Surfaces Master Ticket

[Tom Goddard]

Includes code to compute molecular surface, accessible surface area, basic shape geometry such as sphere, cylinder, icosahedron, splined tube. Compute surface areas and enclosed volumes, connected components, whether holes are present.

[Tom Goddard]

I'm not sure whether this Surfaces project should be responsible for defining the Surface object API or whether that should be thought of as part of the Graphics APIs. Currently in Hydra surfaces are simply Drawing instances where Drawing is part of the graphics module. I think a subclass called Surface is probably desirable. But is not clear to me how to conceptually define a Surface. Currently the atoms of a molecule are drawn as spheres using a Drawing object. This set of spheres is not what we usually think of as a surface, but at a low graphics level it is a surface. Likewise a molecule ribbon tube is currently a Drawing and not a Surface. A volume contour surface is a Drawing -- would that be a Surface? Probably. Functionally all of these renderings appear to be surfaces.

Aside from the task of defining a Surface object, other parts of this project such as computing molecular surfaces and accessible surface area are partially done. There is no command for accessible area calculation. The ability to create spheres, cylinders, icosahedra, as done by the Chimera 1 shape command is not implemented.

[Tom Goddard]

APIs are not final, but the code is in Chimera 2.

[Tom Goddard]

No longer using "master" tickets. Instead use individual tickets for specific features.