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 name1, std::string name2, std::string name3, std::string 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 name1, std::string name2, std::string name3, std::string 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 (double tgtTemp)
void	calcKineticEnergy (float &ekin, float &Temp)
void	applyForces_BeeMan (float &kin, float &temp)
void	applyForces_LangevinIntegration (double 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

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

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

Member Function Documentation

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

private

References calcKineticEnergy(), cartom, protocols::comparative_modeling::features::E, and t.

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

private

References cartom, and numeric::xyzVector< class >::dot().

Referenced by doMinimising().

void protocols::cartesian::MolecularDynamics::applyForces_LangevinIntegration ( double  T, float &  kin, float &  temp  )

private

References calcKineticEnergy(), cartom, protocols::comparative_modeling::features::E, numeric::random::gaussian(), protocols::cartesian::sqr(), and t.

Referenced by doMD().

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

private

References cartom, and inner_product().

Referenced by applyForces_BeeMan(), and applyForces_LangevinIntegration().

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, numeric::xyzVector< class >::distance(), protocols::cartesian::MD_Angle::index1, protocols::cartesian::MD_Angle::index2, protocols::cartesian::MD_Angle::index3, j, protocols::cartesian::MD_Angle::length, pose, and core::pose::Pose::xyz().

Referenced by MolecularDynamics().

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(), numeric::xyzVector< class >::distance(), protocols::cartesian::MD_Bond::index1, protocols::cartesian::MD_Bond::index2, j, protocols::cartesian::MD_Bond::length, nres, pose, core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

Referenced by MolecularDynamics().

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, nres, 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::pose::Pose::residue(), core::pose::Pose::total_residue(), protocols::cartesian::CartesianAtom::velocity, and core::pose::Pose::xyz().

Referenced by MolecularDynamics(), and testCartesianDerivatives().

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

private

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

private

References protocols::cartesian::CartesianAtom::atom_id, cartom, core::optimization::MinimizerMap::domain_map(), protocols::cartesian::CartesianAtom::force, protocols::cartesian::CartesianAtom::index, protocols::cartesian::CartesianAtom::mass, min_map, nres, 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::pose::Pose::residue(), core::pose::Pose::total_residue(), and protocols::cartesian::CartesianAtom::velocity.

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

private

References protocols::cartesian::MD_HarmonicDihedral::atom_id_1, core::conformation::Residue::atom_index(), exit, findCartomAtom(), and core::conformation::Residue::seqpos().

Referenced by createDihedralList().

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  name1, std::string  name2, std::string  name3, std::string  name4  )

private

References protocols::cartesian::MD_HarmonicDihedral::atom_id_1, core::conformation::Residue::atom_index(), exit, findCartomAtom(), and core::conformation::Residue::seqpos().

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(), createDihedral(), dihedrallist, core::conformation::Residue::has(), pose, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by MolecularDynamics().

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

private

References anglelist, cartom, numeric::xyzVector< class >::distance(), length, pose, protocols::cartesian::sqr(), and core::pose::Pose::xyz().

Referenced by doMD(), and doMinimising().

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

private

References bondlist, cartom, numeric::xyzVector< class >::distance(), length, pose, protocols::cartesian::sqr(), and core::pose::Pose::xyz().

Referenced by doMD(), and doMinimising().

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

private

References cartom, dihedrallist, protocols::stepwise::sampling::protein::phi(), protocols::cartesian::sqr(), numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by doMD(), and doMinimising().

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

References applyForces_LangevinIntegration(), doAngleDerivatives(), doBondDerivatives(), doDihedralDerivatives(), core::pose::Pose::dump_pdb(), filename(), getCartesianDerivatives(), protocols::abinitio::abscript::I, pose, setInitialSpeeds(), and setPosePositionsFromCartesian().

void protocols::cartesian::MolecularDynamics::doMinimising

(

core::scoring::ScoreFunction const &

scorefxn

)

References applyForces_ConjugateGradient(), doAngleDerivatives(), doBondDerivatives(), doDihedralDerivatives(), core::pose::Pose::dump_pdb(), filename(), getCartesianDerivatives(), protocols::abinitio::abscript::I, pose, setPosePositionsFromCartesian(), and zeroForces().

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().

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

private

References core::optimization::MinimizerMap::begin(), cartom, core::pose::Pose::conformation(), core::optimization::DOF_Node::dof_id(), core::optimization::MinimizerMap::domain_map(), core::optimization::MinimizerMap::end(), findCartomAtom(), core::conformation::Conformation::get_torsion_angle_atom_ids(), min_map, nres, pose, core::pose::Pose::residue(), protocols::cartesian::sqr(), core::optimization::DOF_Node::torsion_id(), core::pose::Pose::total_residue(), and numeric::xyzVector< class >::x().

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

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

private

References cartom, pose, and core::pose::Pose::xyz().

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

private

References cartom, dihedrallist, protocols::stepwise::sampling::protein::phi(), protocols::cartesian::sqr(), numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by MolecularDynamics().

void protocols::cartesian::MolecularDynamics::setInitialSpeeds ( double  tgtTemp )

private

References cartom, protocols::comparative_modeling::features::E, numeric::random::gaussian(), and mass().

Referenced by doMD().

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

private

References cartom, pose, and core::pose::Pose::set_xyz().

Referenced by doMD(), and doMinimising().

void protocols::cartesian::MolecularDynamics::testCartesianDerivatives

(

core::scoring::ScoreFunction const &

scorefxn

)

References cartom, core::scoring::Energies::clear(), createCartesianArray(), core::pose::Pose::energies(), getCartesianDerivatives(), nres, pose, core::scoring::Energies::reset_nblist(), core::pose::Pose::residue(), core::pose::Pose::set_xyz(), core::pose::Pose::total_residue(), numeric::xyzVector< class >::x(), core::pose::Pose::xyz(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

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

private

References cartom.

Referenced by doMinimising().

Member Data Documentation

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

private

Referenced by createAngleList(), and doAngleDerivatives().

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

private

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

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().

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

private

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

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

private

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

private

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

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

private

Referenced by MolecularDynamics().

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:

• symlinks/rosetta/src/protocols/cartesian/md.hh
• symlinks/rosetta/src/protocols/cartesian/md.cc