protocols::normalmode::NormalMode Class Reference

#include <NormalMode.hh>

Public Member Functions
	NormalMode ()
	NormalMode (std::string const mode, core::Real distcut)
	~NormalMode ()
void	set_harmonic_constants (core::Real const &k_uniform)
void	set_harmonic_constants (core::Real const &k_short, core::Real const &k_SS, core::Real const &k_long)
void	set_torsions_using (core::Size const seqpos)
void	clear_torsions_using ()
void	torsion (bool const bool_in, bool const use_phi=true, bool const use_psi=true, bool const eckart_correction=true)
void	eckart_correction (bool const bool_in)
void	solve (core::pose::Pose const &pose)
bool	torsion () const
core::Size	natm () const
core::Size	ntor () const
core::Size	nmode () const
std::string	mode () const
core::Real	dist2_cut () const
utility::vector1 < core::id::AtomID >	get_atomID () const
utility::vector1 < core::id::TorsionID >	get_torID () const
utility::vector1 < utility::vector1 < core::Vector > >	get_eigvec_cart () const
utility::vector1< core::Vector >	get_eigvec_cart (core::Size const imode) const
utility::vector1 < utility::vector1< core::Real > >	get_eigvec_tor () const
utility::vector1< core::Real >	get_eigvec_tor (core::Size const imode) const
utility::vector1< core::Real >	get_eigval () const
core::Real	get_eigval (core::Size const imode) const
utility::vector1< core::Real >	get_importance () const
core::Real	get_importance (core::Size const imode) const
core::Real	get_k (core::Size const i, core::Size const j) const
core::Vector	xyz (core::Size const i) const
core::Size	a_to_i (core::Size const a) const
core::Size	i_to_a (core::Size const i) const

Private Member Functions
void	prepare_coord (core::pose::Pose const &pose)
void	set_harmonic_constant_map (core::pose::Pose const &pose)
utility::vector1 < utility::vector1< core::Real > >	make_Hessian_ANM ()
utility::vector1 < utility::vector1< core::Real > >	make_Hessian_TNM ()
utility::vector1 < utility::vector1< core::Real > >	convert_to_torsion_crd (utility::vector1< utility::vector1< core::Real > > const &U)
void	update_inertia_tensor (core::Size const a, core::Real &Ma, core::Vector &Ra, numeric::MathMatrix< core::Real > &Icorr, numeric::MathMatrix< core::Real > &Ia, utility::vector1< core::Vector > const xyz_com)
void	calculate_Jacobi_correction (core::Size const a, core::Real const &Ma, core::Vector const &Ra, core::Real const &Msum, numeric::MathMatrix< core::Real > const &Ia, numeric::MathMatrix< core::Real > const &i_Isum, core::Vector &Aa, core::Vector &ta)
numeric::MathMatrix< core::Real >	calc_inertia_tensor (numeric::MathMatrix< core::Real > const Icorr, core::Vector const &Ra, core::Real const Msum)
void	eigsrt (utility::vector1< utility::vector1< core::Real > > &eigvec, utility::vector1< core::Real > &eigval)

Private Attributes
bool	torsion_
std::string	mode_
core::Real	dist2_cut_
bool	use_uniform_k_
core::Real	k_uniform_
core::Real	k_short_
core::Real	k_SS_
core::Real	k_long_
bool	use_phi_
bool	use_psi_
bool	eckart_correction_
utility::vector1< core::Size >	torsions_using_
bool	torsions_using_assigned_
utility::vector1 < utility::vector1< core::Real > >	k_
utility::vector1< core::Size >	a_to_i_
utility::vector1< core::Size >	i_to_a_
utility::vector1< core::Vector >	e_
utility::vector1< core::Vector >	s_
utility::vector1< core::Vector >	tau_
utility::vector1< core::Vector >	xyz_
utility::vector1< core::Real >	importance_
utility::vector1 < core::id::AtomID >	atomID_
utility::vector1 < core::id::TorsionID >	torID_
utility::vector1< core::Real >	eigval_
utility::vector1 < utility::vector1 < core::Vector > >	eigvec_cart_
utility::vector1 < utility::vector1< core::Real > >	eigvec_tor_

