom.class,“C”);

adenine.addAtom(a6);

IAtom a7 = builder.newInstance(IAtom.class,“C”);

adenine.addAtom(a7);

IAtom a8 = builder.newInstance(IAtom.class,“C”);

adenine.addAtom(a8);

IAtom a9 = builder.newInstance(IAtom.class,“C”);

adenine.addAtom(a9);

IAtom a10 = builder.newInstance(IAtom.class,“C”);

adenine.addAtom(a10);

IAtom a11 = builder.newInstance(IAtom.class,“H”);

adenine.addAtom(a11);

IAtom a12 = builder.newInstance(IAtom.class,“H”);

adenine.addAtom(a12);

IAtom a13 = builder.newInstance(IAtom.class,“H”);

adenine.addAtom(a13);

IAtom a14 = builder.newInstance(IAtom.class,“H”);

adenine.addAtom(a14);

IAtom a15 = builder.newInstance(IAtom.class,“H”);

adenine.addAtom(a15);

IBond b1 = builder.newInstance(IBond.class,a1, a6, IBond.Order.SINGLE);

adenine.addBond(b1);

IBond b2 = builder.newInstance(IBond.class,a1, a9, IBond.Order.SINGLE);

adenine.addBond(b2);

IBond b3 = builder.newInstance(IBond.class,a1, a11, IBond.Order.SINGLE);

adenine.addBond(b3);

IBond b4 = builder.newInstance(IBond.class,a2, a7, IBond.Order.SINGLE);

adenine.addBond(b4);

IBond b5 = builder.newInstance(IBond.class,a2, a9, IBond.Order.DOUBLE);

adenine.addBond(b5);

IBond b6 = builder.newInstance(IBond.class,a3, a7, IBond.Order.DOUBLE);

adenine.addBond(b6);

IBond b7 = builder.newInstance(IBond.class,a3, a10, IBond.Order.SINGLE);

adenine.addBond(b7);

IBond b8 = builder.newInstance(IBond.class,a4, a8, IBond.Order.SINGLE);

adenine.addBond(b8);

IBond b9 = builder.newInstance(IBond.class,a4, a10, IBond.Order.DOUBLE);

adenine.addBond(b9);

IBond b10 = builder.newInstance(IBond.class,a5, a8, IBond.Order.SINGLE);

adenine.addBond(b10);

IBond b11 = builder.newInstance(IBond.class,a5, a14, IBond.Order.SINGLE);

adenine.addBond(b11);

IBond b12 = builder.newInstance(IBond.class,a5, a15, IBond.Order.SINGLE);

adenine.addBond(b12);

IBond b13 = builder.newInstance(IBond.class,a6, a7, IBond.Order.SINGLE);

adenine.addBond(b13);

IBond b14 = builder.newInstance(IBond.class,a6, a8, IBond.Order.DOUBLE);

adenine.addBond(b14);

IBond b15 = builder.newInstance(IBond.class,a9, a12, IBond.Order.SINGLE);

adenine.addBond(b15);

IBond b16 = builder.newInstance(IBond.class,a10, a13, IBond.Order.SINGLE);

adenine.addBond(b16);

smilesGenerator = new SmilesGenerator();

AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(

adenine

);

tautomerGenerator = new InChITautomerGenerator();

tautomers = tautomerGenerator.getTautomers(adenine)

for (tautomer in tautomers) {

println smilesGenerator.createSMILES(tautomer)

}

This script can be run with Groovy from the command line with CDK 1.4.7 on the CLASSPATH. Caveat is that the experimental /Ket and /15T options are currently not used.

Apr 20, 2012

Egon, can you put this text rather in an answer not into a comment? Thanks, cheers, Joerg

Apr 21, 2012

6 answers

**Noel O'Boyle [ Admin ] from Cork, Ireland** Apr 18, 2012 (Edited Apr 21, 2012)

Tim Vandermeersch implemented Sayle’s method in the dev version of OpenBabel:

>obtautomer.exe
Usage: obtautomer.exe [-c] 
-c: Canonical tautomer only

NN comments

Hi Noel, so this means normal SVN/trunc checkout and compile? Is the code already validated, aka are the results reliable?

Apr 18, 2012

Yup, it’s on the trunk. I did not check the results too much. The unit tests contain a test for Guanine tautomers. See http://openbabel.svn.sourceforge.net/viewvc/openbabel/openbabel/trunk/test/tautomertest.cpp?revision=4657&view=markup

Apr 18, 2012

In theory I would like to use the function, in practice I consider it as having two bugs, see bug report on the mailing list. Help is appreciated! http://goo.gl/N9dvG

Apr 23, 2012

More discussions here http://goo.gl/HrJwH

Apr 25, 2012

**Mikhail Rybalkin [ Editor ] from Российская Федерация** Apr 18, 2012 (Edited Oct 17, 2012)

You can generate InChI for your molecule, and then convert this InChI into a molecule again. The result molecule will to be a standardized tautomer.

NN comments

Nice! Did not think about it this way.

Apr 21, 2012

Do you have an example? How to handle stereochemistry? Aka, Ido not want to loose the sterochemistry!

Apr 23, 2012

This will work, but the results are not always pretty. A tautomer re-constituted from InChI is quite often one which looks rather peculiar. Also, the tautomer processing of the InChI library is quite limited (actually, it is now being reworked for the next release).

