I guess I should have just tried harder. Anyway, attached please find the updated download-inchi.sh script which works for me on Ubuntu 10.10, just in case anyone is interested. This script also downloads the InchI 1.04 source instead of 1.03. (this file should go in $RDKIT_SOURCE/External/INCHI-API)
There is a small twist on the instructions offered by the RDKit distro.
In $RDKIT_SOURCE/CMakeLists.txt, this has to be ON (rather then OFF) - line
22
option(RDK_BUILD_INCHI_SUPPORT "build the rdkit inchi wrapper" ON )
Then start from your build directory cmake .. and you should see something
like
-- Could NOT find InChI in system locations (missing: INCHI_LIBRARY
INCHI_INCLUDE_DIR)
-- Found InChI software locally
The last line means, the download worked and everything is fine. make &&
make install and from python:
>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem
>>> AllChem.INCHI_AVAILABLE
True
>>> m = Chem.MolFromSmiles('CCCC')
>>> m
<rdkit.Chem.rdchem.Mol object at 0x1314de0>
>>> AllChem.MolToInchi(m)
'InChI=1S/C4H10/c1-3-4-2/h3-4H2,1-2H3'
What I still cannot figure out is what "options" are allowed in the method
call.
How do I get the InchI without the H layer for example? Do I python split
the string?
Thanks
JP
-
Jean-Paul Ebejer
Early Stage Researcher
On 26 January 2012 14:05, JP <[email protected]> wrote:
> AllChem.INCHI_AVAILABLE
download-inchi.sh
Description: Bourne shell script
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