Dear Alfredo,
if you wish to keep only the largest disconnected fragment you may try
the following:
mols = list(rdmolops.GetMolFrags(mol, asMols = True))
if (mols):
mols.sort(reverse = True, key = lambda m: m.GetNumAtoms())
mol = mols[0]
Hope that helps, cheers
p.
On 06/28/18 19:38, Alfredo Quevedo wrote:
Good afternoon,
I would like to filter out small fragments from a list of molecules
using the below strategy:
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import SaltRemover fragment
remover=SaltRemover.SaltRemover()
mol=Chem.MolFromSmiles('CCC.CC')
res=remover.StripMol(mol)
print(res.GetNumAtoms())
I am getting 5 atoms as output, so the ´CC´ is not being stripped (the
script workd ok for salts). Is there any way of filtering non salts
small fragments?
thank you very much in advance,
regards,
Alfredo
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