Re: [Rdkit-discuss] canonicalization of two aromatic molecules returning two different forms (kekule and aromatic)
Thanks Paolo, I'll try that. Sorry about the misleading title of my email, I forgot to change it. Best, Alexis On Fri, 4 Dec 2020 at 13:40, Paolo Tosco wrote: > Hi Alexis, > > you may cast the _vectdouble to a list or a tuple and then you'll be able > to pickle it. > The 2020.09.01 is just an oversight; you are indeed the 2020.09.02 > version. > > Cheers, > p. > > On Fri, Dec 4, 2020 at 1:32 PM Alexis Parenty < > alexis.parenty.h...@gmail.com> wrote: > >> Dear Rdkiters, >> >> I could not pickle my models when using the new chemical descriptors, >> therefore, I have re-installed the latest patched version of rdkit >> 2020.09.02 through conda-forge. (ref Fixes #3511 #3513) >> >> https://anaconda.org/conda-forge/rdkit >> >> However, this new version still does not let me pickle my models: >> >> RuntimeError: Pickling of "rdkit.rdBase._vectdouble" instances is not >> enabled (http://www.boost.org/libs/python/doc/v2/pickle.html) >> >> Also, I have noticed that the newly installed version of rdkit on my >> windows64 machine is still labelled as 2020.09.01 (according to conda list) >> despite having conda-installed the 2020.09.02 version. >> >> Am I installing the wrong fixe? >> >> Many thanks and regards, >> >> Alexis >> >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] canonicalization of two aromatic molecules returning two different forms (kekule and aromatic)
Hi Alexis, you may cast the _vectdouble to a list or a tuple and then you'll be able to pickle it. The 2020.09.01 is just an oversight; you are indeed the 2020.09.02 version. Cheers, p. On Fri, Dec 4, 2020 at 1:32 PM Alexis Parenty wrote: > Dear Rdkiters, > > I could not pickle my models when using the new chemical descriptors, > therefore, I have re-installed the latest patched version of rdkit > 2020.09.02 through conda-forge. (ref Fixes #3511 #3513) > > https://anaconda.org/conda-forge/rdkit > > However, this new version still does not let me pickle my models: > > RuntimeError: Pickling of "rdkit.rdBase._vectdouble" instances is not > enabled (http://www.boost.org/libs/python/doc/v2/pickle.html) > > Also, I have noticed that the newly installed version of rdkit on my > windows64 machine is still labelled as 2020.09.01 (according to conda list) > despite having conda-installed the 2020.09.02 version. > > Am I installing the wrong fixe? > > Many thanks and regards, > > Alexis > > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] canonicalization of two aromatic molecules returning two different forms (kekule and aromatic)
Dear Rdkiters, I could not pickle my models when using the new chemical descriptors, therefore, I have re-installed the latest patched version of rdkit 2020.09.02 through conda-forge. (ref Fixes #3511 #3513) https://anaconda.org/conda-forge/rdkit However, this new version still does not let me pickle my models: RuntimeError: Pickling of "rdkit.rdBase._vectdouble" instances is not enabled (http://www.boost.org/libs/python/doc/v2/pickle.html) Also, I have noticed that the newly installed version of rdkit on my windows64 machine is still labelled as 2020.09.01 (according to conda list) despite having conda-installed the 2020.09.02 version. Am I installing the wrong fixe? Many thanks and regards, Alexis ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] canonicalization of two aromatic molecules returning two different forms (kekule and aromatic)
Dear Peter and Paolo, Wahoo! many thanks to both of you for having researched that much on this issue. No worries, I can live with a kekulé form of my smiles1! I only noticed that strange behaviour when I fragmented a dihydro imidazo pyridine derivative of smiles1 and saw that some of its fragments had lost aromaticity and were no longer a substructure match for their parent... Best, Alexis On Sat, 28 Nov 2020 at 03:49, Peter S. Shenkin wrote: > Yes, I've seen the same phenomenon in multiple SMILES generators. > > Even Daylight's (when they had it up on a public web site). > > From a chemical perspective, it isn't sensible that the pyridone-like ring > in molecule 1 should not be seen as aromatic in the canonical > SMILES, especially since the same ring is seen as aromatic in molecule2. > The counter-argument has often been that "only exocyclic substituents are > considered". But of course that =N is indeed exocyclic to the ring in > question. > > In a famous quote, Dave Weininger said: > > It is important to remember that the purpose of the SMILES aromaticity > detection algorithm is for the purposes of chemical information > representation only! To this end, rigorous rules are provided for > determining the "aromaticity" of charged, heterocyclic, and electron > deficient ring systems. The"aromaticity" designation as used here is not > intended to imply anything about the reactivity, magnetic resonance > spectra, heat of formation, or odor of substances. > > As an example of the utility of this definition, consider o-xylene. You > don't want to see the VB structure with a double bond connecting the > methyl-attached carbons as different from the form with a single bond in > that position. Hence, aromaticity enables SMILES to avoid that issue, since > the (canonical) SMILES does not contain any double bonds, but only aromatic > bonds within the ring. > > And the fact is that there is no ambiguity in any of the structures I've > seen (including the one shown SMILES1) that exhibit the problem. There's > only one way to draw the resonance structure, anyway, so you could argue > that you don't need to make it aromatic at all. > > Of course, if you had the courage of that particular conviction, you > wouldn't bother making pyrrole aromatic, either, because there's only one > resonance structure you can draw. But SMILES does define pyrrole as > aromatic. > > When I've discussed this with developers who have worked on SMILES > systems, they say that looking for cases like exocyclic > aromaticity-producing substituents in adjacent non-aromatic rings would > slow the SMILES generator down. > > But the problem is that when you are using a SMARTS to look for one of > these pyridone-like rings that you see in the first structure, you're not > going to find it, even though it's there. Chemists do expect an aromatic > SMARTS to find an aromatic ring, which is no doubt the secret reason for > making pyrrole aromatic. > > I've never liked this situation, but it boils down to the fact that > Daylight, which produced the original reference SMILES implementation, > "done it that-a-way". It has the advantage of *stare decisis*. > > -P. > > P. S. By the way, if any of you have ever seen a SMILES generator that > displays the 6-membered ring as aromatic in the first example, could you > please tell us which one that is? > > On Fri, Nov 27, 2020 at 1:55 PM Paolo Tosco > wrote: > >> (Now with link - you can tell it's Friday night) >> >> Hi Mark, Alexis, >> >> Yes, I was too fast in composing my previous reply and I did not pay >> enough attention to the molecules. >> After reading Alexis' reply, I looked more carefully at his original >> question and at that point I remembered having seen a similar behaviour >> before from RDKit on condensed ring systems featuring exocyclic bonds and >> relative mailing list discussions. >> So I did a bit of searching and I fished out the (long) thread that deals >> with exactly this behaviour. >> >> >> https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/CAAsqebGxOwJtH32T5jC%3DoBZN6G1JE_NwsEqKUO8%2BmUCqmABCzQ%40mail.gmail.com/#msg36448625 >> >> I hope that helps, cheers >> p. >> >> On Fri, Nov 27, 2020 at 7:31 PM Mark Mackey >> wrote: >> >>> Hi Paolo, >>> >>> >>> >>> Hmmm, I think this is displaying a bug (or at the very least unexpected >>> behaviour) in the aromaticity code. The issue isn’t the aromaticity of the >>> imidazole/dihydroimidazole, but the aromaticity of the pyridyl. Alexis’ >>> second molecule is identical to the first except that o
Re: [Rdkit-discuss] canonicalization of two aromatic molecules returning two different forms (kekule and aromatic)
Yes, I've seen the same phenomenon in multiple SMILES generators. Even Daylight's (when they had it up on a public web site). >From a chemical perspective, it isn't sensible that the pyridone-like ring in molecule 1 should not be seen as aromatic in the canonical SMILES, especially since the same ring is seen as aromatic in molecule2. The counter-argument has often been that "only exocyclic substituents are considered". But of course that =N is indeed exocyclic to the ring in question. In a famous quote, Dave Weininger said: It is important to remember that the purpose of the SMILES aromaticity detection algorithm is for the purposes of chemical information representation only! To this end, rigorous rules are provided for determining