Topology Class Reference

#include <topology.hh>

Public Member Functions
	Topology (const std::vector< Real > &masses)
	Topology ()
void	Save (const String &filename)
uint	AddHarmonicBond (uint index_one, uint index_two, Real bond_length, Real force_constant)
uint	AddHarmonicAngle (uint index_one, uint index_two, uint index_three, Real angle, Real force_constant)
uint	AddUreyBradleyAngle (uint index_one, uint index_two, uint index_three, Real angle, Real angle_force_constant, Real bond_length, Real bond_force_constant)
uint	AddPeriodicDihedral (uint index_one, uint index_two, uint index_three, uint index_four, int multiplicity, Real phase, Real force_constant)
uint	AddPeriodicImproper (uint index_one, uint index_two, uint index_three, uint index_four, int multiplicity, Real phase, Real force_constant)
uint	AddHarmonicImproper (uint index_one, uint index_two, uint index_three, uint index_four, Real angle, Real force_constant)
uint	AddCMap (uint index_one, uint index_two, uint index_three, uint index_four, uint index_five, int dimension, std::vector< Real > values)
uint	AddLJPair (uint index_one, uint index_two, Real sigma, Real epsilon)
uint	AddDistanceConstraint (uint index_one, uint index_two, Real distance)
uint	AddExclusion (uint index_one, uint index_two)
void	AddPositionConstraint (uint index)
void	ResetPositionConstraints ()
void	ResetExclusions ()
uint	AddHarmonicPositionRestraint (uint index, const geom::Vec3 &ref_position, Real k, Real x_scale=1.0, Real y_scale=1.0, Real z_scale=1.0)
uint	AddHarmonicDistanceRestraint (uint index_one, uint index_two, Real length, Real force_constant)
uint	AddFGMDHBondDonor (uint index_one, uint index_two, Real length, Real k_length, Real alpha, Real k_alpha, Real beta, Real k_beta)
uint	AddFGMDHBondAcceptor (uint index_one, uint index_two)
void	SetSigmas (const std::vector< Real > &sigmas)
void	SetSigma (uint index, Real sigma)
void	SetEpsilons (const std::vector< Real > &epsilons)
void	SetEpsilon (uint index, Real epsilon)
void	SetGBSARadii (const std::vector< Real > &gbsa_radii)
void	SetGBSARadius (uint index, Real radius)
void	SetOBCScalings (const std::vector< Real > &obc_scaling)
void	SetOBCScaling (uint index, Real scaling)
void	SetCharges (const std::vector< Real > &charges)
void	SetCharge (uint index, Real charge)
void	SetMasses (const std::vector< Real > &masses)
void	SetMass (uint index, Real mass)
void	SetFudgeQQ (Real fudge)
void	SetFudgeLJ (Real fudge)
void	GetHarmonicBondParameters (uint index, uint &index_one, uint &index_two, Real &bond_length, Real &force_constant) const
void	GetHarmonicAngleParameters (uint index, uint &index_one, uint &index_two, uint &index_three, Real &angle, Real &force_constant) const
void	GetUreyBradleyAngleParameters (uint index, uint &index_one, uint &index_two, uint &index_three, Real &angle, Real &angle_force_constant, Real &bond_length, Real &bond_force_constant) const
void	GetPeriodicDihedralParameters (uint index, uint &index_one, uint &index_two, uint &index_three, uint &index_four, int &multiplicity, Real &phase, Real &force_constant) const
void	GetPeriodicImproperParameters (uint index, uint &index_one, uint &index_two, uint &index_three, uint &index_four, int &multiplicity, Real &phase, Real &force_constant) const
void	GetHarmonicImproperParameters (uint index, uint &index_one, uint &index_two, uint &index_three, uint &index_four, Real &angle, Real &force_constant) const
