Dear Markus,
On Sat, Feb 6, 2010 at 6:41 PM, markus kossner <[email protected]> wrote:
> Dear All,
> I read about a CompressedSDMolSupplier (assuming it is a Supplier for
> zipped sd files, isn't it?) in the release Notes for Q32009_1.
> However I could neither find a function like that in the rdkit.Chem
> Module nor any hint in the docs. Could anyone please give me a pointer?
The CompressedSDMolSupplier is not built by default because it
introduces a couple of extra dependencies and I couldn't get it
working properly on windows. If you'd like to use it and are building
the code on linux (or the mac) using bjam, you should go into
$RDBASE/Code/GraphMol/Wrap/Jamfile and change the lines:
# uncomment the block below to include compressed SDMolSupplier support:
# CompressedSDMolSupplier.cpp /boost/iostreams//boost_iostreams
<toolset>msvc:/boost/iostreams//boost_zlib
#:
# <define>RDK_NOGZIP <define>RDK_NOBZIP2
# <define>SUPPORT_COMPRESSED_SUPPLIERS
to:
# uncomment the block below to include compressed SDMolSupplier support:
CompressedSDMolSupplier.cpp /boost/iostreams//boost_iostreams
<toolset>msvc:/boost/iostreams//boost_zlib
#:
# <define>RDK_NOGZIP <define>RDK_NOBZIP2
<define>SUPPORT_COMPRESSED_SUPPLIERS
After rebuilding, you should then be able to do:
from rdkit import Chem
suppl = Chem.CompressedSDMolSupplier('input.sdf.gz')
and have things work.
-greg
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