Public Member Functions
int	getAtomIndex (int restrained_atom_number) const

int	getOrder () const
	Get the order of this restraint.

int	getInitialStep () const
	Get the initial step at which to begin applying this restraint.

int	getFinalStep () const
	Get the simulation step at which to finish applying this restraint.

double2	getStiffness (int step_number=0) const
	Get the stiffnesses of a restraint at a given step in the simulation.

double2	getInitialStiffness () const
	Get the initial stiffnesses to use when applying this restraint.

double2	getFinalStiffness () const
	Get the final stiffnesses of the restraint in its complete form.

double4	getDisplacements (int step_number=0) const
	Get the displacement parameters of a restraint at a given step in the simulation.

double4	getInitialDisplacements () const
	Get the initial displacement parameters to use in applying this restraint.

double4	getFinalDisplacements () const
	Get the final displacement parameters of the restraint in its complete form.

double3	getTargetSite (int step_number=0) const
	Get the target site of a positional restraint at a given step in the simulation.

double3	getInitialTargetSite () const
	Get the initial target of a positional restraint.

double3	getFinalTargetSite () const
	Get the final target of a positional restraint.

const AtomGraph *	getTopologyPointer () const
	Get the topology pointer.

void	setInitialStep (int new_init_step)
	Modify the initial step at which the restraint is applied.

void	setFinalStep (int new_final_step)
	Modify the final step at which the restraint application reaches its final value.

void	setStiffness (double new_keq)
	Modify the stiffness parameters, set with a single value. This member function is only applicable if there is no time dependence in the restraint and will throw an error otherwise.

void	setStiffnesses (double new_k2, double new_k3)
	Modify the stiffness parameters. This member function is only applicable if there is no time dependence in the restraint and will throw an error otherwise.

void	setInitialStiffness (double new_init_keq)
	Modify the initial stiffness parameters, setting both to a single value. This member function is only applicable if there is time dependence in the restraint.

void	setInitialStiffnesses (double new_init_k2, double new_init_k3)
	Modify the initial stiffness parameters. This member function is only applicable if there is time dependence in the restraint.

void	setFinalStiffness (double new_init_keq)
	Modify the final stiffness parameters, setting both to a single value. This member function is only applicable if there is time dependence in the restraint.

void	setFinalStiffnesses (double new_init_k2, double new_init_k3)
	Modify the final stiffness parameters. This member function is only applicable if there is time dependence in the restraint.

void	setDisplacements (double new_r1, double new_r2, double new_r3, double new_r4)
	Modify the displacements over which each segment of the flat-bottom restraint applies. This member function requires that the restraint be time-independent.

void	setInitialDisplacements (double new_r1, double new_r2, double new_r3, double new_r4)
	Modify the initial displacements over which each segment of the flat-bottom restraint applies. This member function requires that the restraint be time-dependent.

void	setFinalDisplacements (double new_r1, double new_r2, double new_r3, double new_r4)
	Modify the final displacements over which each segment of the flat-bottom restraint applies. This member function requires that the restraint be time-dependent.


	BoundedRestraint (const AtomGraph *ag_in)

	BoundedRestraint (const std::string &mask_i_in, const std::string &mask_j_in, const std::string &mask_k_in, const std::string &mask_l_in, const AtomGraph *ag_in, const ChemicalFeatures &chemfe, const CoordinateFrameReader &cfr, int init_step_in, int final_step_in, double init_k2_in, double init_k3_in, double init_r1_in, double init_r2_in, double init_r3_in, double init_r4_in, double final_k2_in, double final_k3_in, double final_r1_in, double final_r2_in, double final_r3_in, double final_r4_in, const double3 init_ref_crd_in={ 0.0, 0.0, 0.0 }, const double3 final_ref_crd_in={ 0.0, 0.0, 0.0 })

	BoundedRestraint (const std::string &mask_i_in, const std::string &mask_j_in, const std::string &mask_k_in, const AtomGraph *ag_in, const ChemicalFeatures &chemfe, const CoordinateFrameReader &cfr, int init_step_in, int final_step_in, double init_k2_in, double init_k3_in, double init_r1_in, double init_r2_in, double init_r3_in, double init_r4_in, double final_k2_in, double final_k3_in, double final_r1_in, double final_r2_in, double final_r3_in, double final_r4_in)