void	GetCMapParameters (uint index, uint &index_one, uint &index_two, uint &index_three, uint &index_four, uint &index_five, int &dimension, std::vector< Real > &map) const
void	GetLJPairParameters (uint index, uint &index_one, uint &index_two, Real &sigma, Real &epsilon) const
void	GetDistanceConstraintParameters (uint index, uint &index_one, uint &index_two, Real &distance) const
void	GetHarmonicPositionRestraintParameters (uint index, uint &atom_index, geom::Vec3 &ref_position, Real &k, Real &x_scale, Real &y_scale, Real &z_scale) const
void	GetHarmonicDistanceRestraintParameters (uint index, uint &atom_one, uint &atom_two, Real &length, Real &force_constant) const
void	GetFGMDHBondDonorParameters (uint index, uint &index_one, uint &index_two, Real &length, Real &k_length, Real &alpha, Real &k_alpha, Real &beta, Real &k_beta) const
void	GetFGMDHBondAcceptorParameters (uint index, uint &index_one, uint &index_two) const
void	SetHarmonicBondParameters (uint index, const Real bond_length, const Real force_constant)
void	SetHarmonicAngleParameters (uint index, const Real angle, const Real force_constant)
void	SetUreyBradleyAngleParameters (uint index, const Real angle, const Real angle_force_constant, const Real bond_length, const Real bond_force_constant)
void	SetPeriodicDihedralParameters (uint index, const int multiplicity, const Real phase, const Real force_constant)
void	SetPeriodicImproperParameters (uint index, const int multiplicity, const Real phase, const Real force_constant)
void	SetHarmonicImproperParameters (uint index, const Real angle, const Real force_constant)
void	SetCMapParameters (uint index, const int dimension, const std::vector< Real > &map)
void	SetLJPairParameters (uint index, const Real sigma, const Real epsilon)
void	SetDistanceConstraintParameters (uint index, const Real distance)
void	SetHarmonicPositionRestraintParameters (uint index, const geom::Vec3 &ref_position, Real k, Real x_scale=1.0, Real y_scale=1.0, Real z_scale=1.0)
void	SetHarmonicDistanceRestraintParameters (uint index, Real length, Real force_constant)
void	SetFGMDHBondDonorParameters (uint index, Real length, Real k_length, Real alpha, Real k_alpha, Real beta, Real k_beta)
const std::vector< std::pair< Index< 2 >, std::vector< Real > > > &	GetHarmonicBonds () const
const std::vector< std::pair< Index< 3 >, std::vector< Real > > > &	GetHarmonicAngles () const
const std::vector< std::pair< Index< 3 >, std::vector< Real > > > &	GetUreyBradleyAngles () const
const std::vector< std::pair< Index< 4 >, std::vector< Real > > > &	GetPeriodicDihedrals () const
const std::vector< std::pair< Index< 4 >, std::vector< Real > > > &	GetPeriodicImpropers () const
const std::vector< std::pair< Index< 4 >, std::vector< Real > > > &	GetHarmonicImpropers () const
const std::vector< std::pair< Index< 5 >, std::vector< Real > > > &	GetCMaps () const
const std::vector< std::pair< Index< 2 >, std::vector< Real > > > &	GetLJPairs () const
const std::vector< std::pair< Index< 2 >, std::vector< Real > > > &	GetDistanceConstraints () const
const std::vector< std::pair< Index< 1 >, std::vector< Real > > > &	GetHarmonicPositionRestraints () const
const std::vector< std::pair< Index< 2 >, std::vector< Real > > > &	GetHarmonicDistanceRestraints () const
const std::vector< Index< 2 > > &	GetExclusions () const
const std::vector< uint > &	GetPositionConstraints () const
