Actin sets up a filament-like scenerio, where there is one type of Subunit
with a single Conformation and Domain and two binding sites on opposite ends.
BindingSite holds information about a specific BindingSite including the
BindingSiteType, binding state, partner BindingSite (if bound), ID, Domain
ID, Subunit ID, Assembly Name, BindingSiteGraphic, and "up" vector.
Constructs a BindingSite with specified BindingSiteType, ID, domain ID,
subunit ID, assembly name, position (relative to the Subunit), rotation
(reative to the Subunit), and up vector (relative to the Subunit).
Carries out the FormBondEvent e by binding bindasm to this through a bond
between bsSub1 in this Assembly and bsSub2 in bindasm.Both Assembly(s)
should be different.
Constructs ConfChangeEvent which extends Event, with the specified Curent
time, end time and names of Assemblies and Subunit involved, int domainID
and Conformation conf
Conformation holds information about a particular conformation Domain of a
Subunit (energy, SubunitType, Domain, BindingSites present in this
Conformation)
Cube sets up a cube-like Simulation, where there is one type of Subunit with
a single Conformation and Domain and three binding sites arranged at angles
of pi/2, pi/2, pi/2 apart The initial number of Subunits, and the binding and
breaking times control the assembly of Cube
Composes Assembly and Subunit transforms so that the Subunits hold all
the significant location information and the Assembly location
information is all the identity function
Icosahedral sets up a viral truncated-Icosahedron-like Simulation, where
there is one type of Subunit with a single Conformation and Domain and three
binding sites arranged at angles of 120, 120, and 109 degrees apart (allowing
an icosahedral-shaped superstructure).
Creates the loading frame and all the buttons, labels, text boxes for it
the values displayed are read in from the Test.java file and those are
used as defaults
NeighborGroups stores assembly subunits in neighborgroups for fast collision
detection.That is, it divides the subunits in an Assembly into groups of
physically close neighbors for that methods which need to compare physically
close subunits.
Creates a Simulation with specified Solution s, Vector of Assemblies a,
double current time, and HashMap of bonding times (detailed in private
variable definitions), and HashMap of conformation changing times
(detailed in private variable definitions)
extends JPanel, displays the current simulation in a panel, allows user to
observe the simulation in 3-D space, allows user to use mouse to control the
view of simulation
Subunit holds information about a specific Subunit including its SubunitType,
current Conformations, ID, Solution, location/velocity mass, radius, bound
Subunits, and graphic.
Constructs a Subunit with the specified SubunitType, current
Conformations, Solution, ID, position, rotation, velocity, angular
velocity, mass, and radius.
Return a string representation of this BindingSite, detailing it's ID,
the ID of it's BindingSite, whether this BindingSite is bound, and if so,
its partner BindingSite's ID.