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protocols::cartesian::MolecularDynamics Class Reference

#include <md.hh>

Public Member Functions

 MolecularDynamics (core::pose::PoseOP &inputpose, core::scoring::ScoreFunction const &scorefxn)
 
void doMinimising (core::scoring::ScoreFunction const &scorefxn)
 
void doMD (core::scoring::ScoreFunction const &scorefxn, int Steps, float startTemp, float endTemp)
 
void testCartesianDerivatives (core::scoring::ScoreFunction const &scorefxn)
 

Private Member Functions

void createCartesianArray ()
 
void setCartesianPositionsFromPose ()
 
void setPosePositionsFromCartesian ()
 
void zeroForces ()
 
int findCartomAtom (const core::id::AtomID &id1)
 
void getCartesianDerivatives (core::scoring::ScoreFunction const &scorefxn)
 
void createBondList ()
 
void createAngleList ()
 
void createDihedralList ()
 Yes i know this is hard coded stuff. Read warning at the top of this file. More...
 
MD_HarmonicDihedral createDihedral (const core::conformation::Residue &rsd, std::string const &name1, std::string const &name2, std::string const &name3, std::string const &name4)
 
MD_HarmonicDihedral createDihedral (const core::conformation::Residue &rsd1, const core::conformation::Residue &rsd2, const core::conformation::Residue &rsd3, const core::conformation::Residue &rsd4, std::string const &name1, std::string const &name2, std::string const &name3, std::string const &name4)
 
void setDihedralDerivatives ()
 
void doBondDerivatives (float &totalepot)
 
void doAngleDerivatives (float &totalepot)
 
void doDihedralDerivatives (float &totalepot)
 
void createCartesianDerivatives (core::pose::Pose &pose, core::scoring::ScoreFunction const &scorefxn)
 
void setInitialSpeeds (core::Real tgtTemp)
 
void calcKineticEnergy (float &ekin, float &Temp)
 
void applyForces_BeeMan (float &kin, float &temp)
 
void applyForces_LangevinIntegration (core::Real T, float &kin, float &temp)
 
void applyForces_ConjugateGradient (int Step, float &current_energy, float &m_OldEnergy)
 
void createCartesianDerivatives (core::scoring::ScoreFunction const &scorefxn)
 

Private Attributes

utility::vector1< CartesianAtom > cartom
 
utility::vector1< MD_Bond > bondlist
 
utility::vector1< MD_Angle > anglelist
 
utility::vector1< MD_HarmonicDihedral > dihedrallist
 
core::kinematics::MoveMap mm
 
core::optimization::MinimizerMap min_map
 
core::kinematics::DomainMap domain_map
 
core::pose::PoseOP pose
 

Constructor & Destructor Documentation

◆ MolecularDynamics()

protocols::cartesian::MolecularDynamics::MolecularDynamics ( core::pose::PoseOP &  inputpose,
core::scoring::ScoreFunction const &  scorefxn 
)

References createAngleList(), createBondList(), createCartesianArray(), createDihedralList(), core::optimization::MinimizerMap::domain_map(), min_map, mm, pose, core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), setDihedralDerivatives(), core::optimization::MinimizerMap::setup(), and core::scoring::ScoreFunction::setup_for_minimizing().

Member Function Documentation

◆ applyForces_BeeMan()

void protocols::cartesian::MolecularDynamics::applyForces_BeeMan ( float &  kin,
float &  temp 
)
private

References calcKineticEnergy(), cartom, and protocols::hybridization::t.

◆ applyForces_ConjugateGradient()

void protocols::cartesian::MolecularDynamics::applyForces_ConjugateGradient ( int  Step,
float &  current_energy,
float &  m_OldEnergy 
)
private

References cartom.

Referenced by doMinimising().

◆ applyForces_LangevinIntegration()

void protocols::cartesian::MolecularDynamics::applyForces_LangevinIntegration ( core::Real  T,
float &  kin,
float &  temp 
)
private

References calcKineticEnergy(), cartom, protocols::simple_filters::gt, protocols::cartesian::sqr(), and protocols::hybridization::t.

Referenced by doMD().

◆ calcKineticEnergy()

void protocols::cartesian::MolecularDynamics::calcKineticEnergy ( float &  ekin,
float &  Temp 
)
private

References cartom.

Referenced by applyForces_BeeMan(), and applyForces_LangevinIntegration().

◆ createAngleList()

void protocols::cartesian::MolecularDynamics::createAngleList ( )
private

References anglelist, protocols::cartesian::MD_Angle::atom_id_1, protocols::cartesian::MD_Angle::atom_id_2, protocols::cartesian::MD_Angle::atom_id_3, bondlist, cartom, protocols::cartesian::MD_Angle::index1, protocols::cartesian::MD_Angle::index2, protocols::cartesian::MD_Angle::index3, protocols::cartesian::MD_Angle::length, and pose.

Referenced by MolecularDynamics().

◆ createBondList()

void protocols::cartesian::MolecularDynamics::createBondList ( )
private

References protocols::cartesian::MD_Bond::atom_id_1, protocols::cartesian::MD_Bond::atom_id_2, core::conformation::Residue::bonded_neighbor(), bondlist, cartom, core::conformation::Residue::connect_atom(), protocols::cartesian::MD_Bond::index1, protocols::cartesian::MD_Bond::index2, core::conformation::Residue::is_bonded(), protocols::cartesian::MD_Bond::length, and pose.

Referenced by MolecularDynamics().

◆ createCartesianArray()

void protocols::cartesian::MolecularDynamics::createCartesianArray ( )
private

References protocols::cartesian::CartesianAtom::atom_id, cartom, protocols::cartesian::CartesianAtom::force, protocols::cartesian::CartesianAtom::index, protocols::cartesian::CartesianAtom::mass, core::conformation::Residue::natoms(), protocols::cartesian::CartesianAtom::old_force, protocols::cartesian::CartesianAtom::old_position, protocols::cartesian::CartesianAtom::old_velocity, pose, protocols::cartesian::CartesianAtom::position, protocols::cartesian::CartesianAtom::res, and protocols::cartesian::CartesianAtom::velocity.

Referenced by MolecularDynamics(), and testCartesianDerivatives().

◆ createCartesianDerivatives() [1/2]

void protocols::cartesian::MolecularDynamics::createCartesianDerivatives ( core::pose::Pose &  pose,
core::scoring::ScoreFunction const &  scorefxn 
)
private

◆ createCartesianDerivatives() [2/2]

void protocols::cartesian::MolecularDynamics::createCartesianDerivatives ( core::scoring::ScoreFunction const &  scorefxn)
private

References protocols::cartesian::CartesianAtom::atom_id, cartom, core::optimization::MinimizerMap::domain_map(), core::scoring::ScoreFunction::eval_npd_atom_derivative(), protocols::cartesian::CartesianAtom::force, protocols::cartesian::CartesianAtom::index, protocols::cartesian::CartesianAtom::mass, min_map, core::conformation::Residue::natoms(), protocols::cartesian::CartesianAtom::old_force, protocols::cartesian::CartesianAtom::old_position, protocols::cartesian::CartesianAtom::old_velocity, pose, protocols::cartesian::CartesianAtom::position, protocols::cartesian::CartesianAtom::res, core::scoring::ScoreFunction::setup_for_derivatives(), and protocols::cartesian::CartesianAtom::velocity.

◆ createDihedral() [1/2]

MD_HarmonicDihedral protocols::cartesian::MolecularDynamics::createDihedral ( const core::conformation::Residue &  rsd,
std::string const &  name1,
std::string const &  name2,
std::string const &  name3,
std::string const &  name4 
)
private

Referenced by createDihedralList().