const std::vector< std::pair< Index< 2 >, std::vector< Real > > > &	GetFGMDHBondDonors () const
const std::vector< Index< 2 > > &	GetFGMDHBondAcceptors () const
std::vector< Real >	GetSigmas () const
std::vector< Real >	GetEpsilons () const
std::vector< Real >	GetGBSARadii () const
std::vector< Real >	GetOBCScalings () const
std::vector< Real >	GetCharges () const
Real	GetCharge (uint index) const
Real	GetMass (uint index) const
Real	GetSigma (uint index) const
Real	GetEpsilon (uint index) const
Real	GetGBSARadius (uint index) const
Real	GetOBCScaling (uint index) const
std::vector< Real >	GetMasses () const
Real	GetFudgeQQ () const
Real	GetFudgeLJ () const
std::vector< uint >	GetHarmonicBondIndices (uint index_one, uint index_two) const
std::vector< uint >	GetHarmonicAngleIndices (uint index_one, uint index_two, uint index_three) const
std::vector< uint >	GetUreyBradleyAngleIndices (uint index_one, uint index_two, uint index_three) const
std::vector< uint >	GetPeriodicDihedralIndices (uint index_one, uint index_two, uint index_three, uint index_four) const
std::vector< uint >	GetPeriodicImproperIndices (uint index_one, uint index_two, uint index_three, uint index_four) const
std::vector< uint >	GetHarmonicImproperIndices (uint index_one, uint index_two, uint index_three, uint index_four) const
std::vector< uint >	GetCMapIndices (uint index_one, uint index_two, uint index_three, uint index_four, uint index_five) const
int	GetLJPairIndex (uint index_one, uint index_two) const
int	GetDistanceConstraintIndex (uint index_one, uint index_two) const
std::vector< uint >	GetHarmonicDistanceRestraintIndices (uint index_one, uint index_two) const
std::vector< uint >	GetFGMDHBondDonorIndices (uint index_one, uint index_two) const
std::vector< uint >	GetFGMDHBondAcceptorIndices (uint index_one, uint index_two) const
std::vector< uint >	GetHarmonicBondIndices (uint atom_index) const
std::vector< uint >	GetHarmonicAngleIndices (uint atom_index) const
std::vector< uint >	GetUreyBradleyAngleIndices (uint atom_index) const
std::vector< uint >	GetPeriodicDihedralIndices (uint atom_index) const
std::vector< uint >	GetPeriodicImproperIndices (uint atom_index) const
std::vector< uint >	GetHarmonicImproperIndices (uint atom_index) const
std::vector< uint >	GetCMapIndices (uint atom_index) const
std::vector< uint >	GetLJPairIndices (uint atom_index) const
std::vector< uint >	GetDistanceConstraintIndices (uint atom_index) const
std::vector< uint >	GetHarmonicPositionRestraintIndices (uint atom_index) const
std::vector< uint >	GetHarmonicDistanceRestraintIndices (uint atom_index) const
std::vector< uint >	GetFGMDHBondDonorIndices (uint atom_index) const
std::vector< uint >	GetFGMDHBondAcceptorIndices (uint atom_index) const
uint	GetNumParticles ()
uint	GetNumHarmonicBonds ()
uint	GetNumHarmonicAngles ()
uint	GetNumUreyBradleyAngles ()
uint	GetNumPeriodicDihedrals ()
uint	GetNumPeriodicImpropers ()
uint	GetNumHarmonicImpropers ()
uint	GetNumCMaps ()
uint	GetNumLJPairs ()
uint	GetNumDistanceConstraints ()
uint	GetNumPositionConstraints ()
uint	GetNumHarmonicPositionRestraints ()
uint	GetNumHarmonicDistanceRestraints ()
uint	GetNumExclusions ()
uint	GetNumFGMDHBondDonors ()
uint	GetNumFGMDHBondAcceptors ()
void	Merge (ost::mol::EntityHandle &ent, TopologyPtr other, const ost::mol::EntityHandle &other_ent)
void	Merge (TopologyPtr other)
template<typename DS >
void	Serialize (DS &ds)

