#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< 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) |
Definition at line 53 of file topology.hh.
Topology | ( | ) | [inline] |
Definition at line 59 of file topology.hh.
uint AddCMap | ( | uint | index_one, | |
uint | index_two, | |||
uint | index_three, | |||
uint | index_four, | |||
uint | index_five, | |||
int | dimension, | |||
std::vector< Real > | values | |||
) |
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 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 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 | ) |
std::vector<Real> GetCharges | ( | ) | const [inline] |
Definition at line 299 of file topology.hh.
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.
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.
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.
const std::vector<Index<2> >& GetFGMDHBondAcceptors | ( | ) | const [inline] |
Definition at line 286 of file topology.hh.
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.
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.
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.
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 | 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.
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.
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.
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.
std::vector<Real> GetOBCScalings | ( | ) | const [inline] |
Definition at line 297 of file topology.hh.
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 | 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.
std::vector<Real> GetSigmas | ( | ) | const [inline] |
Definition at line 291 of file topology.hh.
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 SetCharges | ( | const std::vector< Real > & | charges | ) |
void SetDensity | ( | const ost::img::ImageHandle & | d, | |
Real | r, | |||
Real | s = 1.0 | |||
) |
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 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 SetMasses | ( | const std::vector< Real > & | masses | ) |
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 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 | |||
) |