Hi,
I've found this (http://code.google.com/p/rdkit/wiki/Generating3DCoordinates)
wiki page suggesting how to compute 3D coordinates:
from rdkit import Chem
from rdkit.Chem import AllChem
m = Chem.MolFromSmiles('c1c1C(=O)O')
AllChem.EmbedMolecule(m)
# the molecule now has a crude
I don't know about the ultimate way: but this works for me (to generate n
conformers):
writer = Chem.SDWriter('some_file.sdf')
# add Hydrogens
molH = Chem.AddHs(mol)
# create n conformers for molecule
confIds = AllChem.EmbedMultipleConfs(molH, n)
# E optimize
for confId in confIds:
Michal: from my experience, MMFF in rdkit is slower than UFF (ca. 2x
for my test cases) but converges faster, so in certain cases the
overall execution time (embedding+optimization) won't be much shorter
for UFF. It really depends on what molecules you work on. AFAIK
rdkit's 3d coord generation
On 05/04/14 19:04, Michal Krompiec wrote:
For example, it does not work well
for long conjugated oligomers - sometimes it produces molecular knots
instead of straight strands, and is quite slow for large systems.
Can you expand on that? What sort of long conjugated oligomers were you
On 5 April 2014 19:11, Paul Emsley pems...@mrc-lmb.cam.ac.uk wrote:
On 05/04/14 19:04, Michal Krompiec wrote:
For example, it does not work well
for long conjugated oligomers - sometimes it produces molecular knots
instead of straight strands, and is quite slow for large systems.
Can you
Hi Michal,
JP gave a good answer already, I'll just add a few things.
First: thanks for pointing out the missing call to AddHs in the
documentation. I've fixed that.
On Sat, Apr 5, 2014 at 1:35 PM, Michał Nowotka mmm...@gmail.com wrote:
Hi,
I've found this (
On Sat, Apr 5, 2014 at 8:44 PM, Michal Krompiec
michal.kromp...@gmail.comwrote:
On 5 April 2014 19:11, Paul Emsley pems...@mrc-lmb.cam.ac.uk wrote:
On 05/04/14 19:04, Michal Krompiec wrote:
For example, it does not work well
for long conjugated oligomers - sometimes it produces
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