◆ createDihedral() [2/2]

MD_HarmonicDihedral protocols::cartesian::MolecularDynamics::createDihedral ( const core::conformation::Residue &  rsd1,
const core::conformation::Residue &  rsd2,
const core::conformation::Residue &  rsd3,
const core::conformation::Residue &  rsd4,
std::string const &  name1,
std::string const &  name2,
std::string const &  name3,
std::string const &  name4 
)
private

References protocols::cartesian::MD_HarmonicDihedral::angle, protocols::cartesian::MD_HarmonicDihedral::atom_id_1, protocols::cartesian::MD_HarmonicDihedral::atom_id_2, protocols::cartesian::MD_HarmonicDihedral::atom_id_3, protocols::cartesian::MD_HarmonicDihedral::atom_id_4, core::conformation::Residue::atom_index(), core::id::AtomID::atomno(), findCartomAtom(), protocols::cartesian::MD_HarmonicDihedral::index1, protocols::cartesian::MD_HarmonicDihedral::index2, protocols::cartesian::MD_HarmonicDihedral::index3, protocols::cartesian::MD_HarmonicDihedral::index4, core::id::AtomID::rsd(), and core::conformation::Residue::seqpos().

◆ createDihedralList()

void protocols::cartesian::MolecularDynamics::createDihedralList ( )
private

Yes i know this is hard coded stuff. Read warning at the top of this file.

References core::conformation::Residue::aa(), core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_his, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_trp, core::chemical::aa_tyr, createDihedral(), dihedrallist, core::conformation::Residue::has(), and pose.

Referenced by MolecularDynamics().

◆ doAngleDerivatives()

void protocols::cartesian::MolecularDynamics::doAngleDerivatives ( float &  totalepot)
private

References anglelist, cartom, pose, and protocols::cartesian::sqr().

Referenced by doMD(), and doMinimising().

◆ doBondDerivatives()

void protocols::cartesian::MolecularDynamics::doBondDerivatives ( float &  totalepot)
private

References bondlist, cartom, pose, and protocols::cartesian::sqr().

Referenced by doMD(), and doMinimising().

◆ doDihedralDerivatives()

void protocols::cartesian::MolecularDynamics::doDihedralDerivatives ( float &  totalepot)
private

References cartom, dihedrallist, and protocols::cartesian::sqr().

Referenced by doMD(), and doMinimising().

◆ doMD()

void protocols::cartesian::MolecularDynamics::doMD ( core::scoring::ScoreFunction const &  scorefxn,
int  Steps,
float  startTemp,
float  endTemp 
)

References applyForces_LangevinIntegration(), doAngleDerivatives(), doBondDerivatives(), doDihedralDerivatives(), protocols::abinitio::filename(), getCartesianDerivatives(), core::chemical::element::I, protocols::mean_field::max(), core::conformation::membrane::out, pose, setInitialSpeeds(), and setPosePositionsFromCartesian().

◆ doMinimising()

void protocols::cartesian::MolecularDynamics::doMinimising ( core::scoring::ScoreFunction const &  scorefxn)

References applyForces_ConjugateGradient(), doAngleDerivatives(), doBondDerivatives(), doDihedralDerivatives(), protocols::abinitio::filename(), getCartesianDerivatives(), core::chemical::element::I, core::conformation::membrane::out, pose, setPosePositionsFromCartesian(), and zeroForces().

◆ findCartomAtom()

int protocols::cartesian::MolecularDynamics::findCartomAtom ( const core::id::AtomID &  id1)
private

References core::id::AtomID::atomno(), cartom, and core::id::AtomID::rsd().

Referenced by createDihedral(), and getCartesianDerivatives().

◆ getCartesianDerivatives()

void protocols::cartesian::MolecularDynamics::getCartesianDerivatives ( core::scoring::ScoreFunction const &  scorefxn)
private

References core::optimization::MinimizerMap::begin(), cartom, core::optimization::DOF_Node::dof_id(), core::optimization::MinimizerMap::domain_map(), core::optimization::MinimizerMap::end(), core::scoring::ScoreFunction::eval_dof_derivative(), core::scoring::ScoreFunction::eval_npd_atom_derivative(), findCartomAtom(), min_map, core::conformation::Residue::natoms(), pose, core::scoring::ScoreFunction::setup_for_derivatives(), and core::optimization::DOF_Node::torsion_id().

