Colloid shapes

Overview

hoobas.GenShape.shape

Generic object describing the shape of a colloid in hoobas.

Details

Genshape provides classes to represent colloid shapes in hoobas.

class hoobas.GenShape.Cube(Num, properties=None, Radius=None)

class hoobas.GenShape.Cylinder(Num, properties=None, RadiusOverLength=None)

class hoobas.GenShape.ElongatedRhombicDodecahedron(Num, ratio=None, properties=None)

class hoobas.GenShape.Octahedron(Num, properties=None)

class hoobas.GenShape.PdbProtein(surf_plane=None, lattice=None, properties=None, filename=None, units=None)

Provides a class to import PDB protein files into hoobas in a simple fashion

Methods :

parse_pdb_protein(filename = None) will load a protein from a pdb file. Calculates mass, moment of inertia. If filename is left to none, assumes legacy filename behavior.

add_shell(key, shell_name = None) parses the keys in the pdb list and adds a shell representation of the parsed keys. Giving it a name allows to bind stuff onto the shell

set_ext_shell_grafts(ext_obj, num = None, linker_bond_type = None, shell_name = None) binds num ext_objs onto the shell with name shell_name. A bond of linker_bond_type is added between the shell and external object

pdb_build_table() needs to be called once all shells / grafts are set

add_shell(key, qualifier=None)

Adds a shell to the protein object. Able to key multiple commands onto the same shell

self.flags[‘shell’] is defined as a list of [ shell_name, positions, [dictionaries] ], this backtracks all previous shells to make sure that no particle is added twice. It is possible to create an empty shell

Parameters:

• key –
• qualifier – qualifier to describe the current set of shell beads, this can be any class that is then compared

with a supplied qualifier during the add_grafts if required. The add_graft can also be supplied with a lambda function that has a key arguement ‘qualifier’ that will receive this paramter. :return:

build()

creates the list for build, keeping only keyed particles. :return:

parse_pdb_protein(filename)

Parses a pdbml protein and stores the file in self._pdb :param filename: :return:

class hoobas.GenShape.ProteinResidueCG(surf_plane=None, lattice=None, properties=None, filename=None, filters=None, CG_model=None)

class hoobas.GenShape.RhombicDodecahedron(Num, properties=None)

class hoobas.GenShape.ShellShape(properties=None, units=None)

class hoobas.GenShape.Sphere(Num, properties=None, **kwargs)

class hoobas.GenShape.SquareRod(Num, surf_plane=None, lattice=None, properties=None, SideOverLength=None)

class hoobas.GenShape.Tetrahedron(Num, properties=None)

class hoobas.GenShape.TruncatedTetrahedron(ratio=0.5, spacing=0.05, properties=None)

Creates a truncated tetrahedron

V4 V1

. . . .

V5….V6 . V4 .

. . . . . .

. . . V5 …. V6 .

Side View-> V2…………V3 Top View-> V2 … … . .V3

class hoobas.GenShape.shape(properties=None, units=None)

Generic object describing the shape of a colloid in hoobas. The object has a shape.table array which contains points representing the shape. New shapes can easily be added by adding new objects inheriting the shape class

self.flags is a dictionary for building directives, which can be set by using shape.set_properties

properties is a dict object for additional properties useful for non-trivial cases (read xyz / pdb parsed files): ‘normalized’ : set to either True or False, defines if the shape is a geometric representation (eg cube) or a finite size object (eg protein)

‘surface’ : used by normalized shapes to calculate surface of an object ‘density’ : used by normalized shapes to calculate mass ‘volume’ : used by normalized shapes to calculate volume properties (eg mass) ‘mass’ : mass of the object, mainly used for proteins, overrides the density*volume value ‘size’ : scaling factor for normalized shapes

Constructor : :param surf_plane : rotation to give every object to match given z axis crystal axis :param lattice : used to specify crystal lattice in conjuction with surf_plane :param properties : dictionary used to set flags :param units: units to be used by the shape.

General methods :

set_properties : sets the additional properties required for building such as density, mass, etc.

Other internals :

Bonded types : self.internal_bonds is a list of length N, containing N bonds in the form of [i, j, r0, type] self.internal_angles is a list of length N, containing N angle potentials in the form [i, j, k, theta0, type]

Rigid body characteristics : self.Itensor is the inertia tensor of the shape, in the form of 1 x 3 values for principal axis self.quaternion is the quaternion of the shape, relating the supplied table to the inertia tensor principal axis

get_N_idx(N, **sortargs)

gets the N smallest indexes of norm values in self.table calculates offsets so whatever is defined in self.additional_points is not taken into account.

This is made for geometric shapes, but can be used for other things.

:param N number of largest norm values to return :return list of indexes

set_geometric_quaternion(tol_eps_rel=2.0)

calculates the tensor of the structure in self.table; uses diagonalization methods and has numerical precision issues :return: