Hi Brian,
Many thanks
I will look into this.
Best regards,
Richard
From: Brian Cole [mailto:[email protected]]
Sent: 19 February 2018 23:19
To: Richard Marchese Robinson <[email protected]>
Cc: [email protected]
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
<[email protected]<mailto:[email protected]>>
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
[email protected]<mailto:[email protected]>
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
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
