Hello,
Imagine I have a compound with some 2D coordinates I really like:
mol
Now I would like to add hydrogens to it:
mol = Chem.AddHs(mol)
The problem is, all new hydrogen atoms will have (0,0,0) coordinates,
which doesn't look to good...
I could force recomputing 2D coords for the
Dear Michal,
Chem.AddHs() has the option “addCoords” which is normally set to False.
So, using
mol = Chem.AddHs(mol, addCoords=True)
should solve your problem.
Best,
Sereina
On 20 Aug 2014, at 19:07, Michał Nowotka mmm...@gmail.com wrote:
Hello,
Imagine I have a compound with some 2D
Perfect, thank you!
On Wed, Aug 20, 2014 at 6:13 PM, Sereina sereina.rini...@gmail.com wrote:
Dear Michal,
Chem.AddHs() has the option “addCoords” which is normally set to False.
So, using
mol = Chem.AddHs(mol, addCoords=True)
should solve your problem.
Best,
Sereina
On 20 Aug
Hmm,
I've just checked and actually adding this flag doesn't solve my problem.
It seems that adding this flag actually calls Compute2dCoords (at
least this is how it looks like), because all coordinates are computed
from scratch, for example if my compound was translated by some vector
on 2D
On Wednesday, August 20, 2014, Michał Nowotka mmm...@gmail.com wrote:
I've just checked and actually adding this flag doesn't solve my problem.
It seems that adding this flag actually calls Compute2dCoords (at
least this is how it looks like), because all coordinates are computed
from
On 08/20/2014 12:34 PM, Greg Landrum wrote:
On Wednesday, August 20, 2014, Michał Nowotka mmm...@gmail.com wrote:
It seems that adding this flag actually calls Compute2dCoords (at
least this is how it looks like), because all coordinates are computed
from scratch,
Hmmm, that doesn't sound
I can't seem to reproduce the problem.
Here's an example showing that the original atom coordinates are preserved
when Chem.AddHs is called with the addCoords argument:
#
In [9]: mb=
...: Mrv0541 08211405312D
...:
...: 6 6 0 0 0 0999
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