Re: [Rdkit-discuss] drawing code

[Greg Landrum]

On Wed, Aug 14, 2019 at 10:42 PM Nicola Zonta 
wrote:

>
> btw here’s that same structure when opened in maestro (coordinates
> generated with coordgen)
>
>
Interesting. That looks much better than when I used coordgen from inside
the RDKit. I wonder if I'm doing something wrong with the parameters.

-greg
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] drawing code

[Dimitri Maziuk via Rdkit-discuss]

On 8/14/19 3:42 PM, Nicola Zonta wrote:
> Hi Greg,
> yeah, coordgen issues are probably the best way to keep track of where we 
> perform poorly.

So... is it "schrodinger/coordgenlibs"? I can open an issue and upload
the sdf.

(And yes, since we actually need all the protons with labels, I am
painfully aware of how crowded the image becomes. Perhaps some day I'll
manage to persuade my spectroscopist to use a 3D image instead -- her
argument is that having to move the mouse to the other screen to rotate
that thing all the time is too distracting.)

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



signature.asc
Description: OpenPGP digital signature
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] drawing code

[Nicola Zonta]

Hi Greg,
yeah, coordgen issues are probably the best way to keep track of where we 
perform poorly.

btw here’s that same structure when opened in maestro (coordinates generated 
with coordgen)



> On 14 Aug 2019, at 06:02, Greg Landrum  wrote:
> 
> Hi Dimitri,
> 
> Here's a notebook demonstrating the extent of the problem (which you've 
> already seen, but this maybe makes it easier for others):
> https://nbviewer.jupyter.org/gist/greglandrum/461c52169e51f9b9e742a5996832ab3c
>  
> 
> 
> To be fair to all depiction algorithms: when you turn on the Hs, this is a 
> really, really crowded molecule. It's going to be very difficult to do 
> anything at all here that doesn't end up looking like crap in one way or 
> another.
> 
> @Nic: how do you want people from the RDKit community to deal with things 
> like this? Is it productive to add them as issues in the coordgen issue 
> tracker or do you have some other way you'd prefer to collect particularly 
> ugly results from coordgen?
> 
> -greg
> 
> 
> 
> On Wed, Aug 14, 2019 at 12:22 AM Dimitri Maziuk via Rdkit-discuss 
>  > wrote:
> PS I played with it a bit: the least ugly version is if you
> MMFF94-optimize it after rdkit.Chem.rdCoordGen.AddCoords()
> 
> It's still far from perfect.
> -- 
> Dimitri Maziuk
> Programmer/sysadmin
> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu 
> 
> 
> ___
> 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] drawing code

[Greg Landrum]

Hi Dimitri,

Here's a notebook demonstrating the extent of the problem (which you've
already seen, but this maybe makes it easier for others):
https://nbviewer.jupyter.org/gist/greglandrum/461c52169e51f9b9e742a5996832ab3c

To be fair to all depiction algorithms: when you turn on the Hs, this is a
really, really crowded molecule. It's going to be very difficult to do
anything at all here that doesn't end up looking like crap in one way or
another.

@Nic: how do you want people from the RDKit community to deal with things
like this? Is it productive to add them as issues in the coordgen issue
tracker or do you have some other way you'd prefer to collect particularly
ugly results from coordgen?

-greg



On Wed, Aug 14, 2019 at 12:22 AM Dimitri Maziuk via Rdkit-discuss <
rdkit-discuss@lists.sourceforge.net> wrote:

> PS I played with it a bit: the least ugly version is if you
> MMFF94-optimize it after rdkit.Chem.rdCoordGen.AddCoords()
>
> It's still far from perfect.
> --
> Dimitri Maziuk
> Programmer/sysadmin
> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>
> ___
> 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