I would like to implement the following in Python but not sure where to start. Are there good modules for shortest path problems of this type?
I am trying to define the shortest path from a particular atom (node) to all other atoms (nodes) in a given collection of xyz coordinates for a 3D chemical structure (the graph). The bonds between the atoms (nodes) are the edges for which travel from node to node is allowed.
I am trying to filter out certain atoms (nodes) from the molecule (graph) based on the connectivity outward from a selected central node.
**For the paths considered, I want to FORBID certain atoms (nodes) from being crossed. If the shortest path from A to B is through forbidden node, this answer is disallowed. The shortest path from A to B must not include the forbidden node **
If the shortest path from the selected centre atom (A) to another other node(B) INCLUDES the forbidden node, AND there is no other path available from A to B through the available edges (bonds), then node B should be deleted from the final set of xyz coordinates (nodes) to be saved.
This should be repeated for A to C, A to D, A to E, etc. for all other atoms (nodes) in the structure (graph).
Thanks in advance for any help you can offer.
Make sure all edges that would lead to the forbidden node(s) have an infinite cost, and whichever graph-traversing algorithm you use will deal with it automatically. 
Alternatively, just remove the forbidden nodes from being considered by the graph traversal algorithm.
Calculating shortest path from set node to all other nodes, with some nodes forbidden from path