# Molecule Module¶

Module to define a molecule to use for simulation.

class sdanalysis.molecules.Dimer(radius=0.637556, distance=1.0, moment_inertia_scale=1)[source]

Defines a Dimer molecule for initialisation within a hoomd context.

This defines a molecule of three particles, shaped somewhat like Mickey Mouse. The central particle is of type ‘A’ while the outer two particles are of type ‘B’. The type ‘B’ particles, have a variable radius and are positioned at a specified distance from the central type ‘A’ particle. The angle between the two type ‘B’ particles, subtended by the type ‘A’ particle is the other degree of freedom.

class sdanalysis.molecules.Disc[source]

Defines a 2D particle.

class sdanalysis.molecules.Molecule(dimensions=3, particles=NOTHING, positions=NOTHING, radii=NOTHING, rigid=False, moment_inertia_scale=1)[source]

Bases: object

A template class for the generation of molecules for analysis.

The positions of all molecules will be adjusted to ensure the center of mass is at the position (0, 0, 0).

get_radii()[source]

Return type

ndarray

get_types()[source]

Get the types of particles present in a molecule.

Return type
property num_particles

Count of particles in the molecule

Return type

int

class sdanalysis.molecules.Sphere[source]

Define a 3D sphere.

class sdanalysis.molecules.Trimer(radius=0.637556, distance=1.0, angle=120, moment_inertia_scale=1.0)[source]

Defines a Trimer molecule for initialisation within a hoomd context.

This defines a molecule of three particles, shaped somewhat like Mickey Mouse. The central particle is of type ‘A’ while the outer two particles are of type ‘B’. The type ‘B’ particles, have a variable radius and are positioned at a specified distance from the central type ‘A’ particle. The angle between the two type ‘B’ particles, subtended by the type ‘A’ particle is the other degree of freedom.

property rad_angle
Return type

float