Referenced by doMD(), doMinimising(), and testCartesianDerivatives().

◆ setCartesianPositionsFromPose()

void protocols::cartesian::MolecularDynamics::setCartesianPositionsFromPose ( )
private

References cartom, and pose.

◆ setDihedralDerivatives()

void protocols::cartesian::MolecularDynamics::setDihedralDerivatives ( )
private

References cartom, dihedrallist, and protocols::cartesian::sqr().

Referenced by MolecularDynamics().

◆ setInitialSpeeds()

void protocols::cartesian::MolecularDynamics::setInitialSpeeds ( core::Real  tgtTemp)
private

References cartom, and core::pose::mass().

Referenced by doMD().

◆ setPosePositionsFromCartesian()

void protocols::cartesian::MolecularDynamics::setPosePositionsFromCartesian ( )
private

References cartom, and pose.

Referenced by doMD(), and doMinimising().

◆ testCartesianDerivatives()

void protocols::cartesian::MolecularDynamics::testCartesianDerivatives ( core::scoring::ScoreFunction const &  scorefxn)

References cartom, createCartesianArray(), getCartesianDerivatives(), core::conformation::Residue::natoms(), pose, and core::scoring::ScoreFunction::show().

◆ zeroForces()

void protocols::cartesian::MolecularDynamics::zeroForces ( )
private

References cartom.

Referenced by doMinimising().

Member Data Documentation

◆ anglelist

utility::vector1< MD_Angle > protocols::cartesian::MolecularDynamics::anglelist
private

Referenced by createAngleList(), and doAngleDerivatives().

◆ bondlist

utility::vector1< MD_Bond > protocols::cartesian::MolecularDynamics::bondlist
private

Referenced by createAngleList(), createBondList(), and doBondDerivatives().

◆ cartom

utility::vector1< CartesianAtom > protocols::cartesian::MolecularDynamics::cartom
private

Referenced by applyForces_BeeMan(), applyForces_ConjugateGradient(), applyForces_LangevinIntegration(), calcKineticEnergy(), createAngleList(), createBondList(), createCartesianArray(), createCartesianDerivatives(), doAngleDerivatives(), doBondDerivatives(), doDihedralDerivatives(), findCartomAtom(), getCartesianDerivatives(), setCartesianPositionsFromPose(), setDihedralDerivatives(), setInitialSpeeds(), setPosePositionsFromCartesian(), testCartesianDerivatives(), and zeroForces().

◆ dihedrallist

utility::vector1< MD_HarmonicDihedral > protocols::cartesian::MolecularDynamics::dihedrallist
private

Referenced by createDihedralList(), doDihedralDerivatives(), and setDihedralDerivatives().

◆ domain_map

core::kinematics::DomainMap protocols::cartesian::MolecularDynamics::domain_map
private

◆ min_map

core::optimization::MinimizerMap protocols::cartesian::MolecularDynamics::min_map
private

Referenced by createCartesianDerivatives(), getCartesianDerivatives(), and MolecularDynamics().

◆ mm

core::kinematics::MoveMap protocols::cartesian::MolecularDynamics::mm
private

Referenced by MolecularDynamics().

◆ pose

core::pose::PoseOP protocols::cartesian::MolecularDynamics::pose
private

Referenced by createAngleList(), createBondList(), createCartesianArray(), createCartesianDerivatives(), createDihedralList(), doAngleDerivatives(), doBondDerivatives(), doMD(), doMinimising(), getCartesianDerivatives(), MolecularDynamics(), setCartesianPositionsFromPose(), setPosePositionsFromCartesian(), and testCartesianDerivatives().

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