Awesome! Thank you all so much!!!
Here is my implementation of the function for reference:
def passed_NA2SR(mol): #no atom shared by two small rings
rings = mol.GetRingInfo().AtomRings()
small_rings = []
for ring in rings:
if len(ring) < 5:
small_rings.append(ring)
Peter, quite correct.
To do that, you'll need to do operations on the rings themselves:
>>> m = Chem.MolFromSmiles("C1CC12CCC2")
>>> list(m.GetRingInfo().AtomRings())
[(0, 1, 2), (3, 4, 5, 2)]
And set operations are probably your friend
>>> m = Chem.MolFromSmiles("C1CCC12CCC2")
>>> list(m.Ge
But Brian's solution won't help Jonathan find atoms that are in two
three-membered or two four-membered rings, which I thought Jonathan also
wanted, based on the wording of the original query.
-P.
On Tue, Apr 11, 2017 at 4:12 PM, Curt Fischer
wrote:
> Brian's solution is obviously better (short
Brian's solution is obviously better (shorter, uses less functions) than
mine. (Although mine assumes that you want atoms that are part of
_exactly_ two rings, not atoms that are part of _at least_ two rings as
Brian's does. Probably Brian's solution is what you want but worth noting.)
CF
On Tu
You are so close!
>>> from rdkit import Chem
>>> m = Chem.MolFromSmiles("C1CC12CCC2")
>>> for atom in m.GetAtoms():
... if atom.IsInRingSize(3) and atom.IsInRingSize(4): print atom.GetIdx()
...
2
>>>
Cheers,
Brian
On Tue, Apr 11, 2017 at 1:38 PM, Jonathan Saboury wrote:
> Hello All,
>
Hello All,
I'm trying to make a function to check if a mol has an atom that is part of
two small rings (3 or 4 atoms). Using GetRingInfo()/NumAtomRings() I can
find out how many ring systems each atom is in, but not the details of the
rings. atom.IsInRingSize(size) returns a bool so I couldn't use
Hello,
Not directly related to rdkit, but if someone that have
the original PDF of this file format could place it
online permanently, that would be wonderful.
The official URL at tripos.com is dead since quite some time
apparently.
And that's bad because it's a quite popular file format
and its
Just from the slides, it's not clear that Roger had a solution; the slides
seem to just suggest an approach. Am I missing something here?
That is, he defined the invariants that all tautomers of a compound have to
share and expressed it as a SMARTS + constraints; but I didn't see that he
provided
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