Hi Greg
Well, I managed to have a go at this earlier than I expected. So first some
apologies, provisos, and caveats to warn you, and other readers, that your eyes
will soon experience things inelegant and unpythonic, but it's the best I could
come up with, with my limited faculties and experience!
On the plus side - I think it is doing what I wanted - ie giving a count of the
number of aromatic systems (if you always want count a fused aromatic as 1
aromatic system). The downside is that the way I have done this now makes your
script eg output (6,1) for anthracene - where the 1 is the count of aromatic
systems (fused or otherwise). It would be most generic if it maybe returned
(6,3,1) as (all unique aromatic substructures, unique mono-cyclic
substructures, aromatic systems). I'm sure this is fairly straightforward, but
for another day!
So what I added was:
def GetOuterSet(rings):
# Initialise a counter for parent aromatic 'super' rings
result = 0
# Set-up a dictionary so that items can be referenced and deleted
ring_set = {}
for k, v in enumerate(rings):
ring_set[k] = v
# While there is something to process
while len(ring_set):
# Set the ring to be checked as the last in the list - should be the
biggest
reference = sorted(ring_set)[-1]
for k,v in sorted(ring_set.iteritems()):
# if current item is contained in last item - remove current from
dictionary
if v&ring_set[reference]:
ring_set.pop(k)
# If we are at the reference, then we have found our 'super'
ring
if k == reference:
result += 1
break
return result
and I passed in the aromaticRings list from your script, then returned both the
length of the aromaticRings list (as before) plus the output of GetOuterSet().
ie:
superRings = GetOuterSet(aromaticRings)
return len(aromaticRings), superRings
So once again, thanks for the help, and I would welcome any pointers from
anyone on tidying-up and improving this modification! (or corrections if
anyone spots them - I have only briefly tested this)
Kind regards
James
-----Original Message-----
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 11 June 2010 06:02
To: James Davidson
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Number of Aromatic Rings
Dear James,
On Thu, Jun 10, 2010 at 2:35 PM, James Davidson <j.david...@vernalis.com> wrote:
>
> I have been trying figure-out how to return the count of aromatic
> rings for molecules (in Python), and am going to have to admit defeat!
> I saw in an earlier message
> (http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg00
> 153.html) a similar query, but I'm afraid it didn't help me very much.
> I also read the section on Aromaticity in the rdkit book, and realised
> that maybe this isn't a trivial exercise!
Correct. Counting the number of non-fused rings that are aromatic, like the
post you reference does, is pretty easy; including the fused rings that are
aromatic is more challenging.
> I would like the count to count aromatic ring-systems such that
> bicyclic (eg indole or naphthalene) would only count as 1. For
> reference, this appears to be the behaviour of the OpenEye
> OEDetermineAromaticRingSystems function - where the molecule derived
> from the smiles "C(O)(=O)c1cccc2c1[nH]c(C3CCCc4c3cccc4)c2" (which
> contains an indole and a
> tetrahydronaphthalene) gives a count of 2.
>
> Any help would be greatly appreciated.
I've attached a script that's not quite what you want, but it gets you almost
there: it finds all aromatic ring systems, including fused ones. Anthracene,
for example, gives 6 rings. The modifications to this to get what you're
looking for aren't a straightforward post-processing step, but shouldn't be too
bad. If there's not enough here, let me know and I will take a look at adding
the extra code.
This code isn't perfectly polished and could certainly be faster, but it does
seem mostly functional.
-greg
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