Static Public Member Functions
static TopologyPtr	Load (const String &filename)

Detailed Description

Definition at line 52 of file topology.hh.

Constructor & Destructor Documentation

Topology() [1/2]

Topology

(

const std::vector< Real > &

masses

)

Topology() [2/2]

Topology ( )

inline

Definition at line 58 of file topology.hh.

Member Function Documentation

AddCMap()

uint AddCMap	(	uint	index_one,
		uint	index_two,
		uint	index_three,
		uint	index_four,
		uint	index_five,
		int	dimension,
		std::vector< Real >	values
	)

AddDistanceConstraint()

uint AddDistanceConstraint	(	uint	index_one,
		uint	index_two,
		Real	distance
	)

AddExclusion()

uint AddExclusion	(	uint	index_one,
		uint	index_two
	)

AddFGMDHBondAcceptor()

uint AddFGMDHBondAcceptor	(	uint	index_one,
		uint	index_two
	)

AddFGMDHBondDonor()

uint AddFGMDHBondDonor	(	uint	index_one,
		uint	index_two,
		Real	length,
		Real	k_length,
		Real	alpha,
		Real	k_alpha,
		Real	beta,
		Real	k_beta
	)

AddHarmonicAngle()

uint AddHarmonicAngle	(	uint	index_one,
		uint	index_two,
		uint	index_three,
		Real	angle,
		Real	force_constant
	)

AddHarmonicBond()

uint AddHarmonicBond	(	uint	index_one,
		uint	index_two,
		Real	bond_length,
		Real	force_constant
	)

AddHarmonicDistanceRestraint()

uint AddHarmonicDistanceRestraint	(	uint	index_one,
		uint	index_two,
		Real	length,
		Real	force_constant
	)

AddHarmonicImproper()

uint AddHarmonicImproper	(	uint	index_one,
		uint	index_two,
		uint	index_three,
		uint	index_four,
		Real	angle,
		Real	force_constant
	)

AddHarmonicPositionRestraint()

uint AddHarmonicPositionRestraint	(	uint	index,
		const geom::Vec3 &	ref_position,
		Real	k,
		Real	x_scale = 1.0,
		Real	y_scale = 1.0,
		Real	z_scale = 1.0
	)

AddLJPair()

uint AddLJPair	(	uint	index_one,
		uint	index_two,
		Real	sigma,
		Real	epsilon
	)

AddPeriodicDihedral()

uint AddPeriodicDihedral	(	uint	index_one,
		uint	index_two,
		uint	index_three,
		uint	index_four,
		int	multiplicity,
		Real	phase,
		Real	force_constant
	)

AddPeriodicImproper()

uint AddPeriodicImproper	(	uint	index_one,
		uint	index_two,
		uint	index_three,
		uint	index_four,
		int	multiplicity,
		Real	phase,
		Real	force_constant
	)

AddPositionConstraint()

void AddPositionConstraint

(

uint

index

)

AddUreyBradleyAngle()

uint AddUreyBradleyAngle	(	uint	index_one,
		uint	index_two,
		uint	index_three,
		Real	angle,
		Real	angle_force_constant,
		Real	bond_length,
		Real	bond_force_constant
	)

GetCharge()

Real GetCharge

(

uint

index

)

const

GetCharges()

std::vector<Real> GetCharges ( ) const

inline

Definition at line 284 of file topology.hh.

GetCMapIndices() [1/2]

std::vector<uint> GetCMapIndices

(

uint

atom_index

)

const

GetCMapIndices() [2/2]

std::vector<uint> GetCMapIndices	(	uint	index_one,
		uint	index_two,
		uint	index_three,
		uint	index_four,
		uint	index_five
	)		const

GetCMapParameters()

void GetCMapParameters	(	uint	index,
		uint &	index_one,
		uint &	index_two,
		uint &	index_three,
		uint &	index_four,
		uint &	index_five,
		int &	dimension,
		std::vector< Real > &	map
	)		const

GetCMaps()

const std::vector<std::pair<Index<5>, std::vector<Real> > >& GetCMaps ( ) const

inline

Definition at line 257 of file topology.hh.

GetDistanceConstraintIndex()

int GetDistanceConstraintIndex	(	uint	index_one,
		uint	index_two
	)		const

GetDistanceConstraintIndices()

std::vector<uint> GetDistanceConstraintIndices

(

uint

atom_index

)

const

GetDistanceConstraintParameters()

void GetDistanceConstraintParameters	(	uint	index,
		uint &	index_one,
		uint &	index_two,
		Real &	distance
	)		const

GetDistanceConstraints()

const std::vector<std::pair<Index<2>, std::vector<Real> > >& GetDistanceConstraints ( ) const

inline

Definition at line 261 of file topology.hh.

GetEpsilon()

Real GetEpsilon

(

uint

index

)

const

GetEpsilons()

std::vector<Real> GetEpsilons ( ) const

inline

Definition at line 278 of file topology.hh.

GetExclusions()

const std::vector<Index<2> >& GetExclusions ( ) const

inline

Definition at line 267 of file topology.hh.

GetFGMDHBondAcceptorIndices() [1/2]

std::vector<uint> GetFGMDHBondAcceptorIndices

(

uint

atom_index

)

const

GetFGMDHBondAcceptorIndices() [2/2]

std::vector<uint> GetFGMDHBondAcceptorIndices	(	uint	index_one,
		uint	index_two
	)		const

GetFGMDHBondAcceptorParameters()

void GetFGMDHBondAcceptorParameters	(	uint	index,
		uint &	index_one,
		uint &	index_two
	)		const

GetFGMDHBondAcceptors()

const std::vector<Index<2> >& GetFGMDHBondAcceptors ( ) const

inline

Definition at line 273 of file topology.hh.

GetFGMDHBondDonorIndices() [1/2]

std::vector<uint> GetFGMDHBondDonorIndices

(

uint

atom_index

)

const

GetFGMDHBondDonorIndices() [2/2]

std::vector<uint> GetFGMDHBondDonorIndices	(	uint	index_one,
		uint	index_two
	)		const

GetFGMDHBondDonorParameters()

void GetFGMDHBondDonorParameters	(	uint	index,
		uint &	index_one,
		uint &	index_two,
		Real &	length,
		Real &	k_length,
		Real &	alpha,
		Real &	k_alpha,
		Real &	beta,
		Real &	k_beta
	)		const

GetFGMDHBondDonors()

const std::vector<std::pair<Index<2>, std::vector<Real> > >& GetFGMDHBondDonors ( ) const

inline

Definition at line 271 of file topology.hh.

GetFudgeLJ()

Real GetFudgeLJ ( ) const

inline

Definition at line 302 of file topology.hh.

GetFudgeQQ()

Real GetFudgeQQ ( ) const

inline

Definition at line 300 of file topology.hh.

GetGBSARadii()

std::vector<Real> GetGBSARadii ( ) const

inline

Definition at line 280 of file topology.hh.

GetGBSARadius()

Real GetGBSARadius

(

uint

index

)

const

GetHarmonicAngleIndices() [1/2]

std::vector<uint> GetHarmonicAngleIndices

(

uint

atom_index

)

const

GetHarmonicAngleIndices() [2/2]

std::vector<uint> GetHarmonicAngleIndices	(	uint	index_one,
		uint	index_two,
		uint	index_three
	)		const

GetHarmonicAngleParameters()

void GetHarmonicAngleParameters	(	uint	index,
		uint &	index_one,
		uint &	index_two,
		uint &	index_three,
		Real &	angle,
		Real &	force_constant
	)		const

GetHarmonicAngles()

const std::vector<std::pair<Index<3>, std::vector<Real> > >& GetHarmonicAngles ( ) const

inline

Definition at line 247 of file topology.hh.

GetHarmonicBondIndices() [1/2]

std::vector<uint> GetHarmonicBondIndices

(

uint

atom_index

)

const

GetHarmonicBondIndices() [2/2]

std::vector<uint> GetHarmonicBondIndices	(	uint	index_one,
		uint	index_two
	)		const

GetHarmonicBondParameters()

void GetHarmonicBondParameters	(	uint	index,
		uint &	index_one,
		uint &	index_two,
		Real &	bond_length,
		Real &	force_constant
	)		const

GetHarmonicBonds()

const std::vector<std::pair<Index<2>, std::vector<Real> > >& GetHarmonicBonds ( ) const

inline

Definition at line 245 of file topology.hh.

GetHarmonicDistanceRestraintIndices() [1/2]

std::vector<uint> GetHarmonicDistanceRestraintIndices

(

uint

atom_index

)

const

GetHarmonicDistanceRestraintIndices() [2/2]

std::vector<uint> GetHarmonicDistanceRestraintIndices	(	uint	index_one,
		uint	index_two
	)		const

GetHarmonicDistanceRestraintParameters()

void GetHarmonicDistanceRestraintParameters	(	uint	index,
		uint &	atom_one,
		uint &	atom_two,
		Real &	length,
		Real &	force_constant
	)		const

GetHarmonicDistanceRestraints()

const std::vector<std::pair<Index<2>, std::vector<Real> > >& GetHarmonicDistanceRestraints ( ) const

inline

Definition at line 265 of file topology.hh.

GetHarmonicImproperIndices() [1/2]

std::vector<uint> GetHarmonicImproperIndices

(

uint

atom_index

)

const

GetHarmonicImproperIndices() [2/2]

std::vector<uint> GetHarmonicImproperIndices	(	uint	index_one,
		uint	index_two,
		uint	index_three,
		uint	index_four
	)		const

GetHarmonicImproperParameters()

void GetHarmonicImproperParameters	(	uint	index,
		uint &	index_one,
		uint &	index_two,
		uint &	index_three,
		uint &	index_four,
		Real &	angle,
		Real &	force_constant
	)		const

GetHarmonicImpropers()

const std::vector<std::pair<Index<4>, std::vector<Real> > >& GetHarmonicImpropers ( ) const

inline

Definition at line 255 of file topology.hh.

GetHarmonicPositionRestraintIndices()

std::vector<uint> GetHarmonicPositionRestraintIndices

(

uint

atom_index

)

const

GetHarmonicPositionRestraintParameters()

void GetHarmonicPositionRestraintParameters	(	uint	index,
		uint &	atom_index,
		geom::Vec3 &	ref_position,
		Real &	k,
		Real &	x_scale,
		Real &	y_scale,
		Real &	z_scale
	)		const

GetHarmonicPositionRestraints()

const std::vector<std::pair<Index<1>, std::vector<Real> > >& GetHarmonicPositionRestraints ( ) const

inline

Definition at line 263 of file topology.hh.

GetLJPairIndex()

int GetLJPairIndex	(	uint	index_one,
		uint	index_two
	)		const

GetLJPairIndices()

std::vector<uint> GetLJPairIndices

(

uint

atom_index

)

const

GetLJPairParameters()

void GetLJPairParameters	(	uint	index,
		uint &	index_one,
		uint &	index_two,
		Real &	sigma,
		Real &	epsilon
	)		const

GetLJPairs()

const std::vector<std::pair<Index<2>, std::vector<Real> > >& GetLJPairs ( ) const

inline

Definition at line 259 of file topology.hh.

GetMass()

Real GetMass

(

uint

index

)

const

GetMasses()

std::vector<Real> GetMasses ( ) const

inline

Definition at line 298 of file topology.hh.

GetNumCMaps()

uint GetNumCMaps ( )

inline

Definition at line 393 of file topology.hh.

GetNumDistanceConstraints()

uint GetNumDistanceConstraints ( )

inline

Definition at line 397 of file topology.hh.

GetNumExclusions()

uint GetNumExclusions ( )

inline

Definition at line 405 of file topology.hh.

GetNumFGMDHBondAcceptors()

uint GetNumFGMDHBondAcceptors ( )

inline

Definition at line 409 of file topology.hh.

GetNumFGMDHBondDonors()

uint GetNumFGMDHBondDonors ( )

inline

Definition at line 407 of file topology.hh.

GetNumHarmonicAngles()

uint GetNumHarmonicAngles ( )

inline

Definition at line 383 of file topology.hh.

GetNumHarmonicBonds()

uint GetNumHarmonicBonds ( )

inline

Definition at line 381 of file topology.hh.

GetNumHarmonicDistanceRestraints()

uint GetNumHarmonicDistanceRestraints ( )

inline

Definition at line 403 of file topology.hh.

GetNumHarmonicImpropers()

uint GetNumHarmonicImpropers ( )

inline

Definition at line 391 of file topology.hh.

GetNumHarmonicPositionRestraints()

uint GetNumHarmonicPositionRestraints ( )

inline

Definition at line 401 of file topology.hh.

GetNumLJPairs()

uint GetNumLJPairs ( )

inline

Definition at line 395 of file topology.hh.

GetNumParticles()

uint GetNumParticles ( )

inline

Definition at line 379 of file topology.hh.

GetNumPeriodicDihedrals()

uint GetNumPeriodicDihedrals ( )

inline

Definition at line 387 of file topology.hh.

GetNumPeriodicImpropers()

uint GetNumPeriodicImpropers ( )

inline

Definition at line 389 of file topology.hh.

GetNumPositionConstraints()

uint GetNumPositionConstraints ( )

inline

Definition at line 399 of file topology.hh.

GetNumUreyBradleyAngles()

uint GetNumUreyBradleyAngles ( )

inline

Definition at line 385 of file topology.hh.

GetOBCScaling()

Real GetOBCScaling

(

uint

index

)

const

GetOBCScalings()

std::vector<Real> GetOBCScalings ( ) const

inline

Definition at line 282 of file topology.hh.

GetPeriodicDihedralIndices() [1/2]

std::vector<uint> GetPeriodicDihedralIndices

(

uint

atom_index

)

const

GetPeriodicDihedralIndices() [2/2]

std::vector<uint> GetPeriodicDihedralIndices	(	uint	index_one,
		uint	index_two,
		uint	index_three,
		uint	index_four
	)		const

GetPeriodicDihedralParameters()

void GetPeriodicDihedralParameters	(	uint	index,
		uint &	index_one,
		uint &	index_two,
		uint &	index_three,
		uint &	index_four,
		int &	multiplicity,
		Real &	phase,
		Real &	force_constant
	)		const

GetPeriodicDihedrals()

const std::vector<std::pair<Index<4>, std::vector<Real> > >& GetPeriodicDihedrals ( ) const

inline

Definition at line 251 of file topology.hh.

GetPeriodicImproperIndices() [1/2]

std::vector<uint> GetPeriodicImproperIndices

(

uint

atom_index

)

const

GetPeriodicImproperIndices() [2/2]

std::vector<uint> GetPeriodicImproperIndices	(	uint	index_one,
		uint	index_two,
		uint	index_three,
		uint	index_four
	)		const

GetPeriodicImproperParameters()

void GetPeriodicImproperParameters	(	uint	index,
		uint &	index_one,
		uint &	index_two,
		uint &	index_three,
		uint &	index_four,
		int &	multiplicity,
		Real &	phase,
		Real &	force_constant
	)		const

GetPeriodicImpropers()

const std::vector<std::pair<Index<4>, std::vector<Real> > >& GetPeriodicImpropers ( ) const

inline

Definition at line 253 of file topology.hh.

GetPositionConstraints()

const std::vector<uint>& GetPositionConstraints ( ) const

inline

Definition at line 269 of file topology.hh.

GetSigma()

Real GetSigma

(

uint

index

)

const

GetSigmas()

std::vector<Real> GetSigmas ( ) const

inline

Definition at line 276 of file topology.hh.

GetUreyBradleyAngleIndices() [1/2]

std::vector<uint> GetUreyBradleyAngleIndices

(

uint

atom_index

)

const

GetUreyBradleyAngleIndices() [2/2]

std::vector<uint> GetUreyBradleyAngleIndices	(	uint	index_one,
		uint	index_two,
		uint	index_three
	)		const

GetUreyBradleyAngleParameters()

void GetUreyBradleyAngleParameters	(	uint	index,
		uint &	index_one,
		uint &	index_two,
		uint &	index_three,
		Real &	angle,
		Real &	angle_force_constant,
		Real &	bond_length,
		Real &	bond_force_constant
	)		const

GetUreyBradleyAngles()

const std::vector<std::pair<Index<3>, std::vector<Real> > >& GetUreyBradleyAngles ( ) const

inline

Definition at line 249 of file topology.hh.

