On 10/16/2019 1:50 PM, Andrew Dalke wrote:
... I would expect to see a "SyntaxError: invalid character in identifier" as
Python doesn't recognize left-handed or right-handed double quotes in a way that doesn't
cause an error. Instead, the MolFromSmiles() appears to be evaluated.
Is that a
On Thu, 14 Mar 2019 13:19:00 -0600
Phuong Chau wrote:
> Could anyone tell me any possible solution to solve this problem?
1. Go to ligand expo search @ http://ligand-expo.rcsb.org/ld-search.html
2. Search for UNL and consider the topology of an "unknown ligand".
The solution is to fiter your
On Mon, 21 Jan 2019 09:43:48 +0100
Markus Sitzmann wrote:
> There is no need for objects with SQLAlchemy, SQLAlchemy's Core and
> its expression language is pretty excellent without objects ...
I spent weeks last year rewriting code that I myself wrote back when I
believed that... When I wrote
On Sun, 20 Jan 2019 12:03:50 +0100
Shojiro Shibayama wrote:
> ... I guess SQLalchemy
> in python might be good, but I'm not sure. Hope that you'll find out
> a good library of SQL OR mapper for python.
SQLalchemy creates a fairly specific ecosystem that you have to buy
into for it to make
On Mon, 17 Dec 2018 14:23:32 +0100
JEAN-MARC NUZILLARD wrote:
...
> returns DIFFERENT.
>
> Removing the EmbedMolecule step returns EQUAL.
>
> How could I change that?
You could try generating multiple conformers instead and checking if
one of them returns EQUAL.
--
Dmitri Maziuk
On Fri, 30 Nov 2018 05:32:13 +0100
Greg Landrum wrote:
> I don’t think you should be getting NaNs, and that’s worth looking into,
> but they are technically numeric values : that’s the double value younger
> when you divide by zero.
NaNs are great because you can tell "invalid result" from 0,
On Wed, 3 Oct 2018 06:21:06 +0200
Greg Landrum wrote:
> The atom ordering in the RDKit molecule created from a SMILES or Mol block
> will always be the same and will corresponds to the ordering of the atoms
> in the input
... provided your molecule has no protons and/or you don't removeH/addH
On 7/5/2018 1:39 PM, Paolo Tosco wrote:
As the PDB format includes no stereochemistry, no coordinates are
needed, and by default they are zero, as the molecule does not have a
conformation yet.
Hmm. One could argue that PDB format *is* 3D coordinates, so a block
with all zeroes is quite
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