Re: [Rdkit-discuss] compound mass calculation

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

Peter,

Thanks. Yes, I am only interested in the mass. Could you please let me know
the function for getting the charge? By the way, how do I the charge is
caused by losing or getting protons instead of electrons?

Yingfeng

On Wed, Dec 18, 2013 at 10:43 PM, Peter Gedeck <pet...@gm...>wrote:

> Hello,
>
> Here is RDkit code that will neutralize a compound:
> http://code.google.com/p/rdkit/wiki/NeutralisingCompounds
>
> If you are only interested in the mass, you could get the charge of the
> compound and add or delete hydrogen masses.
>
> Also, ask on the RDkit list.
>
> Best,
>
> Peter
>
>
>
>
>
> On 19 December 2013 11:18, Yingfeng Wang <ywa...@gm...> wrote:
>
>> 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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>>
>