Hi Jason,
I hope the following codes will help you a little.
from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem import AllChem
size = (120, 120)
m = Chem.MolFromSmiles('C#C')
m2=Chem.rdmolops.AddHs(m)
AllChem.EmbedMolecule(m2, AllChem.ETKDG())
Draw.MolToMPL(m2, size=size)
*** sou
Thank you Malitha,
If I'm understanding the Draw code (not a given, my python ist nicht gut),
then MolToMPL (or MolToImage) is just using the 3D conformation generated
by EmbedMolecule. Is it just chopping off the z-coordinate? For
acetylene, this works out because it gets embedded mostly in the
Dear Jason,
The geometry that you/me visualized in a 2D plot necessarily doesn't exist
in real world except a few planner molecules. To view 3D geometry of a
molecule, 2D representation doesn't work. Please feel free to do whatever
you want to do with your molecule while producing 2D graph. Everyon
Maciek
The 'cpack -G RPM' command does not seem to create a rdkit_package_file.rpm.
The ones that are created are:
RDKit-2018.03.1.dev1-Linux-Development.rpm
RDKit-2018.03.1.dev1-Linux-Extras.rpm
RDKit-2018.03.1.dev1-Linux-Python.rpm
RDKit-2018.03.1.dev1-Linux-Runtime.rpm
Tim
On 28/11/2017 08
Francois,
I'm assuming you are meaning to install those packages on the debian
system prior to installing the RDKit-2018.03.1.dev1-Linux-*.deb files.
Unfortunately that didn't help.
Tim
On 27/11/2017 23:50, Francois BERENGER wrote:
On 11/28/2017 12:42 AM, Tim Dudgeon wrote:
I see exactly t
Hi RDkit users,
I was wondering if RDkit has a means of downloading compounds from Pubchem.
Also let me other ways that helps here.
Thanks,
Jubi
--
Check out the vibrant tech community on one of the world's most
engaging
On Fri, Dec 1, 2017 at 6:04 PM, Tim Dudgeon wrote:
> Maciek
>
> The 'cpack -G RPM' command does not seem to create a rdkit_package_file.rpm.
> The ones that are created are:
>
> RDKit-2018.03.1.dev1-Linux-Development.rpm
> RDKit-2018.03.1.dev1-Linux-Extras.rpm
> RDKit-2018.03.1.dev1-Linux-Python.r
Read back to the top of this thread for all the details, but the key bit
is this:
In the bugtracker, there is an issue about the .deb:
https://github.com/rdkit/rdkit/issues/911
and there is a pull request by Patrick Avery
to fix them:
https://github.com/rdkit/rdkit/pull/1580
Tim
On 01/1
In what way? Given a single PubChem compound or substance ID you just
want to pull the smiles or molfile into RDKit?
Tim
On 01/12/17 17:26, Sundar wrote:
Hi RDkit users,
I was wondering if RDkit has a means of downloading compounds from
Pubchem.
Also let me other ways that helps here.
Than
If upgrading PostgreSQL to a new version of the RDKit cartridge is any
maintenance needed?
Either rebuild the indexes or regenerate the fingerprints and rebuild
the indexes?
--
Check out the vibrant tech community on
On 12/01/2017 11:55 AM, Tim Dudgeon wrote:
> In what way? Given a single PubChem compound or substance ID you just
> want to pull the smiles or molfile into RDKit?
Furthermore what's your definition of "a compound"? If it includes
stereochemistry, pubchem usually has 3d mol files, except where it
I would like to download at least SMILES (great if I can also download mol
files).
And the same is true for Pubchem Compound ID or using Substance ID.
Or even download the whole data set using an assay id. Anything could help.
Thanks,
Jubi
On Fri, Dec 1, 2017 at 11:55 AM, Tim Dudgeon wrote:
> I
Hi,
If you would like get compounds from ChEMBL instead of PubChem you can
use this Python client:
https://github.com/chembl/chembl_webresource_client
and get access to 1.7M+ unique compounds as molfiles, smiles, inchis,
inch keys and images.
Cheers,
Michał
On Fri, Dec 1, 2017 at 6:51 PM, Sundar
Pubchem has an easy to use rest API, described here:
https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest
If you have a compound ID, you can query properties via something
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/property/CanonicalSMILES,IsomericSMILES,InChI/JSON
It comes back in JS
Hi Jubi,
If you need the entire dataset and are not creating queries via the API, you
can download all PubChem Data via ftp here:
ftp://ftp.ncbi.nlm.nih.gov/pubchem/
Then download the SDFs, and extract out SMILES (I’ve used regular expressions
that match the appropriate data tag with good succ
Hi Jason,
This is great. I would really benefit from this.
At present I am looking for a way to download smiles or mol data of a few
compound which only have SIDs and CIDs.
Can we do it? I failed after trying the following,
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/sid/144205334/property
Sundar,
What you do will depend on whether you have an SID or a CID number. Read
https://pubchemblog.ncbi.nlm.nih.gov/2014/06/19/what-is-the-difference-between-a-substance-and-a-compound-in-pubchem/
for more info.
In PubChem terminology, a *substance* is a chemical sample description
> provided b
Hi Jason,
Thanks for the info.
That's exactly what I want. I want to download the compound in any format
(smiles/mol/sdf) for which I only have the Substance ID.
Sundar
On Fri, Dec 1, 2017 at 8:06 PM, Jason Biggs wrote:
> Sundar,
> What you do will depend on whether you have an SID or a CID n
18 matches
Mail list logo