Files
rdkit/External/AvalonTools

To use the Avalon Toolkit support in the RDKit, first download a copy of the
source from:
http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.1_beta/AvalonToolkit_1.1_beta.source.tar/download

Note that the version number is important.

Extract the tar file in $RDBASE/External/AvalonTools; the source required by the RDKit is in
the SourceDistribution directory.

cd to $RDBASE/External/AvalonTools and apply AvalonToolkit_1.1_beta_patch.txt:

$ patch -p0 < AvalonToolkit_1.1_beta_patch.txt