On 20/03/2020 08:43, JW Feng wrote:
iwatobipen blog was where I found instructions for installing RDKit on
Colab. It works but I found waiting for miniconda to install to be
too annoying. A one line apt-get command to install RDKit is easier
and faster (~10 seconds) but it only works with Python 2. Running
following command in a Python 3 environment results in the error
below. Getting apt-get to install RDKit correctly for Python 3 is a
good solution.
!apt-get install python-rdkit librdkit1 rdkit-data
from rdkit import Chem...
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call
last)
<ipython-input-1-96d31abe2ca9> [4] in <module>()
1 get_ipython().system('apt-get install python-rdkit librdkit1
rdkit-data')
----> 2 from rdkit import Chem
ModuleNotFoundError: No module named 'rdkit'
Try python2 instead of python3.
Your Linux distribution is probably shipping an old version of rdkit,
which only works with Python 2.
You can also push for your distribution to ship a recent version
of rdkit.
Altenatively, there is Scripts/create_deb_packages.sh
in the source tree that can create up to date packages on Ubuntu/Debian.
You need to remove your current rdkit installed packages prior to
installing those
though.
Regards,
F.
---------------------------------------------------------------------------
Best,
JW
On Mon, Mar 16, 2020 at 4:48 AM Taka Seri <serit...@gmail.com> wrote:
Dear Steve, Greg and All,
Recently I moved from clab to Binder to make cloud env with python.
However I'll try to make my code more compact and share it.
Thanks for following my blog post. ;)
https://iwatobipen.wordpress.com/
Best regards,
Taka (tiwtter account / iwatobipen)
2020年3月16日(月) 16:03 Greg Landrum <greg.land...@gmail.com>:
Thanks Steve,
That's really helpful. Given that we're unlikely to end up with a
decent pip-installable RDkit, I guess the snippet approach would be
the best way to go. I will try to make some time for this (or
convince iwatobipen to do it) in the reasonably near future.
Best,
-greg
On Sun, Mar 15, 2020 at 5:58 PM Steven Kearnes <kear...@google.com>
wrote:
re: rdkit+colab
In talking with folks outside of Google about rdkit+colab, I haven't
been able to establish that it's worth the trouble of making rdkit a
default dependency. It seems that a rather compact incantation [1]
does the job fairly well. This could be compressed even further, or
even turned into a colab snippet [2] for easier use.
Also, since colab doesn't play well with conda (as far as
pre-installed deps are concerned), we would at least need a
pip-installable rdkit to consider making this work.
Thanks,
Steve
On Mon, Mar 9, 2020 at 4:43 PM JW Feng <jw.a.f...@gmail.com> wrote:
Are you sure depictions in GSheet wouldn't be a good GSoC project?
I will ask around to find volunteers to connect with you on GSheets
and Colab.
On Fri, Mar 6, 2020 at 8:14 PM Greg Landrum <greg.land...@gmail.com>
wrote:
Hi JW,
I don't think it's a great GSoC project for a couple of reasons, but
I'd love to have RDKit integration in Google Sheets and am willing
to do some work to make that happen. I can poke around a bit to see
about how we could use the new RDKit-JS wrappers, but having access
to someone with experience writing Sheets add-ins would help. If you
know someone internally meeting that description, please put them in
touch with me.
I think making the code easily available in Colab can only be done
by someone inside google. I'm happy to help however I can with that
if you (or anyone else) can identify the right person.
Best,
-greg
On Sat, Mar 7, 2020 at 2:22 AM JW Feng <jw.a.f...@gmail.com> wrote:
Project suggestion:
Project 1:Implement 2D structure depiction in Google Spreadsheets.
My colleagues at Google think this is very doable. Being able to
depict structures in Google Spreadsheets will dramatically increase
collaboration between scientists. Imaging being able to provide
comments for a structure, design idea, or virtual screening hit in a
live Google Spreadsheet. While there are commercial (Vortex,
Spotfire, MarvinView, Stardrop ...) and open source (Datawarrior)
packages that can read CSV files containing smiles and depict
structures, none comes close to GSheets for collaboration and ease
of use.
* Cells in columns named SMILES, or have SMILES as a substring in
the header, will be depicted in 2D using RDKit
* Cells with depicted structures move with other columns when
sorting, filtering, etc.
* Optional: depictions update when SMILES string is edited
* Bonus: calculate properties using formulas. Ex:
Descriptors.MolWt(A1) calculates MW of SMILES in A1
Project 2:
* Make it easy to use RDKit in Google Colab [3]
* No need to install RDKit, from rdkit import Chem just works out
of the box
Best,
JW
On Sun, Feb 23, 2020 at 11:48 PM Greg Landrum
<greg.land...@gmail.com> wrote:
Dear all,
I'm happy to share that the RDKit will once again be part of Google
Summer of Code in 2020. This is a program where Google funds
students to work on open-source projects for a couple of months over
the summer. We've participated in each of the last three years and
had some cool stuff come out of it.
We're looking for a few more project ideas (along with possible
mentors!) as well as students.
Applications start in the middle of March. There's more info about
timelines here:
https://developers.google.com/open-source/gsoc/timeline
The current set of project ideas is here and we could use a few
more:
http://wiki.openchemistry.org/GSoC_Ideas_2020#RDKit_Project_Ideas
I'm going to try and come up with something, but if you have
something to add, please let me know.
Best,
-greg
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Links:
------
[1]
https://iwatobipen.wordpress.com/2018/11/01/run-rdkit-and-deep-learning-on-google-colab-rdkit/
[2] https://stackoverflow.com/a/53875826
[3] https://colab.sandbox.google.com/notebooks/intro.ipynb#recent=true
[4]
https://61qi2f4hjw5-496ff2e9c6d22116-0-colab.googleusercontent.com/outputframe.html?vrz=colab-20200318-085600-RC00_301599018#
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