protocols::md::Rattle Class Reference

#include <Rattle.hh>

Public Member Functions
	Rattle ()
	Rattle (core::pose::Pose const &pose, core::optimization::CartesianMinimizerMap const &min_map)
	~Rattle ()=default
core::Size	ncst ()
void	run_rattle1 (core::Real const &dt, core::optimization::Multivec &xyz, core::optimization::Multivec &vel, core::optimization::Multivec const &mass)
void	run_rattle2 (core::Real const &dt, core::optimization::Multivec &xyz, core::optimization::Multivec &vel, core::optimization::Multivec const &mass)

Private Member Functions
void	setup_constraint (core::pose::Pose const &pose, core::optimization::CartesianMinimizerMap const &min_map)

Private Attributes
core::Size	maxiter_
core::Real	sor_
utility::vector1< Constraint >	cst_
utility::vector1< bool >	use_
utility::vector1< bool >	moved_
utility::vector1< bool >	update_

Constructor & Destructor Documentation

Rattle() [1/2]

protocols::md::Rattle::Rattle ( )

inline

Rattle() [2/2]

protocols::md::Rattle::Rattle ( core::pose::Pose const &  pose, core::optimization::CartesianMinimizerMap const &  min_map  )

inline

References maxiter_, moved_, core::optimization::CartesianMinimizerMap::natoms(), setup_constraint(), sor_, update_, and use_.

~Rattle()

protocols::md::Rattle::~Rattle ( )

default

Member Function Documentation

ncst()

core::Size protocols::md::Rattle::ncst ( )

inline

References cst_.

Referenced by protocols::md::CartesianMD::do_MD().

run_rattle1()

void protocols::md::Rattle::run_rattle1 ( core::Real const &  dt, core::optimization::Multivec &  xyz, core::optimization::Multivec &  vel, core::optimization::Multivec const &  mass  )

inline

References protocols::md::Constraint::a, protocols::md::Constraint::b, cst_, protocols::md::Constraint::k, core::pose::mass(), maxiter_, moved_, sor_, update_, use_, and protocols::kinmatch::xyz().

Referenced by protocols::md::CartesianMD::VelocityVerlet_Integrator().

run_rattle2()

void protocols::md::Rattle::run_rattle2 ( core::Real const &  dt, core::optimization::Multivec &  xyz, core::optimization::Multivec &  vel, core::optimization::Multivec const &  mass  )

inline

References protocols::md::Constraint::a, protocols::md::Constraint::b, cst_, protocols::md::Constraint::k, core::pose::mass(), maxiter_, moved_, sor_, update_, use_, and protocols::kinmatch::xyz().

Referenced by protocols::md::CartesianMD::VelocityVerlet_Integrator().

setup_constraint()

void protocols::md::Rattle::setup_constraint ( core::pose::Pose const &  pose, core::optimization::CartesianMinimizerMap const &  min_map  )

inlineprivate

References protocols::md::Constraint::a, core::conformation::Residue::atom_base(), core::conformation::Residue::atom_is_hydrogen(), core::id::AtomID::atomno(), protocols::md::Constraint::b, cst_, core::chemical::AtomICoor::d(), core::optimization::CartesianMinimizerMap::get_atom(), core::optimization::CartesianMinimizerMap::get_atom_index(), core::conformation::Residue::icoor(), protocols::md::Constraint::k, core::optimization::CartesianMinimizerMap::natoms(), core::pose::Pose::residue(), core::id::AtomID::rsd(), and use_.

Referenced by Rattle().

Member Data Documentation

cst_

utility::vector1< Constraint > protocols::md::Rattle::cst_

private

Referenced by ncst(), run_rattle1(), run_rattle2(), and setup_constraint().

maxiter_

core::Size protocols::md::Rattle::maxiter_

private

Referenced by Rattle(), run_rattle1(), and run_rattle2().

moved_

utility::vector1< bool > protocols::md::Rattle::moved_

private

Referenced by Rattle(), run_rattle1(), and run_rattle2().

sor_

core::Real protocols::md::Rattle::sor_

private

Referenced by Rattle(), run_rattle1(), and run_rattle2().

update_

utility::vector1< bool > protocols::md::Rattle::update_

private

Referenced by Rattle(), run_rattle1(), and run_rattle2().

use_

utility::vector1< bool > protocols::md::Rattle::use_

private

Referenced by Rattle(), run_rattle1(), run_rattle2(), and setup_constraint().

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

• src/protocols/md/Rattle.hh