+1 for Symmetrizer too, A must!
De : Michal Krompiec
Date : jeudi, 18 janvier 2018 à 08:18
À : Jason Biggs
Cc : RDKit Discuss, Greg Landrum
Objet : Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018
+1 vote for Symmetrizer. It would be very useful for preparing input for
computational
+1 vote for Symmetrizer. It would be very useful for preparing input for
computational chemistry codes.
Best,
Michal Krompiec
Merck KGaA
On Mon, 15 Jan 2018 at 15:21, Jason Biggs wrote:
>
>- I've had this on my to-do list for a few months now, implementing
>the
Hi Andy,
A better option is to sanitize the products of a reaction enumeration
before using them as reactants.
Look at this example from RDKit "Getting Started" documentation.
Note that the molecules that are produced by the chemical reaction
processing code are not sanitized, as this artificial
Hi Christos,
Many thanks for the reply. I hadn't appreciated that the presence of a
single invalid reagent would bring the entire thing crashing down, rather
than issuing a warning/error and moving onto other molecules in the set.
Good to know, and I'll have to be less lazy in my code ;-)
Best,
Hi Andy,
The reason that your code breaks is that the second product of the third
iteration ( 'NN(Cc1c1)(Cc1c1)Cc1c1') is not a valid
molecule.
And when calling Chem.MolFromSmiles( 'NN(Cc1c1)(Cc1c1)Cc1c1')
it creates a None object.
So you have to filter out the
I don't think there's a way to do this using RDKit itself, but it appears
to be straightforward using Python with numpy and networkx, e.g.
import numpy as np
import networkx as nx
a = np.matrix([[0, 1, 0, 0, 0],[1, 0, 1, 1, 0],[0, 1, 0, 0, 0],[0, 1, 0, 0,
1],[0, 0, 0, 1, 0]])
b =
Correct, I am looking for a rdkit-hidden-option to do it :D
On Wed, Jan 17, 2018 at 5:56 PM, Jason Biggs wrote:
> I am a novice when it comes to graph theory, but it seems like what is
> wanted here is the adjacency matrix of the corresponding line graph (
>
I am a novice when it comes to graph theory, but it seems like what is
wanted here is the adjacency matrix of the corresponding line graph (
http://mathworld.wolfram.com/LineGraph.html).
I don't know how to do this in python, but if I use mathematica, it goes
like this
adjacencyMatrix = {{0, 1,
Dear Marta and Guillaume,
Thank you both.
Your solutions are giving the same output, which is the vertices-adjacency
matrix.
There is something called the edge-adjaceny matrix. Its defined in several
papers by Trinajstic to calculate the M2 Zagreb indices, eg. "The Zagreb
Indices 30 Years After"
On 2018-01-17 10:25, Jason Biggs wrote:
For the case in question, I find that if I read in a mol file containing
2D coordinates, and I skip the sanitization step altogether, then the 3D
embedding algorithms fail.
Well, yes, as I mentioned in the other thread: the only way you can get
it to
Hi Mario,
What exactly do you mean by 'edge matrix'? Are you sure you provided a
correct example? If you want to get an adjacency matrix of a molecular
graph you can iterate over bonds to get it:
from rdkit.Chem import MolFromSmiles
import numpy as np
m = MolFromSmiles('CC(C)CC')
n =
Dear Mario,
There is a adjacency matrix available:
from rdkit import Chem
mol = Chem.MolFromSmiles('CC(C)CC')
adj = Chem.GetAdjacencyMatrix(mol)
print adj
[[0 1 0 0 0]
[1 0 1 1 0]
[0 1 0 0 0]
[0 1 0 0 1]
[0 0 0 1 0]]
But this is not what you want…
Can you explain your output
Dear all,
I am using Constrained embed to generate conformers. I AddHs before I use
ConstrainedEmbed but I am finding that some of the conformers have Hs which
overlap (have the same coordinates).
Here is one example below.
from rdkit import Chem
from rdkit.Chem import AllChem, rdFMCS
from
On Wed, Jan 17, 2018 at 10:12 AM, Dimitri Maziuk
wrote:
> On 2018-01-16 22:46, Greg Landrum wrote:
>
> It might be worth thinking about adding an option to the aromaticity
>> perception code to maintain the original bond types and just set the
>> "isAromatic" flag on the
Hi RDKitters,
I have a question and an observation on the topic of library enumeration.
First, the question: is there a call within RDKit to trigger the exhaustive
reaction of reagents? For example, if I have two reagents - a primary amine
and an akyl chloride - can I tell RDKit to enumerate the
On 2018-01-16 22:46, Greg Landrum wrote:
It might be worth thinking about adding an option to the aromaticity
perception code to maintain the original bond types and just set the
"isAromatic" flag on the bonds.
This is how it's modeled in mmCIF chem. comp. It may or may not come
from
Dear all,
Does any one have an idea how to get an edge matrix (graph theory) out of
Rdkit, I digged deep but didnt find anything.
F.example for:
'CC(C)CC'
it would be:
array([[0, 1, 1, 0],
[1, 0, 1, 0],
[1, 1, 0, 1],
[0, 0, 1, 0]])
Thanks.
--
Mario Lovrić
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