Thanks Greg, I suspected that might be the case. I certainly don't
want to turn off all sanitization, but I could write a bit of code to
convert these salts back to my desired form as a separate step.
Alternatively, I guess I could disable or rewrite halogenCleanup() in
MolOps.cpp. Is this the only function which would need to be changed?
Best regards,
Chris
On 22 November 2017 at 07:59, Greg Landrum <greg.land...@gmail.com> wrote:
> At the moment the only way to do this is to disable the "cleanup"
> functionality in SanitizeMol(). This can be done, but it will also have the
> consequence that things like the hypervalent N in nitro groups (i.e.
> "-N(=O)=O") is not cleaned up.
>
> In [2]: m = Chem.MolFromSmiles('O=Cl(=O)(=O)[O-]',sanitize=False)
>
> In [3]: m.UpdatePropertyCache(strict=False)
>
> In [4]:
> Chem.SanitizeMol(m,sanitizeOps=Chem.SANITIZE_ALL^Chem.SANITIZE_CLEANUP^Chem.SANITIZE_PROPERTIES)
> Out[4]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
>
> In [5]: Chem.MolToSmiles(m)
> Out[5]: 'O=Cl(=O)(=O)[O-]'
>
> In [6]: m2 = Chem.MolFromSmiles('CN(=O)=O',sanitize=False)
>
> In [7]: m2.UpdatePropertyCache(strict=False)
>
> In [8]:
> Chem.SanitizeMol(m2,sanitizeOps=Chem.SANITIZE_ALL^Chem.SANITIZE_CLEANUP^Chem.SANITIZE_PROPERTIES)
> Out[8]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
>
> In [10]: Chem.MolToSmiles(m2)
> Out[10]: 'CN(=O)=O'
>
>
> Note that this way of doing things disables all "unreasonable" valence
> checking.
>
> -greg
>
>
> On Tue, Nov 21, 2017 at 10:12 AM, Chris Earnshaw <cgearns...@gmail.com>
> wrote:
>>
>> Hi
>>
>> Sometime between 2014 and now there appears to have been a change in
>> the way hypervalent halogen structures are handled. The old behaviour
>> (involving some tweaking of atomic_data.cpp to allow the higher
>> oxidation states) was to have a neutral halogen with double bonds to
>> most of the oxygens, e.g.
>> chlorate O=Cl(=O)[O-]
>> perchlorate O=Cl(=O)(=O)[O-]
>>
>> The current behaviour is to 'charge separate' the dative bonds, giving
>> chlorate [O-][Cl2+]([O+])[O-]
>> perchlorate [O-][Cl3+]([O-])([O+])[O-]
>>
>> Although this may be regarded as 'correct' (arguable!), it can cause
>> problems of compatibility with other software and looks remarkably
>> ugly. It's also inconsistent with the handling of hypervalent P and S
>> compounds. Using the same convention, we should have -
>>
>> trimethylphosphine oxide C[P+]([O-])(C)C
>> dimethylsulfoxide C[S+]([O-])C
>> dimethylsulfone C[S2+]([O-])([O-])C
>>
>> - and I really don't want this to happen!
>>
>> Does anyone know a way to restore the old behaviour for chlorites,
>> bromates, periodates etc.?
>>
>> Best regards,
>> Chris Earnshaw
>>
>>
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