API reference¶
Molecule¶
molecule.Molecule([name, short, inp]) |
This class defines a molecule object, which is basically a list of Atom objects. |
atom.Atom(pos, atom_type[, name, residue]) |
This class defines an atom object containing the position, the atom type and optionally a specific name. |
store.Store(inp[, link, sort_list]) |
This class converts a molecule object to a structure file of different possible formats. |
Pore¶
pore.Pore(block, matrix) |
This class prepares and converts a given molecule block into a pore system. |
system.PoreSystem() |
This class is a container class for further pore system classes. |
system.PoreCylinder(size, diam[, res, hydro]) |
This class carves a cylindric pore system out of a \(\beta\)-cristobalite block. |
system.PoreSlit(size, height) |
This class carves a slit-pore out of a \(\beta\)-cristobalite block. |
system.PoreCapsule(size, diam, sep[, res]) |
This class carves a capsule pore system out of a \(\beta\)-cristobalite block. |
Pattern¶
pattern.Pattern() |
This class is a container for individual pattern classes. |
pattern.BetaCristobalit() |
This class defines the minimal structure of a \(\beta\)-cristobalite molecule. |
Shape¶
shape.Shape(inp) |
This class is a container for individual shape classes. |
shape.Cylinder(inp) |
This class defines a cylindric shape. |
shape.Sphere(inp) |
This class defines a sphere shape. |
shape.Cuboid(inp) |
This class defines a cuboid shape. |
Optimization¶
dice.Dice(mol, size, is_pbc) |
This class splits the molecule into smaller sub boxes and provides parallelized functions for pair-search. |
matrix.Matrix(bonds) |
The aim of this class is preserving all information of the grid bonds. |