On Sep 7, 2016, at 11:53 AM, Stephen O'hagan wrote:
> How would I find the molecular weight (fraction) of that substructure within
> a compounds expressed as a SMILES string, e.g.:
I don't know if a built-in function which does this. It's possible to write
one. Here's a function which will compute the molecular weight given the
molecule and the atom indices for the fragment.
def get_fragment_molwt(mol, atom_indices):
assert len(atom_indices) == len(set(atom_indices)) # quick duplicate check
molwt = 0.0
for atom_index in atom_indices:
atom = mol.GetAtomWithIdx(atom_index)
molwt += atom.GetMass()
return molt
If you want to include the hydrogen mass, then use this variant:
from rdkit import Chem
_H_mass = Chem.Atom(1).GetMass()
def get_fragment_molwt(mol, atom_indices):
assert len(atom_indices) == len(set(atom_indices)) # quick duplicate check
molwt = 0.0
for atom_index in atom_indices:
atom = mol.GetAtomWithIdx(atom_index)
molwt += atom.GetMass() + atom.GetTotalNumHs() * _H_mass
return molt
Here's an example of how to use the function:
#======
from rdkit import Chem
def get_fragment_molwt():
... as above ...
smiles = "CC(=O)O[C@H]1CC[C@@]2(C)C(=CCC3C4CC=C(c5cccnc5)[C@@]4(C)CCC32)C1"
smarts =
"[#6](:,-[#6]:,-[#6](-[#6]):,-[#6]-[#6](:[#6]:[#7]):[#6]:[#6]):,-[#6]:,-[#6]"
mol = Chem.MolFromSmiles(smiles)
assert mol is not None, smiles
pat = Chem.MolFromSmarts(smarts)
assert pat is not None, smarts
matches = mol.GetSubstructMatches(pat)
molwt = MolWt(mol)
for match_no, match in enumerate(matches, 1):
fragment_molwt = get_fragment_molwt(mol, match)
print("#{}: {:.2%}".format(match_no, fragment_molwt/molwt))
#======
If I don't include the hydrogens in the fragment weight calculation then I get:
#1: 37.32%
#2: 37.32%
#3: 37.32%
...
If I include the hydrogens, then I get:
#1: 40.15%
#2: 39.64%
#3: 40.15%
...
Cheers,
Andrew
[email protected]
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