Dear Greg,
Yes, Eigen was found (I used brew install rdkit/rdkit/rdkit --with-inchi
--with-avalon -v --HEAD command)
==> cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/HEAD-4f2ec84'
-DCMAKE_BUILD_TYPE=None -DCMAKE_FIND_FRAMEWORK=LAST -Wno-dev
-DRDK_INSTALL_INTREE=OFF -DRDK_BUILD_AVALON_SUPPORT=ON
-DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_CPP_TESTS=ON
-DRDK_INSTALL_STATIC_LIBS=OFF
-DPYTHON_EXECUTABLE='/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/python'
-DPYTHON_INCLUDE_DIR='/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7'
-DPYTHON_LIBRARY='/Library/Frameworks/Python.framework/Versions/2.7/Python'
-DPYTHON_NUMPY_INCLUDE_PATH='/usr/local/lib/python2.7/site-packages/numpy/core/include'
.
-- The C compiler identification is AppleClang 8.0.0.8000038
-- The CXX compiler identification is AppleClang 8.0.0.8000038
-- Check for working C compiler: /usr/local/Library/Homebrew/shims/super/clang
-- Check for working C compiler: /usr/local/Library/Homebrew/shims/super/clang
-- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler:
/usr/local/Library/Homebrew/shims/super/clang++
-- Check for working CXX compiler:
/usr/local/Library/Homebrew/shims/super/clang++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Could NOT find InChI in system locations (missing: INCHI_INCLUDE_DIR)
Downloading
http://www.inchi-trust.org/wp/wp-content/uploads/2014/06/INCHI-1-API.zip...
-- Found PythonInterp:
/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/python
(found version "2.7.11")
-- Found PythonLibs: /Library/Frameworks/Python.framework/Versions/2.7/Python
(found version "2.7.11")
-- Boost version: 1.61.0
-- Found the following Boost libraries:
-- python
Python Install directory
/usr/local/Cellar/rdkit/HEAD-4f2ec84/lib/python2.7/site-packages
-- Boost version: 1.61.0
-- Found the following Boost libraries:
-- regex
== OSX: CHECKING for libc++
== BOOST USES LIBC++
-- Found Eigen3: /usr/local/include/eigen3 (Required is at least version
"2.91.0")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Boost version: 1.61.0
-- Found the following Boost libraries:
-- thread
-- system
-- chrono
-- date_time
-- atomic
-- Boost version: 1.61.0
-- Found the following Boost libraries:
-- serialization
== Using strict rotor definition
Downloading
http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.2/AvalonToolkit_1.2.0.source.tar...
== Updating Filters.cpp from pains file
== Done updating pains files
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/rdkit-20161011-53375-95rv1i
==> make
Scanning dependencies of target inchi_support
Scanning dependencies of target hc
maybe the python files were not updated correctly, I will check.
thanks, best regards,
Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645
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Firmenich SA
RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
________________________________
De : Greg Landrum <[email protected]>
Envoyé : mardi 11 octobre 2016 18:39
À : Guillaume GODIN
Cc : [email protected]
Objet : Re: [Rdkit-discuss] Descriptor3d not exposed in python
Guillaume,
Are you sure that the 3D descriptors built? If you don't have the eigen library
installed ("conda install -c conda-forge eigen" if you are using anaconda
python), the 3D descriptor build will be automatically disabled.
If eigen is not present, when you run cmake, you will see a message like this:
-- Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK)
(Required is at least version "2.91.0")
Eigen3 not found, disabling the Descriptors3D build.
as part of the output of cmake.
-greg
On Tue, Oct 11, 2016 at 6:00 PM, Guillaume GODIN
<[email protected]<mailto:[email protected]>> wrote:
Dear all,
I'm trying to use 3D descriptors in Python after compiling without issue, there
is no new descriptors available in Python, is it normal?
Best regards,
Guillaume
Envoyé de mon iPhone
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