the "aromaticity" of charged, heterocyclic, and electron deficient ring systems. The"aromaticity" designation as used here is not intended to imply anything about the reactivity, magnetic resonance spectra, heat of formation, or odor of substances. As an example of the utility of this definition, consider o-xylene. You don't want to see the VB structure with a double bond connecting the methyl-attached carbons as different from the form with a single bond in that position. Hence, aromaticity enables SMILES to avoid that issue, since the (canonical) SMILES does not contain any double bonds, but only aromatic bonds within the ring. And the fact is that there is no ambiguity in any of the structures I've seen (including the one shown SMILES1) that exhibit the problem. There's only one way to draw the resonance structure, anyway, so you could argue that you don't need to make it aromatic at all. Of course, if you had the courage of that particular conviction, you wouldn't bother making pyrrole aromatic, either, because there's only one resonance structure you can draw. But SMILES does define pyrrole as aromatic. When I've discussed this with developers who have worked on SMILES systems, they say that looking for cases like exocyclic aromaticity-producing substituents in adjacent non-aromatic rings would slow the SMILES generator down. But the problem is that when you are using a SMARTS to look for one of these pyridone-like rings that you see in the first structure, you're not going to find it, even though it's there. Chemists do expect an aromatic SMARTS to find an aromatic ring, which is no doubt the secret reason for making pyrrole aromatic. I've never liked this situation, but it boils down to the fact that Daylight, which produced the original reference SMILES implementation, "done it that-a-way". It has the advantage of *stare decisis*. -P. P. S. By the way, if any of you have ever seen a SMILES generator that displays the 6-membered ring as aromatic in the first example, could you please tell us which one that is? On Fri, Nov 27, 2020 at 1:55 PM Paolo Tosco wrote: > (Now with link - you can tell it's Friday night) > > Hi Mark, Alexis, > > Yes, I was too fast in composing my previous reply and I did not pay > enough attention to the molecules. > After reading Alexis' reply, I looked more carefully at his original > question and at that point I remembered having seen a similar behaviour > before from RDKit on condensed ring systems featuring exocyclic bonds and > relative mailing list discussions. > So I did a bit of searching and I fished out the (long) thread that deals > with exactly this behaviour. > > > https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/CAAsqebGxOwJtH32T5jC%3DoBZN6G1JE_NwsEqKUO8%2BmUCqmABCzQ%40mail.gmail.com/#msg36448625 > > I hope that helps, cheers > p. > > On Fri, Nov 27, 2020 at 7:31 PM Mark Mackey > wrote: > >> Hi Paolo, >> >> >> >> Hmmm, I think this is displaying a bug (or at the very least unexpected >> behaviour) in the aromaticity code. The issue isn’t the aromaticity of the >> imidazole/dihydroimidazole, but the aromaticity of the pyridyl. Alexis’ >> second molecule is identical to the first except that one bond in the >> 5-membered ring was broken, and that (to my eyes at least) should not >> affect whether the 6-membered ring is seen as aromatic. >> >> >> >> Regards, >> >> Mark. >> >> >> >> *From:* Paolo Tosco >> *Sent:* 27 November 2020 17:04 >> *To:* Alexis Parenty >> *Cc:* RDKit Discuss >> *Subject:* Re: [Rdkit-discuss] canonicalization of two aromatic >> molecules returning two different forms (kekule and aromatic) >> >> >> >> Hi Alexis, >> >> >> >> The second molecule (smiles2) is indeed aromatic, but the first (smiles1) >> is not, as the imidazole ring condensed to the pyridine is partially >> saturated. >> >> The smiles1a analogue where I have added a double bond is aromatic, a
Re: [Rdkit-discuss] canonicalization of two aromatic molecules returning two different forms (kekule and aromatic)
Hi Paolo,
Hmmm, I think this is displaying a bug (or at the very least unexpected
behaviour) in the aromaticity code. The issue isn’t the aromaticity of the
imidazole/dihydroimidazole, but the aromaticity of the pyridyl. Alexis’ second
molecule is identical to the first except that one bond in the 5-membered ring
was broken, and that (to my eyes at least) should not affect whether the
6-membered ring is seen as aromatic.
Regards,
Mark.
