Dear Greg,
Thank you very much! I think 'C6H5' is good enough to me.
Yingfeng
On Sun, Jun 2, 2013 at 12:25 AM, Greg Landrum <[email protected]>wrote:
>
> On Sat, Jun 1, 2013 at 6:46 AM, Yingfeng Wang <[email protected]> wrote:
>
>> Dear Greg,
>>
>> Thanks.
>>
>> As for
>> In [19]: frags = Chem.GetMolFrags(nm,asMols=True)
>> In [20]: [AllChem.CalcMolFormula(x) for x in frags]
>> Out[20]: ['C4H5N3O', 'C6H6']
>>
>> Is it possible to directly get 'C6H5+' instead of 'C6H6'?
>>
>
> You can't get C6H5+, because there's not really any way for the code to
> know here to assign charges if you just call break bonds, but as of this
> morning (I just committed it) you can tell the RDKit not to sanitize the
> fragments:
>
> In [10]: frags = Chem.GetMolFrags(nm,asMols=True,sanitizeFrags=False)
>
> In [11]: [AllChem.CalcMolFormula(x) for x in frags]
> Out[11]: ['C4H4N3O', 'C6H5']
>
> In [10]: frags = Chem.GetMolFrags(nm,asMols=True,sanitizeFrags=False)
>
> In [11]: [AllChem.CalcMolFormula(x) for x in frags]
> Out[11]: ['C4H4N3O', 'C6H5']
>
>
>
>>
>> As for the difference between ExactMolWt() and MolWt(). The confusion is
>> from the following case:
>>
>> >>>[Chem.MolToSmiles(x) for x in frags]
>> ['Cc1nncc(O)n1', 'c1ccccc1']
>>
>> >>> Descriptors.MolWt(Chem.MolFromSmiles('Cc1nncc(O)n1'))
>> 111.10399999999998
>> >>> Descriptors.MolWt(Chem.MolFromSmiles('c1ccccc1'))
>> 78.11399999999999
>> >>> [Descriptors.ExactMolWt(x) for x in frags]
>> [111.04326178, 78.046950192]
>>
>> By far, every thing is perfect.
>>
>> But if I use
>>
>> >>>[Descriptors.MolWt(x) for x in frags]
>> [5.04, 6.048]
>>
>> It looks I can get correct mass by MolWt() if I transfer mol to Smiles
>> format, and transfer Smiles format back to mol. However, if I directly
>> apply MolWt() on the original mol, I got weird results.
>>
>
> I can reproduce this and it looks like a bug. I'll get it fixed.
>
> -greg
>
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