OpenStructure
Public Member Functions | Static Public Member Functions
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< RealGetSigmas () const
 
std::vector< RealGetEpsilons () const
 
std::vector< RealGetGBSARadii () const
 
std::vector< RealGetOBCScalings () const
 
std::vector< RealGetCharges () 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< RealGetMasses () const
 
Real GetFudgeQQ () const
 
Real GetFudgeLJ () const
 
std::vector< uintGetHarmonicBondIndices (uint index_one, uint index_two) const
 
std::vector< uintGetHarmonicAngleIndices (uint index_one, uint index_two, uint index_three) const
 
std::vector< uintGetUreyBradleyAngleIndices (uint index_one, uint index_two, uint index_three) const
 
std::vector< uintGetPeriodicDihedralIndices (uint index_one, uint index_two, uint index_three, uint index_four) const
 
std::vector< uintGetPeriodicImproperIndices (uint index_one, uint index_two, uint index_three, uint index_four) const
 
std::vector< uintGetHarmonicImproperIndices (uint index_one, uint index_two, uint index_three, uint index_four) const
 
std::vector< uintGetCMapIndices (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< uintGetHarmonicDistanceRestraintIndices (uint index_one, uint index_two) const
 
std::vector< uintGetFGMDHBondDonorIndices (uint index_one, uint index_two) const
 
std::vector< uintGetFGMDHBondAcceptorIndices (uint index_one, uint index_two) const
 
std::vector< uintGetHarmonicBondIndices (uint atom_index) const
 
std::vector< uintGetHarmonicAngleIndices (uint atom_index) const
 
std::vector< uintGetUreyBradleyAngleIndices (uint atom_index) const
 
std::vector< uintGetPeriodicDihedralIndices (uint atom_index) const
 
std::vector< uintGetPeriodicImproperIndices (uint atom_index) const
 
std::vector< uintGetHarmonicImproperIndices (uint atom_index) const
 
std::vector< uintGetCMapIndices (uint atom_index) const
 
std::vector< uintGetLJPairIndices (uint atom_index) const
 
std::vector< uintGetDistanceConstraintIndices (uint atom_index) const
 
std::vector< uintGetHarmonicPositionRestraintIndices (uint atom_index) const
 
std::vector< uintGetHarmonicDistanceRestraintIndices (uint atom_index) const
 
std::vector< uintGetFGMDHBondDonorIndices (uint atom_index) const
 
std::vector< uintGetFGMDHBondAcceptorIndices (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: