On 06/15/2017 01:14 PM, Brian Kelley wrote:
> Sorry to hear about the flooding.
>> Unfortunately we got flooded day before yesterday and the servers doing
>> the crunching are currently down.
I should have mentioned that the server (URL is in the article), which
I'll hopefully get back up today,
Sorry to hear about the flooding.
As an aside if you want to get they smiles atom output order, it is saved as a
property on the molecule after a call to MolToSmiles,
To get to the property, use mol.GetPropsAsDict(True,True) and it will be there
with the key named something like "_smilesAtomOut
On 06/15/2017 10:13 AM, Maciek Wójcikowski wrote:
> Hi,
>
> If you really want to rely on the order of atom you can renumber them
> anyhow you like with Chem.RenumberAtoms()
> http://rdkit.org/Python_Docs/rdkit.Chem.rdmolops-module.html#RenumberAtoms
> There is also a function which returns canoni
Hi,
If you really want to rely on the order of atom you can renumber them
anyhow you like with Chem.RenumberAtoms()
http://rdkit.org/Python_Docs/rdkit.Chem.rdmolops-module.html#RenumberAtoms
There is also a function which returns canonical order of atoms for
you: Chem.CanonicalRankAtoms() As I rem
Yes, atoms are always added in file order. It would take a major change in
rdkit to change/violate this.
Brian Kelley
> On Jun 15, 2017, at 7:52 AM, Francois BERENGER
> wrote:
>
> Hello,
>
> If I read a molecule from a .sdf file, will the atom indexes be
> conserved/preserved?
>
> 1s
Hello,
If I read a molecule from a .sdf file, will the atom indexes be
conserved/preserved?
1st atom in the file will have index 0,
2nd index 1, etc.
And, will this always hold in the future?
Is this an invariant of rdkit?
Thanks,
F.
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