	BoundedRestraint (const std::string &mask_i_in, const std::string &mask_j_in, const AtomGraph *ag_in, const ChemicalFeatures &chemfe, const CoordinateFrameReader &cfr, int init_step_in, int final_step_in, double init_k2_in, double init_k3_in, double init_r1_in, double init_r2_in, double init_r3_in, double init_r4_in, double final_k2_in, double final_k3_in, double final_r1_in, double final_r2_in, double final_r3_in, double final_r4_in)

	BoundedRestraint (const std::string &mask_i_in, const AtomGraph *ag_in, const ChemicalFeatures &chemfe, const CoordinateFrameReader &cfr, int init_step_in, int final_step_in, double init_k2_in, double init_k3_in, double init_r1_in, double init_r2_in, double init_r3_in, double init_r4_in, double final_k2_in, double final_k3_in, double final_r1_in, double final_r2_in, double final_r3_in, double final_r4_in, const double3 init_ref_crd_in, const double3 final_ref_crd_in)

	BoundedRestraint (const std::string &mask_i_in, const std::string &mask_j_in, const std::string &mask_k_in, const std::string &mask_l_in, const AtomGraph *ag_in, const ChemicalFeatures &chemfe, const CoordinateFrameReader &cfr, double k2_in, double k3_in, double r1_in, double r2_in, double r3_in, double r4_in)

	BoundedRestraint (const std::string &mask_i_in, const std::string &mask_j_in, const std::string &mask_k_in, const AtomGraph *ag_in, const ChemicalFeatures &chemfe, const CoordinateFrameReader &cfr, double k2_in, double k3_in, double r1_in, double r2_in, double r3_in, double r4_in)

	BoundedRestraint (const std::string &mask_i_in, const std::string &mask_j_in, const AtomGraph *ag_in, const ChemicalFeatures &chemfe, const CoordinateFrameReader &cfr, double k2_in, double k3_in, double r1_in, double r2_in, double r3_in, double r4_in)

	BoundedRestraint (const std::string &mask_i_in, const AtomGraph *ag_in, const ChemicalFeatures &chemfe, const CoordinateFrameReader &cfr, double k2_in, double k3_in, double r1_in, double r2_in, double r3_in, double r4_in, const double3 ref_crd_in)

	BoundedRestraint (const std::string &mask_i_in, const AtomGraph *ag_in, const ChemicalFeatures &chemfe, const CoordinateFrameReader &cfr, double k2_in, double k3_in, double r1_in, double r2_in, double r3_in, double r4_in, const std::string &mask_ref_in)

	BoundedRestraint (int atom_i_in, int atom_j_in, int atom_k_in, int atom_l_in, const AtomGraph *ag_in, int init_step_in, int final_step_in, double init_k2_in, double init_k3_in, double init_r1_in, double init_r2_in, double init_r3_in, double init_r4_in, double final_k2_in, double final_k3_in, double final_r1_in, double final_r2_in, double final_r3_in, double final_r4_in, const double3 init_ref_crd_in={ 0.0, 0.0, 0.0}, const double3 final_ref_crd_in={ 0.0, 0.0, 0.0 })

	BoundedRestraint (int atom_i_in, int atom_j_in, int atom_k_in, const AtomGraph *ag_in, int init_step_in, int final_step_in, double init_k2_in, double init_k3_in, double init_r1_in, double init_r2_in, double init_r3_in, double init_r4_in, double final_k2_in, double final_k3_in, double final_r1_in, double final_r2_in, double final_r3_in, double final_r4_in)

	BoundedRestraint (int atom_i_in, int atom_j_in, const AtomGraph *ag_in, int init_step_in, int final_step_in, double init_k2_in, double init_k3_in, double init_r1_in, double init_r2_in, double init_r3_in, double init_r4_in, double final_k2_in, double final_k3_in, double final_r1_in, double final_r2_in, double final_r3_in, double final_r4_in)

	BoundedRestraint (int atom_i_in, const AtomGraph *ag_in, int init_step_in, int final_step_in, double init_k2_in, double init_k3_in, double init_r1_in, double init_r2_in, double init_r3_in, double init_r4_in, double final_k2_in, double final_k3_in, double final_r1_in, double final_r2_in, double final_r3_in, double final_r4_in, const double3 init_ref_crd_in, const double3 final_ref_crd_in)

	BoundedRestraint (int atom_i_in, int atom_j_in, int atom_k_in, int atom_l_in, const AtomGraph *ag_in, double k2_in, double k3_in, double r1_in, double r2_in, double r3_in, double r4_in)

	BoundedRestraint (int atom_i_in, int atom_j_in, int atom_k_in, const AtomGraph *ag_in, double k2_in, double k3_in, double r1_in, double r2_in, double r3_in, double r4_in)

	BoundedRestraint (int atom_i_in, int atom_j_in, const AtomGraph *ag_in, double k2_in, double k3_in, double r1_in, double r2_in, double r3_in, double r4_in)

	BoundedRestraint (int atom_i_in, const AtomGraph *ag_in, double k2_in, double k3_in, double r1_in, double r2_in, double r3_in, double r4_in, const double3 ref_crd_in)

	BoundedRestraint (int atom_index, const AtomGraph *ag_in, const CoordinateFrameReader &cfr, double k2_in, double k3_in, double r1_in, double r2_in, double r3_in, double r4_in, int refr_index=-1)


	BoundedRestraint (const BoundedRestraint &original)=default
	Take the default copy, copy assignment, move, and move assignment constructors.

	BoundedRestraint (BoundedRestraint &&original)=default

BoundedRestraint &	operator= (const BoundedRestraint &original)=default

BoundedRestraint &	operator= (BoundedRestraint &&original)=default


void	setTargetSite (double new_ref_x, double new_ref_y, double new_ref_z)
	Set the target site. This function can only apply to a time-independent positional restraint with only one active atom.

void	setTargetSite (double3 new_ref_crd)


void	setInitialTargetSite (double new_ref_x, double new_ref_y, double new_ref_z)
	Set the initial target site. This function can only apply to a time-dependent positional restraint with only one active atom.

void	setInitialTargetSite (double3 new_ref_crd)


void	setFinalTargetSite (double new_ref_x, double new_ref_y, double new_ref_z)
	Set the final target site. This function can only apply to a time-dependent positional restraint with only one active atom.

void	setFinalTargetSite (double3 new_ref_crd)

Constructor & Destructor Documentation

◆ BoundedRestraint()

stormm::restraints::BoundedRestraint::BoundedRestraint ( const AtomGraph * ag_in )

Constructors take either four atom masks (each of whcih must evaluate to exactly one atom) or four atom numbers (numbers are given for a series 1... atom_count in the topology pointer, decremented when constructing the mask to index into the actual memory)

Overloaded:

Empty constructor (creates a restraint of order zero but for a particular topology)
Accept up to four atom masks and all other inputs
Accept up to four atom numbers and all other inputs
Accept up to four atom masks and basic inputs
Accept up to four atom numbers and basic inputs
If only a single atom is specified by mask or by number, reference coordinates should also be supplied

Parameters

mask_i_in	Atom mask identifying the first atom
mask_j_in	Atom mask identifying the second atom (empty string for no atom)
mask_k_in	Atom mask identifying the third atom (empty string for no atom)
mask_l_in	Atom mask identifying the fourth atom (empty string for no atom)
atom_i_in	Topological index of the first atom (starts from 0, skip atom mask)
atom_i_in	Topological index of the second atom (starts from 0, skip atom mask)
atom_i_in	Topological index of the third atom (starts from 0, skip atom mask)
atom_i_in	Topological index of the fourth atom (starts from 0, skip atom mask)
ag_in	Topology of the system in question
chemfe	Chemical perception output for the system in question
cfr	Coordinates of the system in question (for positional restraints)
init_step_in	Step at which to begin to apply the restraints
final_step_in	Step at which the retraint is to take on its mature values
init_k2_in	Start value of the stiffness of the left-hand parabola
init_k3_in	Start value of the stiffness of the right-hand parabola
init_r1_in	Start value of the leftmost point of the left-hand half parabola
init_r2_in	Start value of the rightmost point of the left-hand half parabola
init_r3_in	Start value of the leftmost point of the right-hand half parabola
init_r4_in	Start value of the rightmost point of the right-hand half parabola
final_k2_in	Mature value of the stiffness of the left-hand parabola
final_k3_in	Mature value of the stiffness of the right-hand parabola
final_r1_in	Mature value of the leftmost point of the left-hand half parabola
final_r2_in	Mature value of the rightmost point of the left-hand half parabola
final_r3_in	Mature value of the leftmost point of the right-hand half parabola
final_r4_in	Mature value of the rightmost point of the right-hand half parabola
init_ref_crd_in	The initial target location for an atomic positional restraint
final_ref_crd_in	The final target location for an atomic positional restraint

