hi,
I am in the process of a scaffold analysis, printing the scaffolds in
smiles format, and came across some unexpected behaviour:
Whenever I remove hydrogens with RemoveHs() and print out the smiles
string, some hydrogens remain attached (irrespective
if the original input file type is SDF or smiles):
from rdkit import Chem
from rdkit.Chem.Scaffolds import MurckoScaffold
# molecule from zinc:
suppl = Chem.SDMolSupplier("zinc_69443014.sdf");
for mol in suppl:
mol = Chem.RemoveHs(mol)
print 'Mol1: %s' %(Chem.MolToSmiles(mol))
mol = Chem.MolFromSmiles("c1cc(C[NH2+]CC2CNc3ccnn3C2)[nH]n1")
mol = Chem.RemoveHs(mol)
print 'Mol2: %s' %(Chem.MolToSmiles(mol))
Output:
Mol1: Cn1nccc1C[NH2+]CC1CNc2ccnn2C1
Mol2: c1cc(C[NH2+]CC2CNc3ccnn3C2)[nH]n1
This is also the case when extracting the carbon scaffold of a molecule
(even after
resetting all formal charges to zero)
mol = Chem.MolFromSmiles("c1cc(C[NH2+]CC2CNc3ccnn3C2)[nH]n1")
mol = Chem.RemoveHs(mol,implicitOnly=False)
sc = [MurckoScaffold.MakeScaffoldGeneric(mol)]
print 'Scaffold1: %s' %(Chem.MolToSmiles(sc[0]))
mol = Chem.MolFromSmiles("c1cc(C[NH2+]CC2CNc3ccnn3C2)[nH]n1")
sc2 = [MurckoScaffold.MakeScaffoldGeneric(mol)]
sc2[0] = Chem.RemoveHs(sc2[0],implicitOnly=False)
print 'Scaffold2: %s' %(Chem.MolToSmiles(sc2[0]))
mol = Chem.MolFromSmiles("c1cc(C[NH2+]CC2CNc3ccnn3C2)[nH]n1")
mol = Chem.RemoveHs(mol,implicitOnly=False)
for atom in mol.GetAtoms():
atom.SetFormalCharge(0)
sc3 = [MurckoScaffold.MakeScaffoldGeneric(mol)]
sc3[0] = Chem.RemoveHs(sc3[0],implicitOnly=False)
print 'Scaffold3: %s' %(Chem.MolToSmiles(sc3[0]))
Output:
Scaffold1: [CH]1CCCC1C[CH2+]CC1CCC2CCCC2C1
Scaffold2: [CH]1CCCC1C[CH2+]CC1CCC2CCCC2C1
Scaffold3: [CH]1CCCC1CCCC1CCC2CCCC2C1
Are the hydrogen re-added upon mol-> smiles conversion to a string? Do I
have to first reset some atom-based
flag so the hydrogens get removed ?
cheers
Fabian
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