Nomenclatures for topologies 


In the TTD collection the net topologies are designated according to the following nomenclatures (see for a general introduction “Vertex-, face-, point-, Schläfli-, and Delaney-symbols in nets, polyhedra and tilings: recommended terminology”. Blatov V.A., O’Keeffe M., Proserpio D. M. CrystEngComm, 2010, 12, 44-48):

• TOPOS symbols NDn, where N is a sequence of degrees (coordination numbers) of all independent nodes; D is one of the letters C, L, or T designating the dimensionality of the net (C – chain, L – layer, T – three-periodic); n enumerates non-isomorphic nets with a given ND sequence. For instance, the symbol 3,3,4T3 denotes the 3^rd (by the order) three-periodic trinodal net with two 3-coordinated and one 4-coordinated independent nodes. For finite (molecular) graphs the symbols NMk-n are used, where k is the number of vertices (atoms) in the graph.


• RCSR lower-case three-letter symbols, see http://rcsr.anu.edu.au/ for details. See also "The Reticular Chemistry Structure Resource (RCSR) Database of, and Symbols for, Crystal Nets" O'Keeffe, M.; Peskov, M. A.; Ramsden, S. J.; Yaghi, O. M. (2008) Acc. Chem. Res. 41, 1782-1789


• EPINET sqcXXXXX symbols, see http://epinet.anu.edu.au/ for details.


• Fischer's symbols k/m/fn for sphere packings (see e.g. Koch, E., Fischer, W. & Sowa, H. (2006). Acta Cryst. A62, 152-167).


• CSD Reference Codes or ICSD Collection Codes.


• Zeolite capital three-letter symbols, see http://www.iza-structure.org/databases/ for details.


• Subnet s-d-G-n symbols (Blatov, V. A. (2007). Acta Cryst. A63, 329–343), where s is a conventional name of the initial net, d is a set of ascending integers equal to degrees of all inequivalent nodes in the subnet, G is the space group for the most symmetrical embedding of the subnet, n is optional and enumerates non-isomorphic subnets with a given s-d-G sequence.
  Examples: scu-3,6-P42/mnm-2 (is a 3,6-c net derived from 4,8-c scu); acs-4-Pbcn (is a 4-c net derived from 6-c acs)


• Subnet transformation symbols s/G→S1→…→Sn;BS where s is a conventional name of the initial net, G is the space group of the initial net, S1, …, Sn is the sequence of group-subgroup transformations to obtain the symmetry of the resulting subnet, Sn, BS is the set of numbers of non-equivalent edges to be retained in the subnet. For instance, the notation
  
  fny/P 63/m c m->P 63 2 2 (0,0,1/4);Bond sets: 2,3,4,5
  
  means that the subnet is derived from the RCSR net fny by decreasing its space-group symmetry from P6₃/mcm to P6₃22 with shifting the origin by (0, 0, 1/4) vector and breaking all non-equivalent edges in the resulting net except the edges No 2, 3, 4 and 5.
  Subnet transformation symbols can be found for uninodal and binodal nets depending if the transformation start from uninodal or binodal nets.
  The subnet transformation symbols are being gradually replaced in the TTD collection with s-d-G-n symbols whenever an example is found in crystal structures;
  ATTENTION: if you have obtained ToposPro output with a subnet transformation symbol, this means that the topology has not yet been found in crystal structures. Let ToposPro authors know about this case!

Some nets fall into different nomenclatures, in this case ToposPro outputs all possible symbols separated by semicolons with the RCSR name first (if available). For example:

dia Diamond; 4/6/c1; sqc6
crs/dia-e; 6/3/c2; sqc889
fau/faujasite/FAU;infinite polyhedron; 4/4/c17; sqc13519
eth; jbw-3,3-Pmna-1

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