. Author manuscript; available in PMC: 2019 Jun 3.

Published in final edited form as: J Chem Theory Comput. 2018 Nov 29;14(12):6642–6652. doi: 10.1021/acs.jctc.8b00765

Table 1.

Current list of shapes available in BUMPy repository, with associated geometric parameters and shape-specific notes.

Shape	Parameters	Notes
Semisphere	R_sphere	basic building block
Cylinder	R_cylinder L_cylinder	-basic building block -quarter-cylinder used as a junction between orthogonal structures
partial_torus	R_torus R_tube	-basic building block -quarter-torus used as toroidal junction
Flat_bilayer	X_dimension Y_dimension	-basic building block
Sphere	R_sphere
Torus	R_torus R_tube	R_torus > R_tube
Capped_cylinder	R_cylinder L_cylinder	-cap radius is necessarily equal to the cylinder radius
Double_bilayer_cylinder	R_cylinder L_cylinder R_junction L_flat	L flat >= 2 * (R cylinder + R_junction)
Semicylinder_plane	R_cylinder L_cylinder R_junction L_flat	L flat > 2 * (R cylinder + R_junction)
Semisphere_plane	R_sphere R_junction L_flat	L flat > 2 * (R cylinder + R_junction)
Buckle	R_buckle L_buckle	L_buckle is the length in the flat dimension