On Thu, Aug 2, 2018 at 8:59 AM Guillaume GODIN <
guillaume.go...@firmenich.com> wrote:
>
>
> I have a simple question about generating all possible smiles of a given
> molecule:
>
>
It's a simple question, but the answer is somewhat complicated. :-)
>
>
> RDKit provides only 4 differents smiles for my molecule “CCC1CC1“:
>
> C1C(CC)C1
>
> CCC1CC1
>
> C1(CC)CC1
>
> C(C)C1CC1
>
>
>
> While by hand we can write those 7 smiles:
>
> CCC1CC1
>
> C(C)C1CC1
>
> C(C1CC1)C
>
> C1CC(CC)1
>
> C1C(CC)C1
>
> C1CC1CC
>
> C(CC)1CC1
>
>
>
> I use this function for the enumeration:
>
>
>
> def allsmiles(smil):
>
> m = Chem.MolFromSmiles(smil) # Construct a molecule from a SMILES
> string.
>
> if m is None:
>
> return smil
>
> N = m.GetNumAtoms()
>
> if N==0:
>
> return smil
>
> try:
>
> n= np.random.randint(0,high=N)
>
> t= Chem.MolToSmiles(m, rootedAtAtom=n, canonical=False)
>
> except :
>
> return smil
>
> return t
>
>
>
> n= 50
>
> SMILES = [“CCC1CC1”]
>
> SMILES_mult = [allsmiles(S) for S in SMILES for i in range(n)]
>
>
>
> Why we cannot generate all the 7 smiles ?
>
The RDKit has rules that it uses to decide which atom to branch to when
generating a SMILES. These are used regardless of whether you are
generating canonical SMILES or not.
The upshot of this is that it will never generate a SMILES where there's a
branch before a ring closure.
The other important factor here is that atom rank is determined by the
index of the atom in the molecule when you aren't using canonicalization.
So changing the atom order on input can help:
In [12]: set(allsmiles('CCC1CC1') for i in range(50))
Out[12]: {'C(C)C1CC1', 'C1(CC)CC1', 'C1C(CC)C1', 'CCC1CC1'}
In [13]: set(allsmiles('C1CC1CC') for i in range(50))
Out[13]: {'C(C1CC1)C', 'C1(CC)CC1', 'C1CC1CC', 'CCC1CC1'}
You can do this all at once as follows:
```
In [20]: def allsmiles(smil):
...: m = Chem.MolFromSmiles(smil) # Construct a molecule from a
SMILES string.
...: if m is None:
...: return smil
...: N = m.GetNumAtoms()
...: if N==0:
...: return smil
...: aids = list(range(N))
...: random.shuffle(aids)
...: m = Chem.RenumberAtoms(m,aids)
...: try:
...: n= random.randint(0,N-1)
...: t= Chem.MolToSmiles(m, rootedAtAtom=n, canonical=False)
...: except :
...: return smil
...: return t
...:
...:
...:
In [21]:
In [21]: set(allsmiles('C1CC1CC') for i in range(50))
Out[21]: {'C(C)C1CC1', 'C(C1CC1)C', 'C1(CC)CC1', 'C1C(CC)C1', 'C1CC1CC',
'CCC1CC1'}
```
Note that I switched to using python's built in random module instead of
using the one in numpy.
-greg
>
>
> Thanks guys,
>
>
>
> Best regards,
>
>
>
> Guillaume
>
> ***********************************************************************************
> DISCLAIMER
> This email and any files transmitted with it, including replies and
> forwarded copies (which may contain alterations) subsequently transmitted
> from Firmenich, are confidential and solely for the use of the intended
> recipient. The contents do not represent the opinion of Firmenich except to
> the extent that it relates to their official business.
>
> ***********************************************************************************
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
