Package Details: rdkit 2019_03_4-2

Git Clone URL: https://aur.archlinux.org/rdkit.git (read-only)
Package Base: rdkit
Description: RDKit - A collection of cheminformatics and machine-learning software written in C++ and Python.
Upstream URL: http://rdkit.org/
Licenses: New BSD License
Conflicts: rdkit-git, rdkit-python2
Submitter: None
Maintainer: Athemis
Last Packager: Athemis
Votes: 6
Popularity: 0.014841
First Submitted: 2011-03-26 18:34
Last Updated: 2019-09-13 11:50

Latest Comments

1 2 Next › Last »

tyaur27182 commented on 2018-08-06 17:12

Arch updated the Python3 upstream to version 3.7, breaking the RDKit build. I got it to rebuild by changing the -DPYTHON_LIBRARY and -DPYTHON_INCLUDE_DIR to 3.7 instead of 3.6 in the PKGBUILD. This seems to have fixed it.

Athemis commented on 2018-06-06 12:24

@yoowul: Thanks, this has been fixed + bump to current release (2018_03_2)

yoowul commented on 2018-06-05 13:39

This fails to build:

:: Checking rdkit integrity...
==> ERROR: conflicts contains invalid characters: ','
:: failed to verify rdkit integrity

samoturk commented on 2016-02-01 13:13

Weird inchi support works fine for me.. But you are right should be with src. I will rebuild rdkit and rdkit-git packages today and report back.

UPDATE:
rdkit and rdkit-git compile and have working inchi support. Though there some boost related bugs: https://github.com/rdkit/rdkit/issues/738 and an issue with Jupyter: https://github.com/rdkit/rdkit/issues/666

davvelsan commented on 2016-01-27 11:45

Just tried and it does not seem to work yet. Looking at the PKGBUILD, I believe the cause may be this command:

cp INCHI-1-API/INCHI_API/inchi_dll/* ${pkgname}-Release_${pkgver}/External/INCHI-API/

which according to the github docs (https://github.com/rdkit/rdkit/tree/master/External/INCHI-API) should be:

cp INCHI-1-API/INCHI_API/inchi_dll/* ${pkgname}-Release_${pkgver}/External/INCHI-API/src

I'll try modifying the build later when I get the chance, see if that works.

Alternatively, it seems we can now use the included script "$ bash download-inchi.sh" to do this for us prior to compilation. However, I rather prefer the manual solution that you used as well.


------------ EDIT

Yep, that seems to be it. I had to create the src/ dir as well, though, since it wasn't there like the docs say.

Now I am having a different problem, which I believe might be related to the 1.6.x version of lib-boost. I'm leaving it here for future reference, but this is something to be reported elsewhere I'm afraid.

"No to_python (by-value) converter found for C++ type: boost::shared_ptr<RDKit::ROMol>"

Thanks for your efforts to add InChi support, hopefully I'll get it to work eventually.

samoturk commented on 2016-01-07 13:06

I added InChi support.

davvelsan commented on 2016-01-04 14:09

Any chance to compile this with InChI support?

From the install page (http://www.rdkit.org/docs/Install.html):
"If you would like to install the RDKit InChI support (first available in the Q2 2011 release), follow the instructions in $RDBASE/External/INCHI-API to get a copy of the InChI source and put it in the appropriate place."

More info here:
https://github.com/rdkit/rdkit/tree/master/External/INCHI-API

samoturk commented on 2014-11-04 14:28

PKGBUILD for python 2.7:
https://gist.github.com/samoturk/32e36597f0b4aac51ba0

and for python 3.4:
https://gist.github.com/samoturk/4af7b0695c9b9bb937bc

samoturk commented on 2013-09-25 08:44

In order to compile RDKit version 2013_06_1 you need to downgrade bison to 2.7 (you can use AUR packge bison27).

PS: python2-numpy should be added as a dependency.

petecan commented on 2013-05-11 05:37

It has been a while this was not updated. Just changing the version and updating the MD5 works for the latest rdkit (2013_03_2).