2.1 Searching for compounds in a database. Computing and saving an adjacency matrix containing the information on valence and non-valence bonding in the crystal structure. Automated storing coordination numbers of atoms in the database.
2.2 Looking through and editing adjacency matrix.
2.3 Building the adjacency matrix for an artificial net.
Appendix 1. Details of the AutoCN algorithms.
3.1 Drawing an image of a crystal structure, performing standard geometrical calculations, analysis of the system of chemical bonds.
3.2 Search for a given finite fragment in the net.
3.3 Analyzing interpenetrated arrays.
3.4 Determining molecular coordination numbers, analysis of molecular packing and intermolecular bonds.
4.1 Standard methods to simplify valence-bonded, hydrogen-bonded and specific-bonded structures.
4.2 Special methods of simplifications. Constructing edge and ring nets. Simplification of nets with synthons. The cluster and skeleton simplification modes. Hopf ring nets. Augmented nets.
4.3 Appendix 2. The concept of “underlying net” and crystal structure representation. Methods of simplification.
5.1 Computing and checking topological indices (coordination sequences, point and vertex symbols).
5.2 Taxonomy of nets. Working with the TTO and TTR collection.
5.3 Generating different structure representations.
Appendix 3. TTD, TTO, and TTR collections.
Appendix 4. Sources of the TTD collection.
Appendix 5. Nomenclatures for topologies.
Appendix 6. What to do with new topologies?
6.1 Analysis and classification of interpenetrating nets.
6.2 Analysis of self-catenation.
6.3 Analysis of catenation, polycatenation, low-dimensional interpenetration and polythreading.
Appendix 7. Nomenclature for interpenetration parameters and classes of interpenetration.
Appendix 8. Interpenetration vs. polycatenation.