Dan!
- Kovas
From: Dan Nealschneider
Date: Tuesday, December 4, 2018 at 10:05 AM
To: "col...@gmail.com"
Cc: Kovas Palunas , rdkit discuss
Subject: Re: [Rdkit-discuss] Double Bond Stereochemistry in the RDKit
I've done some in-memory translation of molecules to ROMols, and ha
Hi All,
I’m looking for a bit more clarity regarding double bond stereochem in RDKit.
Currently, my understanding is that there are 3 ways to currently store this
information:
1. STEREOE/STEREOZ tags + stereo atoms on either side of bond set by CIP
ranks, as computed when calling
dummy atoms have atomic number 0
if (a1n == 0 || a2n == 0) {
return true;
}
So far, it seems to work great for me. If anyone else cares for this
functionality, I’d be happy to share more details/open a pull request!
- Kovas
From: Kovas Palunas
Date: Thursday, August 23, 2018 at 10
Kannas
Date: Thursday, August 23, 2018 at 7:53 AM
To: Kovas Palunas
Cc: RDKit , Paolo Tosco
Subject: Re: [Rdkit-discuss] Matching Generalized Compounds
Hi Kovas,
You have two fuzzy compounds that you try to match them, because our intuition
says that any atom notation [*:1] from m1 should match
Hi All,
I’m interested in having GetSubstructMatches return non-“null” results in the
following example. The results should lead to a match where atom 1 maps to
atom 11, 2 to 12, etc.
m1 = Chem.MolFromSmiles('[*:1][CH2:2][C:3]([CH3:4])=[CH2:5]')
m2 =
code). I guess the old ones were
overwriting my new ones, since they were in the same namespace.
- Kovas
On 5/31/18, 10:50 AM, "Paul Emsley" wrote:
On 31/05/2018 02:00, Kovas Palunas wrote:
> If anyone has an idea for what is going wrong with my setup, or can point
Hi All,
I’m attempting to write my own small RDKit extension library to store C++
functions I’ll write which will be called from Python. To start out, I have
one function, which is a slightly modified RunReactants from the 2018.03
release. Previously, I directly modified this function in the
Hi all,
I thought I'd share a script I wrote to build RDKit and Boost together which
has worked for me on Linux (CentOS) and Mac machines so far. I run RDKit in a
virtualenv Python environment (not in anaconda), so this may only be helpful
for a small group of RDKitters. Hopefully some of
There should be a post in there about changing the RDKit C++ code to make that
property available. It's a very small change!
- Kovas
From: Jennifer Wei <jennifer...@fas.harvard.edu>
Sent: Friday, September 29, 2017 10:51:02 AM
To: Kovas Palunas;
Hi Jennifer,
I had this same issue a while back. Here is an issue I posted about it on the
github: https://github.com/rdkit/rdkit/issues/1269
I never did make the pull request mentioned in the issue, but all the code that
does what you want should be in there. Let me know if you have any
nesday, September 27, 2017 2:27:04 AM
To: Kovas Palunas
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Masking groups as atoms in RDKit
Where would you want to use this?
Is it for depiction (i.e. drawing molecules) or something else?
-greg
On Tue, Sep 26, 2017 at 10:12 PM, Kovas P
Subject: Re: [Rdkit-discuss] Masking groups as atoms in RDKit
To: Kovas Palunas
Cc: rdkit-discuss@lists.sourceforge.net
I'm afraid that there's likely to be rather a lot of devil hiding in the
details (as is so often the case).
A simple example of one problem: let's take your [But]O case
Hi all,
Has anyone tried implementing or using a group to atom masking strategy in
RDKit? By this I mean taking a piece of a molecule and representing it as a
single atom. Here is an example:
O could be represented as [But]O, where the atom [But] represents the
four carbon chain.
hat innovative
algorithms and software are key to advance synthetic biology and bring to
the market exciting new molecules.
Arzeda Corp. (www.arzeda.com) is an equal opportunity employer promoting
diversity and inclusion in the workspace.
KOVAS PALUNAS
SOFTWARE DEVELOPER
Arzeda Corp.
T: 206.40
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