Hi Jason, Jim,
You are right; I think an alternative could be the following:
>>> from rdkit import Chem
>>> suppl=Chem.ResonanceMolSupplier(Chem.MolFromSmiles('c1ccccc1'),Chem.KEKULE_ALL)
>>>
>>> q=Chem.MolFromSmarts('C-C=C')
>>> for mol in suppl:
... molCopy=Chem.Mol(mol)
... for a in molCopy.GetAtoms():
... a.SetIsAromatic(False)
... for b in molCopy.GetBonds():
... b.SetIsAromatic(False)
... print molCopy.GetSubstructMatches(q)
...
((0, 5, 4), (1, 2, 3), (2, 1, 0), (3, 4, 5), (4, 3, 2), (5, 0, 1))
((0, 1, 2), (1, 0, 5), (2, 3, 4), (3, 2, 1), (4, 5, 0), (5, 4, 3))
>>>
Cheers,
p.
> On 11 Sep 2017, at 23:38, Jason Biggs <jasondbi...@gmail.com> wrote:
>
> But keep in mind that the kekulized mols you create with the resonance
> supplier will not match the SMARTS patterns given.
>
> Chem.MolToSmiles(mol2, kekuleSmiles = True)
>
> >'C1C=CC=CC=1'
>
> mol2.HasSubstructMatch(Chem.MolFromSmarts('[C]=[C]-[C]'))
>
> > False
>
> mol2.HasSubstructMatch(Chem.MolFromSmarts('[c]=[c]-[c]'))
>
> > True
>
> So at the very least, you need to change the smarts strings to use [#6]
> instead of [C]
>
>
>
> Jason Biggs
>
>
>> On Mon, Sep 11, 2017 at 2:53 PM, Paolo Tosco <paolo.to...@unito.it> wrote:
>> Hi Jim,
>>
>> you can indeed enumerate all Kekulè structures for a molecule within the
>> RDKit using Chem.ResonanceMolSupplier():
>>
>> from rdkit import Chem
>> mol = Chem.MolFromSmiles('c1ccccc1')
>> suppl = Chem.ResonanceMolSupplier(mol, Chem.KEKULE_ALL)
>> len(suppl)
>> 2
>> for i in range(len(suppl)):
>> print (Chem.MolToSmiles(suppl[i], kekuleSmiles=True))
>> C1C=CC=CC=1
>> C1=CC=CC=C1
>>
>> Best,
>> Paolo
>>
>>
>>> On 09/11/2017 05:22 PM, James T. Metz via Rdkit-discuss wrote:
>>> Greg,
>>>
>>> Thanks! Yes, very helpful. I will need to digest the detailed
>>> information
>>> you have provided. I am somewhat familiar with recursive SMARTS. Thanks
>>> again.
>>>
>>> Regards,
>>> Jim Metz
>>>
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: Greg Landrum <greg.land...@gmail.com>
>>> To: James T. Metz <jamestm...@aol.com>
>>> Cc: RDKit Discuss <rdkit-discuss@lists.sourceforge.net>
>>> Sent: Mon, Sep 11, 2017 11:15 am
>>> Subject: Re: [Rdkit-discuss] how to output multiple Kekule structures
>>>
>>>
>>> On Mon, Sep 11, 2017 at 5:55 PM, James T. Metz <jamestm...@aol.com> wrote:
>>> Greg,
>>>
>>> I need to be able to use SMARTS patterns to identify substructures in
>>> molecules
>>> that can be aromatic, and I need to be able to handle cases where there can
>>> be
>>> differences in the way that the molecule was entered or drawn by a user.
>>>
>>> That particular problem is a big part of the reason that we tend to use the
>>> aromatic representation of things.