Load()

static TopologyPtr Load ( const String &  filename )

static

Merge() [1/2]

void Merge	(	ost::mol::EntityHandle &	ent,
		TopologyPtr	other,
		const ost::mol::EntityHandle &	other_ent
	)

Merge() [2/2]

void Merge

(

TopologyPtr

other

)

ResetExclusions()

void ResetExclusions ( )

inline

Definition at line 132 of file topology.hh.

ResetPositionConstraints()

void ResetPositionConstraints ( )

inline

Definition at line 130 of file topology.hh.

Save()

void Save

(

const String &

filename

)

Serialize()

void Serialize ( DS &  ds )

inline

Definition at line 416 of file topology.hh.

SetCharge()

void SetCharge	(	uint	index,
		Real	charge
	)

SetCharges()

void SetCharges

(

const std::vector< Real > &

charges

)

SetCMapParameters()

void SetCMapParameters	(	uint	index,
		const int	dimension,
		const std::vector< Real > &	map
	)

SetDistanceConstraintParameters()

void SetDistanceConstraintParameters	(	uint	index,
		const Real	distance
	)

SetEpsilon()

void SetEpsilon	(	uint	index,
		Real	epsilon
	)

SetEpsilons()

void SetEpsilons

(

const std::vector< Real > &

epsilons

)

SetFGMDHBondDonorParameters()

void SetFGMDHBondDonorParameters	(	uint	index,
		Real	length,
		Real	k_length,
		Real	alpha,
		Real	k_alpha,
		Real	beta,
		Real	k_beta
	)

SetFudgeLJ()

void SetFudgeLJ ( Real  fudge )

inline

Definition at line 173 of file topology.hh.

SetFudgeQQ()

void SetFudgeQQ ( Real  fudge )

inline

Definition at line 171 of file topology.hh.

SetGBSARadii()

void SetGBSARadii

(

const std::vector< Real > &

gbsa_radii

)

SetGBSARadius()

void SetGBSARadius	(	uint	index,
		Real	radius
	)

SetHarmonicAngleParameters()

void SetHarmonicAngleParameters	(	uint	index,
		const Real	angle,
		const Real	force_constant
	)

SetHarmonicBondParameters()

void SetHarmonicBondParameters	(	uint	index,
		const Real	bond_length,
		const Real	force_constant
	)

SetHarmonicDistanceRestraintParameters()

void SetHarmonicDistanceRestraintParameters	(	uint	index,
		Real	length,
		Real	force_constant
	)

SetHarmonicImproperParameters()

void SetHarmonicImproperParameters	(	uint	index,
		const Real	angle,
		const Real	force_constant
	)

SetHarmonicPositionRestraintParameters()

void SetHarmonicPositionRestraintParameters	(	uint	index,
		const geom::Vec3 &	ref_position,
		Real	k,
		Real	x_scale = 1.0,
		Real	y_scale = 1.0,
		Real	z_scale = 1.0
	)

SetLJPairParameters()

void SetLJPairParameters	(	uint	index,
		const Real	sigma,
		const Real	epsilon
	)

SetMass()

void SetMass	(	uint	index,
		Real	mass
	)

SetMasses()

void SetMasses

(

const std::vector< Real > &

masses

)

SetOBCScaling()

void SetOBCScaling	(	uint	index,
		Real	scaling
	)

SetOBCScalings()

void SetOBCScalings

(

const std::vector< Real > &

obc_scaling

)

SetPeriodicDihedralParameters()

void SetPeriodicDihedralParameters	(	uint	index,
		const int	multiplicity,
		const Real	phase,
		const Real	force_constant
	)

SetPeriodicImproperParameters()

void SetPeriodicImproperParameters	(	uint	index,
		const int	multiplicity,
		const Real	phase,
		const Real	force_constant
	)

SetSigma()

void SetSigma	(	uint	index,
		Real	sigma
	)

SetSigmas()

void SetSigmas

(

const std::vector< Real > &

sigmas

)

SetUreyBradleyAngleParameters()

void SetUreyBradleyAngleParameters	(	uint	index,
		const Real	angle,
		const Real	angle_force_constant,
		const Real	bond_length,
		const Real	bond_force_constant
	)

---

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

• build-2.9.0-doc/stage/include/ost/mol/mm/topology.hh