connection /adjacency


Does anyone know how to extract the adjacency matrix /connection table from a molecule/sdf file? The output should be compatible with the connection table/ ad matrix 'network' nodes in Knime.


Many thanks


Unfortunately, there is no such a node, at least, Indigo nodes do not contain the adjacency matrix / connection table extraction possibility. But if you provide some examples of real usages of such a functionality, we will consider your request and implement the method in future releases.

With best regards,

Savelyev Alexander,

GGA Software Services LLC

Well my plan was to use the network nodes to use mine for conserved nodes[atoms] and edges[bonds] when one has multiple molecules in an sdf file.

The centrality of a node in network theory, e.g. how many other nodes it is connected to and the least distance etc indicates the important in the network. My intention was find such pharmacophores. 

One would think this would be an interesting application for pharmacophore discovery and complement other approaches very well.