Member Function Documentation

◆ getAtomIndex()

int stormm::restraints::BoundedRestraint::getAtomIndex ( int restrained_atom_number ) const

Obtain the topology index of an atom in this restraint

Parameters

restrained_atom_number The 1st, 2nd, 3rd, or 4th atom (specify 1, 2, 3, or 4)

◆ getDisplacements()

double4 stormm::restraints::BoundedRestraint::getDisplacements ( int step_number = 0 ) const

Get the displacement parameters of a restraint at a given step in the simulation.

Parameters

step_number The step at which to compute the target site

◆ getStiffness()

double2 stormm::restraints::BoundedRestraint::getStiffness ( int step_number = 0 ) const

Get the stiffnesses of a restraint at a given step in the simulation.

Parameters

step_number The step at which to compute the target site

◆ getTargetSite()

double3 stormm::restraints::BoundedRestraint::getTargetSite ( int step_number = 0 ) const

Get the target site of a positional restraint at a given step in the simulation.

Parameters

step_number The step at which to compute the target site

◆ setDisplacements()

void stormm::restraints::BoundedRestraint::setDisplacements	(	double	new_r1,
		double	new_r2,
		double	new_r3,
		double	new_r4 )

Modify the displacements over which each segment of the flat-bottom restraint applies. This member function requires that the restraint be time-independent.

Parameters

new_r1	New value of r1, the leftmost point of a harmonic potential scaled by k2
new_r2	New value of r2, the rightmost point of a harmonic potential scaled by k2
new_r3	New value of r3, the leftmost point of a harmonic potential scaled by k3
new_r4	New value of r4, the rightmost point of a harmonic potential scaled by k3

◆ setFinalDisplacements()

void stormm::restraints::BoundedRestraint::setFinalDisplacements	(	double	new_r1,
		double	new_r2,
		double	new_r3,
		double	new_r4 )

Modify the final displacements over which each segment of the flat-bottom restraint applies. This member function requires that the restraint be time-dependent.

Parameters

new_r1	New final r1, the leftmost point of a harmonic potential scaled by k2
new_r2	New final r2, the rightmost point of a harmonic potential scaled by k2
new_r3	New final r3, the leftmost point of a harmonic potential scaled by k3
new_r4	New final r4, the rightmost point of a harmonic potential scaled by k3

◆ setFinalStep()

void stormm::restraints::BoundedRestraint::setFinalStep ( int new_final_step )

Modify the final step at which the restraint application reaches its final value.

Parameters

new_final_step The new value for the final application step

◆ setFinalStiffness()

void stormm::restraints::BoundedRestraint::setFinalStiffness ( double new_init_keq )

Modify the final stiffness parameters, setting both to a single value. This member function is only applicable if there is time dependence in the restraint.

Parameters

new_init_keq New final value of both k2 and k3

◆ setFinalStiffnesses()

void stormm::restraints::BoundedRestraint::setFinalStiffnesses	(	double	new_init_k2,
		double	new_init_k3 )

Modify the final stiffness parameters. This member function is only applicable if there is time dependence in the restraint.

Parameters

new_init_k2	New final value of k2
new_init_k3	New final value of k3

◆ setFinalTargetSite()

void stormm::restraints::BoundedRestraint::setFinalTargetSite	(	double	new_ref_x,
		double	new_ref_y,
		double	new_ref_z )

Set the final target site. This function can only apply to a time-dependent positional restraint with only one active atom.

