Molecule Module¶
Module to define a molecule to use for simulation.
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class
sdanalysis.molecules.
Dimer
(radius=0.637556, distance=1.0, moment_inertia_scale=1)[source]¶ Bases:
sdanalysis.molecules.Molecule
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.
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class
sdanalysis.molecules.
Disc
[source]¶ Bases:
sdanalysis.molecules.Molecule
Defines a 2D particle.
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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).
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class
sdanalysis.molecules.
Sphere
[source]¶ Bases:
sdanalysis.molecules.Molecule
Define a 3D sphere.
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class
sdanalysis.molecules.
Trimer
(radius=0.637556, distance=1.0, angle=120, moment_inertia_scale=1.0)[source]¶ Bases:
sdanalysis.molecules.Molecule
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.