Re: [Rdkit-discuss] how to output multiple Kekule structures
Hi Jason, Jim,
You are right; I think an alternative could be the following:
>>> from rdkit import Chem
>>> suppl=Chem.ResonanceMolSupplier(Chem.MolFromSmiles('c1c1'),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('c1c1')
>> 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('')
>>>
>>> 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]-=,:[*])]')
>>>
>&g
Re: [Rdkit-discuss] how to output multiple Kekule structures
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('c1c1')
>
> 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> <greg.land...@gmail.com>
> To: James T. Metz <jamestm...@aol.com> <jamestm...@aol.com>
> Cc: RDKit Discuss <rdkit-discuss@lists.sourceforge.net>
> <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>
> 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('')
>
> 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,
&g
Re: [Rdkit-discuss] how to output multiple Kekule structures
Paolo,
Exactly what I was looking for. Very helpful. Thank you.
Regards,
Jim Metz
-Original Message-
From: Paolo Tosco <paolo.to...@unito.it>
To: James T. Metz <jamestm...@aol.com>; greg.landrum <greg.land...@gmail.com>;
rdkit-discuss <rdkit-discuss@lists.sourceforge.net>
Sent: Mon, Sep 11, 2017 2:53 pm
Subject: Re: [Rdkit-discuss] how to output multiple Kekule structures
Hi Jim,
you can indeed enumerate all Kekulè structures for a molecule withinthe
RDKit using Chem.ResonanceMolSupplier():
from rdkit import Chem
mol = Chem.MolFromSmiles('c1c1')
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
-OriginalMessage-
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 SMARTSpatterns to
identify substructures inmolecules
that can be aromatic, and I need to beable to
handle cases where there can be
differences in the way that the moleculewas 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 cando 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('')
Re: [Rdkit-discuss] how to output multiple Kekule structures
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('c1c1')
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
<mailto: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('')
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
<mailto:greg.land...@gmail.com>>
To: James T. Metz <jamestm...@aol.com <mailto:jamestm...@aol.com>>
Cc: RDKit Discuss <rdkit-discuss@lists.sourceforge.net
<mailto: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
c1c1
I would like to generate the major canonical resonance forms
and save the results as two separate molecules. Essentially
I am trying to generate
Re: [Rdkit-discuss] how to output multiple Kekule structures
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('')
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
c1c1
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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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('')
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
>
> c1c1
>
> 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
>
>
>
>
>
>
>
>
> --
> 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
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> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
>
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Re: [Rdkit-discuss] how to output multiple Kekule structures
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.
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'
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
c1c1
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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engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
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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 > > c1c1 > > 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 > > > > > > > > > -- > 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 > Rdkit-discuss@lists.sourceforge.net > 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 Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
