Hello! Is there a recommended stable format for long-term storage of RDKit
molecules? Will ToBinary() give me what I need? (the documentation /
purpose seems to be a bit... spartan) I'd like to save topology,
conformers, and properties (at the atom, bond, and molecule level) to disk
a format that
I think Nils is right here. An RDKit fingerprint with a max length of 12 is
going to set A LOT of bits. Try it and see.
Collisions are almost guaranteed
There are many possible reasons why you may not be getting the results you
expect (that’s the fun in machine learning), but if you suspect that t
Thanks Paolo,
That would be a really nice contribution to the RDKit Cookbook. hint hint.
:-)
-greg
On Fri, Oct 5, 2018 at 12:20 AM Paolo Tosco
wrote:
> Hi Eric,
>
> I may be a bit late, but here's a gist that shows how to convert a
> molecule in XYZ format to an RDKit molecule with bond order
6 digits seems perfectly fine for me.
On Fri, 5 Oct 2018 at 14:26, Greg Landrum wrote:
>
> On Fri, Oct 5, 2018 at 2:42 PM Ivan Tubert-Brohman <
> ivan.tubert-broh...@schrodinger.com> wrote:
>
>> In the newer "V3000", the atom line is not column-based, which I believe
>> gives more freedom to imp
On Fri, Oct 5, 2018 at 2:42 PM Ivan Tubert-Brohman <
ivan.tubert-broh...@schrodinger.com> wrote:
> In the newer "V3000", the atom line is not column-based, which I believe
> gives more freedom to implementers to decide the precision of the
> coordinates. You can force RDKit to write in this format
Hi Michal,
The old SDF format (aka V2000 CTAB) is column-based, as things often were
in the era of Fortran 77 and punch cards. Not only the precision but also
the exact position of each value on the line is specified! Here's what the
spec says:
The Atom Block is made up of atom lines, one line pe
Hi Jan,
Thanks, 6 digits is OK! Forcing V3000 did the trick:
sdf_out=Chem.SDWriter(outfile)
sdf_out.SetForceV3000(True)
Best,
Michal
On Fri, 5 Oct 2018 at 12:59, Jan Holst Jensen wrote:
> Hi Michal,
>
> V2000 format is restricted by its specification to fixed format with 4
> decimals. V3000 out
Hi Michal,
V2000 format is restricted by its specification to fixed format with 4
decimals. V3000 output is not restricted to a fixed format, but the
current code still rounds it in practice as seen below.
To get extra precision you could change the formatting of x, y, and z
coordinate outpu
Hi Maria,
Which version of the RDKit do you have installed and which python version?
-greg
On Fri, 5 Oct 2018 at 12:18, MARIA BRANDL via Rdkit-discuss <
rdkit-discuss@lists.sourceforge.net> wrote:
> Dear all,
>
> I have installed rdkit on Windows 10 under Anaconda 3.
>
>
> Everything runs smoot
Dear all,
I have installed rdkit on Windows 10 under Anaconda 3.
Everything runs smoothly, but depictions on jupyter notebooks return the warning
Warning: unable to load font metrics from dir
C:\Users\MB\Anaconda3\lib\site-packages\rdkit\sping\PIL\pilfonts
and are quite low in resolution.
Is ther
Hello,
Is it possible to control the number of significant digits of XYZ
coordinates? I am modifying coordinates of my molecules
using SetAtomPosition but when I save them into an SDF it seems that the
precision is limited to 4 digits after the decimal point (I'd like 10
instead...).
Best wishes,
M
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