From: Paolo Tosco
Sent: 27 November 2020 17:04
To: Alexis Parenty
Cc: RDKit Discuss
Subject: Re: [Rdkit-discuss] canonicalization of two aromatic molecules
returning two different forms (kekule and aromatic)
Hi Alexis,
The second molecule (smiles2) is indeed aromatic, but the first (smiles1) is
not, as the imidazole ring condensed to the pyridine is partially saturated.
The smiles1a analogue where I have added a double bond is aromatic, and upon
canonicalization it yields an aromatic SMILES as expected.
Cheers,
p.
from rdkit import Chem
In [2]:
mol1 = Chem.MolFromSmiles("N12C=CC=CC1=NCC2")
In [3]:
mol1
Out[3]:
[cid:image001.png@01D6C4EB.7D142840]
In [4]:
smiles1 = Chem.MolToSmiles(mol1)
In [5]:
smiles1
Out[5]:
'C1=CC2=NCCN2C=C1'
In [6]:
mol2 = Chem.MolFromSmiles("CN=C1C=CC=CN1C")
In [7]:
mol2
Out[7]:
[cid:image002.png@01D6C4EB.7D142840]
In [8]:
smiles2 = Chem.MolToSmiles(mol2)
In [9]:
smiles2
Out[9]:
'CN=c1n1C'
In [10]:
mol1a = Chem.MolFromSmiles("N12C=CC=CC1=NC=C2")
In [11]:
mol1a
Out[11]:
[cid:image003.png@01D6C4EB.7D142840]
In [12]:
smiles1a = Chem.MolToSmiles(mol1a)
In [13]:
smiles1a
Out[13]:
'c1ccn2ccnc2c1'
On Fri, Nov 27, 2020 at 5:09 PM Alexis Parenty
mailto:alexis.parenty.h...@gmail.com>> wrote:
Hi everyone,
Why is it that when I canonicalize the following smiles_1 I get its unexpected
kekule form, whereas when I canonicalize a similar smiles_2, I get its expected
aromatic form?
From rdkit import Chem
smiles1 = Chem.CanonSmiles("N12C=CC=CC1=NCC2")
smiles
==> 'C1=CC2=NCCN2C=C1'
smiles2 = Chem.CanonSmiles("CN=C1C=CC=CN1C")
smiles2
==> 'CN=c1n1C'
I would like to get the aromatic form in both cases... Is there a way to force
the aromatic form?
Best,
Alexis
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] canonicalization of two aromatic molecules returning two different forms (kekule and aromatic)
(Now with link - you can tell it's Friday night)
Hi Mark, Alexis,
Yes, I was too fast in composing my previous reply and I did not pay enough
attention to the molecules.
After reading Alexis' reply, I looked more carefully at his original
question and at that point I remembered having seen a similar behaviour
before from RDKit on condensed ring systems featuring exocyclic bonds and
relative mailing list discussions.
So I did a bit of searching and I fished out the (long) thread that deals
with exactly this behaviour.
https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/CAAsqebGxOwJtH32T5jC%3DoBZN6G1JE_NwsEqKUO8%2BmUCqmABCzQ%40mail.gmail.com/#msg36448625
I hope that helps, cheers
p.
On Fri, Nov 27, 2020 at 7:31 PM Mark Mackey wrote:
> Hi Paolo,
>
>
>
> Hmmm, I think this is displaying a bug (or at the very least unexpected
> behaviour) in the aromaticity code. The issue isn’t the aromaticity of the
> imidazole/dihydroimidazole, but the aromaticity of the pyridyl. Alexis’
> second molecule is identical to the first except that one bond in the
> 5-membered ring was broken, and that (to my eyes at least) should not
> affect whether the 6-membered ring is seen as aromatic.
>
>
>
> Regards,
>
> Mark.
>
>
>
> *From:* Paolo Tosco
> *Sent:* 27 November 2020 17:04
> *To:* Alexis Parenty
> *Cc:* RDKit Discuss
> *Subject:* Re: [Rdkit-discuss] canonicalization of two aromatic molecules
> returning two different forms (kekule and aromatic)
>
>
>
> Hi Alexis,
>
>
>
> The second molecule (smiles2) is indeed aromatic, but the first (smiles1)
> is not, as the imidazole ring condensed to the pyridine is partially
> saturated.
