|
| 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) |
|