Apr 24, 2012

Actually, this works only for inchi, but not if used with the tautomer function 13T or 15T. Those created identifiers can’t be backtranslated. Finally, the 13T and 15T are not really working properly.

Jan 7, 2013

**rajarshi guha [ Editor ] from Bethesda, United States of America** Apr 17, 2012 (Edited Apr 20, 2012)

See this blog post which provides a GUI generator (http://tripod.nih.gov/ws/tautomer/tautomer.jnlp, limited to 1000 tautomers). Would be easy enough to convert to a command line tool

NN comments

**Matteo Floris [ Editor ] from Amendolara, Italia** Apr 18, 2012 (Edited Apr 20, 2012)

Hi, have a look at this open access paper:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2886898/

you can find there both the set of SMIRKS transforms for the enumeration of “all” possible tautomers (see Table 1)

and the rules used for the definition of a canonical tautomer (see Table 2).

You can easily copy and past these transforms, and include them in a CACTVS or RDkit script.

NN comments

Matteo, practically, do you know if anyonw has done this already, e.g. in combination with the CDK, RDKit, or Openbabel?

The issue is ... Is the code already validated, aka are the results reliable? I do not have the time to do the validation myself.

Apr 18, 2012

The transforms mentioned in the paper are a standard component of the Cactvs toolkit and included in both the academic and commercial versions.

Apr 18, 2012

O.k., great to hear, can you remind me about a download and command line option to do this? Thanks!

Apr 18, 2012

Academic downloads at www.xemistry.com/academic.

Simple interactive command to create a SMILES of a canonic tautomer:

cactvs>ens get [ens get [ens create C=CO] E_CANONIC_TAUTOMER] E_SMILES

CC=O

Apr 19, 2012

**Joerg Kurt Wegner [ Editor ] from Raritan, United States of America** Oct 15, 2012 (Edited Oct 15, 2012)

Ambit http://ambit.sourceforge.net/ can also calculate tautomers!

NN comments

Yes, code examples & command line Java application here http://ideaconsult.github.com/examples-ambit/

Oct 31, 2012

**wdiwdi [ Editor ] from Frankfurt am Main, Deutschland** Apr 18, 2012 (Edited Apr 18, 2012)

The Cactvs toolkit contains a standard property (E_CANONIC_TAUTOMER) for this. See www.xemistry.com/academic for free academic versions.

The transforms are the same as mentioned in the paper cited below (its computations were actually performed by this software).

The canonic tautomer is selected from the tautomer set with a rating function, which includes both rule-of-thumb energetic terms and topological criteria (for example, avoid double bonds which look like they could be stereogenic), and in case of ties a Cactvs hashcode is the final resort to select the unique form.

NN comments

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Which open source tools can calculate canonical tautomers? Code? Command line?

6 answers

**Noel O'Boyle [ Admin ] from Cork, Ireland** Apr 18, 2012 (Edited Apr 21, 2012)

**Mikhail Rybalkin [ Editor ] from Российская Федерация** Apr 18, 2012 (Edited Oct 17, 2012)

**rajarshi guha [ Editor ] from Bethesda, United States of America** Apr 17, 2012 (Edited Apr 20, 2012)

**Matteo Floris [ Editor ] from Amendolara, Italia** Apr 18, 2012 (Edited Apr 20, 2012)

**Joerg Kurt Wegner [ Editor ] from Raritan, United States of America** Oct 15, 2012 (Edited Oct 15, 2012)

**wdiwdi [ Editor ] from Frankfurt am Main, Deutschland** Apr 18, 2012 (Edited Apr 18, 2012)

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Which open source tools can calculate canonical tautomers? Code? Command line?

6 answers

Noel O'Boyle [ Admin ] from Cork, Ireland Apr 18, 2012 (Edited Apr 21, 2012)

Mikhail Rybalkin [ Editor ] from Российская Федерация Apr 18, 2012 (Edited Oct 17, 2012)

rajarshi guha [ Editor ] from Bethesda, United States of America Apr 17, 2012 (Edited Apr 20, 2012)

Matteo Floris [ Editor ] from Amendolara, Italia Apr 18, 2012 (Edited Apr 20, 2012)

Joerg Kurt Wegner [ Editor ] from Raritan, United States of America Oct 15, 2012 (Edited Oct 15, 2012)

wdiwdi [ Editor ] from Frankfurt am Main, Deutschland Apr 18, 2012 (Edited Apr 18, 2012)

Your answer

**Noel O'Boyle [ Admin ] from Cork, Ireland** Apr 18, 2012 (Edited Apr 21, 2012)

**Mikhail Rybalkin [ Editor ] from Российская Федерация** Apr 18, 2012 (Edited Oct 17, 2012)

**rajarshi guha [ Editor ] from Bethesda, United States of America** Apr 17, 2012 (Edited Apr 20, 2012)

**Matteo Floris [ Editor ] from Amendolara, Italia** Apr 18, 2012 (Edited Apr 20, 2012)

**Joerg Kurt Wegner [ Editor ] from Raritan, United States of America** Oct 15, 2012 (Edited Oct 15, 2012)

**wdiwdi [ Editor ] from Frankfurt am Main, Deutschland** Apr 18, 2012 (Edited Apr 18, 2012)