Hello Yingfeng,
The molecular formula in the inchi key is not the same as the one from the
molecule that is encoded. It ignores charges. You can see this when you
convert the mol to a SMILES:
>>> sInchi =
"InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-1/t3-/m0/s1"
>>> current_mol = Chem.MolFromInchi(sInchi)
>>> Descriptors.ExactMolWt(current_mol)
146.04533273600001
>>> Chem.MolToSmiles(current_mol)
'NC(CCC(=O)[O-])C(=O)O'
>>> sInchi =
"InChI=1S/C5H9NO4/c6-4(5(9)10)1-3(8)2-7/h2-4,8H,1,6H2,(H,9,10)/t3-,4+/m1/s1"
>>> current_mol = Chem.MolFromInchi(sInchi)
>>> Descriptors.ExactMolWt(current_mol)
147.05315776800001
>>> Chem.MolToSmiles(current_mol)
'NC(CC(O)C=O)C(=O)O'
The first molecule is negatively charged and has a proton less than the
second molecule which is neutral. This explains the difference in molecular
weight.
Best,
Peter
On 19 December 2013 06:50, Yingfeng Wang <[email protected]> wrote:
> I have two different compounds with the same formula. But I got different
> mass.
>
> >>> sInchi =
> "InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-1/t3-/m0/s1"
> >>> current_mol = Chem.MolFromInchi(sInchi)
> >>> current_mass = Descriptors.ExactMolWt(current_mol)
> >>> print current_mass
> 146.045332736
> >>> sInchi =
> "InChI=1S/C5H9NO4/c6-4(5(9)10)1-3(8)2-7/h2-4,8H,1,6H2,(H,9,10)/t3-,4+/m1/s1"
> >>> current_mol = Chem.MolFromInchi(sInchi)
> >>> current_mass = Descriptors.ExactMolWt(current_mol)
> >>> print current_mass
> 147.053157768
>
> Could you please check this problem?
>
> Thanks.
>
> Yingfeng
>
>
>
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