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 SetDensity (const ost::img::ImageHandle &d, Real r, Real s=1.0)
void DefineDensityBody (const std::vector< int > &indices)
int GetNumDensityBodies () const
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
ost::img::ImageHandle GetDensity ()
Real GetDensityResolution ()
Real GetDensityScaling ()
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
const std::vector< std::vector
< int > > & 
GetDensityBodies () 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 53 of file topology.hh.


Constructor & Destructor Documentation

Topology ( const std::vector< Real > &  masses  ) 
Topology (  )  [inline]

Definition at line 59 of file topology.hh.


Member Function Documentation

uint AddCMap ( uint  index_one,
uint  index_two,
uint  index_three,
uint  index_four,
uint  index_five,
int  dimension,
std::vector< Real values 
)
uint AddDistanceConstraint ( uint  index_one,
uint  index_two,
Real  distance 
)
uint AddExclusion ( uint  index_one,
uint  index_two 
)
uint AddFGMDHBondAcceptor ( uint  index_one,
uint  index_two 
)
uint AddFGMDHBondDonor ( uint  index_one,
uint  index_two,
Real  length,
Real  k_length,
Real  alpha,
Real  k_alpha,
Real  beta,
Real  k_beta 
)
uint AddHarmonicAngle ( uint  index_one,
uint  index_two,
uint  index_three,
Real  angle,
Real  force_constant 
)
uint AddHarmonicBond ( uint  index_one,
uint  index_two,
Real  bond_length,
Real  force_constant 
)
uint AddHarmonicDistanceRestraint ( uint  index_one,
uint  index_two,
Real  length,
Real  force_constant 
)
uint AddHarmonicImproper ( uint  index_one,
uint  index_two,
uint  index_three,
uint  index_four,
Real  angle,
Real  force_constant 
)
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 AddLJPair ( uint  index_one,
uint  index_two,
Real  sigma,
Real  epsilon 
)
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 
)
void AddPositionConstraint ( uint  index  ) 
uint AddUreyBradleyAngle ( uint  index_one,
uint  index_two,
uint  index_three,
Real  angle,
Real  angle_force_constant,
Real  bond_length,
Real  bond_force_constant 
)
void DefineDensityBody ( const std::vector< int > &  indices  ) 
Real GetCharge ( uint  index  )  const
std::vector<Real> GetCharges (  )  const [inline]

Definition at line 299 of file topology.hh.

std::vector<uint> GetCMapIndices ( uint  atom_index  )  const
std::vector<uint> GetCMapIndices ( uint  index_one,
uint  index_two,
uint  index_three,
uint  index_four,
uint  index_five 
) 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
const std::vector<std::pair<Index<5>, std::vector<Real> > >& GetCMaps (  )  const [inline]

Definition at line 270 of file topology.hh.

ost::img::ImageHandle GetDensity (  )  [inline]

Definition at line 222 of file topology.hh.

const std::vector<std::vector<int> >& GetDensityBodies (  )  const [inline]

Definition at line 288 of file topology.hh.

Real GetDensityResolution (  )  [inline]

Definition at line 224 of file topology.hh.

Real GetDensityScaling (  )  [inline]

Definition at line 226 of file topology.hh.

int GetDistanceConstraintIndex ( uint  index_one,
uint  index_two 
) const
std::vector<uint> GetDistanceConstraintIndices ( uint  atom_index  )  const
void GetDistanceConstraintParameters ( uint  index,
uint index_one,
uint index_two,
Real distance 
) const
const std::vector<std::pair<Index<2>, std::vector<Real> > >& GetDistanceConstraints (  )  const [inline]

Definition at line 274 of file topology.hh.

Real GetEpsilon ( uint  index  )  const
std::vector<Real> GetEpsilons (  )  const [inline]

Definition at line 293 of file topology.hh.

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

Definition at line 280 of file topology.hh.

std::vector<uint> GetFGMDHBondAcceptorIndices ( uint  atom_index  )  const
std::vector<uint> GetFGMDHBondAcceptorIndices ( uint  index_one,
uint  index_two 
) const
void GetFGMDHBondAcceptorParameters ( uint  index,
uint index_one,
uint index_two 
) const
const std::vector<Index<2> >& GetFGMDHBondAcceptors (  )  const [inline]

Definition at line 286 of file topology.hh.

std::vector<uint> GetFGMDHBondDonorIndices ( uint  atom_index  )  const
std::vector<uint> GetFGMDHBondDonorIndices ( uint  index_one,
uint  index_two 
) 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
const std::vector<std::pair<Index<2>, std::vector<Real> > >& GetFGMDHBondDonors (  )  const [inline]

Definition at line 284 of file topology.hh.

Real GetFudgeLJ (  )  const [inline]

Definition at line 317 of file topology.hh.

Real GetFudgeQQ (  )  const [inline]

Definition at line 315 of file topology.hh.

std::vector<Real> GetGBSARadii (  )  const [inline]

Definition at line 295 of file topology.hh.

Real GetGBSARadius ( uint  index  )  const
std::vector<uint> GetHarmonicAngleIndices ( uint  atom_index  )  const
std::vector<uint> GetHarmonicAngleIndices ( uint  index_one,
uint  index_two,
uint  index_three 
) const
void GetHarmonicAngleParameters ( uint  index,
uint index_one,
uint index_two,
uint index_three,
Real angle,
Real force_constant 
) const
const std::vector<std::pair<Index<3>, std::vector<Real> > >& GetHarmonicAngles (  )  const [inline]

Definition at line 260 of file topology.hh.

std::vector<uint> GetHarmonicBondIndices ( uint  atom_index  )  const
std::vector<uint> GetHarmonicBondIndices ( uint  index_one,
uint  index_two 
) const
void GetHarmonicBondParameters ( uint  index,
uint index_one,
uint index_two,
Real bond_length,
Real force_constant 
) const
const std::vector<std::pair<Index<2>, std::vector<Real> > >& GetHarmonicBonds (  )  const [inline]

Definition at line 258 of file topology.hh.

std::vector<uint> GetHarmonicDistanceRestraintIndices ( uint  atom_index  )  const
std::vector<uint> GetHarmonicDistanceRestraintIndices ( uint  index_one,
uint  index_two 
) const
void GetHarmonicDistanceRestraintParameters ( uint  index,
uint atom_one,
uint atom_two,
Real length,
Real force_constant 
) const
const std::vector<std::pair<Index<2>, std::vector<Real> > >& GetHarmonicDistanceRestraints (  )  const [inline]

Definition at line 278 of file topology.hh.

std::vector<uint> GetHarmonicImproperIndices ( uint  atom_index  )  const
std::vector<uint> GetHarmonicImproperIndices ( uint  index_one,
uint  index_two,
uint  index_three,
uint  index_four 
) const
void GetHarmonicImproperParameters ( uint  index,
uint index_one,
uint index_two,
uint index_three,
uint index_four,
Real angle,
Real force_constant 
) const
const std::vector<std::pair<Index<4>, std::vector<Real> > >& GetHarmonicImpropers (  )  const [inline]

Definition at line 268 of file topology.hh.

std::vector<uint> GetHarmonicPositionRestraintIndices ( uint  atom_index  )  const
void GetHarmonicPositionRestraintParameters ( uint  index,
uint atom_index,
geom::Vec3 ref_position,
Real k,
Real x_scale,
Real y_scale,
Real z_scale 
) const
const std::vector<std::pair<Index<1>, std::vector<Real> > >& GetHarmonicPositionRestraints (  )  const [inline]

Definition at line 276 of file topology.hh.

int GetLJPairIndex ( uint  index_one,
uint  index_two 
) const
std::vector<uint> GetLJPairIndices ( uint  atom_index  )  const
void GetLJPairParameters ( uint  index,
uint index_one,
uint index_two,
Real sigma,
Real epsilon 
) const
const std::vector<std::pair<Index<2>, std::vector<Real> > >& GetLJPairs (  )  const [inline]

Definition at line 272 of file topology.hh.

Real GetMass ( uint  index  )  const
std::vector<Real> GetMasses (  )  const [inline]

Definition at line 313 of file topology.hh.

uint GetNumCMaps (  )  [inline]

Definition at line 408 of file topology.hh.

int GetNumDensityBodies (  )  const [inline]

Definition at line 135 of file topology.hh.

uint GetNumDistanceConstraints (  )  [inline]

Definition at line 412 of file topology.hh.

uint GetNumExclusions (  )  [inline]

Definition at line 420 of file topology.hh.

uint GetNumFGMDHBondAcceptors (  )  [inline]

Definition at line 424 of file topology.hh.

uint GetNumFGMDHBondDonors (  )  [inline]

Definition at line 422 of file topology.hh.

uint GetNumHarmonicAngles (  )  [inline]

Definition at line 398 of file topology.hh.

uint GetNumHarmonicBonds (  )  [inline]

Definition at line 396 of file topology.hh.

uint GetNumHarmonicDistanceRestraints (  )  [inline]

Definition at line 418 of file topology.hh.

uint GetNumHarmonicImpropers (  )  [inline]

Definition at line 406 of file topology.hh.

uint GetNumHarmonicPositionRestraints (  )  [inline]

Definition at line 416 of file topology.hh.

uint GetNumLJPairs (  )  [inline]

Definition at line 410 of file topology.hh.

uint GetNumParticles (  )  [inline]

Definition at line 394 of file topology.hh.

uint GetNumPeriodicDihedrals (  )  [inline]

Definition at line 402 of file topology.hh.

uint GetNumPeriodicImpropers (  )  [inline]

Definition at line 404 of file topology.hh.

uint GetNumPositionConstraints (  )  [inline]

Definition at line 414 of file topology.hh.

uint GetNumUreyBradleyAngles (  )  [inline]

Definition at line 400 of file topology.hh.

Real GetOBCScaling ( uint  index  )  const
std::vector<Real> GetOBCScalings (  )  const [inline]

Definition at line 297 of file topology.hh.

std::vector<uint> GetPeriodicDihedralIndices ( uint  atom_index  )  const
std::vector<uint> GetPeriodicDihedralIndices ( uint  index_one,
uint  index_two,
uint  index_three,
uint  index_four 
) 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
const std::vector<std::pair<Index<4>, std::vector<Real> > >& GetPeriodicDihedrals (  )  const [inline]

Definition at line 264 of file topology.hh.

std::vector<uint> GetPeriodicImproperIndices ( uint  atom_index  )  const
std::vector<uint> GetPeriodicImproperIndices ( uint  index_one,
uint  index_two,
uint  index_three,
uint  index_four 
) 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
const std::vector<std::pair<Index<4>, std::vector<Real> > >& GetPeriodicImpropers (  )  const [inline]

Definition at line 266 of file topology.hh.

const std::vector<uint>& GetPositionConstraints (  )  const [inline]

Definition at line 282 of file topology.hh.

Real GetSigma ( uint  index  )  const
std::vector<Real> GetSigmas (  )  const [inline]

Definition at line 291 of file topology.hh.

std::vector<uint> GetUreyBradleyAngleIndices ( uint  atom_index  )  const
std::vector<uint> GetUreyBradleyAngleIndices ( uint  index_one,
uint  index_two,
uint  index_three 
) 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
const std::vector<std::pair<Index<3>, std::vector<Real> > >& GetUreyBradleyAngles (  )  const [inline]

Definition at line 262 of file topology.hh.

static TopologyPtr Load ( const String filename  )  [static]
void Merge ( TopologyPtr  other  ) 
void Merge ( ost::mol::EntityHandle ent,
TopologyPtr  other,
const ost::mol::EntityHandle other_ent 
)
void ResetExclusions (  )  [inline]

Definition at line 139 of file topology.hh.

void ResetPositionConstraints (  )  [inline]

Definition at line 137 of file topology.hh.

void Save ( const String filename  ) 
void Serialize ( DS &  ds  )  [inline]

Definition at line 431 of file topology.hh.

void SetCharge ( uint  index,
Real  charge 
)
void SetCharges ( const std::vector< Real > &  charges  ) 
void SetCMapParameters ( uint  index,
const int  dimension,
const std::vector< Real > &  map 
)
void SetDensity ( const ost::img::ImageHandle d,
Real  r,
Real  s = 1.0 
)
void SetDistanceConstraintParameters ( uint  index,
const Real  distance 
)
void SetEpsilon ( uint  index,
Real  epsilon 
)
void SetEpsilons ( const std::vector< Real > &  epsilons  ) 
void SetFGMDHBondDonorParameters ( uint  index,
Real  length,
Real  k_length,
Real  alpha,
Real  k_alpha,
Real  beta,
Real  k_beta 
)
void SetFudgeLJ ( Real  fudge  )  [inline]

Definition at line 180 of file topology.hh.

void SetFudgeQQ ( Real  fudge  )  [inline]

Definition at line 178 of file topology.hh.

void SetGBSARadii ( const std::vector< Real > &  gbsa_radii  ) 
void SetGBSARadius ( uint  index,
Real  radius 
)
void SetHarmonicAngleParameters ( uint  index,
const Real  angle,
const Real  force_constant 
)
void SetHarmonicBondParameters ( uint  index,
const Real  bond_length,
const Real  force_constant 
)
void SetHarmonicDistanceRestraintParameters ( uint  index,
Real  length,
Real  force_constant 
)
void SetHarmonicImproperParameters ( uint  index,
const Real  angle,
const Real  force_constant 
)
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 SetLJPairParameters ( uint  index,
const Real  sigma,
const Real  epsilon 
)
void SetMass ( uint  index,
Real  mass 
)
void SetMasses ( const std::vector< Real > &  masses  ) 
void SetOBCScaling ( uint  index,
Real  scaling 
)
void SetOBCScalings ( const std::vector< Real > &  obc_scaling  ) 
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 SetSigma ( uint  index,
Real  sigma 
)
void SetSigmas ( const std::vector< Real > &  sigmas  ) 
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:
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