Individual skill
framework-topology
Turns a crystal structure (CIF) of a hydrogen-bonded, coordination or covalent framework into its underlying net and the quantities a topology question asks for: node definition, the periodic quotient graph, connectivity as distinct neighbours rather than bond counts, degree of interpenetration, coordination sequences and RCSR three-letter symbols, and internodal distances. Use whenever a task asks for the topology, connectivity, interpenetration or net symbol of a HOF, MOF, COF or molecular crystal from CIF or coordinate data; use atomistic-workflows for simulation setup and cheminformatics-definitions for molecular descriptors.
backend/cli/skills/chemistry/framework-topology/SKILL.md
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# Framework topology from a crystal structure
A framework's topology is a property of a graph you construct, and every wrong answer in
this area is a wrong construction: a node that should have been two, an edge counted
twice, a guest kept, a symmetry image missed, two independent nets read as one. Build the
graph explicitly, print what it is at each stage, and identify the net from the graph's own
invariants rather than from what the chemistry "usually" gives.
## Procedure
1. **Expand the structure completely.** Apply every symmetry operation to the asymmetric
unit, merge atoms that coincide modulo the lattice (special positions), and keep the
lattice vectors. Work in fractional coordinates with an explicit image vector per
neighbour, so that a contact to a molecule in the next cell is a different edge from a