Re: [Rdkit-discuss] GenerateDepictionMatching[23]DStructure (a bit off-topic)

[Peter S. Shenkin]

That's a really nice presentation.

-P.

On Fri, Nov 18, 2016 at 3:16 AM, Greg Landrum <greg.land...@gmail.com>
wrote:

> This is a very big topic, and one where I would very much like to improve
> the RDKit. John Mayfield gave a great talk on the issues (and some ideas
> about fixing them based on his work with the CDK) at the UGM that some of
> you may find interesting :
> https://github.com/rdkit/UGM_2016/blob/master/Presentations/JohnMayfield_
> Depiction.pdf
>
> Fixing the larger problems is a *lot* of work and not something that is
> likely to happen quickly, but there is some low-hanging fruit (like cutting
> crossed bonds) that I ought to be able to do something about.[1]
>
> -greg
> [1] the trick is to avoid, as much as possible, creating drawings that
> look like Möbius strips.
> _
> From: Peter S. Shenkin <shen...@gmail.com>
> Sent: Thursday, November 17, 2016 11:23 PM
> Subject: Re: [Rdkit-discuss] GenerateDepictionMatching[23]DStructure (a
> bit off-topic)
> To: <rdkit-discuss@lists.sourceforge.net>
>
>
>
>
> On 17 Nov 2016, at 4:12 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu> wrote:
>
> Philosophically speaking, there must exist molecules for which a legible
> 2D projection is simply not possible.
>
>
> Hi,
>
> I don't think that 2D projection of a 3D structure is an appropriate
> paradigm for 2D depiction, in general. I think of it as being more about 2D
> construction. I don't think camphor is a particularly difficult example,
> though, and I think that the hidden-line elimination (for lack of a better
> term) that Marvin does gives it a leg up on RDKit's representation.
>
> By the way, I do not think that Marvin is the best there is out there;
> it's just what I happen to have available for comparison.
>
> Stereochemistry adds complications, because 3D information has to be
> encoded in some way. Camphor (your suggestion) has a little of this. I gave
> Marvin a non-stereo SMILES and it picked an enantiomer. I drew the same
> enantiomer. I did not specify stereochemistry to RDKit, so, despite the
> visual confusion of the bond crossings, I suppose it's good that it didn't
> depict an explicit enantiomer.
>
> And labels add further complications. The two approaches I've seen for
> labels are using them as the atomic vertices, as RDKit does, and adding
> them adjacent to the vertices. I personally prefer the latter, because to
> my eye, it's easier to see the connectivity without being distracted by the
> labels.
>
> But my philosophical point was that different forms of 2D depiction work
> better for different purposes. Stéphane wants to see sugars drawn as
> carbohydrate chemists are used to seeing them. I would like to see the 2D
> connectivity as clearly as possible and would sacrifice some conventions
> for that purpose. And so on.
>
> -P.
>
>
>
>
> 
> --
>
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Re: [Rdkit-discuss] GenerateDepictionMatching[23]DStructure (a bit off-topic)

[Téletchéa Stéphane]

Le 18/11/2016 à 09:16, Greg Landrum a écrit :
> Fixing the larger problems is a *lot* of work and not something that 
> is likely to happen quickly, but there is some low-hanging fruit (like 
> cutting crossed bonds) that I ought to be able to do something about.[1]
>
> -greg
> [1] the trick is to avoid, as much as possible, creating drawings that 
> look like Möbius strips.

Dear Greg,

I appreciate your tremendous, and I have always wanted to give back to 
the community when possible.

Do you have any guidelines about getting something better (a draft or 
links to ideas / papers?), I do have the possibility to mentor some 
students and this kind of subjects would be a perfect C++ / python 
project for them ...

Just my two cents :-)

Stéphane

-- 
Team Protein Design In Silico
UFIP, UMR 6286 CNRS, UFR Sciences et Techniques,
2, rue de la Houssinière, Bât. 25, Nantes cedex 03, France
Tél : +33 251 125 636 - Fax : +33 251 125 632
http://www.ufip.univ-nantes.fr/ - http://www.steletch.org


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Re: [Rdkit-discuss] GenerateDepictionMatching[23]DStructure (a bit off-topic)

[David Cosgrove]

As Greg says, this is a large area and somewhat of a diversion from my
original intention. All I was asking for was a set of test cases so I can
ensure that my port of the original Python code in AllChem.py to C++
behaves correctly. That seems like a sensible first step before embarking
on something more ambitious.

Dave

On Fri, 18 Nov 2016 at 08:17, Greg Landrum <greg.land...@gmail.com> wrote:

> This is a very big topic, and one where I would very much like to improve
> the RDKit. John Mayfield gave a great talk on the issues (and some ideas
> about fixing them based on his work with the CDK) at the UGM that some of
> you may find interesting :
>
> https://github.com/rdkit/UGM_2016/blob/master/Presentations/JohnMayfield_Depiction.pdf
>
> Fixing the larger problems is a *lot* of work and not something that is
> likely to happen quickly, but there is some low-hanging fruit (like cutting
> crossed bonds) that I ought to be able to do something about.[1]
>
> -greg
> [1] the trick is to avoid, as much as possible, creating drawings that
> look like Möbius strips.
> _
> From: Peter S. Shenkin <shen...@gmail.com>
> Sent: Thursday, November 17, 2016 11:23 PM
> Subject: Re: [Rdkit-discuss] GenerateDepictionMatching[23]DStructure (a
> bit off-topic)
> To: <rdkit-discuss@lists.sourceforge.net>
>
>
>
>
> On 17 Nov 2016, at 4:12 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu> wrote:
>
> Philosophically speaking, there must exist molecules for which a legible
> 2D projection is simply not possible.
>
>
> Hi,
>
> I don't think that 2D projection of a 3D structure is an appropriate
> paradigm for 2D depiction, in general. I think of it as being more about 2D
> construction. I don't think camphor is a particularly difficult example,
> though, and I think that the hidden-line elimination (for lack of a better
> term) that Marvin does gives it a leg up on RDKit's representation.
>
> By the way, I do not think that Marvin is the best there is out there;
> it's just what I happen to have available for comparison.
>
> Stereochemistry adds complications, because 3D information has to be
> encoded in some way. Camphor (your suggestion) has a little of this. I gave
> Marvin a non-stereo SMILES and it picked an enantiomer. I drew the same
> enantiomer. I did not specify stereochemistry to RDKit, so, despite the
> visual confusion of the bond crossings, I suppose it's good that it didn't
> depict an explicit enantiomer.
>
> And labels add further complications. The two approaches I've seen for
> labels are using them as the atomic vertices, as RDKit does, and adding
> them adjacent to the vertices. I personally prefer the latter, because to
> my eye, it's easier to see the connectivity without being distracted by the
> labels.
>
> But my philosophical point was that different forms of 2D depiction work
> better for different purposes. Stéphane wants to see sugars drawn as
> carbohydrate chemists are used to seeing them. I would like to see the 2D
> connectivity as clearly as possible and would sacrifice some conventions
> for that purpose. And so on.
>
> -P.
>
>
>
>
> --
> ___
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Re: [Rdkit-discuss] GenerateDepictionMatching[23]DStructure (a bit off-topic)

[Greg Landrum]

This is a very big topic, and one where I would very much like to improve the 
RDKit. John Mayfield gave a great talk on the issues (and some ideas about 
fixing them based on his work with the CDK) at the UGM that some of you may 
find interesting 
:https://github.com/rdkit/UGM_2016/blob/master/Presentations/JohnMayfield_Depiction.pdf

Fixing the larger problems is a *lot* of work and not something that is likely 
to happen quickly, but there is some low-hanging fruit (like cutting crossed 
bonds) that I ought to be able to do something about.[1]
-greg[1] the trick is to avoid, as much as possible, creating drawings that 
look like Möbius strips.
_
From: Peter S. Shenkin <shen...@gmail.com>
Sent: Thursday, November 17, 2016 11:23 PM
Subject: Re: [Rdkit-discuss] GenerateDepictionMatching[23]DStructure (a bit 
off-topic)
To:  <rdkit-discuss@lists.sourceforge.net>



On 17 Nov 2016, at 4:12 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu> wrote:
Philosophically speaking, there must exist molecules for which a legible
2D projection is simply not possible.
Hi,
I don't think that 2D projection of a 3D structure is an appropriate paradigm 
for 2D depiction, in general. I think of it as being more about 2D 
construction. I don't think camphor is a particularly difficult example, 
though, and I think that the hidden-line elimination (for lack of a better 
term) that Marvin does gives it a leg up on RDKit's representation. 
By the way, I do not think that Marvin is the best there is out there; it's 
just what I happen to have available for comparison.
Stereochemistry adds complications, because 3D information has to be encoded in 
some way. Camphor (your suggestion) has a little of this. I gave Marvin a 
non-stereo SMILES and it picked an enantiomer. I drew the same enantiomer. I 
did not specify stereochemistry to RDKit, so, despite the visual confusion of 
the bond crossings, I suppose it's good that it didn't depict an explicit 
enantiomer.
And labels add further complications. The two approaches I've seen for labels 
are using them as the atomic vertices, as RDKit does, and adding them adjacent 
to the vertices. I personally prefer the latter, because to my eye, it's easier 
to see the connectivity without being distracted by the labels.
But my philosophical point was that different forms of 2D depiction work better 
for different purposes. Stéphane wants to see sugars drawn as carbohydrate 
chemists are used to seeing them. I would like to see the 2D connectivity as 
clearly as possible and would sacrifice some conventions for that purpose. And 
so on.
-P.



