Re: [Rdkit-discuss] how to output multiple Kekule structures
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Re: [Rdkit-discuss] how to output multiple Kekule structures
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From: Jason B. <jas...@gm...> - 2017-09-11 21:38:09
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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 <pao...@un...> 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 <gre...@gm...> <gre...@gm...>
> To: James T. Metz <jam...@ao...> <jam...@ao...>
> Cc: RDKit Discuss <rdk...@li...>
> <rdk...@li...>
> 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 < <jam...@ao...>
> jam...@ao...> 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 < <gre...@gm...>gre...@gm...>
> To: James T. Metz < <jam...@ao...>jam...@ao...>
> Cc: RDKit Discuss <rdk...@li...>
> 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 <
> rdk...@li...> 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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