Package ffx.potential.bonded

Class RestrainPosition

java.lang.Object

javax.swing.tree.DefaultMutableTreeNode

ffx.potential.bonded.MSNode

ffx.potential.bonded.BondedTerm

ffx.potential.bonded.RestrainPosition

All Implemented Interfaces:

BondedEnergy, LambdaInterface, ROLS, Serializable, Cloneable, Comparable<BondedTerm>, MutableTreeNode, TreeNode

public class RestrainPosition
extends BondedTerm
implements LambdaInterface

Restrain the position of atoms to their initial coordinates.

Since:

1.0

Author:

Michael J. Schnieders

See Also:

• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class ffx.potential.bonded.BondedTerm

BondedTerm.BondedComparator

Field Summary

Fields inherited from class ffx.potential.bonded.BondedTerm

atoms, bonds, energy, id, value

Fields inherited from class ffx.potential.bonded.MSNode

selected

Fields inherited from class javax.swing.tree.DefaultMutableTreeNode

allowsChildren, children, EMPTY_ENUMERATION, parent, userObject

Fields inherited from interface ffx.potential.bonded.ROLS

MaxLengthScale

Constructor Summary

Constructors

Constructor	Description
RestrainPosition(Atom[] atoms, double[][] equilibriumCoordinates, double forceConst, double flatBottom, boolean lambdaTerm)	Restrain atoms to a position in the global coordinate frame.

Method Summary

Modifier and Type	Method	Description
double	energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	Calculates energy and gradients for this coordinate restraint.
Atom[]	getAtoms()	Returns a copy of the atoms array.
double	getd2EdL2()	Get the 2nd partial derivative of the energy with respect to lambda.
double	getdEdL()	Get the partial derivative of the energy with respect to lambda.
void	getdEdXdL(double[] gradient)	Get the gradient of dEdL with respect to each parameter.
double[][]	getEquilibriumCoordinates()	Returns the original coordinates of this restraint, indexed by atoms then x,y,z.
double	getForceConstant()	Returns the force constant in kcal/mol/Angstrom^2.
double	getLambda()	Get the current value of the state variable.
int	getNumAtoms()	getNumAtoms.
static RestrainPosition	parseRestrainPosition(String line, Atom[] atoms, boolean useLambda)	Parse a Restrain-Position line and return a RestrainPosition instance.
static RestrainPosition[]	parseRestrainPositions(MolecularAssembly molecularAssembly)
void	setLambda(double lambda)	Set the current value of the state variable.

Methods inherited from class ffx.potential.bonded.BondedTerm

applyLambda, compareTo, containsHydrogen, containsResolution, destroy, equals, getAtom, getAtomArray, getAtomArray, getBond, getID, getUse, getValue, hashCode, isConstrained, isLambdaScaled, isNeuralNetwork, print, removeNeuralNetworkTerms, setAtoms, setBonds, setColor, setConstraint, setID, setID_Key, setSelected, setValue, setView, toString

Methods inherited from class ffx.potential.bonded.MSNode

contains, drawLabel, getAngleList, getAngleTorsionList, getAtomList, getAtomList, getBondList, getCenter, getChildList, getExtent, getImproperTorsionList, getList, getList, getMSCount, getMSNode, getMW, getName, getOutOfPlaneBendList, getPiOrbitalTorsionList, getStretchBendList, getStretchTorsionList, getTorsionList, getTorsionTorsionList, getTotalMass, getUreyBradleyList, isSelected, removeChild, setName, update

Methods inherited from class javax.swing.tree.DefaultMutableTreeNode

add, breadthFirstEnumeration, children, clone, depthFirstEnumeration, getAllowsChildren, getChildAfter, getChildAt, getChildBefore, getChildCount, getDepth, getFirstChild, getFirstLeaf, getIndex, getLastChild, getLastLeaf, getLeafCount, getLevel, getNextLeaf, getNextNode, getNextSibling, getParent, getPath, getPathToRoot, getPreviousLeaf, getPreviousNode, getPreviousSibling, getRoot, getSharedAncestor, getSiblingCount, getUserObject, getUserObjectPath, insert, isLeaf, isNodeAncestor, isNodeChild, isNodeDescendant, isNodeRelated, isNodeSibling, isRoot, pathFromAncestorEnumeration, postorderEnumeration, preorderEnumeration, remove, remove, removeAllChildren, removeFromParent, setAllowsChildren, setParent, setUserObject

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface ffx.potential.bonded.BondedEnergy

energy, energy, update

Methods inherited from interface ffx.potential.bonded.LambdaInterface

dEdLZeroAtEnds

Constructor Details

RestrainPosition

public RestrainPosition(Atom[] atoms,
 double[][] equilibriumCoordinates,
 double forceConst,
 double flatBottom,
 boolean lambdaTerm)

Restrain atoms to a position in the global coordinate frame.

Parameters:

atoms - The atoms to restrain.

equilibriumCoordinates - The equilibrium coordinates.

forceConst - The force constant in kcal/mol/A^2.

flatBottom - The flat bottom radius in Angstroms.

lambdaTerm - If true, apply lambda to this restraint.

Method Details

getAtoms

public Atom[] getAtoms()

Returns a copy of the atoms array.

Overrides:

getAtoms in class BondedTerm

Returns:

Copy of the atom array.

getForceConstant

public double getForceConstant()

Returns the force constant in kcal/mol/Angstrom^2.

Returns:

a double.

getLambda

public double getLambda()

Get the current value of the state variable.

Specified by:

getLambda in interface LambdaInterface

Returns:

state

setLambda

public void setLambda(double lambda)

Set the current value of the state variable. May be ignored if lambda is not being applied.

Specified by:

setLambda in interface LambdaInterface

Parameters:

lambda - a double.

getNumAtoms

public int getNumAtoms()

getNumAtoms.

Returns:

a int.

getEquilibriumCoordinates

public double[][] getEquilibriumCoordinates()

Returns the original coordinates of this restraint, indexed by atoms then x,y,z. This is the opposite order of the internal storage.

Returns:

Original coordinates [atoms][xyz]

getd2EdL2

public double getd2EdL2()

Get the 2nd partial derivative of the energy with respect to lambda.

Specified by:

getd2EdL2 in interface LambdaInterface

Returns:

d2EdL2

getdEdL

public double getdEdL()

Get the partial derivative of the energy with respect to lambda.

Specified by:

getdEdL in interface LambdaInterface

Returns:

dEdL

getdEdXdL

public void getdEdXdL(double[] gradient)

Get the gradient of dEdL with respect to each parameter.

Specified by:

getdEdXdL in interface LambdaInterface

Parameters:

gradient - - A double array of length the number of parameters in the model (commonly 3 * number of atoms).

energy

public double energy(boolean gradient,
 int threadID,
 AtomicDoubleArray3D grad,
 AtomicDoubleArray3D lambdaGrad)

Calculates energy and gradients for this coordinate restraint.

Specified by:

energy in interface BondedEnergy

Parameters:

gradient - Calculate gradients

threadID - The thread ID.

grad - a AtomicDoubleArray3D object.

lambdaGrad - a AtomicDoubleArray3D object.

Returns:

Energy in the coordinate restraint

parseRestrainPositions

public static RestrainPosition[] parseRestrainPositions(MolecularAssembly molecularAssembly)

parseRestrainPosition

public static RestrainPosition parseRestrainPosition(String line,
 Atom[] atoms,
 boolean useLambda)

Parse a Restrain-Position line and return a RestrainPosition instance.

Parameters:

line - The restraint line.

atoms - The atoms in the system.

useLambda - If true, apply lambda to this restraint.

Returns:

A RestrainPosition object.