ModelOperations

Model operations are processed after the models are added. These components apply transformations to the coordinates of the particles. VLMP has both simple transformations, like rotation or fixing the position of the particle, and more complex ones, such as distributing models within a volume:

# Model Operations
"modelOperations":[{
 "type":"rotation",
 "parameters":{"axis":[1.0,0.0,0.0],
               "angle":3.14,
               "selection":"all"}},{
 "type":"distributeRandomly",
 "parameters":{"mode":{
                    "sphere":{
                        "radius":40.0,
                        "center":[0.0,0.0,0.0]
                    }
                },
               "avoidClashes":True,
               "selection":"all"}}
              ]

As seen, in most cases, model operations require specifying a selection of particles to apply them. In the above example, the keyword “all” is used, which selects all particles added to the simulation. As mentioned, models can also define selections:

# Model Operations Selection
"modelOperations":[{
  "type":"setCenterOfMassPosition",
  "parameters":{"position":[0.0,0.0,0.0],
                "selection":"dna basePairIndex 2"}}
                ]

In this case, we would fix the position of the center of mass formed by the particles of the model named “dna” that belong to the second base pair. Model operations can be combined, and like the rest of the components, their processing order is ensured.

The full list of model operations is as follows:

alignInertiaMomentAlongVector
distributeRandomly
rotation
setCenterOfMassPosition
setContactDistance
setParticleLowestPosition
setParticlePositions
setParticleXYPosition

alignInertiaMomentAlongVector

author

Pablo Ibáñez-Freire

Aligns the largest inertia moment of selected particles along a specified vector.

Required Parameters
Name	Description	Type	Default
vector	Vector along which to align the largest inertia moment.	list of float

Required Selections
Name	Description	Type
selection	Selection of particles to align.	list of ids

Example:

{
        "type": "alignInertiaMomentAlongVector",
        "parameters":{
                "vector": [0.0, 0.0, 1.0],
                "selection": "model1 chain A"
        }
}

distributeRandomly

author

Pablo Ibáñez-Freire

Distributes selected particles randomly within specified bounds.

Optional Parameters
Name	Description	Type	Default
mode	Distribution mode, either ‘box’ or ‘sphere’.	str	box
randomRotation	Whether to apply random rotations to the particles.	bool	True
avoidClashes	Number of attempts to avoid particle clashes. If 0, clashes are not avoided.	int	0

Required Selections
Name	Description	Type
selection	Selection of particles to distribute.	list of ids

Example:

{
        "type": "distributeRandomly",
        "parameters":{
                "mode": "sphere",
                "avoidClashes": 100,
                "randomRotation": True,
                "selection": "model1 all"
        }
}

rotation

author

Pablo Ibáñez-Freire

Applies a rotation to selected particles around a specified axis.

Required Parameters
Name	Description	Type	Default
angle	Angle of rotation in radians.	float
axis	Axis of rotation.	list of float

Required Selections
Name	Description	Type
selection	Selection of particles to rotate.	list of ids

Example:

{
        "type": "rotation",
        "parameters":{
                "axis": [0.0, 0.0, 1.0],
                "angle": 3.14159,
                "selection": "model1 resid 1 to 10"
        }
}

setCenterOfMassPosition

author

Pablo Ibáñez-Freire

Sets the center of mass of a selection of particles to a specified position.

Required Parameters
Name	Description	Type	Default
position	Target position for the center of mass.	list of float

Required Selections
Name	Description	Type
selection	Selection of particles to move.	list of ids

Example:

{
        "type": "setCenterOfMassPosition",
        "parameters":{
                "position": [0.0, 0.0, 0.0],
                "selection": "model1 type A B C"
        }
}

setContactDistance

author

Pablo Ibáñez-Freire

Sets the contact distance between two selections of particles.

Required Parameters
Name	Description	Type	Default
distance	Target contact distance between the selections.	float
resolution	Resolution for the contact distance adjustment.	float	0.1

Optional Parameters
Name	Description	Type	Default
inverse	Whether to invert the direction of the contact.	bool	False

Required Selections
Name	Description	Type
reference	Reference selection of particles.	list of ids
mobile	Mobile selection of particles to be moved.	list of ids

Example:

{
        "type": "setContactDistance",
        "parameters":{
                "distance": 5.0,
                "resolution": 0.01,
                "inverse": False,
                "reference": "model1 type A",
                "mobile": "model2 type B"
        }
}

setParticleLowestPosition

author

Pablo Ibáñez-Freire

Sets the lowest particle in the selection to a specified Z position.

Required Parameters
Name	Description	Type	Default
position	Z coordinate to set for the lowest particle.	float

Optional Parameters
Name	Description	Type	Default
radiusFactor	Factor to multiply the radius by when considering it.	float	1.0
considerRadius	Whether to consider particle radius when setting the position.	bool	False

Required Selections
Name	Description	Type
selection	Selection of particles to consider.	list of ids

Example:

{
        "type": "setParticleLowestPosition",
        "parameters":{
                "position": 0.0,
                "considerRadius": True,
                "radiusFactor": 1.1,
                "selection": "model1 all"
        }
}

setParticlePositions

author

Pablo Ibáñez-Freire

Sets the positions of a group of particles to specified coordinates.

Required Parameters
Name	Description	Type	Default
ids	List of particle IDs to move.	list of int
positions	List of new positions for the selected particles.	list of list of float

Example:

{
        "type": "setParticlePositions",
        "parameters":{
                "positions": [[1.0, 2.0, 3.0], [4.0, 5.0, 6.0]],
                "ids": [0, 1]
        }
}

setParticleXYPosition

author

Pablo Ibáñez-Freire

Sets the XY position of selected particles to a specified value.

Required Parameters
Name	Description	Type	Default
position	New XY position for the particles.	list of float

Required Selections
Name	Description	Type
selection	Selection of particles to move.	list of ids

Example:

{
        "type": "setParticleXYPosition",
        "parameters":{
                "position": [1.0, 2.0],
                "selection": "model1 type A"
        }
}