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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::AtomIDget_atomID () const
 
utility::vector1< core::id::TorsionIDget_torID () const
 
utility::vector1< utility::vector1< core::Vector > > get_eigvec_cart () const
 
utility::vector1< core::Vectorget_eigvec_cart (core::Size const imode) const
 
utility::vector1< utility::vector1< core::Real > > get_eigvec_tor () const
 
utility::vector1< core::Realget_eigvec_tor (core::Size const imode) const
 
utility::vector1< core::Realget_eigval () const
 
core::Real get_eigval (core::Size const imode) const
 
utility::vector1< core::Realget_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::Realcalc_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::Sizetorsions_using_
 
bool torsions_using_assigned_
 
utility::vector1< utility::vector1< core::Real > > k_
 
utility::vector1< core::Sizea_to_i_
 
utility::vector1< core::Sizei_to_a_
 
utility::vector1< core::Vectore_
 
utility::vector1< core::Vectors_
 
utility::vector1< core::Vectortau_
 
utility::vector1< core::Vectorxyz_
 
utility::vector1< core::Realimportance_
 
utility::vector1< core::id::AtomIDatomID_
 
utility::vector1< core::id::TorsionIDtorID_
 
utility::vector1< core::Realeigval_
 
utility::vector1< utility::vector1< core::Vector > > eigvec_cart_
 
utility::vector1< utility::vector1< core::Real > > eigvec_tor_
 

Constructor & Destructor Documentation

◆ NormalMode() [1/2]

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

◆ NormalMode() [2/2]

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

◆ ~NormalMode()

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

Member Function Documentation

◆ a_to_i()

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

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

◆ calc_inertia_tensor()

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

◆ calculate_Jacobi_correction()

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

◆ clear_torsions_using()

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

◆ convert_to_torsion_crd()

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

◆ dist2_cut()

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

References dist2_cut_.

◆ eckart_correction()

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

References eckart_correction_.

◆ eigsrt()

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

◆ get_atomID()

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

References atomID_.

◆ get_eigval() [1/2]

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

References eigval_.

◆ get_eigval() [2/2]

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

References eigval_, and torsion().

◆ get_eigvec_cart() [1/2]

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

References eigvec_cart_.

◆ get_eigvec_cart() [2/2]

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

References eigvec_cart_.

◆ get_eigvec_tor() [1/2]

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

◆ get_eigvec_tor() [2/2]

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

References eigvec_tor_.

◆ get_importance() [1/2]

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

◆ get_importance() [2/2]

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

References importance_.

◆ get_k()

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

References k_.

◆ get_torID()

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

◆ i_to_a()

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

References i_to_a_.

◆ make_Hessian_ANM()

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

◆ make_Hessian_TNM()

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

◆ mode()

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

References mode_.

◆ natm()

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

◆ nmode()

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

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

◆ ntor()

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

◆ prepare_coord()

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

◆ set_harmonic_constant_map()

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

◆ set_harmonic_constants() [1/2]

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

◆ set_harmonic_constants() [2/2]

void protocols::normalmode::NormalMode::set_harmonic_constants ( core::Real const &  k_uniform)

◆ set_torsions_using()

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

◆ solve()

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

◆ torsion() [1/2]

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

References torsion_.

Referenced by get_eigval(), and nmode().

◆ torsion() [2/2]

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

◆ update_inertia_tensor()

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

◆ xyz()

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

References xyz_.

Member Data Documentation

◆ a_to_i_

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

Referenced by a_to_i().

◆ atomID_

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

Referenced by get_atomID().

◆ dist2_cut_

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

Referenced by dist2_cut().

◆ e_

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

Referenced by ntor().

◆ eckart_correction_

bool protocols::normalmode::NormalMode::eckart_correction_
private

Referenced by eckart_correction().

◆ eigval_

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

Referenced by get_eigval().

◆ eigvec_cart_

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

Referenced by get_eigvec_cart().

◆ eigvec_tor_

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

Referenced by get_eigvec_tor().

◆ i_to_a_

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

Referenced by i_to_a().

◆ importance_

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

Referenced by get_importance().

◆ k_

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

Referenced by get_k().

◆ k_long_

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

◆ k_short_

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

◆ k_SS_

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

◆ k_uniform_

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

◆ mode_

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

Referenced by mode().

◆ s_

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

◆ tau_

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

◆ torID_

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

Referenced by get_torID().

◆ torsion_

bool protocols::normalmode::NormalMode::torsion_
private

Referenced by torsion().

◆ torsions_using_

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

◆ torsions_using_assigned_

bool protocols::normalmode::NormalMode::torsions_using_assigned_
private

◆ use_phi_

bool protocols::normalmode::NormalMode::use_phi_
private

◆ use_psi_

bool protocols::normalmode::NormalMode::use_psi_
private

◆ use_uniform_k_

bool protocols::normalmode::NormalMode::use_uniform_k_
private

◆ xyz_

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: