System¶
- class openmm.openmm.System(*args)¶
This class represents a molecular system. The definition of a System involves four elements:
The particles and constraints are defined directly by the System object, while forces are defined by objects that extend the Force class. After creating a System, call addParticle() once for each particle, addConstraint() for each constraint, and addForce() for each Force.
In addition, particles may be designated as “virtual sites”. These are particles whose positions are computed automatically based on the positions of other particles. To define a virtual site, call setVirtualSite(), passing in a VirtualSite object that defines the rules for computing its position.
Methods
__init__(-> System)Create a new System.
addConstraint(self, particle1, particle2, …)Add a constraint to the System.
addForce(self, force)Add a Force to the System.
addParticle(self, mass)Add a particle to the System.
getConstraintParameters(self, index)Get the parameters defining a distance constraint.
Get the default values of the vectors defining the axes of the periodic box (measured in nm).
getForce(-> Force)Get a writable reference to one of the Forces in this System.
Get the list of Forces in this System
getNumConstraints(self)Get the number of distance constraints in this System.
getNumForces(self)Get the number of Force objects that have been added to the System.
getNumParticles(self)Get the number of particles in this System.
getParticleMass(self, index)Get the mass (in atomic mass units) of a particle.
getVirtualSite(self, index)Get VirtualSite object for a particle.
isVirtualSite(self, index)Get whether a particle is a VirtualSite.
removeConstraint(self, index)Remove a constraint from the System.
removeForce(self, index)Remove a Force from the System.
setConstraintParameters(self, index, …)Set the parameters defining a distance constraint.
setDefaultPeriodicBoxVectors(self, a, b, c)Set the default values of the vectors defining the axes of the periodic box (measured in nm).
setParticleMass(self, index, mass)Set the mass (in atomic mass units) of a particle.
setVirtualSite(self, index, virtualSite)Set a particle to be a virtual site.
Returns whether or not any forces in this System use periodic boundaries.
Attributes
The membership flag
- property thisown¶
The membership flag
- getNumParticles(self) → int¶
Get the number of particles in this System.
- addParticle(self, mass) → int¶
Add a particle to the System. If the mass is 0, Integrators will ignore the particle and not modify its position or velocity. This is most often used for virtual sites, but can also be used as a way to prevent a particle from moving.
- Parameters
mass (double) – the mass of the particle (in atomic mass units)
- Returns
the index of the particle that was added
- Return type
int
- getParticleMass(self, index) → double¶
Get the mass (in atomic mass units) of a particle. If the mass is 0, Integrators will ignore the particle and not modify its position or velocity. This is most often used for virtual sites, but can also be used as a way to prevent a particle from moving.
- Parameters
index (int) – the index of the particle for which to get the mass
- setParticleMass(self, index, mass)¶
Set the mass (in atomic mass units) of a particle. If the mass is 0, Integrators will ignore the particle and not modify its position or velocity. This is most often used for virtual sites, but can also be used as a way to prevent a particle from moving.
- Parameters
index (int) – the index of the particle for which to set the mass
mass (double) – the mass of the particle
- setVirtualSite(self, index, virtualSite)¶
Set a particle to be a virtual site. The VirtualSite object should have been created on the heap with the “new” operator. The System takes over ownership of it, and deletes it when the System itself is deleted.
- Parameters
index (int) – the index of the particle that should be treated as a virtual site
virtualSite (VirtualSite *) – a pointer to the VirtualSite object describing it
- isVirtualSite(self, index) → bool¶
Get whether a particle is a VirtualSite.
- Parameters
index (int) – the index of the particle to check
- getVirtualSite(self, index) → VirtualSite¶
Get VirtualSite object for a particle. If the particle is not a virtual site, this throws an exception.
- Parameters
index (int) – the index of the particle to get
- getNumConstraints(self) → int¶
Get the number of distance constraints in this System.
- addConstraint(self, particle1, particle2, distance) → int¶
Add a constraint to the System. Particles whose mass is 0 cannot participate in constraints.
- Parameters
particle1 (int) – the index of the first particle involved in the constraint
particle2 (int) – the index of the second particle involved in the constraint
distance (double) – the required distance between the two particles, measured in nm
- Returns
the index of the constraint that was added
- Return type
int
- getConstraintParameters(self, index)¶
Get the parameters defining a distance constraint.
- Parameters
index (int) – the index of the constraint for which to get parameters
- Returns
particle1 (int) – the index of the first particle involved in the constraint
particle2 (int) – the index of the second particle involved in the constraint
distance (double) – the required distance between the two particles, measured in nm
- setConstraintParameters(self, index, particle1, particle2, distance)¶
Set the parameters defining a distance constraint. Particles whose mass is 0 cannot participate in constraints.
- Parameters
index (int) – the index of the constraint for which to set parameters
particle1 (int) – the index of the first particle involved in the constraint
particle2 (int) – the index of the second particle involved in the constraint
distance (double) – the required distance between the two particles, measured in nm
- removeConstraint(self, index)¶
Remove a constraint from the System.
- Parameters
index (int) – the index of the constraint to remove
- addForce(self, force) → int¶
Add a Force to the System. The Force should have been created on the heap with the “new” operator. The System takes over ownership of it, and deletes the Force when the System itself is deleted.
- Parameters
force (Force *) – a pointer to the Force object to be added
- Returns
the index within the System of the Force that was added
- Return type
int
- getNumForces(self) → int¶
Get the number of Force objects that have been added to the System.
- getForce(self, index) → Force¶
- getForce(self, index) → Force
Get a writable reference to one of the Forces in this System.
- Parameters
index (int) – the index of the Force to get
- removeForce(self, index)¶
Remove a Force from the System. The memory associated with the removed Force object is deleted.
- Parameters
index (int) – the index of the Force to remove
- getDefaultPeriodicBoxVectors(self)¶
Get the default values of the vectors defining the axes of the periodic box (measured in nm). Any newly created Context will have its box vectors set to these. They will affect any Force added to the System that uses periodic boundary conditions.
- Returns
a (Vec3) – the vector defining the first edge of the periodic box
b (Vec3) – the vector defining the second edge of the periodic box
c (Vec3) – the vector defining the third edge of the periodic box
- setDefaultPeriodicBoxVectors(self, a, b, c)¶
Set the default values of the vectors defining the axes of the periodic box (measured in nm). Any newly created Context will have its box vectors set to these. They will affect any Force added to the System that uses periodic boundary conditions.
Triclinic boxes are supported, but the vectors must satisfy certain requirements. In particular, a must point in the x direction, b must point “mostly” in the y direction, and c must point “mostly” in the z direction. See the documentation for details.
- usesPeriodicBoundaryConditions(self) → bool¶
Returns whether or not any forces in this System use periodic boundaries.
If a force in this System does not implement usesPeriodicBoundaryConditions a OpenMM::OpenMMException is thrown
- Returns
true if at least one force uses PBC and false otherwise
- Return type
bool
- getForces()¶
Get the list of Forces in this System
