A versatile object for collecting the parameters and scope of applicability of any molecular mechanics force field term. This relies on enumerations to inform whether the term applies to atom types or atom and residue names and the nature of the term. More...

#include <forcefield_element.h>

Public Member Functions
ParameterKind	getKind () const
	Get the force field parameter kind.

char4	getNameOfAtom (char atom_rank='I') const
	Get the atom name of the I atom in the term.

char4	getTypeOfAtom (char atom_rank='I') const
	Get the atom type of atom I in the term.

char4	getNameOfResidue (char atom_rank='I') const
	Get the resiude name of atom I in the term.

double	getCharge () const
	Get the charge of an atom with a given atom name and residue nam.

double	getSigma () const
	Get the Lennard-Jones sigma parameter of an atom.

double	getEpsilon () const
	Get the Lennard-Jones epsilon parameter of an atom.

double	getRho () const
	Get the Lennard-Jones rho parameter of an atom (the third parameter, for 12-6-4 potentials)

double	getStiffnessConstant () const
	Get the stiffness constant of a bond, angle, Urey-Bradley, or CHARMM improper term.

double	getEquilibriumConstant () const
	Get the equilibrium constant of a bond, angle, or Urey-Bradley term.

double	getAmplitude () const
	Get the amplitude of a cosine-based dihedral term.

double	getPhaseAngle () const
	Get the phase angle of a cosine-based dihedral or CHARMM improper dihedral term.

double	getPeriodicity () const
	Get the periodicity of a cosine-based dihedral term.

double	getElectrostaticScaling () const
	Get the electrostatic scaling factor for an attenuated 1:4 non-bonded interaction.

double	getVanDerWaalsScaling () const
	Get the van-der Waals scaling factor for an attenuated 1:4 non-bonded interaction.

TorsionKind	getTorsionKind () const
	Get the torsion kind, indicating whether these four atoms describe a proper or improper torsion interaction.

std::vector< double >	getSurfaceValues () const
	Get the surface value edits associated with a CMAP term.

std::vector< int2 >	getSurfaceIndices () const
	Get the locations of point edits on a CMAP term's energy surface.

VirtualSiteKind	getVirtualSiteFrameType () const
	Get the virtual site frame type.

bool	testSigmaModification () const
	Test whether the sigma value of a van-der Waals parameter is being modified.

bool	testEpsilonModification () const
	Test whether the epsilon value of a van-der Waals parameter is being modified.

bool	testRhoModification () const
	Test whether the rho value of a van-der Waals parameter is being modified.

bool	testStiffnessModification () const
	Test whether the stiffness constant of a valence parameter is being modified.

bool	testEquilibriumModification () const
	Test whether the equilibrium constant of a valence parameter is being modified.

bool	testAmplitudeModification () const
	Test whether the amplitude of a dihedral parameter is being modified.

bool	testPhaseAngleModification () const
	Test whether the phase angle of a dihedral or improper dihedral is being modified.

bool	testPeriodicityModification () const
	Test whether the periodicity of a dihedral parameter is being modified.

void	setStiffness (double stiffness_in)
	Set the stiffness property of one of the valence terms.

void	setEquilibrium (double equilbrium_in)
	Set the equilibrium property of one of the valence terms.

void	setPhaseAngle (double phase_angle_in)
	Set the phase angle property of one of the valence terms.

void	setAmplitude (double amplitude_in)
	Set the amplitude of a cosine-based dihedral term.

void	setPeriodicity (double periodicity_in)
	Set the periodicity of a cosine-based dihedral term.

void	setChargeScaling (double scaling_in)
	Set the electrostatic scaling factor for an attenuated 1:4 interaction.

void	setVanDerWaalsScaling (double scaling_in)
	Set the van-der Waals scaling factor for an attenuated 1:4 interaction.

void	setCharge (double charge_in)
	Set the charge parameter of an atom.

void	setSigma (double sigma_in)
	Set the sigma parameter of an atom.

void	setEpsilon (double epsilon_in)
	Set the epsilon parameter of an atom.

void	setRho (double rho_in)
	Set the rho parameter of an atom.

void	apply (AtomGraph *ag, ExceptionResponse policy=ExceptionResponse::SILENT) const
	Apply these force field parameters to any terms found in a specific topology.


