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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