This is the MELD Force. More...

#include <MeldForce.h>

Inheritance diagram for MeldForce:

Public Member Functions
	MeldForce ()
	Default constructor. More...

void	updateParametersInContext (OpenMM::Context &context)
	Update the per-restraint parameters in a Context to match those stored in this Force object. More...

int	getNumDistRestraints () const

int	getNumHyperbolicDistRestraints () const

int	getNumTorsionRestraints () const

int	getNumDistProfileRestraints () const

int	getNumDistProfileRestParams () const

int	getNumTorsProfileRestraints () const

int	getNumTorsProfileRestParams () const

int	getNumTotalRestraints () const

int	getNumGroups () const

int	getNumCollections () const

void	getDistanceRestraintParams (int index, int &atom1, int &atom2, float &r1, float &r2, float &r3, float &r4, float &forceConstant, int &globalIndex) const
	Get the parameters for a distance restraint. More...

void	getHyperbolicDistanceRestraintParams (int index, int &atom1, int &atom2, float &r1, float &r2, float &r3, float &r4, float &forceConstant, float &asymptote, int &globalIndex) const
	Get the parameters for a hyperbolic distance restraint. More...

void	getTorsionRestraintParams (int index, int &atom1, int &atom2, int &atom3, int &atom4, float &phi, float &deltaPhi, float &forceConstant, int &globalIndex) const
	Get the parameters for a torsion restraint. More...

void	getDistProfileRestraintParams (int index, int &atom1, int &atom2, float &rMin, float &rMax, int &nBins, std::vector< double > &a0, std::vector< double > &a1, std::vector< double > &a2, std::vector< double > &a3, float &scaleFactor, int &globalIndex) const
	Get the parameters for a distance profile restraint. More...

void	getTorsProfileRestraintParams (int index, int &atom1, int &atom2, int &atom3, int &atom4, int &atom5, int &atom6, int &atom7, int &atom8, int &nBins, std::vector< double > &a0, std::vector< double > &a1, std::vector< double > &a2, std::vector< double > &a3, std::vector< double > &a4, std::vector< double > &a5, std::vector< double > &a6, std::vector< double > &a7, std::vector< double > &a8, std::vector< double > &a9, std::vector< double > &a10, std::vector< double > &a11, std::vector< double > &a12, std::vector< double > &a13, std::vector< double > &a14, std::vector< double > &a15, float &scaleFactor, int &globalIndex) const
	Get the parameters for a torsion profile restraint. More...

void	getGroupParams (int index, std::vector< int > &indices, int &numActive) const
	Get the parameters for a group of restraints. More...

void	getCollectionParams (int index, std::vector< int > &indices, int &numActive) const
	Get the parameters for a collection of restraint groups. More...

int	addDistanceRestraint (int particle1, int particle2, float r1, float r2, float r3, float r4, float force_constant)
	Create a new distance restraint. More...

void	modifyDistanceRestraint (int index, int particle1, int particle2, float r1, float r2, float r3, float r4, float force_constant)
	Modify an existing distance restraint. More...

int	addHyperbolicDistanceRestraint (int particle1, int particle2, float r1, float r2, float r3, float r4, float force_constant, float asymptote)
	Create a new hyperbolic distance restraint. More...

void	modifyHyperbolicDistanceRestraint (int index, int particle1, int particle2, float r1, float r2, float r3, float r4, float force_constant, float asymptote)
	Modify an existing hyperbolic distance restraint. More...

int	addTorsionRestraint (int atom1, int atom2, int atom3, int atom4, float phi, float deltaPhi, float forceConstant)
	Create a new torsion restraint. More...

void	modifyTorsionRestraint (int index, int atom1, int atom2, int atom3, int atom4, float phi, float deltaPhi, float forceConstant)
	Modify an existing torsion restraint. More...

int	addDistProfileRestraint (int atom1, int atom2, float rMin, float rMax, int nBins, std::vector< double > a0, std::vector< double > a1, std::vector< double > a2, std::vector< double > a3, float scaleFactor)
	Create a new distance profile restraint. More...

