Package Details: rdkit 2019_09_3-1

Git Clone URL: https://aur.archlinux.org/rdkit.git (read-only, click to copy)
Package Base: rdkit
Description: RDKit - A collection of cheminformatics and machine-learning software written in C++ and Python.
Upstream URL: http://rdkit.org/
Licenses: BSD
Conflicts: rdkit-git, rdkit-python2
Provides: rdkit
Submitter: None
Maintainer: Athemis
Last Packager: Athemis
Votes: 7
Popularity: 0.019051
First Submitted: 2011-03-26 18:34
Last Updated: 2020-02-20 09:36

Latest Comments

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ptrxyz commented on 2021-05-11 16:10

I'd also be interested in a new release/an update. Is this still maintained?

joanmanel commented on 2021-05-10 10:57

The installation seems to be OK, but I don't have rdkit.chem, is this normal? otherwise how can I get rdkit.chem?

zsurnz commented on 2021-01-06 21:59

@riteme: I also got a compilation crash on Manjaro, gcc 10.2.0 when updating to Python3.9. Following your suggestion the package did compile but was broken and Chem could not even be imported from rdkit. To my surprise recompiling maeparser 1.2.4-3 and coordgen 1.4.2-2 from source did solve the issue, although I had previously up-to-date versions from "extra" installed.

riteme commented on 2020-06-06 03:30

Consider adding -DRDK_BUILD_CPP_TESTS=OFF to cmake. Some tests got compile errors on my system (Manjaro, GCC 10.1.0). Meanwhile, CMakeLists.txt says "disabling (it) can speed up builds".

dviktor commented on 2020-02-19 17:18

Please update PKGBUILD:

--- PKGBUILD.old    2020-02-19 20:17:30.912687743 +0300
+++ PKGBUILD    2020-02-19 20:16:58.946353419 +0300
@@ -1,31 +1,38 @@
 # Maintainer: Samo Turk <samo.turk@gmail.com> 
+
 pkgname=rdkit
-_pkgname=RDKit
-pkgver=2019_09_1
+pkgver=2019_09_3
 pkgrel=1
 pkgdesc="RDKit - A collection of cheminformatics and machine-learning software written in C++ and Python."
 arch=("i686" "x86_64" "armv7h")
 url="http://rdkit.org/"
-license=('New BSD License')
-depends=( 'bison' 'boost' 'boost-libs' 'cmake' 'flex' 'python' 'python-numpy' 'sqlite3' 'python-cairocffi' 'python-pillow' 'eigen3' )
+license=(custom)
+depends=(python python-numpy boost boost-libs sqlite cairo eigen)
+makedepends=('gcc>=4.8' 'clang>=3.9' 'cmake>=3.1')
 source=("https://github.com/rdkit/rdkit/archive/Release_${pkgver}.tar.gz")
-sha256sums=('bfcb3c094cd0e7ec6fbebacde71f29f61df71601eb3d577eb295fd45771513eb')
-conflicts=('rdkit-python2' 'rdkit-git')
+sha256sums=('88bbc298eb6c17584471b17a34e202b1da3d59d92ea5b6b6dcda635b739f76f2')
+conflicts=(rdkit-git)
+provides=(rdkit)

 build() {
   cd ${srcdir}/${pkgname}-Release_${pkgver}
-  cmake . \
+
+  mkdir -p build
+  cd build
+
+  cmake .. \
     -DCMAKE_BUILD_TYPE=Release \
-    -DRDK_INSTALL_INTREE=0 \
+    -DRDK_INSTALL_INTREE=OFF \
     -DCMAKE_INSTALL_PREFIX=/usr \
-    -DPYTHON_LIBRARY=/usr/lib/libpython3.7m.so \
-    -DPYTHON_INCLUDE_DIR=/usr/include/python3.7m/ \
-    -DPYTHON_EXECUTABLE=/usr/bin/python \
-    -DRDK_BUILD_INCHI_SUPPORT=OFF
+    -DBoost_NO_BOOST_CMAKE=ON \
+    -DRDK_BUILD_INCHI_SUPPORT=OFF \
+    -DRDK_BUILD_CAIRO_SUPPORT=ON
+
   make
 }

 package() {
-  cd ${srcdir}/${pkgname}-Release_${pkgver}
+  cd ${srcdir}/${pkgname}-Release_${pkgver}/build
+
   make DESTDIR=${pkgdir} install 
 }

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.