Constructor & Destructor Documentation

protocols::normalmode::NormalMode::NormalMode

(

)

protocols::normalmode::NormalMode::NormalMode	(	std::string const	mode,
		core::Real	distcut
	)

protocols::normalmode::NormalMode::~NormalMode ( )

default

Member Function Documentation

core::Size protocols::normalmode::NormalMode::a_to_i ( core::Size const  a ) const

inline

References core::pose::motif::a(), and a_to_i_.

numeric::MathMatrix< Real > protocols::normalmode::NormalMode::calc_inertia_tensor ( numeric::MathMatrix< core::Real > const  Icorr, core::Vector const &  Ra, core::Real const  Msum  )

private

References protocols::hybridization::r2.

void protocols::normalmode::NormalMode::calculate_Jacobi_correction ( core::Size const  a, core::Real const &  Ma, core::Vector const &  Ra, core::Real const &  Msum, numeric::MathMatrix< core::Real > const &  Ia, numeric::MathMatrix< core::Real > const &  i_Isum, core::Vector &  Aa, core::Vector &  ta  )

private

References core::pose::motif::a().

void protocols::normalmode::NormalMode::clear_torsions_using ( )

inline

References torsions_using_, and torsions_using_assigned_.

Referenced by protocols::normalmode::NormalModeRelaxMover::initialize_NM_for_movemap().

utility::vector1< utility::vector1< Real > > protocols::normalmode::NormalMode::convert_to_torsion_crd ( utility::vector1< utility::vector1< core::Real > > const &  U )

private

References core::pose::motif::a(), core::chemical::element::Ra, core::chemical::element::U, and protocols::kinmatch::xyz().

core::Real protocols::normalmode::NormalMode::dist2_cut ( ) const

inline

References dist2_cut_.

void protocols::normalmode::NormalMode::eckart_correction ( bool const  bool_in )

inline

References eckart_correction_.

void protocols::normalmode::NormalMode::eigsrt ( utility::vector1< utility::vector1< core::Real > > &  eigvec, utility::vector1< core::Real > &  eigval  )

private

utility::vector1< core::id::AtomID > protocols::normalmode::NormalMode::get_atomID ( ) const

inline

References atomID_.

utility::vector1< core::Real > protocols::normalmode::NormalMode::get_eigval ( ) const

inline

References eigval_.

core::Real protocols::normalmode::NormalMode::get_eigval ( core::Size const  imode ) const

inline

References eigval_, and torsion().

utility::vector1< utility::vector1< core::Vector > > protocols::normalmode::NormalMode::get_eigvec_cart ( ) const

inline

References eigvec_cart_.

utility::vector1< core::Vector > protocols::normalmode::NormalMode::get_eigvec_cart ( core::Size const  imode ) const

inline

References eigvec_cart_.

utility::vector1< utility::vector1< core::Real > > protocols::normalmode::NormalMode::get_eigvec_tor ( ) const

inline

References eigvec_tor_.

Referenced by protocols::normalmode::NormalModeMultifunc::dEddofs_to_dEdvars(), protocols::normalmode::NormalModeMultifunc::dofs_to_vars(), and protocols::normalmode::NormalModeMultifunc::vars_to_dofs().

utility::vector1< core::Real > protocols::normalmode::NormalMode::get_eigvec_tor ( core::Size const  imode ) const

inline

References eigvec_tor_.

utility::vector1< core::Real > protocols::normalmode::NormalMode::get_importance ( ) const

inline

References importance_.