void	modifyDistProfileRestraint (int index, int atom1, int atom2, float rMin, float rMax, int nBins, std::vector< double > a0, std::vector< double > a1, std::vector< double > a2, std::vector< double > a3, float scaleFactor)
	Modify an existing distance profile restraint. More...

int	addTorsProfileRestraint (int atom1, int atom2, int atom3, int atom4, int atom5, int atom6, int atom7, int atom8, int nBins, std::vector< double > a0, std::vector< double > a1, std::vector< double > a2, std::vector< double > a3, std::vector< double > a4, std::vector< double > a5, std::vector< double > a6, std::vector< double > a7, std::vector< double > a8, std::vector< double > a9, std::vector< double > a10, std::vector< double > a11, std::vector< double > a12, std::vector< double > a13, std::vector< double > a14, std::vector< double > a15, float scaleFactor)
	Create a new torsion profile restraint. More...

void	modifyTorsProfileRestraint (int index, int atom1, int atom2, int atom3, int atom4, int atom5, int atom6, int atom7, int atom8, int nBins, std::vector< double > a0, std::vector< double > a1, std::vector< double > a2, std::vector< double > a3, std::vector< double > a4, std::vector< double > a5, std::vector< double > a6, std::vector< double > a7, std::vector< double > a8, std::vector< double > a9, std::vector< double > a10, std::vector< double > a11, std::vector< double > a12, std::vector< double > a13, std::vector< double > a14, std::vector< double > a15, float scaleFactor)
	Modify an existing torsion profile restraint. More...

int	addGroup (std::vector< int > restraint_indices, int n_active)
	Create a new group of restraints. More...

int	addCollection (std::vector< int > group_indices, int n_active)
	Create a new collection of restraint groups. More...

Protected Member Functions
OpenMM::ForceImpl *	createImpl () const

Detailed Description

This is the MELD Force.

Constructor & Destructor Documentation

MeldForce ( )

Default constructor.

Member Function Documentation

int addCollection	(	std::vector< int >	group_indices,
		int	n_active
	)

Create a new collection of restraint groups.

Parameters

group_indices	the indices of the groups in the collection
n_active	the number of active groups in the collection

Returns: the index of the collection that was created

int addDistanceRestraint	(	int	particle1,
		int	particle2,
		float	r1,
		float	r2,
		float	r3,
		float	r4,
		float	force_constant
	)

Create a new distance restraint.

There are five regions:

I: r < r1

II: r1 < r < r2

III: r2 < r < r3

IV: r3 < r < r4

V: r4 < r

The energy is linear in regions I and V, quadratic in II and IV, and zero in III.

Parameters

particle1	the first atom
particle2	the second atom
r1	the upper bound of region 1
r2	the upper bound of region 2
r3	the upper bound of region 3
r4	the upper bound of region 4
forceConstant	the force constant

Returns: the index of the restraint that was created

int addDistProfileRestraint	(	int	atom1,
		int	atom2,
		float	rMin,
		float	rMax,
		int	nBins,
		std::vector< double >	a0,
		std::vector< double >	a1,
		std::vector< double >	a2,
		std::vector< double >	a3,
		float	scaleFactor
	)

Create a new distance profile restraint.

bin = floor( (r - rMin) / (rMax - rMin) * nBins) )

binWidth = (rMax - rMin) / nBins

t = (r - bin * binWidth + rMin) / binWidth;

E = scaleFactor * (a0 + a1 * t + a2 * t^2 + a3 * t^3)

Parameters

atom1	the first atom
atom2	the second atom
rMin	the lower bound of the restraint
rMax	the upper bound of the restraint
nBins	the number of bins
aN	the Nth spline parameter where N is in (0,1,2,3)
scaleFactor	the scale factor

Returns: the index of the restraint that was created

int addGroup	(	std::vector< int >	restraint_indices,
		int	n_active
	)

Create a new group of restraints.

Parameters

restraint_indices	the indices of the restraints in the group
n_active	the number of active restraints in the group

Returns: the index of the group that was created

int addHyperbolicDistanceRestraint	(	int	particle1,
		int	particle2,
		float	r1,
		float	r2,
		float	r3,
		float	r4,
		float	force_constant,
		float	asymptote
	)

Create a new hyperbolic distance restraint.

There are five regions:

I: r < r1

II: r1 < r < r2

III: r2 < r < r3

IV: r3 < r < r4

V: r4 < r

The energy is linear in region I, quadratic in II and IV, and zero in III.

The energy is hyperbolic in region V, with an asymptotic value set by the parameter asymptote. The energy will be 1/3 of the asymptotic value at r=r4. The distance between r3 and r4 controls the steepness of the potential.

Parameters

particle1	the first atom
particle2	the second atom
r1	the upper bound of region 1
r2	the upper bound of region 2
r3	the upper bound of region 3
r4	the upper bound of region 4
forceConstant	the force constant in regions I and II
asymptote	the asymptotic value in region V, also controls the steepness in region IV.

Returns: the index of the restraint that was created

int addTorsionRestraint	(	int	atom1,
		int	atom2,
		int	atom3,
		int	atom4,
		float	phi,
		float	deltaPhi,
		float	forceConstant
	)

Create a new torsion restraint.

If (x - phi) < -deltaPhi: E = 1/2 * forceConstant * (x - phi + deltaPhi)^2

Else if (x - phi) > deltaPhi: E = 1/2 * forceConstant * (x - phi - deltaPhi)^2

Else: E = 0

Parameters

atom1	the first atom
atom2	the second atom
atom3	the third atom
atom4	the fourth atom
phi	the equilibrium torsion (degrees)
deltaPhi	the deltaPhi parameter (degrees)
forceConstant	the force constant

Returns: the index of the restraint that was created

int addTorsProfileRestraint	(	int	atom1,
		int	atom2,
		int	atom3,
		int	atom4,
		int	atom5,
		int	atom6,
		int	atom7,
		int	atom8,
		int	nBins,
		std::vector< double >	a0,
		std::vector< double >	a1,
		std::vector< double >	a2,
		std::vector< double >	a3,
		std::vector< double >	a4,
		std::vector< double >	a5,
		std::vector< double >	a6,
		std::vector< double >	a7,
		std::vector< double >	a8,
		std::vector< double >	a9,
		std::vector< double >	a10,
		std::vector< double >	a11,
		std::vector< double >	a12,
		std::vector< double >	a13,
		std::vector< double >	a14,
		std::vector< double >	a15,
		float	scaleFactor
	)

Create a new torsion profile restraint.

Parameters

atom1	the first atom
atom2	the second atom
atom3	the third atom
atom4	the fourth atom
atom5	the fifth atom
atom6	the sixth atom
atom7	the seventh atom
atom8	the eighth atom
nBins	the number of bins
aN	the Nth spline parameter where N is in (0,1,...,14,15)
scaleFactor	the scale factor

Returns: the index of the restraint that was created

OpenMM::ForceImpl* createImpl ( ) const

protected

void getCollectionParams	(	int	index,
		std::vector< int > &	indices,
		int &	numActive
	)		const

Get the parameters for a collection of restraint groups.

Parameters

index	the index of the collection
indices	the indices of the groups in the collection
numActive	the number of active groups in the collection

void getDistanceRestraintParams	(	int	index,
		int &	atom1,
		int &	atom2,
		float &	r1,
		float &	r2,
		float &	r3,
		float &	r4,
		float &	forceConstant,
		int &	globalIndex
	)		const

Get the parameters for a distance restraint.

See addDistanceRestraint() for more details about the parameters.

Parameters

index	the index of the restraint
atom1	the first atom
atom2	the second atom
r1	the upper bound of region 1
r2	the upper bound of region 2
r3	the upper bound of region 3
r4	the upper bound of region 4
forceConstant	the force constant
globalIndex	the global index of the restraint

void getDistProfileRestraintParams	(	int	index,
		int &	atom1,
		int &	atom2,
		float &	rMin,
		float &	rMax,
		int &	nBins,
		std::vector< double > &	a0,
		std::vector< double > &	a1,
		std::vector< double > &	a2,
		std::vector< double > &	a3,
		float &	scaleFactor,
		int &	globalIndex
	)		const

Get the parameters for a distance profile restraint.

See addDistProfileRestraint() for more details about the parameters.