	ForceFieldElement (ParameterKind kind_in=ParameterKind::NONE)
	A variety of constructors can load one or more atoms and their properties.

	ForceFieldElement (ParameterKind kind_in, char4 atom_i_in)

	ForceFieldElement (ParameterKind kind_in, char4 atom_i_in, char4 atom_j_in)

	ForceFieldElement (ParameterKind kind_in, char4 atom_i_in, char4 atom_j_in, char4 atom_k_in)

	ForceFieldElement (ParameterKind kind_in, char4 atom_i_in, char4 atom_j_in, char4 atom_k_in, char4 atom_l_in, TorsionKind tkind_in=TorsionKind::PROPER)

	ForceFieldElement (ParameterKind kind_in, VirtualSiteKind frame_type_in, char4 atom_i_in, char4 atom_j_in, char4 atom_k_in, char4 residue_i_in, char4 residue_j_in, char4 residue_k_in)

	ForceFieldElement (ParameterKind kind_in, VirtualSiteKind frame_type_in, char4 atom_i_in, char4 atom_j_in, char4 atom_k_in, char4 atom_l_in, char4 residue_i_in, char4 residue_j_in, char4 residue_k_in, char4 residue_l_in)

	ForceFieldElement (ParameterKind kind_in, VirtualSiteKind frame_type_in, char4 atom_i_in, char4 atom_j_in, char4 atom_k_in, char4 atom_l_in, char4 atom_m_in, char4 residue_i_in, char4 residue_j_in, char4 residue_k_in, char4 residue_l_in, char4 residue_m_in)

	ForceFieldElement (ParameterKind kind_in, char4 atom_i_in, char4 atom_j_in, char4 atom_k_in, char4 atom_l_in, char4 atom_m_in, char4 residue_i_in, char4 residue_j_in, char4 residue_k_in, char4 residue_l_in, char4 residue_m_in, const std::vector< double > &surface_in, const std::vector< int2 > &locations_in)

Detailed Description

A versatile object for collecting the parameters and scope of applicability of any molecular mechanics force field term. This relies on enumerations to inform whether the term applies to atom types or atom and residue names and the nature of the term.

Constructor & Destructor Documentation

◆ ForceFieldElement()

stormm::modeling::ForceFieldElement::ForceFieldElement ( ParameterKind kind_in = ParameterKind::NONE )

A variety of constructors can load one or more atoms and their properties.

Overloaded:

Create an empty element with only a ParameterKind (default NONE)
Load non-bonded terms describing a specific atom
Load valence terms describing a bond, angle, dihedral, Urey-Bradley, or CHARMM improper
Load an entire CMAP surface
Load a virtual site with frame specifications

Parameters

kind_in	The kind of force field parameter, obligatory for every constructor
atom_i_in	Name or type of atom I in the term
atom_j_in	Name or type of atom J in the term
atom_k_in	Name or type of atom K in the term
atom_l_in	Name or type of atom L in the term
atom_m_in	Name or type of atom M in the term
resi_i_in	Name or type of residue I in the term
resi_j_in	Name or type of residue J in the term
resi_k_in	Name or type of residue K in the term
resi_l_in	Name or type of residue L in the term
resi_m_in	Name or type of residue M in the term
surface_in	Surface values for an entire CMAP
frame_type_in	Frame type of the virtual site, if that is what this object contains

Member Function Documentation

◆ apply()

void stormm::modeling::ForceFieldElement::apply	(	AtomGraph *	ag,
		ExceptionResponse	policy = ExceptionResponse::SILENT ) const

Apply these force field parameters to any terms found in a specific topology.