My two cents: Brian's suggestion to use _CalcLabuteASAContribs is what I
would do here.
For what it's worth, the original Python versions of the RDKit's
implementations of the MOE VSA descriptors is here:
https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/MolSurf.py
The current code has reimplemented most of this in C++, but what's there
may still be educational.
-greg
On Tue, Feb 20, 2018 at 12:18 AM, Brian Cole <col...@gmail.com> wrote:
> Hi Richard,
>
> You can calculate the per-atom contributions to the surface area with
> _CalcLabuteASAContribs:
> http://www.rdkit.org/Python_Docs/rdkit.Chem.rdMolDescriptors-module.html#_
> CalcLabuteASAContribs
>
> If you have the MOE SMARTS for "pure hydrogen bond acceptors", the
> following is the Python I currently use to convert MOE SMARTS to 'standard'
> SMARTS, I expand the dictionary as I encounter the needL
>
> from collections import OrderedDict
>
> # Note, the order these are applied by moe_smarts_to_real_smarts is
> important!
> MOE_SMARTS_TO_REAL_SMARTS = OrderedDict([
> ('i', '*!-*'),
> ('#X', '!#1;!#6'),
> ('#G4', '#6,#14,#32,#50,#82'),
> ('#G5', '#7,#15,#33,#51,#83'),
> ('#G6', '#8,#16,#34,#52,#84'),
> ('#G7', '#9,#17,#35,#53,#85'),
> ('#N', '#8,#7,#9,#17,#35'),
> ('#O7', '#9,#17,#35,#53'),
> ('#O4', '#6'),
> ('#O', '#6,#7,#8,#9,#15,#16,#17,#35,#53'),
> ('q3', '*(@*)(@*)@*'),
> ('#R2', '#3,#4,#5,#6,#7,#8,#9,#10'),
> ('#Q', '!#1'),
> ('Q1', '$(*[!#1]);!$(*([!#1])[!#1])'),
> ])
>
> def moe_smarts_to_real_smarts(smarts):
> for pat, repl in MOE_SMARTS_TO_REAL_SMARTS.items():
> smarts = smarts.replace(pat, '$([%s])' % repl)
> return smarts
>
> Cheers,
> Brian
>
> On Mon, Feb 19, 2018 at 1:36 PM, Richard Marchese Robinson <
> r.l.marcheserobin...@leeds.ac.uk> wrote:
>
>> Dear Rdkit Team,
>>
>>
>>
>> Please excuse me if I am overlooking something, but it does not seem
>> possible to calculate the MOE vsa_acc descriptor using the Rdkit. Is that
>> correct?
>>
>> [https://www.chemcomp.com/journal/descr.htm#VSA][http://www.
>> rdkit.org/docs/GettingStartedInPython.html#list-of-available-descriptors]
>>
>>
>>
>> I did wonder whether it might be possible to implement the descriptor in
>> Python using the Rdkit, but there seems to be no obvious way to do that. (I
>> can see how it would be possible to use the Rdkit to identify all “pure
>> hydrogen bond acceptors”, as defined in the MOE documentation, using SMARTS
>> patterns, but identifying the contribution of each atom to the van der
>> Waals surface area seems decidedly non-trivial, based on my reading of
>> Labute [http://www.chemcomp.com/journal/vsadesc.htm].)
>>
>>
>>
>> Whilst I appreciate I may need to simply persevere, I would be grateful
>> if any guidance could be provided as to how this descriptor might be
>> calculated using the rdkit (e.g. is there a straightforward way of getting
>> those van der Waals surface area contributions that I have embarrassingly
>> overlooked) or some other Open Source tool that I may have overlooked?
>>
>>
>>
>> Otherwise, are there any plans to implement this descriptor in a
>> forthcoming version of the rdkit?
>>
>>
>>
>> As ever, the efforts of the Rdkit Team in making this great resource
>> available to the community are much appreciated.
>>
>>
>>
>> Best regards,
>>
>>
>>
>> Richard
>>
>>
>>
>>
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>
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