at might be a bit foolish as I'm not an
accomplished chemist, but does the SMARTS for O11 deal correctly when
the Oxygen in question is bonded to aromatic atoms? If I understand
correctly it should match either aromatic or aliphatic elements (apart
from the Carbon), but the SMARTS as written will onl
delete mol;
}
}
cout << "We found " << molCount << " molecules in file \"" << argv[1]
<< "\"." << endl;
in.close();
}
Yours,
Toby Wright
--
InhibOx Ltd.
---
t; On 10 October 2012 14:24, Greg Landrum wrote:
>>
>> On Tue, Oct 9, 2012 at 4:44 PM, Toby Wright
>> wrote:
>> >
>> > Working in C++, I am calling ForwardsSDMolSupplier's method "atEnd()",
>> > expecting that it returns false if there
a smiles string before the second
sanitization I get C[b-]1c1 but C[B-]1C=CC=CC1 after the second.
Any ideas what's going on?
Yours,
Toby Wright
--
InhibOx
--
T
smi now contains:
[H]OC(=O)C([H])(N([H])[H])C([H])([H])[H] L-alanine
[H]OC(=O)C([H])(N([H])[H])C([H])([H])[H] D-alanine
and ChiralTest2.smi contains:
C[C@H](N)C(=O)O L-alanine
C[C@@H](N)C(=O)O D-alanine
My question is why do I get different outputs depending on when
sanitization was pe
- so
I will. How it represented hydrogens was just a byproduct of the simplest
example I could create to illustrate the issue.
Thanks,
Toby
--
InhibOx Ltd
On 14 August 2013 16:19, Greg Landrum wrote:
> Hi Toby,
>
> On Wed, Aug 14, 2013 at 2:00 PM, Toby Wright wrote:
>
>>
0
>>> mol.Debug()
Atoms:
0 6 C chg: 0 deg: 0 exp: 0 imp: 4 hyb: 4 arom?: 0 chi: 0
Bonds:
Any ideas why this might be?
Yours,
Toby Wright
--
InhibOx Ltd
--
Introducing Performance Central, a new site f
Hi,
I've observed an odd behaviour in RDKit with listing explicit hydrogens in
smiles where the original molecules were generated from SD files. As the
code below shows if I ask "What is the smiles for a single C atom?" I get
"C" but if I ask for silicon I get "[SiH4]". Any reason why this might b
= Chem.MolFromSmarts('CC')
>>> print Chem.MolToSmiles(Chem.DeleteSubstructs(query, remove_as_smiles,
onlyFrags=True))
C
>>> print Chem.MolToSmiles(Chem.DeleteSubstructs(query, remove_as_smarts,
onlyFrags=True))
C
So now I know to use "[C!r][C!r][C!r][C!r][C!r][C!
While this doesn't answer your core question of can RDKit do what you want
without manually editing the smarts strings, if you do end up hacking it
using 'C[CX3v4](~O)~O' might be cleaner than 'CC(~O)~O)' as it would
exclude the case where both Os were singly bon
esign decision or a
feature?
The below code snippet shows the problem:
>>> import rdkit
>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem
>>> mol = Chem.MolFromSmiles('NC(=O)C1CC[NH+](CC(=O)NC(N)=O)CC1')
>>> print AllChem
en though this connection is not
made by the N-C bond in question.
Thanks again,
Yours,
Toby Wright
--
InhibOx Ltd
Oxford
On 24 December 2013 15:46, Gerebtzoff, Gregori wrote:
> Hi Toby,
>
> One additional note on what Greg wrote:
> you can define another smarts pattern for the i
e for the new function/variable.
Yours,
Toby Wright
--
InhibOx Ltd
Oxford
On 31 January 2014 11:05, JP wrote:
> My 2p worth:
>
> I am not a big fan of outright replacing the NumRotatableBonds
> implementation (option 2). This is quite a popular descriptor which is
> used in
= Chem.MolFromSmarts("[C:3][C:4](=[O:5])[O;H:6]")
>>> m3 = Chem.MolFromSmiles("CC(=O)O")
>>> m3H = Chem.AddHs(m3)
>>> m3.HasSubstructMatch(m1)
False
>>> m3H.HasSubstructMatch(m1)
True
>>> m3.HasSubstructMatch(m2)
True
>
: 0
1 1->2 order: 1 conj?: 1 aromatic?: 0
2 2->3 order: 2 conj?: 1 aromatic?: 0
3 3->4 order: 1 conj?: 0 aromatic?: 0
4 4->0 order: 1 conj?: 0 aromatic?: 0
>>> Chem.MolFromSmiles('n1
Thanks all for informative and helpful responses, the behaviour I was
struggling to understand now makes perfect sense.
