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Re: [Joelib-help] Canonified version?
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From: Joerg K. W. <we...@in...> - 2004-12-06 16:32:52
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Hi Andreas,
morgan.renumber(tMol); returns the renumbered molecule (no salts!).
In detail:
- Applying a modified BFS search which assigns the initial values
- The rest of the algorithm uses this numbers to get an unique=20
renumbering for this molecule. If renumbering ties occur, there are=20
several tie resolvers using different atom labels.
- Finally, the returned molecule should be uniquely renumbered, as far=20
as the morgan algorithm and the tie resolvers can grant this.
If you put then this molecule into a SMILES generator, it should always=20
return the same SMILES, even, if the original molecules used another=20
numbering scheme.
Kind regards, Joerg
> If I use
>=20
> ------------------CODE BEGIN---------------------
> // create mol object out of this smiles string
> JOESmilesParser.smiToMol(mol, smiles, smiles);
> =09
> // clone the molecule
> // and recalculate
> // numbers
> JOEMol tMol =3D (JOEMol) mol.clone(false);
> morgan.calculate(tMol);
> JOEMol rMol =3D morgan.renumber(tMol); // (*)
> JOEMol rMol =3D tMol;
>=20
> // create mol to smiles converter=20
> m2s.init();
>=20
> // do some correction
> m2s.correctAromaticAmineCharge(rMol);
>=20
> // String buffer to hold the canonified string
> m2s.createSmiString(rMol, smilesb);
> return smilesb.toString();
> ------------------CODE BEGIN---------------------
>=20
> I get a NULL pointer exception at (*) with the following:
> Exception in thread "main" java.lang.NullPointerException
> at joelib.algo.morgan.Morgan.getBFS(Morgan.java:329)
> at joelib.algo.morgan.Morgan.renumber(Morgan.java:261)
> at SmilesCanonifier.canonify(SmilesCanonifier.java:35)
> at SmilesCanonifier.main(SmilesCanonifier.java:52)
> =09
> Without (*), however, it works quite well, too.
> Only in some molecules it switches from (for example)
> 'C12CC3CC(CC(C3)C2)C1' to
> 'C12CC3CC(CC(C3)C1)C2',
> but that's not so problematic.
> Also, the missing salt support is no acute problem.
> What does (*) do, exactly?
>=20
> Greetings,
> Andreas
> =09
> On Tue, Nov 30, 2004 at 08:17:37AM +0100, Joerg K. Wegner wrote:
>=20
>>Hi Andreas,
>>
>>here is the code fragment used by joelib.io.types.Smiles. Please note=20
>>that the actual morgan algorithm can not deal with salts. A solution=20
>>would be to get all contiguous fragments in decreasing order (method=20
>>mol.contiguousFragments(List)) and apply the morgan algorithm to each=20
>>fragment. Then you must simply connect those fragments in the SMILES=20
>>String with frag1smiles.frag2smiles.frag3smiles
>>
>>Mmhh, its not a big deal but i'm at the moment heavily busy with the=20
>>JOELib2 refactoring. Anyway, here is the code:
>>
>>if (doCanonical)
>>{
>> JOEMol tMol =3D (JOEMol) mol.clone(false);
>> morgan.calculate(tMol);
>> JOEMol rMol =3D morgan.renumber(tMol);
>> m2s.correctAromaticAmineCharge(rMol);
>> m2s.createSmiString(rMol, smilesb);
>>}
>>else
>>{
>> m2s.correctAromaticAmineCharge(mol);
>> m2s.createSmiString(mol, smilesb);
>>}
>>
>>MfG, Joerg
>>
>>
>>>with the following code I read in a SMILES, build a molecule out of=20
>>>it and reencode it as a string:
>>>
>>>----------------- BEGIN CODE --------------------------------
>>>
>>>import joelib.molecule.*;
>>>import joelib.smiles.*;
>>>
>>>public class SmilesCanonifier {
>>> =20
>>> public String canonify(String smiles) {
>>> JOEMol mol=3Dnew JOEMol();
>>> JOEMol2Smi m2s =3D new JOEMol2Smi(); m2s.init();
>>> StringBuffer smilesb =3D new StringBuffer(1000);
>>>
>>> // create mol object out of this smiles string
>>> JOESmilesParser.smiToMol(mol, smiles, smiles);
>>>
>>> // create mol to smiles converter
>>> m2s.init();
>>> // do some correction
>>> m2s.correctAromaticAmineCharge(mol);
>>>
>>> // String buffer to hold the canonified string
>>> m2s.createSmiString(mol, smilesb);
>>> return smilesb.toString();
>>> }
>>>
>>> public static void main(String args[]) {
>>> String smiles =3D args[0];
>>> System.out.println(smiles);
>>> SmilesCanonifier sc =3D new SmilesCanonifier();
>>> System.out.println(sc.canonify(smiles));
>>> }
>>>}
>>>
>>>----------------- END CODE ----------------------------------
>>>
>>>When I try this on a SMILES s0 I get an equivalent output smiles s1.
>>>When I try it on s1, I get an equivalent output smiles s2, which is=20
>>>different from s1.
>>>When I try it on s2, I get an equivalent output smiles s3, which is=20
>>>the same as s1, s3=3Ds1.
>>>When I try it on s3=3Ds1, I get an equivalent output smiles s4, which=20
>>>is the same as s2, s4=3Ds2.
>>>
>>>The process repeats from now on, switching between two SMILES=20
>>>versions.
>>>Is there no canonical version? Otherwise, how can I get one?
>>>
>>>Greetings,
>>>Andi
>>>
>>>
>>>
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>>>
>>
>>
>>--=20
>>Dipl. Chem. Joerg K. Wegner
>>Center of Bioinformatics Tuebingen (ZBIT)
>>Department of Computer Architecture
>>Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
>>Phone: (+49/0) 7071 29 78970
>>Fax: (+49/0) 7071 29 5091
>>E-Mail: mailto:we...@in...
>>WWW: http://www-ra.informatik.uni-tuebingen.de
>>--
>>Never mistake motion for action.
>> (E. Hemingway)
>>
>>Never mistake action for meaningful action.
>> (Hugo Kubinyi,2004)
>>
>>
>>
>>-------------------------------------------------------
>>SF email is sponsored by - The IT Product Guide
>>Read honest & candid reviews on hundreds of IT Products from real=20
>>users.
>>Discover which products truly live up to the hype. Start reading now.=20
>>http://productguide.itmanagersjournal.com/
>>_______________________________________________
>>Joelib-help mailing list
>>Joe...@li...
>>https://lists.sourceforge.net/lists/listinfo/joelib-help
>=20
>=20
> Viele Gr=FC=DFe,
> Andi
--=20
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW: http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
(E. Hemingway)
Never mistake action for meaningful action.
(Hugo Kubinyi,2004)
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