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Re: [Rdkit-discuss] GenerateDepictionMatching[23]DStructure (a bit off-topic)

[Peter S. Shenkin]

> On 17 Nov 2016, at 4:12 PM, Dimitri Maziuk  wrote:
> 
> Philosophically speaking, there must exist molecules for which a legible
> 2D projection is simply not possible.

Hi,

I don't think that 2D projection of a 3D structure is an appropriate paradigm 
for 2D depiction, in general. I think of it as being more about 2D 
construction. I don't think camphor is a particularly difficult example, 
though, and I think that the hidden-line elimination (for lack of a better 
term) that Marvin does gives it a leg up on RDKit's representation. 

By the way, I do not think that Marvin is the best there is out there; it's 
just what I happen to have available for comparison.

Stereochemistry adds complications, because 3D information has to be encoded in 
some way. Camphor (your suggestion) has a little of this. I gave Marvin a 
non-stereo SMILES and it picked an enantiomer. I drew the same enantiomer. I 
did not specify stereochemistry to RDKit, so, despite the visual confusion of 
the bond crossings, I suppose it's good that it didn't depict an explicit 
enantiomer.

And labels add further complications. The two approaches I've seen for labels 
are using them as the atomic vertices, as RDKit does, and adding them adjacent 
to the vertices. I personally prefer the latter, because to my eye, it's easier 
to see the connectivity without being distracted by the labels.

But my philosophical point was that different forms of 2D depiction work better 
for different purposes. Stéphane wants to see sugars drawn as carbohydrate 
chemists are used to seeing them. I would like to see the 2D connectivity as 
clearly as possible and would sacrifice some conventions for that purpose. And 
so on.

-P.

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Re: [Rdkit-discuss] GenerateDepictionMatching[23]DStructure (a bit off-topic)

[Dimitri Maziuk]

On 11/17/2016 02:41 PM, Peter S. Shenkin wrote:

...

> I have to say that Marvin displays the connectivity of the structures much 
> more 
> clearly than RDKit.

Philosophically speaking, there must exist molecules for which a legible
2D projection is simply not possible. PubChem CID 2537 comes close.
Marvin doesn't do much better on this one even if you don't turn on all
the labels.

-- 
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu


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Re: [Rdkit-discuss] GenerateDepictionMatching[23]DStructure (a bit off-topic)

[Téletchéa Stéphane]

Le 17/11/2016 à 18:01, David Cosgrove a écrit :
> Hi All,
>
> I'm currently working on transferring the 2 Python functions
> GenerateDepictionMatching2DStructure and the 3D equivalent into the C++
> core so they will be available to all users of the toolkit.  Can anyone
> supply example test cases for me? In particular, I would appreciate
> examples of the 2D version using the optional referencePattern argument,
> and, for the 3D version, examples where it works well and less well.
> SMILES and/or SDFs would be enough, but if you have pictures of the
> output and/or comments on them, that would be a bonus.
>
> Many thanks,
> Dave

Dear Dave, thanks a lot for the move.

One thing which is not very well handled in rdkit (and elsewhere) is 
carbohydrates. Since you are moving things, do you want test scenarios 
and examples to adjust it?

For instance "classical" representations of carbohydrates:
https://en.wikibooks.org/wiki/File:Chairenvelopeboat*.png

or better :

http://oregonstate.edu/instruct/bb450/450material/stryer7/11/figure_11_07.jpg

Actually they look pretty flat in rdkit, unfortunately. This is also 
true in pubchem for instance :
https://pubchem.ncbi.nlm.nih.gov/compound/D-glucose

Sorry for this off-topic demand, but if there is room for improvements, 
I would be intersted :-)

Best,

Stéphane

-- 
Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein 
Design In Silico
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 
Nantes cedex 03, France
Tél : +33 251 125 636 / Fax : +33 251 125 632
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