protocols::normalmode::NormalMode Class Reference

#include <NormalMode.hh>

Public Member Functions
	NormalMode ()
	NormalMode (std::string const mode, Real distcut)
	~NormalMode ()
void	set_harmonic_constants (Real const &k_uniform)
void	set_harmonic_constants (Real const &k_short, Real const &k_SS, Real const &k_long)
void	set_torsions_using (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
Size	natm () const
Size	ntor () const
Size	nmode () const
std::string	mode () const
Real	dist2_cut () const
utility::vector1< id::AtomID >	get_atomID () const
utility::vector1< id::TorsionID >	get_torID () const
utility::vector1 < utility::vector1< Vector > >	get_eigvec_cart () const
utility::vector1< Vector >	get_eigvec_cart (Size const imode) const
utility::vector1 < utility::vector1< Real > >	get_eigvec_tor () const
utility::vector1< Real >	get_eigvec_tor (Size const imode) const
utility::vector1< Real >	get_eigval () const
Real	get_eigval (Size const imode) const
utility::vector1< Real >	get_importance () const
Real	get_importance (Size const imode) const
Real	get_k (Size const i, Size const j) const
Vector	xyz (Size const i) const
Size	a_to_i (Size const a) const
Size	i_to_a (Size const i) const

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

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

Constructor & Destructor Documentation

protocols::normalmode::NormalMode::NormalMode

(

)

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

protocols::normalmode::NormalMode::~NormalMode

(

)

Member Function Documentation

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

inline

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

private

References j, and r2.

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

private

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

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

inline

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

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

private

References cross(), numeric::xyzVector< class >::cross(), numeric::MathMatrix< T >::inverse_square_matrix(), j, numeric::MathMatrix< T >::transpose(), and protocols::kinmatch::xyz().

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

inline

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

inline

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

private

References j.

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

inline

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

inline

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

inline

References torsion().

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

inline

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

inline

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

inline

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

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

inline

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

inline

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

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

inline

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

inline

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

inline

Referenced by protocols::normalmode::TorsionNormalModeMover::extrapolate_mode(), protocols::normalmode::NormalModeMultifunc::get_dofs_map(), and protocols::normalmode::NormalModeMultifunc::vars_to_dofs().

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

inline

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

private

References numeric::xyzVector< class >::dot(), j, protocols::TR, and protocols::kinmatch::xyz().

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

private

References protocols::normalmode::ContactStruct::c21, co, cross(), protocols::normalmode::ContactStruct::d2, numeric::xyzVector< class >::dot(), dot(), j, protocols::normalmode::ContactStruct::k, l, protocols::normalmode::ContactStruct::r21, protocols::normalmode::ContactStruct::tor1, protocols::normalmode::ContactStruct::tor2, protocols::TR, protocols::kinmatch::xyz(), and zero.

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

inline

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

inline

Referenced by protocols::normalmode::CartesianNormalModeMover::extrapolate_mode(), protocols::normalmode::CartesianNormalModeMover::gen_coord_constraint(), and protocols::normalmode::TorsionNormalModeMover::gen_coord_constraint().

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

inline

References torsion().

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

inline

Referenced by protocols::normalmode::NormalModeMultifunc::dofs_to_vars(), protocols::normalmode::TorsionNormalModeMover::extrapolate_mode(), protocols::normalmode::NormalModeMultifunc::NormalModeMultifunc(), and protocols::normalmode::NormalModeMultifunc::set_default_modes().

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

private

References core::id::BB, protocols::fldsgn::topology::compare(), mode, core::pose::Pose::residue(), core::pose::Pose::total_residue(), and protocols::TR.

Real protocols::normalmode::NormalMode::pythag ( Real  a, Real  b  )

private

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

private

References numeric::xyzVector< class >::dot(), dssp, core::scoring::dssp::Dssp::insert_ss_into_pose(), core::pose::Pose::residue(), core::pose::Pose::secstruct(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

void protocols::normalmode::NormalMode::set_harmonic_constants

(

Real const &

k_uniform

)

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

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

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

inline

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

Real protocols::normalmode::NormalMode::sign ( Real  a, Real  b  )

inlineprivate

void protocols::normalmode::NormalMode::solve

(

core::pose::Pose const &

pose

)

References j, torsion(), and protocols::TR.

Referenced by protocols::normalmode::NormalModeMinimizer::apply(), protocols::normalmode::CartesianNormalModeMover::apply(), and protocols::normalmode::TorsionNormalModeMover::apply().

void protocols::normalmode::NormalMode::svdcmp ( utility::vector1< utility::vector1< Real > > &  a, Size const  m, Size const  n, utility::vector1< Real > &  w, utility::vector1< utility::vector1< Real > > &  v  )

private

References c, j, l, s, and sign().

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(), and protocols::normalmode::TorsionNormalModeMover::TorsionNormalModeMover().

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

inline

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

private

References end, j, and protocols::loops::start.

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

inline

Member Data Documentation

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

private

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

private

Real protocols::normalmode::NormalMode::dist2_cut_

private

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

private

bool protocols::normalmode::NormalMode::eckart_correction_

private

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

private

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

private

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

private

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

private

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

private

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

private

Real protocols::normalmode::NormalMode::k_long_

private

Real protocols::normalmode::NormalMode::k_short_

private

Real protocols::normalmode::NormalMode::k_SS_

private

Real protocols::normalmode::NormalMode::k_uniform_

private

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

private

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

private

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

private

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

private

bool protocols::normalmode::NormalMode::torsion_

private

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

private

bool protocols::normalmode::NormalMode::torsions_using_assigned_

private

bool protocols::normalmode::NormalMode::use_phi_

private

bool protocols::normalmode::NormalMode::use_psi_

private

bool protocols::normalmode::NormalMode::use_uniform_k_

private

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

private

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

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