t shorter way to write this formation of a
benzotriazole would be:
reaction_smarts =
'c1ccc([NX3H2:1])c([NX3H2:2])[cX3]1>>c12[*:1]-[n]=[*:2]c12'
best wishes
wim
On Wed, Nov 23, 2022 at 3:36 PM Alfredo Quevedo
wrote:
Dear users,
I have bee
Dear users,
I have been struggling for days trying to model a specific reaction but
cannot succeed in matching the corresponding SMARTS notation, I am
reproducing my code below,
My molecule is:
/reactant = 'c1ccc(N)c(N)c1'/
I am trying to prepare a second ring by reacting the two primary
les.org/datawarrior/>) to inspect molecules.
Cheers!
Aishvarya
--------
*From:* Alfredo Quevedo
*Sent:* Thursday, October 6, 2022 3:10:20 AM
*To:* RDKit Discuss
*Subject:* [Rdkit-discuss] Generating a pdf file with a grid of molecules
Hell
Hello,
I am trying to out a .pdf file containing a grid of molecules with the
corresponding labels below. For that, I am following these steps:
1- Prepare a dataframe reading a csv file containing the smiles and
molecule names,
2- use
Cheers,
Scott
-Original Message-
From: Alfredo Quevedo
Sent: Sunday, August 28, 2022 7:09 PM
To: RDKit Discuss
Subject: [Rdkit-discuss] problem matching SMART pattern
Dear users,
I am trying to math a triazole scaffold using SMARTS notation. My code is shown
below:
query = 'N1N=NC=C1
Dear users,
I am trying to math a triazole scaffold using SMARTS notation. My code
is shown below:
query = 'N1N=NC=C1'
template = '[NX3H1]1[N]=[N][C]=[C]1'
mol = Chem.MolFromSmiles(query)
mol.HasSubstructMatch(Chem.MolFromSmarts(template))
This results in 'False'. By depicting the structures
Dear all,
I am trying to figure out if there is a way to remove all hydrogens bond
to sp3 carbons in my molecule?
thanks in advance for the help,
kind regards
Alfredo
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thank you Greg for the hint,
Kind regards
Alfredo
Enviado desde BlueMail
En 30 de octubre de 2019 07:03, en 07:03, Greg Landrum
escribió:
>On Wed, Oct 30, 2019 at 10:16 AM Alfredo Quevedo
>
>wrote:
>
>> thank you very much Hongbin for the detailed answe
ot;, then you will understand why they are not the absolute
>chirality.
>>
>> Absolute chirality depends on the chiral tag as well as the CIPRanks
>of
>> the neighbor atoms. That is why the chirality of the two carbons are
>> different while their chiral tags are the same.
En 29 de octubre de 2019 10:10, en 10:10, Alfredo Quevedo
escribió:
>Good morning,
>
>I am trying to manually set/change the stereochemistry of a chiral
>center of a molecule, and I cant understand how to set the
>CHI_TETRAHEDRAL_CW/CHI_TETRAHEDRAL_CCW tag on a certain
Good morning,
I am trying to manually set/change the stereochemistry of a chiral center
of a molecule, and I cant understand how to set the
CHI_TETRAHEDRAL_CW/CHI_TETRAHEDRAL_CCW tag on a certain atom. So far my
script does the following:
-
from rdkit import Chem
from rdkit.Chem import
s('C(C(=O)COc1c(F)c(F)cc(F)c1F)n1cc([C@
>@](C)(NCc2ccn3nccc3n2)C22)nn1',0xf00d)
>1.0405439864921206e-07
>[(4, 'R'), (22, 'S')] [(4, 'R'), (22, 'S')]
>
>In [91]: run_smiles('C(C(=O)COc1c(F)c(F)cc(F)c1F)n1cc([C@
>@](C)(NCc2ccn3nccc3n2)C22)nn1',23)
>0.0
>[(4, 'S'), (
Good afternoon,
I am generating 3D structures in .pdb format starting from smiles
notation. I am working with chiral molecules, and noted that the 3D
structure obtained when generating the molecule explicitly indicating
the configuration of the stereocenter is sligthly different from that
on of the boost-python library that matches
>the
>version of python you are using.
>
>I hope this helps,
>-greg
>
>
>On Mon, Jul 23, 2018 at 7:43 PM Alfredo Quevedo
>
>wrote:
>
>> Dear all,
>>
>> I am trying to build RDKit from source under Ub
Dear all,
I am trying to build RDKit from source under Ubuntu 16.04, on which I
have both Python2.7 and Python3.5.2 installed. Followin the instructions
provided in the RDKit book document I was able to build the module for
the default Python version (2.7) and the 'import rdkit' command is
;Monitoring: MedChemica Limited retains and monitors all email traffic
>data and content for the purposes of the prevention and detection of
>crime, ensuring the security of our computer systems and checking
>compliance with our policies.
>
>> On 29 Jun 2018, at 06:37, Alfredo Queve
thank you much much Andrew for this detailed explanation
regards
Alfredo
Enviado desde BlueMail
En 29 de junio de 2018 07:02, en 07:02, Andrew Dalke
escribió:
>On Jun 28, 2018, at 22:08, Paolo Tosco
>wrote:
>> if you wish to keep only the largest disconnected fragment you may
>try the
may
>try
>> the following:
>>
>> mols = list(rdmolops.GetMolFrags(mol, asMols = True))
>> if (mols):
>> mols.sort(reverse = True, key = lambda m: m.GetNumAtoms())
>> mol = mols[0]
>>
>> Hope that helps, cheers
>> p.
>>
t;
>mols = list(rdmolops.GetMolFrags(mol, asMols = True))
>if (mols):
> mols.sort(reverse = True, key = lambda m: m.GetNumAtoms())
> mol = mols[0]
>
>Hope that helps, cheers
>p.
>
>On 06/28/18 19:38, Alfredo Quevedo wrote:
>> Good afternoon,
>>
>
Good afternoon,
I would like to filter out small fragments from a list of molecules
using the below strategy:
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import SaltRemover
remover=SaltRemover.SaltRemover()
mol=Chem.MolFromSmiles('CCC.CC')
res=remover.StripMol(mol)
N(Cc3ccsc3)C(=O)Cn3nnc4c43)cc2)cn1
(2 rows)
Can you please check to see if this simple test works for you?
To do more detailed troubleshooting I will need to know which version
of the cartridge you are using and one which operating system.
Best,
-greg
On Tue, May 29, 2018 at 8:00 PM Alf
Dear user,
I am trying to perform a substructure search using smiles notation under
the ChEMBL database I have already loaded into my postgreSQL database. I
am here providing two sample molecules in smiles format as read by the
RDKit cartrigde into the database:
Molecule 1:
if there is
another directory instead of 10/
Markus
-
| Markus Sitzmann
| markus.sitzm...@gmail.com <mailto:markus.sitzm...@gmail.com>
On 24. May 2018, at 18:24, Alfredo Quevedo <maquevedo@gmail.com
<mailto:maquevedo@gmail.com>&
Good morning,
I am trying to build RDKit from source, and succeed with that following
the instructions provided in the documentation. Howvere, I am trying to
use the postgres cartridge, which as far as I understand is built during
the main building process.
but after trying to create the
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