>>>
>>> For example, consider the following alkenyl-substituted pyridine, there
>>> are two possible Kekule structures
>>>
>>> m1 = 'C=CC1=NC=CC=C1'
>>> m2 = 'C=CC1N=CC=CC1'
>>>
>>> Fixing what I assume is a typo for m2, I can do the following:
>>>
>>> In [11]: m1 = Chem.MolFromSmiles('C=CC1=NC=CC=C1')
>>>
>>> In [12]: m2 = Chem.MolFromSmiles('C=CC1N=CC=CC=1')
>>>
>>> In [13]: q1 = Chem.MolFromSmarts('cccc')
>>>
>>> In [14]: q2 = Chem.MolFromSmarts('cccn')
>>>
>>> In [15]: list(m1.GetSubstructMatch(q1))
>>> Out[15]: [2, 7, 6, 5]
>>>
>>> In [16]: list(m1.GetSubstructMatch(q2))
>>> Out[16]: [6, 5, 4, 3]
>>>
>>> In [17]: list(m2.GetSubstructMatch(q1))
>>> Out[17]: [2, 7, 6, 5]
>>>
>>> In [18]: list(m2.GetSubstructMatch(q2))
>>> Out[18]: [6, 5, 4, 3]
>>>
>>>
>>> Those particular queries were going for the aromatic species and will only
>>> match inside the ring, but if you want to be more generic you could tune
>>> your queries like this:
>>>
>>> In [28]: q3 =
>>> Chem.MolFromSmarts('[#6;$([#6]=,:[*])]-,=,:[#6;$([#6]=,:[*])]-,=,:[#6;$([#6]=,:[*])]-,=,:[#6;$([#6]-=,:[*])]')
>>>
>>> In [29]: q4 =
>>> Chem.MolFromSmarts('[#6;$([#6]=,:[*])]-,=,:[#6;$([#6]=,:[*])]-,=,:[#6;$([#6]=,:[*])]-,=,:[#7;$([#7]-=,:[*])]')
>>>
>>> In [30]: list(m1.GetSubstructMatch(q3))
>>> Out[30]: [0, 1, 2, 7]
>>>
>>> In [31]: list(m1.GetSubstructMatch(q4))
>>> Out[31]: [0, 1, 2, 3]
>>>
>>> In [32]: list(m2.GetSubstructMatch(q3))
>>> Out[32]: [0, 1, 2, 7]
>>>
>>> In [33]: list(m2.GetSubstructMatch(q4))
>>> Out[33]: [0, 1, 2, 3]
>>>
>>> If you aren't familiar with recursive SMARTS, this construct:
>>> "[#6;$([#6]=,:[*])]" means "a carbon that has either a double bond or an
>>> aromatic bond to another atom". So you can interpret q3 as "four carbons
>>> that each have either a double or aromatic bond and that are
>>> connected to each other by single, double, or aromatic bonds".
>>>
>>> Is this starting to approximate what you're looking for?
>>> -greg
>>>
>>>
>>>
>>>
>>> Now consider two SMARTS
>>>
>>> pattern1 = '[C]=[C]-[C]={C]
>>> pattern2 = '[C]=[C]-[C]=[N]'
>>>
>>> I need to be able to detect the existence of each pattern in the
>>> molecule
>>>
>>> If m1 is the only available generated Kekule structure, then pattern2
>>> will be recognized.
>>> If m2 is the only available generated Kekule structure, then pattern1
>>> will be recognized.
>>>
>>> Hence, I am getting different answers for the same input molecule just
>>> because
>>> it was drawn in different Kekule structures.
>>>
>>> Regards,
>>> Jim Metz
>>>
>>>
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: Greg Landrum <greg.land...@gmail.com>
>>> To: James T. Metz <jamestm...@aol.com>
>>> Cc: RDKit Discuss <rdkit-discuss@lists.sourceforge.net>
>>> Sent: Mon, Sep 11, 2017 10:31 am
>>> Subject: Re: [Rdkit-discuss] how to output multiple Kekule structures
>>>
>>> Hi Jim,
>>>
>>> The code currently has no way to enumerate Kekule structures. I don't
>>> recall this coming up in the past and, to be honest, it doesn't seem all
>>> that generally useful.
>>>
>>> Perhaps there's an alternate way to solve the problem; what are you trying
>>> to do?
>>>
>>> -greg
>>>
>>>
>>> On Mon, Sep 11, 2017 at 5:04 PM, James T. Metz via Rdkit-discuss
>>> <rdkit-discuss@lists.sourceforge.net> wrote:
>>> Hello,
>>>
>>> Suppose I read in an aromatic SMILES e.g.,
>>> for benzene
>>>
>>> c1ccccc1
>>>
>>> I would like to generate the major canonical resonance forms
>>> and save the results as two separate molecules. Essentially
>>> I am trying to generate
>>>
>>> m1 = 'C1=CC=CC-C1'
>>> m2 = 'C1C=CC=CC1'
>>>
>>> Can this be done in RDkit? I have found a KEKULE_ALL
>>> option in the detailed documentation which seems to be what I
>>> am trying to do, but I don't understand how this option is to be used,
>>> or the proper syntax.
>>>
>>> If it is necessary to somehow renumber the atoms and re-generate
>>> Kekule structures, that is OK. Thank you.
>>>
>>> Regards,
>>> Jim Metz
>>>
>>>
>>>
>>>
>>>
>>>
>>>
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>>>
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>>
>>
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