SimTK::DuMM Namespace Reference

This namespace is used for symbols which are useful in conjunction with Molmodel's DuMMForceFieldSubsystem. More...

Classes
class	CustomBondStretch
	Abstract base class for custom bond stretch terms, that is, functional forms that apply a distance-based force along a 1-2 bond between a pair of atoms. More...
class	CustomBondBend
	Abstract base class for custom bond bend functions, that is, functional forms that apply an angle-based torque between the two lines formed by a 1-2-3 triple of bonded atoms. More...
class	CustomBondTorsion
	Abstract base class for custom torsion functions, that is, functional forms that apply a dihedral-angle based torque about the middle bond of a 1-2-3-4 quadruple of bonded atoms. More...
class	AtomIndex
	This is the unique integer index that DuMM assigns to atoms as they are added via addAtom(). More...
class	IncludedAtomIndex
	This is the unique integer index that DuMM assigns to atoms that are to be included in force calculations. These represent a subset of all the atoms and you can map from an IncludedAtomIndex to the corresponding AtomIndex. More...
class	NonbondAtomIndex
	This is the unique integer index that DuMM assigns to included atoms that are involved in nonbonded force calculations (Coulomb, van der Waals, and/or GBSA). These represent a subset of all the included atoms and you can map from a NonbondAtomIndex to the corresponding IncludedAtomIndex. More...
class	BondIndex
	This is the unique integer index that DuMM assigns to bonds as they are added via addBond(). More...
class	ClusterIndex
	This is the unique integer index that DuMM assigns to clusters as they are created via createCluster(). More...
class	AtomClassIndex
	This is a unique integer associated with each "atom class", assigned by the user when the atom class is first introduced via defineAtomClass(). More...
class	ChargedAtomTypeIndex
	This is a unique integer associated with each "charged atom type", assigned by the user when the charged atom type is first introduced via defineChargedAtomType(). More...
Functions
	SimTK_DEFINE_UNIQUE_INDEX_TYPE (AtomIndex)
	SimTK_DEFINE_UNIQUE_INDEX_TYPE (IncludedAtomIndex)
	SimTK_DEFINE_UNIQUE_INDEX_TYPE (NonbondAtomIndex)
	SimTK_DEFINE_UNIQUE_INDEX_TYPE (BondIndex)
	SimTK_DEFINE_UNIQUE_INDEX_TYPE (ClusterIndex)
	SimTK_DEFINE_UNIQUE_INDEX_TYPE (AtomClassIndex)
	SimTK_DEFINE_UNIQUE_INDEX_TYPE (ChargedAtomTypeIndex)
Variables
static const Real	Ang2Nm = (Real)0.1L
	angstroms to nanometers
static const Real	Nm2Ang = (Real)10.L
	nanometers to angstroms
static const Real	Deg2Rad = (Real)SimTK_DEGREE_TO_RADIAN
	degrees to radians
static const Real	Rad2Deg = (Real)SimTK_RADIAN_TO_DEGREE
	radians to degrees
static const Real	KJ2Kcal = (Real)SimTK_KJOULE_TO_KCAL
	kilojoules to kilocalories
static const Real	Kcal2KJ = (Real)SimTK_KCAL_TO_KJOULE
	kilocalories to kilojoules
static const Real	Sigma2Radius = (Real)std::pow(2.L, 1.L/6.L)
	half-Sigma to van der Waals radius; caution -- see discussion in module description.
static const Real	Radius2Sigma = (Real)std::pow(2.L, -1.L/6.L)
	van der Waals radius to half-Sigma; caution -- see discussion in module description.

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Detailed Description

This namespace is used for symbols which are useful in conjunction with Molmodel's DuMMForceFieldSubsystem.