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.PoreKit()

Pore construction kit.

system.PoreCylinder(size, diam[, res, hydro])

This class carves a cylindrical pore system out of a \(\beta\)-cristobalite block.

system.PoreSlit(size, height[, res, hydro])

This class carves a slit-pore out of a \(\beta\)-cristobalite block.

system.PoreCapsule(size, diam, sep[, res, hydro])

This class carves a capsule pore system out of a \(\beta\)-cristobalite block.

system.PoreAmorphCylinder(diam[, res, hydro])

This class carves a cylindrical pore system out of an amorph \(\beta\)-cristobalite block from Vink et al. with dimensions [9.605, 9.605, 9.605] (x, y, z).

Pattern

pattern.Pattern()

This class is a container for individual pattern classes.

pattern.AlphaCristobalit()

This class defines the minimal structure of a \(\alpha\)-cristobalite molecule.

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 cylindrical shape.

shape.Sphere(inp)

This class defines a sphere shape.

shape.Cuboid(inp)

This class defines a cuboid shape.

shape.Cone(inp)

This class defines a conical 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.

Utilities

utils

Here popular basic methods are noted.

generic

This file contains function for generic molecules and serves as an exemplary molecule generation process.

geometry

Here basic geometric functions are noted.

database

Very simple molecule database helper methods.