International
Tables for
Crystallography
Volume B
Reciprocal space
Edited by U. Shmueli

International Tables for Crystallography (2006). Vol. B, ch. 3.3, p. 377   | 1 | 2 |

Section 3.3.2.1.2. Implied connectivity

R. Diamonda*

aMRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England
Correspondence e-mail: rd10@cam.ac.uk

3.3.2.1.2. Implied connectivity

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In cases where software is required to deal only with a certain class of molecule, it may be possible to exploit the characteristics of that class to define an ordering for lists of atoms such that connectivity is implied by the ordering of items in the list. Such an ordering may successfully define one of the three types of connectivity defined in Section 3.3.2.1[link] but it is unlikely to be able to meet the needs of all three simultaneously. It may also be at a disadvantage when required to deal with structures not part of the class for which it is designed. Within these limitations, however, it may be exceedingly efficient. Both proteins and nucleic acids are of a class which permits their logical connectivity to be specified entirely by list ordering, and the software described in Section 3.3.3.2.6[link] uses no connectivity tables for this purpose. The ordering rules concerned are given by Diamond (1976b[link]).

Drawing connectivity needs explicit specification in such a case; this may be done using only one 16-bit integer per atom, which may be stored as part of the atom list without the need of a separate table. This integer consists of two signed bytes which act as relative pointers in the list, positive pointers implying draw-to, negative pointers implying move-to. As each atom is encountered during drawing the right byte is read and utilized, and the two bytes are swapped before proceeding. This allows up to two bonds drawn to an atom and two bonds drawn from it, four in all, with a minimum of storage (Diamond, 1984a[link]).

Brandenburg et al. (1981[link]) handle drawing connectivity by enlarging the molecular list with duplicate atoms such that each is connected to the next in the list, but moves and draws still need to be distinguished.

Levitt (1971[link]) has developed a syntax for specifying structural connectivity implicitly from a list structure which is very general, though designed with biopolymers in mind, and the work of Katz & Levinthal (1972[link]) includes something similar.

References

Brandenburg, N. P., Dempsey, S., Dijkstra, B. W., Lijk, L. J. & Hol, W. G. J. (1981). An interactive graphics system for comparing and model building of macromolecules. J. Appl. Cryst. 14, 274–279.Google Scholar
Diamond, R. (1976b). Model building techniques for macromolecules. In Crystallographic computing techniques, edited by F. R. Ahmed, K. Huml & B. Sedlacek, pp. 336–343. Copenhagen: Munksgaard.Google Scholar
Diamond, R. (1984a). Applications of computer graphics in molecular biology. Comput. Graphics Forum, 3, 3–11.Google Scholar
Katz, L. & Levinthal, C. (1972). Interactive computer graphics and representation of complex biological structures. Annu. Rev. Biophys. Bioeng. 1, 465–504.Google Scholar
Levitt, M. (1971). PhD Dissertation, ch. 2. University of Cambridge, England.Google Scholar








































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