Hi folks
it seems that the “easiest” way to get my coords if I know the ChEBI identifier
is to do something like this in Python3 (note this snippet has no error
checking!):
> import sys # only needed to parse the command-line arguments
> chebi = sys.argv[1] # expect ChEBI identifier without
Maybe more information on that here: https://developer.rsc.org/?
I'm not an expert and only used it interactively...
Julie
On Tue, 6 Dec 2022 at 12:19, Harry Powell
wrote:
> Hi Julie
>
> Ta.
>
> Do you know if there’s an API (pref. Python 3.9 or later) for downloading
> the 3D coordinates from
Hi Oliver
I’d just worked that out when I tried an obviously non-planar molecule (that I
didn’t include with my breakfast this morning)!
PubChem looks like a useful way forward - many thanks.
Harry
> On 6 Dec 2022, at 11:55, Oliver Smart wrote:
>
> Hi Harry,
>
> The SDF found at ChEBI is a
Chemspider can also provide you with a .mol file amongst other things.
http://www.chemspider.com/Chemical-Structure.2424.html?rid=281bd645-a2c9-4d07-af08-c3148b323194
Best wishes
Julie
On Tue, 6 Dec 2022 at 11:55, Oliver Smart wrote:
> Hi Harry,
>
> The SDF found at ChEBI is a 2D SDF with the
Hi Harry,
The SDF found at ChEBI is a 2D SDF with the coordinates used for the diagram. I
do not think that ChEBI has
3D coordinates. Why not use PubChem instead as this does provide 3D sdf files?
For your caffeine example:
https://pubchem.ncbi.nlm.nih.gov/compound/64119
Whoops.
It looks like these entries are not supposed to be 3D models, but
representations of 2D line drawings (which I noticed when I had a look at an
obviously non-planar molecule).
Which is a shame, because I was hoping I could use them in 3D modelling…
Sorry for polluting your inboxes!
Hi folks
Can anyone help with this?
I must have missed something in the documentation, because I don’t understand
why the .mol and .sdf files downloaded from
https://www.ebi.ac.uk/chebi
seem to have aromatic C-C bonds that are 0.825 Å long (it’s a few decades now
since I solved any
