Dear Thomas,
You can get the SMILES of substructures that are extracted via
`GetMorganFingerprint` function as follows. Then, you can append any labels
to the SMILES string but not real numbers.
```python
from rdkit import Chem
mol = Chem.MolFromSmiles('Cc1ncccc1')
info = {}
AllChem.GetMorganFingerprint(mol, radius=2, bitInfo=info)
radius, atom_id = list(info.values())[0][0][::-1]
env = Chem.FindAtomEnvironmentOfRadiusN(mol, radius, atom_id)
sub_struct = Chem.PathToSubmol(mol, env)
type(sub_struct) #=> rdkit.Chem.rdchem.Mol
Chem.MolToSmiles(sub_struct) #=> 'ccc'
```
Best,
On Fri, 22 Nov 2019 at 23:40, Thomas Evangelidis <teva...@gmail.com> wrote:
> Greetings,
>
> Could someone please clarify how can I pass atomic partial charges to the
> ECFP fingerprint generator along with the default atomic properties that it
> considers? Can I pass the real charge values or do I have to group them
> into bins and pass the bin identifier? I found a function in utilsFP.py
> file which generates invariants as follows:
>
> def generateAtomInvariant(mol):
> """
> >>> generateAtomInvariant(Chem.MolFromSmiles("Cc1ncccc1"))
> [341294046, 3184205312, 522345510, 1545984525, 1545984525, 1545984525,
> 1545984525]
> """
> num_atoms = mol.GetNumAtoms()
> invariants = [0]*num_atoms
> for i,a in enumerate(mol.GetAtoms()):
> descriptors=[]
> descriptors.append(a.GetAtomicNum())
> descriptors.append(a.GetTotalDegree())
> descriptors.append(a.GetTotalNumHs())
> descriptors.append(a.IsInRing())
> descriptors.append(a.GetIsAromatic())
> invariants[i]=hash(tuple(descriptors))& 0xffffffff
> return invariants
>
>
> And then generate the fingerprint like this:
>
>
> fp = AllChem.GetMorganFingerprint(mol, radius=3,
> invariants=generateAtomInvariant(mol))
>
>
> Would just suffice to add this extra line in generateAtomInvariant() function?
>
>
> descriptors.append(a.GetFormalCharge())
>
>
>
> I thank you in advance.
> Thomas
>
>
>
> --
>
> ======================================================================
>
> Dr. Thomas Evangelidis
>
> Research Scientist
>
> IOCB - Institute of Organic Chemistry and Biochemistry of the Czech
> Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>,
> Prague,
> Czech Republic
> &
> CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>
> , Brno, Czech Republic
>
> email: teva...@gmail.com, Twitter: tevangelidis
> <https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis
> <https://www.linkedin.com/in/thomas-evangelidis-495b45125/>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>
>
> _______________________________________________
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>
--
----
The University of Tokyo
2nd year Ph.D. candidate
Shojiro Shibayama
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