Hi.
Yes this works for me as per the RDKit docs. But I need to pipe it to a file,
any suggestions?
Thanks.
Mike
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On Tue, Sep 24, 2019 at 10:28 PM +0100, "Lukas Pravda"
wrote:
Hi Mike,
The following code works for me:
import sys
from i
A carboxylate has to be represented as C(=O)[O-]. Use ...[OH] for an
uncharged carboxyl. Similarly, a tetravalent aliphatic N has to be given a
+ charge.
-P.
On Tue, Sep 24, 2019 at 9:15 PM Scalfani, Vincent wrote:
> Dear Navid,
>
>
>
> RDKit rejects tetravalent Nitrogen by default. This thread
Dear Navid,
RDKit rejects tetravalent Nitrogen by default. This thread below may help. It
shows how to load the SMILES with sanitization off, then perform a partial
sanitization.
https://sourceforge.net/p/rdkit/mailman/message/32589379/
Vin
From: Navid Shervani-Tabar
Sent: Tuesday, Septemb
Hello,
I have noticed that RDKit have some problems with some SMILES when trying
to use MolFromSmiles. With further attention, I have noticed that all of
these SMILES include nitrogen atoms. Some examples include:
[NH3]CCC(=O)[O]
NC(=[NH2])C(=O)[O]
NC(=[NH2])[CH2].C(=O)=O
CNC(=[NH2])C(=O)[O]
CNC(
Dear All,
One question why this is not working ?
def mol3D(mol):
tot = AllChem.EmbedMolecule(mol)
try:
X = AllChem.Get3DDistanceMatrix(mol)
except:
print('err')
print(tot)
n = mol.GetNumAtoms()
X = np.zeros(n,n)
return X
mol = Chem.MolFromS
Hi Mike,
The following code works for me:
import sys
from io import StringIO
from rdkit import Chem
saved_std_err = sys.stderr
log = sys.stderr = StringIO()
Chem.WrapLogs()
# do whatever you want with rdkit
whatever_used_to_be_printed_by_rdkit_in_console_as_str = log.getvalu
Hi Mike,
The usual incantation when working with suppliers, and this is shown in a
lot of sample code, is to check to see if the molecule that is returned is
None (which indicates a problem processing it).
The simple way to do this, and to report the error molecules to stdout (you
can change this)
Hello RDKit gurus,
I've found an interesting issue with V2000 SDF files which have a carbon marked
as "Either or unmarked stereocentre", a 3 in the atom-block.
The enclosed molecule throws these errors – note also that the word “begining"
is spelt wrong in the stderr.
Is there a way
Hi Rdkit forum,
Easy question, perhaps difficult to answer…
I’ve been reading a lot of support messages, many a very old about how to get
warnings (only visible at the cmd line) to be send to files.
I can get error messages sent, but not warnings.
The type I’m trying to capture ar
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