ose Manuel Gally , RDKIT mailing
list
*Subject: *Re: [Rdkit-discuss] Which method to prefer for computing 2D
coordinates
Hello Lukas,
I am also struggling with 2D coordinate generation quite a long time
as well as what criteria to use for choosing the most appropriate.
Therefore, I would be
Evangelidis
Date: Tuesday, 9 April 2019 at 15:43
To: Lukas Pravda
Cc: Jose Manuel Gally , RDKIT mailing list
Subject: Re: [Rdkit-discuss] Which method to prefer for computing 2D coordinates
Hello Lukas,
I am also struggling with 2D coordinate generation quite a long time as well as
what
When I was at Schrödinger, I wrote a simple program to find bad 2D
structures. I no longer have access to the code, but I computed two things:
1. Number of bond lengths deviating from the median bond length (MBL) by
50% or more (i.e., <0.5*MBL or >2*MBL)
2. Number of bond crossings
The overall sc
Dear Lukas, Greg, Nic and Thomas,
thank you for your feedback!
I suspected that I would have to combine several methods, but I have to
admit I'm still unsure how to deal with this.
Therefore I (and certainly many others!) would be really interested if
you could share some code, Lukas.
Che
Hello Lukas,
I am also struggling with 2D coordinate generation quite a long time as
well as what criteria to use for choosing the most appropriate. Therefore,
I would be very interest to use your code for 2D coordinate selection.
With best regards,
Thomas
PS: very nice notebook Jose. I also wan
Here's a reply from Nic Zonta, the coordgen author:
As for suggestions, I’d say that the strength of coordgen at the moment is
in macrocycles handling, so if for instance E/Z stereo in a macrocycle is
important I’d say that’s a good idea, and the weak point is intrinsically
3d systems and in perfo
Hi Jose,
As you have shown there is no single method which would be perfect for
everything. If you don’t care that much about speed, the possible solution
could be to compute coordinates with all three approaches and then simply
select the best conformer based on some criteria.
The solution I
Dear all,
This might sound naive, but I want to compute 2D coordinates for a set
of molecules.
For now I am considering the 3 methods below [1].
I was wondering if there was any recommendation to use one method over
another in some cases?
For instance, very large rings are not displayed ro
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