Sorry my fault. The SmilesGenerator removed the stereochemistry. Just
noticed that I have to use .absolute() instead of .unique()
Am 03.09.2015 um 12:36 schrieb Martin Gütlein:
Hi John,
Awesome, thanks. SuppressHydrogens works good, but it suppresses Hs
with stereochem-information as well. Can this be avoided?
> although possible you should perhaps store and index (unique check)
you structures separately.
Thats what we try to not do, if possible.
Martin
Am 03.09.2015 um 11:32 schrieb John M:
Hi Martin,
By design CDK separates out standardisation (H rep, tautomers,
protonation) from canonicalisation (ordering). You've found the
method to "sprout" hydrogens but you actually want the opposite -
suppressHydrogens(mol)
<http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.html#suppressHydrogens%28org.openscience.cdk.interfaces.IAtomContainer%29>.
I think you might be conflating two things, although possible you
should perhaps store and index (unique check) you structures
separately. For your example you could assign a unique tautomer but
you'll be back at square one with your first example.
O=C[CH]1Cc2[nH]cnc2CC1 -> 1,3 proton shift -> C(=O)[CH]1Cc2c(CC1)[nH]cn2
CC(=O)N -> 1,3 proton shift -> CC(O)=N
Thanks,
Regards,
John W May
john.wilkinson...@gmail.com <mailto:john.wilkinson...@gmail.com>
On 3 September 2015 at 09:27, Martin Gütlein <guetl...@uni-mainz.de
<mailto:guetl...@uni-mainz.de>> wrote:
One more thing:
I noticed that unique SMILES differentiate explicit and implicit
Hydrogens, e.g. "[H]Cl" is different form "Cl". This can be
solved by running
AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol).
However, I do not like having my all Hs defined explicitly. Is
there an option in the CDK to convert explict Hs back to
implicit, leaving only thoses Hs as explict that are relevant?
Martin
Am 03.09.2015 um 09:48 schrieb Martin Gütlein:
Hi John,
thanks for your reply, I tried to use unique (kekulized) SMILES
instead of InChIs.
Whats good is that the structure for (most) compounds is stored
correctly (i.e., I can create an IAtomContainer that is
apparently equal).
However, I found an example were the unique SMILES of two
identical structures is different (see below).
Kind regards,
Martin
for (String smi : new String[] { "O=C[CH]1Cc2[nH]cnc2CC1",
"C(=O)[CH]1Cc2c(CC1)[nH]cn2" })
{
IAtomContainer mol = new
SmilesParser(SilentChemObjectBuilder.getInstance()).parseSmiles(smi);
System.out.println(SmilesGenerator.unique().create(mol));
}
Am 02.09.2015 um 20:58 schrieb John M:
Just to add on - if you really want to use InChI (don't) then
you could store the AuxInfo but the CDK doesn't have a
conversion method that accepts it when turning it back into an
AtomContainer.
I also notice you're using unique SMILES (default by old APIs),
you probably want isomeric that a non-canonical but store
stereochemistry.
IAtomContainer mol = SmilesGenerator.isomeric().create(container);
John
Regards,
John W May
john.wilkinson...@gmail.com <mailto:john.wilkinson...@gmail.com>
On 2 September 2015 at 19:54, John M
<john.wilkinson...@gmail.com> wrote:
Hi Martin,
The InChI is an identifier and not a structure
representation it should never be used as such. For maximum
preservation you should store compounds as Kekulé SMILES or
Molfile. You can store additional data such as coordinates
supplementary to the SMILES.
You might find a recent presentation by Noel (O Babel) and
Rajarshi (CDK) useful:
http://baoilleach.blogspot.co.uk/2015/08/the-whole-of-cheminformatics-best.html
John
--
Dr. Martin Gütlein
Phone:
+49 (0)6131 39 23336 <tel:%2B49%20%280%296131%2039%2023336> (office)
+49 (0)177 623 9499 <tel:%2B49%20%280%29177%20623%209499> (mobile)
Email:
guetl...@uni-mainz.de <mailto:guetl...@uni-mainz.de>
--
Dr. Martin Gütlein
Phone:
+49 (0)6131 39 23336 (office)
+49 (0)177 623 9499 (mobile)
Email:
guetl...@uni-mainz.de
--
Dr. Martin Gütlein
Phone:
+49 (0)6131 39 23336 (office)
+49 (0)177 623 9499 (mobile)
Email:
guetl...@uni-mainz.de
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