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. Author manuscript; available in PMC: 2017 Sep 25.
Published in final edited form as: Perspect Sci (Neth). 2016 Oct 20;11:24–30. doi: 10.1016/j.pisc.2016.05.013

Figure 3.

Figure 3

Stick model (A) and abbreviated GLYDE-II representation (B) of an α-D-Manp molecule. (Several lines of XML code are omitted for brevity; the remaining lines are numbered.) The structure of each bound atom is specified by its ref attribute (lines 3, 6 and 33), which points to a GLYDE-II representation of the atom (Fig. 2) serving as the archetype for the bound atom. The molecular topology is fully specified by atom link objects (e.g. lines 60 and 69), which connect bound atom objects. The molecular configuration (stereochemistry) is specified explicitly by listing the coordinates of each bound atom. Alternatively, stereochemistry of the molecule can be inferred from its id (line 2), which by rule corresponds to its representation using a format based on GlycoCT. The conventional orientation and position of the Cartesian axes in the atomistic GLYDE-II representation is defined by the alignment of three key bound atom objects: the anomeric carbon (C1 in this case) is at the origin, the ring oxygen (O5 in this case) is on the x-axis, and the highest-numbered carbon (C2 in this case) that is directly linked to the anomeric carbon is in the first or second quadrant of the x,y-plain (where y > 0).