Parameters

index	the index of the restraint
atom1	the first atom
atom2	the second atom
rMin	the lower bound of the restraint
rMax	the upper bound of the restraint
nBins	the number of bins
aN	the Nth spline parameter where N is in (0,1,2,3)
scaleFactor	the scale factor
globalIndex	the global index of the restraint

void getGroupParams	(	int	index,
		std::vector< int > &	indices,
		int &	numActive
	)		const

Get the parameters for a group of restraints.

Parameters

index	the index of the group
indices	the indices of the restraints in the group
numActive	the number of active restraints in the group

void getHyperbolicDistanceRestraintParams	(	int	index,
		int &	atom1,
		int &	atom2,
		float &	r1,
		float &	r2,
		float &	r3,
		float &	r4,
		float &	forceConstant,
		float &	asymptote,
		int &	globalIndex
	)		const

Get the parameters for a hyperbolic distance restraint.

See addHyperbolicDistanceRestraint() for more details about the parameters.

Parameters

index	the index of the restraint
atom1	the first atom
atom2	the second atom
r1	the upper bound of region 1
r2	the upper bound of region 2
r3	the upper bound of region 3
r4	the upper bound of region 4
forceConstant	the force constant for region 1
asymptote	the asymptotic energy in region 4
globalIndex	the global index of the restraint

int getNumCollections ( ) const

Returns: The number of collections of restraint groups.

int getNumDistProfileRestParams ( ) const

Returns: The number of distance profile restraint parameters.

int getNumDistProfileRestraints ( ) const

Returns: The number of distance profile restraints.

int getNumDistRestraints ( ) const

Returns: The number of distance restraints.

int getNumGroups ( ) const

Returns: The number of restraint groups.

int getNumHyperbolicDistRestraints ( ) const

Returns: The number of hyperbolic distance restraints.

int getNumTorsionRestraints ( ) const

Returns: The number of torsion restraints.

int getNumTorsProfileRestParams ( ) const

Returns: The number of torsion profile restraint parameters.

int getNumTorsProfileRestraints ( ) const

Returns: The number of torsion profile restraints.

int getNumTotalRestraints ( ) const

Returns: The total number of distance and torsion restraints.

void getTorsionRestraintParams	(	int	index,
		int &	atom1,
		int &	atom2,
		int &	atom3,
		int &	atom4,
		float &	phi,
		float &	deltaPhi,
		float &	forceConstant,
		int &	globalIndex
	)		const

Get the parameters for a torsion restraint.

See addTorsionRestraint() for more details about the parameters.

Parameters

index	the index of the restraint
atom1	the first atom
atom2	the second atom
atom3	the third atom
atom4	the fourth atom
phi	the equilibrium torsion (degrees)
deltaPhi	the deltaPhi parameter (degrees)
forceConstant	the force constant
globalIndex	the global index of the restraint

void getTorsProfileRestraintParams	(	int	index,
		int &	atom1,
		int &	atom2,
		int &	atom3,
		int &	atom4,
		int &	atom5,
		int &	atom6,
		int &	atom7,
		int &	atom8,
		int &	nBins,
		std::vector< double > &	a0,
		std::vector< double > &	a1,
		std::vector< double > &	a2,
		std::vector< double > &	a3,
		std::vector< double > &	a4,
		std::vector< double > &	a5,
		std::vector< double > &	a6,
		std::vector< double > &	a7,
		std::vector< double > &	a8,
		std::vector< double > &	a9,
		std::vector< double > &	a10,
		std::vector< double > &	a11,
		std::vector< double > &	a12,
		std::vector< double > &	a13,
		std::vector< double > &	a14,
		std::vector< double > &	a15,
		float &	scaleFactor,
		int &	globalIndex
	)		const

Get the parameters for a torsion profile restraint.

Parameters

index	the index of the restraint
atom1	the first atom
atom2	the second atom
atom3	the third atom
atom4	the fourth atom
atom5	the fifth atom
atom6	the sixth atom
atom7	the seventh atom
atom8	the eighth atom
nBins	the number of bins
aN	the Nth spline parameter where N is in (0,1,...,14,15)
scaleFactor	the scale factor
globalIndex	the global index of the restraint

void modifyDistanceRestraint	(	int	index,
		int	particle1,
		int	particle2,
		float	r1,
		float	r2,
		float	r3,
		float	r4,
		float	force_constant
	)

Modify an existing distance restraint.

