On Nov 18, 2019, at 17:40, David Cosgrove wrote:
>
> Point taken. I don’t think you’d be able to get RDKit to spit such SMILES
> strings out unless you tortured it pretty hard, however.
Did someone mention one of my favorite things to do? :) See:
On Mon, 18 Nov 2019 16:40:28 +
David Cosgrove wrote:
> Point taken. I don’t think you’d be able to get RDKit to spit such SMILES
> strings out unless you tortured it pretty hard, however.
Export smiles with arbitrary given atom order is diffrent problem.
Normally working with mol object you
Hi Rocco,
Point taken. I don’t think you’d be able to get RDKit to spit such SMILES
strings out unless you tortured it pretty hard, however.
Dave
On Mon, 18 Nov 2019 at 16:36, Rocco Moretti wrote:
> Actually, it is possible to get arbitrary orders, if you (ab)use the '.'
> component ("zero
Actually, it is possible to get arbitrary orders, if you (ab)use the '.'
component ("zero order bond") directive and the numeric bonding ("ring
closure") directives:
>>> Chem.MolToSmiles( Chem.MolFromSmiles("O1.Cl2.C12" ) )
'OCCl'
Whether you want to do things that way is another question.
On
Hi Rafal,
It is not always possible to preserve the atom ordering in the SMILES
string because there is an implied bond between contiguous symbols in the
SMILES. I think, for example, that the molecule with the SMILES OCCl
couldn’t have the order in the molecule object O first, Cl second, C third,
Hi all,
Is there any way to preserve atom order from Mol object during
exporting to smiles? I tried MolToSmiles with rootedAtAtom=0 and
canonical=False options but it not always prevent oryginal order.
I know I can use _smilesAtomOutputOrder to map old indices to new one
in canonical smiles but
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