Referenced by protocols::normalmode::NormalModeRelaxMover::set_random_mode().

core::Real protocols::normalmode::NormalMode::get_importance ( core::Size const  imode ) const

inline

References importance_.

core::Real protocols::normalmode::NormalMode::get_k ( core::Size const  i, core::Size const  j  ) const

inline

References k_.

utility::vector1< core::id::TorsionID > protocols::normalmode::NormalMode::get_torID ( ) const

inline

References torID_.

Referenced by protocols::normalmode::NormalModeRelaxMover::extrapolate_mode_on_pose(), protocols::normalmode::NormalModeMultifunc::get_dofs_map(), and protocols::normalmode::NormalModeMultifunc::vars_to_dofs().

core::Size protocols::normalmode::NormalMode::i_to_a ( core::Size const  i ) const

inline

References i_to_a_.

utility::vector1< utility::vector1< Real > > protocols::normalmode::NormalMode::make_Hessian_ANM ( )

private

References core::chemical::element::H, protocols::TR(), and protocols::kinmatch::xyz().

utility::vector1< utility::vector1< Real > > protocols::normalmode::NormalMode::make_Hessian_TNM ( )

private

References protocols::normalmode::ContactStruct::c21, core::scoring::co, protocols::normalmode::ContactStruct::d2, core::chemical::element::H, protocols::normalmode::ContactStruct::k, protocols::normalmode::ContactStruct::r21, protocols::normalmode::ContactStruct::tor1, protocols::normalmode::ContactStruct::tor2, protocols::TR(), and protocols::kinmatch::xyz().

std::string protocols::normalmode::NormalMode::mode ( ) const

inline

References mode_.

core::Size protocols::normalmode::NormalMode::natm ( ) const

inline

References xyz_.

Referenced by protocols::normalmode::NormalModeRelaxMover::extrapolate_mode_on_crd(), protocols::normalmode::NormalModeRelaxMover::gen_coord_constraint(), and nmode().

core::Size protocols::normalmode::NormalMode::nmode ( ) const

inline

References natm(), ntor(), and torsion().

core::Size protocols::normalmode::NormalMode::ntor ( ) const

inline

References e_.

Referenced by protocols::normalmode::NormalModeMultifunc::dofs_to_vars(), protocols::normalmode::NormalModeRelaxMover::extrapolate_mode_on_pose(), nmode(), protocols::normalmode::NormalModeMultifunc::NormalModeMultifunc(), and protocols::normalmode::NormalModeMultifunc::set_default_modes().

void protocols::normalmode::NormalMode::prepare_coord ( core::pose::Pose const &  pose )

private

References core::id::BB, core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::TR().

void protocols::normalmode::NormalMode::set_harmonic_constant_map ( core::pose::Pose const &  pose )

private

References protocols::simple_filters::dssp(), core::conformation::Residue::has(), core::scoring::dssp::Dssp::insert_ss_into_pose(), core::conformation::Residue::is_protein(), core::pose::Pose::residue(), core::pose::Pose::secstruct(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

void protocols::normalmode::NormalMode::set_harmonic_constants

(

core::Real const &

k_uniform

)

Referenced by protocols::normalmode::NormalModeRelaxMover::set_harmonic_constants().

void protocols::normalmode::NormalMode::set_harmonic_constants	(	core::Real const &	k_short,
		core::Real const &	k_SS,
		core::Real const &	k_long
	)

void protocols::normalmode::NormalMode::set_torsions_using ( core::Size const  seqpos )

inline

References torsions_using_, and torsions_using_assigned_.

Referenced by protocols::normalmode::NormalModeRelaxMover::initialize_NM_for_movemap().

void protocols::normalmode::NormalMode::solve

(

core::pose::Pose const &

pose

)

References protocols::TR(), and core::chemical::element::U.

