[Rdkit-discuss] Number of Aromatic Rings
Dear Greg, 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/msg0015 3.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! 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)c12c1[nH]c(C3CCCc4c34)c2" (which contains an indole and a tetrahydronaphthalene) gives a count of 2. Any help would be greatly appreciated. Thanks James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies Oakdene Court 613 Reading Road Winnersh, Berkshire RG41 5UA. Tel: +44 118 977 3133 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the "Company address and registration details" link at the bottom of the page.. __-- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Number of Aromatic Rings
I propose something; it's not a true approach If you've a aromatic you've a smile c1c1 for example. So if you count the number of "1" and divide by 2 you're the number of aromatic If you've lot of cycle in your structure, you're count the number of 1, the number of 2, 3 4 5 6 and you're sum and divide by 2. No ? C From: James Davidson [mailto:j.david...@vernalis.com] Sent: jeudi, 10. juin 2010 14:35 To: rdkit-discuss@lists.sourceforge.net Subject: [Rdkit-discuss] Number of Aromatic Rings Dear Greg, 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/msg00153.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! 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)c12c1[nH]c(C3CCCc4c34)c2" (which contains an indole and a tetrahydronaphthalene) gives a count of 2. Any help would be greatly appreciated. Thanks James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies Oakdene Court 613 Reading Road Winnersh, Berkshire RG41 5UA. Tel: +44 118 977 3133 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the "Company address and registration details" link at the bottom of the page.. __ ** DISCLAIMER This email and any files transmitted with it, including replies and forwarded copies (which may contain alterations) subsequently transmitted from Firmenich, are confidential and solely for the use of the intended recipient. The contents do not represent the opinion of Firmenich except to the extent that it relates to their official business. ** -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Number of Aromatic Rings
Thanks for the suggestion, Cedric. I think something like this could work - but it would not get around the issue of bicyclic aromatics, unless more advanced string parsing were used. For example, indole can be represented as [nH]1ccc2c12 in SMILES, so would give two aromatic rings from your suggestion. However, it does occur to me that for bicyclic systems the 'a12' motif would always be present(?), so maybe... James From: Cedric MORETTI [mailto:cedric.more...@firmenich.com] Sent: 10 June 2010 15:04 To: James Davidson; rdkit-discuss@lists.sourceforge.net Subject: RE: Number of Aromatic Rings I propose something; it's not a true approach If you've a aromatic you've a smile c1c1 for example. So if you count the number of "1" and divide by 2 you're the number of aromatic If you've lot of cycle in your structure, you're count the number of 1, the number of 2, 3 4 5 6 and you're sum and divide by 2. No ? C From: James Davidson [mailto:j.david...@vernalis.com] Sent: jeudi, 10. juin 2010 14:35 To: rdkit-discuss@lists.sourceforge.net Subject: [Rdkit-discuss] Number of Aromatic Rings Dear Greg, 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/msg0015 3.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! 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)c12c1[nH]c(C3CCCc4c34)c2" (which contains an indole and a tetrahydronaphthalene) gives a count of 2. Any help would be greatly appreciated. Thanks James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies Oakdene Court 613 Reading Road Winnersh, Berkshire RG41 5UA. Tel: +44 118 977 3133 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the "Company address and registration details" link at the bottom of the page.. __ ** DISCLAIMER This email and any files transmitted with it, including replies and forwarded copies (which may contain alterations) subsequently transmitted from Firmenich, are confidential and solely for the use of the intended recipient. The contents do not represent the opinion of Firmenich except to the extent that it relates to their official business. ** __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Gr
Re: [Rdkit-discuss] Number of Aromatic Rings
Dear James,
On Thu, Jun 10, 2010 at 2:35 PM, James Davidson 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/msg00153.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)c12c1[nH]c(C3CCCc4c34)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
#
# Copyright (C) 2010 Greg Landrum
#
from rdkit import Chem
def IsRingAromatic(ring,aromaticBonds):
for bidx in ring:
if not aromaticBonds[bidx]:
return False
return True
def HasRingAromatic(ring,aromaticBonds):
for bidx in ring:
if aromaticBonds[bidx]:
return True
return False
def GetFusedRings(rings):
res=rings[:]
pool=[]
for i in range(len(rings)):
for j in range(i+1,len(rings)):
ovl=rings[i]&rings[j]
if ovl:
fused=rings[i]|rings[j]
fused.difference_update(ovl)
pool.append(fused)
while pool:
res.extend(pool)
nextRound=[]
for ringi in rings:
li=len(ringi)
for poolj in pool:
ovl = ringi&poolj
if ovl:
lj = len(poolj)
fused = ringi|poolj
fused.difference_update(ovl)
lf = len(fused)
if lf>li and lf>lj and fused not in nextRound and fused not in res:
nextRound.append(fused)
pool = nextRound
return res
def FindAromaticRings(mol):
# flag whether or not bonds are aromatic:
aromaticBonds = [0]*mol.GetNumBonds()
for bond in mol.GetBonds():
if bond.GetIsAromatic():
aromaticBonds[bond.GetIdx()]=1
# get the list of all rings:
ri = mol.GetRingInfo()
# collect the ones that have at least one aromatic bond:
rings=[set(x) for x in ri.BondRings() if HasRingAromatic(x,aromaticBonds)]
# generate all fused ring systems from that set
fusedRings=GetFusedRings(rings)
aromaticRings = [x for x in fusedRings if IsRingAromatic(x,aromaticBonds)]
return aromaticRings
if __name__=='__main__':
m = Chem.MolFromSmiles('C1=CC2=CC=CC=CC2=C1')
print FindAromaticRings(m)
m = Chem.MolFromSmiles('C1=CC2=C(C=C1)C=C1C=C3C=C4C=C5C(C=CC=C5C5=CC=CC6=C5C=CC=C6)=CC4=CC3=CC1=C2')
print FindAromaticRings(m)
--
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Re: [Rdkit-discuss] Number of Aromatic Rings
Thanks Greg, The code looks pretty shiny to me! I hope I can find time over the weekend to look at doing the post-processing, and will let you know how I get on. 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 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)c12c1[nH]c(C3CCCc4c34)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 __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies Oakdene Court 613 Reading Road Winnersh, Berkshire RG41 5UA. Tel: +44 118 977 3133 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the "Company address and registration details" link at the bottom of the page.. __ -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Number of Aromatic Rings
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 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)c12c1[nH]c(C3CCCc4c34)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
__
PLEASE READ: This email is confidential and may be privileged. It is intended
for the named addressee(s) only and access to it by anyone else is
unauthorised. If you are not an addressee, any disclosure or copying of the
contents of this email or any action taken (or not taken) in reliance on it is
unauthorised and may be unlawful. If you have received this email in error,
please notify the sender or postmas...@vernalis.com. Email is not a secure
method of communication and the Company cannot accept responsibility for the
accuracy or completeness of this message or any attachment(s). Please check
this email for virus infection for which the
