I change MolWt() into ExactMolWt(), and get
Descriptors.ExactMolWt(m)
187.074561908
[Descriptors.ExactMolWt(x) for x in frags]
[111.04326178, 78.046950192]
According to the document, MolWt() outputs the average molecular weight of
the molecule ignoring hydrogens, while ExactMolWt() is for the exact
molecular weight of the molecule. What do I observe so big difference of
mass? By the way, the mass of m calculated by the ExactMolWt () is still
less than summation of its fragments.
Thanks.
Yingfeng
On Fri, May 31, 2013 at 3:58 PM, Yingfeng Wang <[email protected]> wrote:
> Greg,
>
> I got a weird case. With the following code,
>
> >>> from rdkit import Chem
> >>> from rdkit.Chem import Descriptors
> >>> m
> =Chem.MolFromInchi('InChI=1S/C10H9N3O/c1-7-11-10(14)9(13-12-7)8-5-3-2-4-6-8/h2-6H,1H3,(H,11,12,14)')
> >>> Descriptors.MolWt(m)
> 9.072
> >>> em = Chem.EditableMol(m)
> >>> em.RemoveBond(8,7)
> >>> nm = em.GetMol()
> >>> frags = Chem.GetMolFrags(nm,asMols=True)
> >>> [Descriptors.MolWt(x) for x in frags]
> [5.04, 6.048]
>
> It seems the mass of the original molecule is 9.072, while the summation
> of masses of its fragments is 5.04+6.048 > 9.072. I don't think it is
> caused by the precision problem. Could you please let me know how to remove
> the "extra" mass?
>
> Thanks.
>
> Yingfeng
>
>
> On Fri, May 31, 2013 at 8:58 AM, Yingfeng Wang <[email protected]> wrote:
>
>> Greg,
>>
>> Thank you very much.
>>
>> Yingfeng
>>
>>
>> On Fri, May 31, 2013 at 4:14 AM, Greg Landrum <[email protected]>wrote:
>>
>>>
>>> On Fri, May 31, 2013 at 7:53 AM, Yingfeng Wang <[email protected]>wrote:
>>>
>>>>
>>>> I think I need to add masses of all atoms for getting the mass of the
>>>> whole fragment. Am I right?
>>>>
>>>
>>> It's better to just use the built in functionality:
>>>
>>> In [2]: m = Chem.MolFromSmiles('c1ccccc1')
>>>
>>> In [3]: from rdkit.Chem import Descriptors
>>>
>>> In [4]: Descriptors.MolWt(m)
>>> Out[4]: 78.11399999999999
>>>
>>> -greg
>>>
>>
>>
>
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