Hi,
Thanks for the update to the download script. I will incorporate your change
into the svn. The change you made to CMakeLists.txt is not necessary. To turn
on InChI support, you could just add `-DRDK_BUILD_INCHI_SUPPORT=ON` as an
argument when you run the `cmake` command:
cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON
The InChI wrapper supports all options recognized by the InChI software.
Supported options are documented on page 22 of the official user guide found
here. Using your example:
>>> AllChem.MolToInchi(m, '/DoNotAddH')
[09:36:55] WARNING: Accepted unusual valence(s): C(1); C(2)
'InChI=1S/C4/c1-3-4-2'
However, unlike SMILES, hydrogen layer is always explicit. So the above InChI
string actually corresponds to a different molecule:
>>> m = Chem.MolFromInchi('InChI=1S/C4/c1-3-4-2')
>>> Chem.MolToSmiles(m)
'[C-]#CC#[CH2+]'
This is explained here, and I quote:
> Does InChI require all atoms including hydrogens?
>
> While bond orders are not used in the representation, hydrogen atoms are
> required. If there is ambiguity concerning the number of H-atoms in a
> structure (i.e., its chemical formula is not clear), a reliable InChI cannot
> be created.
So use these options with cautions.
Hope this helps.
Regards,
Eddie
On Jan 26, 2012, at 7:01 AM, JP wrote:
> 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>------------------------------------------------------------------------------
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