>
> The smiles1a analogue where I have added a double bond is aromatic, and
> upon canonicalization it yields an aromatic SMILES as expected.
>
>
>
> Cheers,
>
> p.
>
>
>
> *from* rdkit *import* Chem
>
> In [2]:
>
> mol1 *=* Chem*.*MolFromSmiles("N12C=CC=CC1=NCC2")
>
> In [3]:
>
> mol1
>
> Out[3]:
>
> In [4]:
>
> smiles1 *=* Chem*.*MolToSmiles(mol1)
>
> In [5]:
>
> smiles1
>
> Out[5]:
>
> 'C1=CC2=NCCN2C=C1'
>
> In [6]:
>
> mol2 *=* Chem*.*MolFromSmiles("CN=C1C=CC=CN1C")
>
> In [7]:
>
> mol2
>
> Out[7]:
>
> In [8]:
>
> smiles2 *=* Chem*.*MolToSmiles(mol2)
>
> In [9]:
>
> smiles2
>
> Out[9]:
>
> 'CN=c1n1C'
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> In [10]:
>
> mol1a *=* Chem*.*MolFromSmiles("N12C=CC=CC1=NC=C2")
>
> In [11]:
>
> mol1a
>
> Out[11]:
>
> In [12]:
>
> smiles1a *=* Chem*.*MolToSmiles(mol1a)
>
> In [13]:
>
> smiles1a
>
> Out[13]:
>
> 'c1ccn2ccnc2c1'
>
>
>
> On Fri, Nov 27, 2020 at 5:09 PM Alexis Parenty <
> alexis.parenty.h...@gmail.com> wrote:
>
> Hi everyone,
>
>
>
> Why is it that when I canonicalize the following smiles_1 I get its
> unexpected kekule form, whereas when I canonicalize a similar smiles_2, I
> get its expected aromatic form?
>
>
>
> From rdkit import Chem
>
> smiles1 = Chem.CanonSmiles("N12C=CC=CC1=NCC2")
> smiles
>
> ==> 'C1=CC2=NCCN2C=C1'
>
>
>
> smiles2 = Chem.CanonSmiles("CN=C1C=CC=CN1C")
> smiles2
>
> ==> 'CN=c1n1C'
>
>
>
> I would like to get the aromatic form in both cases... Is there a way to
> force the aromatic form?
>
>
>
> Best,
>
> Alexis
>
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] canonicalization of two aromatic molecules returning two different forms (kekule and aromatic)
Hi Mark, Alexis,
I was too fast in composing my previous reply and I did not pay enough
attention to the molecules.
After reading Alexis' reply, I went back to his original question and at
that point I remembered having seen a similar behaviour before from RDKit
on condensed ring systems featuring exocyclic bonds and relative mailing
list discussions.
So I did a bit of searching and I fished out the (long) thread that deals
with exactly this behaviour.
I hope that helps, cheers
p.
On Fri, Nov 27, 2020 at 7:31 PM Mark Mackey wrote:
> Hi Paolo,
>
>
>
> Hmmm, I think this is displaying a bug (or at the very least unexpected
> behaviour) in the aromaticity code. The issue isn’t the aromaticity of the
> imidazole/dihydroimidazole, but the aromaticity of the pyridyl. Alexis’
> second molecule is identical to the first except that one bond in the
> 5-membered ring was broken, and that (to my eyes at least) should not
> affect whether the 6-membered ring is seen as aromatic.
>
>
>
> Regards,
>
> Mark.
>
>
>
> *From:* Paolo Tosco
> *Sent:* 27 November 2020 17:04
> *To:* Alexis Parenty
> *Cc:* RDKit Discuss
> *Subject:* Re: [Rdkit-discuss] canonicalization of two aromatic molecules
> returning two different forms (kekule and aromatic)
>
>
>
> Hi Alexis,
>
>
>
> The second molecule (smiles2) is indeed aromatic, but the first (smiles1)
> is not, as the imidazole ring condensed to the pyridine is partially
> saturated.