Referenced by protocols::normalmode::NormalModeMinimizer::apply(), and protocols::normalmode::NormalModeRelaxMover::apply_on_pose().

void protocols::normalmode::NormalMode::torsion	(	bool const	bool_in,
		bool const	use_phi = true,
		bool const	use_psi = true,
		bool const	eckart_correction = true
	)

Referenced by protocols::normalmode::NormalModeMinimizer::apply(), protocols::normalmode::NormalModeMultifunc::NormalModeMultifunc(), protocols::normalmode::NormalModeRelaxMover::NormalModeRelaxMover(), and protocols::normalmode::NormalModeRelaxMover::parse_my_tag().

bool protocols::normalmode::NormalMode::torsion ( ) const

inline

References torsion_.

Referenced by get_eigval(), and nmode().

void protocols::normalmode::NormalMode::update_inertia_tensor ( core::Size const  a, core::Real &  Ma, core::Vector &  Ra, numeric::MathMatrix< core::Real > &  Icorr, numeric::MathMatrix< core::Real > &  Ia, utility::vector1< core::Vector > const  xyz_com  )

private

References core::sequence::end, and protocols::loops::start.

core::Vector protocols::normalmode::NormalMode::xyz ( core::Size const  i ) const

inline

References xyz_.

Member Data Documentation

utility::vector1< core::Size > protocols::normalmode::NormalMode::a_to_i_

private

Referenced by a_to_i().

utility::vector1< core::id::AtomID > protocols::normalmode::NormalMode::atomID_

private

Referenced by get_atomID().

core::Real protocols::normalmode::NormalMode::dist2_cut_

private

Referenced by dist2_cut().

utility::vector1< core::Vector > protocols::normalmode::NormalMode::e_

private

Referenced by ntor().

bool protocols::normalmode::NormalMode::eckart_correction_

private

Referenced by eckart_correction().

utility::vector1< core::Real > protocols::normalmode::NormalMode::eigval_

private

Referenced by get_eigval().

utility::vector1< utility::vector1< core::Vector > > protocols::normalmode::NormalMode::eigvec_cart_

private

Referenced by get_eigvec_cart().

utility::vector1< utility::vector1< core::Real > > protocols::normalmode::NormalMode::eigvec_tor_

private

Referenced by get_eigvec_tor().

utility::vector1< core::Size > protocols::normalmode::NormalMode::i_to_a_

private

Referenced by i_to_a().

utility::vector1< core::Real > protocols::normalmode::NormalMode::importance_

private

Referenced by get_importance().

utility::vector1< utility::vector1< core::Real > > protocols::normalmode::NormalMode::k_

private

Referenced by get_k().

core::Real protocols::normalmode::NormalMode::k_long_

private

core::Real protocols::normalmode::NormalMode::k_short_

private

core::Real protocols::normalmode::NormalMode::k_SS_

private

core::Real protocols::normalmode::NormalMode::k_uniform_

private

std::string protocols::normalmode::NormalMode::mode_

private

Referenced by mode().

utility::vector1< core::Vector > protocols::normalmode::NormalMode::s_

private

utility::vector1< core::Vector > protocols::normalmode::NormalMode::tau_

private

utility::vector1< core::id::TorsionID > protocols::normalmode::NormalMode::torID_

private

Referenced by get_torID().

bool protocols::normalmode::NormalMode::torsion_

private

Referenced by torsion().

utility::vector1< core::Size > protocols::normalmode::NormalMode::torsions_using_

private

Referenced by clear_torsions_using(), and set_torsions_using().

bool protocols::normalmode::NormalMode::torsions_using_assigned_

private

Referenced by clear_torsions_using(), and set_torsions_using().

bool protocols::normalmode::NormalMode::use_phi_

private

bool protocols::normalmode::NormalMode::use_psi_

private

bool protocols::normalmode::NormalMode::use_uniform_k_

private

utility::vector1< core::Vector > protocols::normalmode::NormalMode::xyz_

private

Referenced by natm(), and xyz().

---

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

• src/protocols/normalmode/NormalMode.hh
• src/protocols/normalmode/NormalMode.cc