Toby Wright
--
InhibOx Ltd
On 4 March 2014 04:06, Greg Landrum wrote:
> Bob hit the nail on the head.
>
> The first case, "N1N=CC=C1", is aromatic bec
tch(O_or_C)
True
We also see:
> C_or_O = Chem.MolFromSmarts('[C,O]')
> C_or_O.HasSubstructMatch(O)
False
> C_or_O.HasSubstructMatch(C)
True
so the order of elements in a SMARTS 'or' statement changes the behaviour,
which is unexpected.
Yours,
Toby Wright
--
In
y make atoms aromatic in SMARTS
if you wish them to match aromatic SMILES rather than relying on the kekule
representation to sort it for you.
Yours,
Toby Wright
--
InhibOx Ltd
On 6 March 2014 04:55, Greg Landrum wrote:
>
>
> On Wed, Mar 5, 2014 at 4:03 PM, Toby Wright wrote:
>
on
specification appears to have been lost. Is this a bug or am I going about
my reaction in the wrong way?
Yours,
Toby Wright
--
InhibOx Ltd
--
Learn Graph Databases - Download FREE O'Reilly Book
"Graph
Oops, forgot to mention: This is with the solution to github issue
#233<https://github.com/rdkit/rdkit/issues/233>patched into my RDKit
build.
Yours,
Toby Wright
--
InhibOx Ltd
On 28 March 2014 15:43, Toby Wright wrote:
> Hi,
>
> I believe I've found a bug in the new
line images 1]
but in the output one is towards and the other is away:
[image: Inline images 2]
Note that I can work around this, if I specify my reaction as
[C:1].[C:2]>>[C:1]C[C@H]1CC[C@@H](C[C:2])CC1 thus apeing the atom ordering
of the product RDKit will give me I get the chirality I w
True)
CC[C@@H]1CC[C@@H](CC)CC1
The output should be the same as the input but plugging those strings into
the daylight website's depiction tool gives chirally different molecules.
This behaviour is observed in RDKit 2013.09 with no custom patches.
Yours,
Toby Wright
--
InhibOx Ltd
On 2
so I don't need a workaround or quick
fix. I just happened across the behaviour and thought it worth reporting.
Yours,
Toby Wright
--
InhibOx Ltd
--
Put Bad Developers to Shame
Dominate Development with Jenkins Cont
xygen
with a property and that property need not be conserved by reaction
transforms, and so isn't. And in the [H]O case it is internally converted
to an [OH] before the reaction takes place.
Thanks once again for your time,
Toby Wright
--
InhibOx Ltd
On 8 April 2014 02:35, Greg Landrum w
h cases above show the same behaviour, considering phenolish things
to be phenols for the sake of MMFF94 atom typing. Alternatively we could
consider phenolish things to be not phenols and implement atom type 21 for
the hydrogen in both cases. Any thoughts?
Yours,
Toby Wright
PS I'm aware t
resented is not covered by the validation suite and so I missed
> that bug until today: thank you very much for reporting it!
>
> Cheers,
> p.
>
>
> On 04/14/2014 03:42 PM, Toby Wright wrote:
>
> Hi,
>
> I've been using the MMFF94 forcefield and noticed an odd
e).SetChiralTag(Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW)
print Chem.MolToSmiles(chiral, isomericSmiles=True)
F[C@@H](Cl)Br
F[C@H](Cl)Br
How to extend this to molecules with multiple chiral centres is left as an
exercise for the reader ;)
Yours,
Toby Wright
--
InhibOx Ltd
On 28 May 2014 13:27, wrote:
> Hi R
If you just want to ignore the error add a try...catch block around the
offending line.
Yours,
Toby Wright
On 31 May 2014 00:03, Matthew Lardy wrote:
> Hi all,
>
> I am having this issue with the Java wrapper while trying to create a
> smiles string from a RWMol class object.
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