>
> The smiles1a analogue where I have added a double bond is aromatic, and
> upon canonicalization it yields an aromatic SMILES as expected.
>
>
>
> Cheers,
>
> p.
>
>
>
> *from* rdkit *import* Chem
>
> In [2]:
>
> mol1 *=* Chem*.*MolFromSmiles("N12C=CC=CC1=NCC2")
>
> In [3]:
>
> mol1
>
> Out[3]:
>
> In [4]:
>
> smiles1 *=* Chem*.*MolToSmiles(mol1)
>
> In [5]:
>
> smiles1
>
> Out[5]:
>
> 'C1=CC2=NCCN2C=C1'
>
> In [6]:
>
> mol2 *=* Chem*.*MolFromSmiles("CN=C1C=CC=CN1C")
>
> In [7]:
>
> mol2
>
> Out[7]:
>
> In [8]:
>
> smiles2 *=* Chem*.*MolToSmiles(mol2)
>
> In [9]:
>
> smiles2
>
> Out[9]:
>
> 'CN=c1n1C'
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> In [10]:
>
> mol1a *=* Chem*.*MolFromSmiles("N12C=CC=CC1=NC=C2")
>
> In [11]:
>
> mol1a
>
> Out[11]:
>
> In [12]:
>
> smiles1a *=* Chem*.*MolToSmiles(mol1a)
>
> In [13]:
>
> smiles1a
>
> Out[13]:
>
> 'c1ccn2ccnc2c1'
>
>
>
> On Fri, Nov 27, 2020 at 5:09 PM Alexis Parenty <
> alexis.parenty.h...@gmail.com> wrote:
>
> Hi everyone,
>
>
>
> Why is it that when I canonicalize the following smiles_1 I get its
> unexpected kekule form, whereas when I canonicalize a similar smiles_2, I
> get its expected aromatic form?
>
>
>
> From rdkit import Chem
>
> smiles1 = Chem.CanonSmiles("N12C=CC=CC1=NCC2")
> smiles
>
> ==> 'C1=CC2=NCCN2C=C1'
>
>
>
> smiles2 = Chem.CanonSmiles("CN=C1C=CC=CN1C")
> smiles2
>
> ==> 'CN=c1n1C'
>
>
>
> I would like to get the aromatic form in both cases... Is there a way to
> force the aromatic form?
>
>
>
> Best,
>
> Alexis
>
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] canonicalization of two aromatic molecules returning two different forms (kekule and aromatic)
Hi Paolo,
Many thanks for your response. I suspected that the dihydro-imidazol ring
was involved in this behaviour.
Still can't get my head around this aromaticity behaviour, but I trust you!
It seems that the fused dihydro-imidazol is somehow "stealing" the
aromaticity of the pyridine ring... I'll try to remember that one.
Have a good WE,
Cheers,
Alexis
On Fri, 27 Nov 2020 at 18:04, Paolo Tosco
wrote:
> Hi Alexis,
>
> The second molecule (smiles2) is indeed aromatic, but the first (smiles1)
> is not, as the imidazole ring condensed to the pyridine is partially
> saturated.
> The smiles1a analogue where I have added a double bond is aromatic, and
> upon canonicalization it yields an aromatic SMILES as expected.
>
> Cheers,
> p.
>
> from rdkit import Chem
>
> In [2]:
>
> mol1 = Chem.MolFromSmiles("N12C=CC=CC1=NCC2")
>
> In [3]:
>
> mol1
>
> Out[3]:
> [image: image.png]
> In [4]:
>
> smiles1 = Chem.MolToSmiles(mol1)
>
> In [5]:
>
> smiles1
>
> Out[5]:
>
> 'C1=CC2=NCCN2C=C1'
>
> In [6]:
>
> mol2 = Chem.MolFromSmiles("CN=C1C=CC=CN1C")
>
> In [7]:
>
> mol2
>
> Out[7]:
> [image: image.png]
> In [8]:
>
> smiles2 = Chem.MolToSmiles(mol2)
>
> In [9]:
>
> smiles2
>
> Out[9]:
>
> 'CN=c1n1C'
>
>
>
>
>
>
>
>
>
> In [10]:
>
> mol1a = Chem.MolFromSmiles("N12C=CC=CC1=NC=C2")
>
> In [11]:
>
> mol1a
>
> Out[11]:
> [image: image.png]
> In [12]:
>
> smiles1a = Chem.MolToSmiles(mol1a)
>
> In [13]:
>
> smiles1a
>
> Out[13]:
>
> 'c1ccn2ccnc2c1'
>
>
> On Fri, Nov 27, 2020 at 5:09 PM Alexis Parenty <
> alexis.parenty.h...@gmail.com> wrote:
>
>> Hi everyone,
>>
>> Why is it that when I canonicalize the following smiles_1 I get its
>> unexpected kekule form, whereas when I canonicalize a similar smiles_2, I
>> get its expected aromatic form?
