Dear James,
On Tue, Jan 28, 2014 at 4:09 PM, James Davidson <j.david...@vernalis.com>wrote:
>
>
> As part of a New Year's resolution, I decided I should try to enjoy the
> benefits of a cutting-edge version of RDKit built from source(!) So far
> this has proven to be much more realistic than eg 'not drinking for
> January' - as I now have a working build to show for my efforts.
>
>
congrats!
>
>
> However, I wonder if I could quickly list the steps I took; and also ask a
> couple of questions (relating to InChi and Avalon)?
>
Attempts at some answers are below.
> For reference I am running on Windows7 64-bit, but use python 2.7.6 32bit,
> so am building 32-bit RDKit. I essentially followed the guide on the wiki (
> https://code.google.com/p/rdkit/wiki/BuildingOnWindows) but thought the
> version info of boost, etc may be of use to others, and the steps may help
> put my questions into context:
>
>
>
> 1. Downloaded Visual Studio Express 2012 for Desktop, installed,
> and accepted the updates
>
> 2. Downloaded matching version of Windows boost binaries
> (boost_1_55_0-msvc-11.0-32.exe) from
> http://sourceforge.net/projects/boost/files/boost-binaries/ and extracted
> to the default path
>
hmm, I didn't know about that source of boost binaries. That is very good
to know; I was afraid there was going to be real hole after the boostpro
guys stopped doing binaries.
> 3. Used TortoiseSVN to add a repository link to
> https://github.com/rdkit/rdkit.git/trunk (and not the SF path as
> currently shown in the wiki guide) in C:/RDKit
>
> 4. Set the environment variables as described on the wiki.
>
> 5. Downloaded the INCHI src as described in the wiki and set the
> RDK_BUILD_INCHI_SUPPORT option later in cmake. Incidentally, the location
> for the downloads from IUPAC have changed (ie the info in the README is out
> of date):
> http://www.iupac.org/home/publications/e-resources/inchi/download.html
>
The link that is in the README, which is to a more recent version (1.04
instead of 1.03), does still work for me. Did you have problems with that?
> 6. Ran CMake configure (GUI) following the wiki, and based on the
> output, made some boost-related additions to environment variables
>
> a. Added C:\local\boost_1_55_0\lib32-msvc-11.0 to PATH
>
> b. Created BOOST_ROOT=C:\local\boost_1_55_0
>
> c. Created BOOST_LIBRARYDIR=C:\local\boost_1_55_0\lib32-msvc-11.0
>
> 7. Re-ran configure, then generate, then followed the rest of the
> wiki instructions to build and test - all tests passed except the dbCli
> one.
>
What was the DbCLI test failure?
Thanks for pointing out the places where the documentation needs to be
updated. Since the wiki docs are out of date, I will go back and replace
them with a pointer to the main documentation (
http://www.rdkit.org/docs/Install.html#installation-from-source) and be
sure that is up to date based on the above.
>
> So now for the questions:
>
> I thought I did everything right for adding INCHI support. However, I see
> the following:
>
>
>
> In [1]: from rdkit import Chem
>
> In [2]: Chem.inchi.INCHI_AVAILABLE
>
> Out[2]: False
>
>
>
> CMake shows:
>
>
>
> Could NOT find InChI in system locations (missing: INCHI_LIBRARY
> INCHI_INCLUDE_DIR)
>
> Found InChI software locally
>
>
>
> Do I also need to download the InChi binary and set these two variables
> appropriately in CMake?
>
No; that should not be necessary.
If you have the source in the right place (and that cmake message makes it
look like you do) and have RDK_BUILD_INCHI_SUPPORT set, run "generate", and
then do a build and an install, it should produce the binaries you need and
update that file so that Chem.inchi.INCHI_AVAILABLE is True. Did you re-run
"generate" after installing the INCHI source?
> Also, I am struggling to build with Avalon support... Choosing the
> RDK_BUILD_AVALON_SUPPORT appears to configure fine, but when I try to
> 'Generate' I see the following error:
>
>
>
> CMake Error at Code/cmake/Modules/RDKitUtils.cmake:26 (add_library):
> Cannot find source file:
>
> /common/layout.c
>
> Tried extensions .c .C .c++ .cc .cpp .cxx .m .M .mm .h .hh .h++ .hm .hpp
> .hxx .in .txx
> Call Stack (most recent call first):
> External/AvalonTools/CMakeLists.txt:43 (rdkit_library)
>
>
>
> Any thought on how to get around this? Do I need to download the Avalon
> project src and put it somewhere?
>
Yeah, you do, but there's no documentation for that (yet...).
Here's a first pass at something
1) download the beta source distribution from sf.net;
http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.1_beta/AvalonToolkit_1.1_beta.source.tar/download
2) extract that tar file somewhere. It's going to create SourceDistribution
and a StandardFiles directories
3) set the cmake variable AVALONTOOLS_DIR to point to the
SourceDistribution directory
3) set RDK_BUILD_AVALON_SUPPORT=ON in cmake
4) run a build and install.
Note: one or two of the avalontools tests may fail on windows. This is
currently expected.
> And final question - can I happily ignore the CMake messages about not
> finding FLEX and BISON, or are these needed when incorporating any of the
> non-default entries (SWIG wrappers, etc)?
>
You can ignore those warnings. We made some changes a couple releases ago
so that flex and bison are no longer necessary unless you want to make
modifications to the SLN, SMILES, or SMARTS parsers. That's can wait for
your 2015 New Years resolution. ;-)
Hope this helps,
-greg
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