Hi Brian,

Many thanks

I will look into this.

Best regards,

Richard

From: Brian Cole [mailto:col...@gmail.com]
Sent: 19 February 2018 23:19
To: Richard Marchese Robinson <r.l.marcheserobin...@leeds.ac.uk>
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Calculating the MOE vsa_acc descriptor using the 
rdkit (or other Open Source software)?

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<mailto: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<https://www.chemcomp.com/journal/descr.htm#VSA][http://www.rdkit.org/docs/GettingStartedInPython.html%23list-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]<http://www.chemcomp.com/journal/vsadesc.htm%5D>.)

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


------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Reply via email to