>>
>> From rdkit import Chem
>> smiles1 = Chem.CanonSmiles("N12C=CC=CC1=NCC2")
>> smiles
>> ==> 'C1=CC2=NCCN2C=C1'
>>
>> smiles2 = Chem.CanonSmiles("CN=C1C=CC=CN1C")
>> smiles2
>> ==> 'CN=c1n1C'
>>
>> I would like to get the aromatic form in both cases... Is there a way to
>> force the aromatic form?
>>
>> Best,
>> Alexis
>> ___
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] canonicalization of two aromatic molecules returning two different forms (kekule and aromatic)
Hi Alexis,
The second molecule (smiles2) is indeed aromatic, but the first (smiles1)
is not, as the imidazole ring condensed to the pyridine is partially
saturated.
The smiles1a analogue where I have added a double bond is aromatic, and
upon canonicalization it yields an aromatic SMILES as expected.
Cheers,
p.
from rdkit import Chem
In [2]:
mol1 = Chem.MolFromSmiles("N12C=CC=CC1=NCC2")
In [3]:
mol1
Out[3]:
[image: image.png]
In [4]:
smiles1 = Chem.MolToSmiles(mol1)
In [5]:
smiles1
Out[5]:
'C1=CC2=NCCN2C=C1'
In [6]:
mol2 = Chem.MolFromSmiles("CN=C1C=CC=CN1C")
In [7]:
mol2
Out[7]:
[image: image.png]
In [8]:
smiles2 = Chem.MolToSmiles(mol2)
In [9]:
smiles2
Out[9]:
'CN=c1n1C'
In [10]:
mol1a = Chem.MolFromSmiles("N12C=CC=CC1=NC=C2")
In [11]:
mol1a
Out[11]:
[image: image.png]
In [12]:
smiles1a = Chem.MolToSmiles(mol1a)
In [13]:
smiles1a
Out[13]:
'c1ccn2ccnc2c1'
On Fri, Nov 27, 2020 at 5:09 PM Alexis Parenty <
alexis.parenty.h...@gmail.com> wrote:
> Hi everyone,
>
> Why is it that when I canonicalize the following smiles_1 I get its
> unexpected kekule form, whereas when I canonicalize a similar smiles_2, I
> get its expected aromatic form?
>
> From rdkit import Chem
> smiles1 = Chem.CanonSmiles("N12C=CC=CC1=NCC2")
> smiles
> ==> 'C1=CC2=NCCN2C=C1'
>
> smiles2 = Chem.CanonSmiles("CN=C1C=CC=CN1C")
> smiles2
> ==> 'CN=c1n1C'
>
> I would like to get the aromatic form in both cases... Is there a way to
> force the aromatic form?
>
> Best,
> Alexis
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] canonicalization of two aromatic molecules returning two different forms (kekule and aromatic)
Hi everyone,
Why is it that when I canonicalize the following smiles_1 I get its
unexpected kekule form, whereas when I canonicalize a similar smiles_2, I
get its expected aromatic form?
>From rdkit import Chem
smiles1 = Chem.CanonSmiles("N12C=CC=CC1=NCC2")
smiles
==> 'C1=CC2=NCCN2C=C1'
smiles2 = Chem.CanonSmiles("CN=C1C=CC=CN1C")
smiles2
==> 'CN=c1n1C'
I would like to get the aromatic form in both cases... Is there a way to
force the aromatic form?
Best,
Alexis
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