See addDistanceRestraint() for more details about the parameters.

Parameters

index	the index of the restraint
particle1	the first atom
particle2	the second atom
r1	the upper bound of region 1
r2	the upper bound of region 2
r3	the upper bound of region 3
r4	the upper bound of region 4
forceConstant	the force constant

void modifyDistProfileRestraint	(	int	index,
		int	atom1,
		int	atom2,
		float	rMin,
		float	rMax,
		int	nBins,
		std::vector< double >	a0,
		std::vector< double >	a1,
		std::vector< double >	a2,
		std::vector< double >	a3,
		float	scaleFactor
	)

Modify an existing distance profile restraint.

See addDistProfileRestraint() for more details about the parameters.

Parameters

index	the index of the restraint
atom1	the first atom
atom2	the second atom
rMin	the lower bound of the restraint
rMax	the upper bound of the restraint
nBins	the number of bins
aN	the Nth spline parameter where N is in (0,1,2,3)
scaleFactor	the scale factor

void modifyHyperbolicDistanceRestraint	(	int	index,
		int	particle1,
		int	particle2,
		float	r1,
		float	r2,
		float	r3,
		float	r4,
		float	force_constant,
		float	asymptote
	)

Modify an existing hyperbolic distance restraint.

See addHyperbolicDistanceRestraint() for more details about the parameters.

Parameters

index	the index of the restraint
particle1	the first atom
particle2	the second atom
r1	the upper bound of region 1
r2	the upper bound of region 2
r3	the upper bound of region 3
r4	the upper bound of region 4
forceConstant	the force constant
asymptote	the asymptotic value

void modifyTorsionRestraint	(	int	index,
		int	atom1,
		int	atom2,
		int	atom3,
		int	atom4,
		float	phi,
		float	deltaPhi,
		float	forceConstant
	)

Modify an existing torsion restraint.

See addTorsionRestraint() for more details about the parameters.

Parameters

index	the index of the restraint
atom1	the first atom
atom2	the second atom
atom3	the third atom
atom4	the fourth atom
phi	the equilibrium torsion (degrees)
deltaPhi	the deltaPhi parameter (degrees)
forceConstant	the force constant

void modifyTorsProfileRestraint	(	int	index,
		int	atom1,
		int	atom2,
		int	atom3,
		int	atom4,
		int	atom5,
		int	atom6,
		int	atom7,
		int	atom8,
		int	nBins,
		std::vector< double >	a0,
		std::vector< double >	a1,
		std::vector< double >	a2,
		std::vector< double >	a3,
		std::vector< double >	a4,
		std::vector< double >	a5,
		std::vector< double >	a6,
		std::vector< double >	a7,
		std::vector< double >	a8,
		std::vector< double >	a9,
		std::vector< double >	a10,
		std::vector< double >	a11,
		std::vector< double >	a12,
		std::vector< double >	a13,
		std::vector< double >	a14,
		std::vector< double >	a15,
		float	scaleFactor
	)

Modify an existing torsion profile restraint.

Parameters

index	the index of the restraint
atom1	the first atom
atom2	the second atom
atom3	the third atom
atom4	the fourth atom
atom5	the fifth atom
atom6	the sixth atom
atom7	the seventh atom
atom8	the eighth atom
nBins	the number of bins
aN	the Nth spline parameter where N is in (0,1,...,14,15)
scaleFactor	the scale factor

void updateParametersInContext ( OpenMM::Context & context )

Update the per-restraint parameters in a Context to match those stored in this Force object.

This method provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it. Simply call modifyDistanceRestaint(), modifyTorsionRestraint(), modifyDistProfileRestraint(), or modifyTorsProfileRestraint() to modify the parameters of a restraint, then call updateParametersInContext() to copy them over to the Context.

This method has several limitations. The only information it updates is the values of per-restraint parameters. All other aspects of the Force (such as the energy function) are unaffected and can only be changed by reinitializing the Context. The set of particles involved in a restraint cannot be changed, nor can new restraints be added.

The documentation for this class was generated from the following file:

MeldForce.h

Public Member Functions

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation