Re: [Rdkit-discuss] compound mass calculation

[Yingfeng W. <ywa...@gm...>]

Peter,

Thanks. Is there is a way to calculate the neutral mass of a compound even
if the Inchi indicates that this compound is negatively charged?

Yingfeng


On Wed, Dec 18, 2013 at 7:50 PM, Peter Gedeck <pet...@gm...>wrote:

> 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 <ywa...@gm...> 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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>