Overloaded:

Take separate x, y, and z coordinate arguments
Take a 3-tuple of real numbers for x, y, and z coordinates

Parameters

new_ref_x	New final reference Cartesian x coordinate
new_ref_y	New final reference Cartesian y coordinate
new_ref_z	New final reference Cartesian z coordinate
new_ref_crd	New final reference Cartesian coordinate tuple

◆ setInitialDisplacements()

void stormm::restraints::BoundedRestraint::setInitialDisplacements	(	double	new_r1,
		double	new_r2,
		double	new_r3,
		double	new_r4 )

Modify the initial displacements over which each segment of the flat-bottom restraint applies. This member function requires that the restraint be time-dependent.

Parameters

new_r1	New initial r1, the leftmost point of a harmonic potential scaled by k2
new_r2	New initial r2, the rightmost point of a harmonic potential scaled by k2
new_r3	New initial r3, the leftmost point of a harmonic potential scaled by k3
new_r4	New initial r4, the rightmost point of a harmonic potential scaled by k3

◆ setInitialStep()

void stormm::restraints::BoundedRestraint::setInitialStep ( int new_init_step )

Modify the initial step at which the restraint is applied.

Parameters

new_init_step The new value for the initial application step

◆ setInitialStiffness()

void stormm::restraints::BoundedRestraint::setInitialStiffness ( double new_init_keq )

Modify the initial stiffness parameters, setting both to a single value. This member function is only applicable if there is time dependence in the restraint.

Parameters

new_init_keq New initial value of both k2 and k3

◆ setInitialStiffnesses()

void stormm::restraints::BoundedRestraint::setInitialStiffnesses	(	double	new_init_k2,
		double	new_init_k3 )

Modify the initial stiffness parameters. This member function is only applicable if there is time dependence in the restraint.

Parameters

new_init_k2	New initial value of k2
new_init_k3	New initial value of k3

◆ setInitialTargetSite()

void stormm::restraints::BoundedRestraint::setInitialTargetSite	(	double	new_ref_x,
		double	new_ref_y,
		double	new_ref_z )

Set the initial target site. This function can only apply to a time-dependent positional restraint with only one active atom.

Overloaded:

Take separate x, y, and z coordinate arguments
Take a 3-tuple of real numbers for x, y, and z coordinates

Parameters

new_ref_x	New initial reference Cartesian x coordinate
new_ref_y	New initial reference Cartesian y coordinate
new_ref_z	New initial reference Cartesian z coordinate
new_ref_crd	New initial reference Cartesian coordinate tuple

◆ setStiffness()

void stormm::restraints::BoundedRestraint::setStiffness ( double new_keq )

Modify the stiffness parameters, set with a single value. This member function is only applicable if there is no time dependence in the restraint and will throw an error otherwise.

Parameters

new_keq New value of both k2 and k3. Both values of the initial stiffness tuple will be set to these values.

◆ setStiffnesses()

void stormm::restraints::BoundedRestraint::setStiffnesses	(	double	new_k2,
		double	new_k3 )

Modify the stiffness parameters. This member function is only applicable if there is no time dependence in the restraint and will throw an error otherwise.

Parameters

new_k2	New value of k2
new_k3	New value of k3

◆ setTargetSite()

void stormm::restraints::BoundedRestraint::setTargetSite	(	double	new_ref_x,
		double	new_ref_y,
		double	new_ref_z )

Set the target site. This function can only apply to a time-independent positional restraint with only one active atom.

Overloaded:

Take separate x, y, and z coordinate arguments
Take a 3-tuple of real numbers for x, y, and z coordinates

Parameters

new_ref_x	New reference Cartesian x coordinate
new_ref_y	New reference Cartesian y coordinate
new_ref_z	New reference Cartesian z coordinate
new_ref_crd	New reference Cartesian coordinate tuple

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

src/Restraints/bounded_restraint.h
src/Restraints/bounded_restraint.cpp

Public Member Functions

Constructor & Destructor Documentation

◆ BoundedRestraint()

Member Function Documentation

◆ getAtomIndex()

◆ getDisplacements()

◆ getStiffness()

◆ getTargetSite()

◆ setDisplacements()

◆ setFinalDisplacements()

◆ setFinalStep()

◆ setFinalStiffness()

◆ setFinalStiffnesses()

◆ setFinalTargetSite()

◆ setInitialDisplacements()

◆ setInitialStep()

◆ setInitialStiffness()

◆ setInitialStiffnesses()

◆ setInitialTargetSite()

◆ setStiffness()

◆ setStiffnesses()

◆ setTargetSite()