> - Adjacency matrix or adjacency list for each graph
> - Label information for each node in a graph (for labeled graphs)
> - Class (+1/-1) information for each graph for classification
>
> I've found some datasets in .mol and .sdf formats (for example, Bursi
> dataset: http://cheminformatics.org/datasets/bursi/) and I can view them with
> OpenBabel, however I am not sure which format I can convert in order to
> simply get an adjacency matrix.
I don't think there's anything even close. File formats are generally
chemically-based, but you want graph information. My suggestion would be to
write a short program in C++ or Python (e.g., through Pybel) to compute the
appropriate adjacency matrix, labels, etc.
I'd iterate through the bonds (i.e., the connections) to do this, but it's also
possible to generate the adjacency list from iterating over the atoms as well.
There are examples online, but if you need more information on using Pybel,
please post again.
-Geoff
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