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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