Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
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::AtomIDget_atomID () const
 
utility::vector1< id::TorsionIDget_torID () const
 
utility::vector1
< utility::vector1< Vector > > 
get_eigvec_cart () const
 
utility::vector1< Vectorget_eigvec_cart (Size const imode) const
 
utility::vector1
< utility::vector1< Real > > 
get_eigvec_tor () const
 
utility::vector1< Realget_eigvec_tor (Size const imode) const
 
utility::vector1< Realget_eigval () const
 
Real get_eigval (Size const imode) const
 
utility::vector1< Realget_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< Realcalc_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< Sizetorsions_using_
 
bool torsions_using_assigned_
 
utility::vector1
< utility::vector1< Real > > 
k_
 
utility::vector1< Sizea_to_i_
 
utility::vector1< Sizei_to_a_
 
utility::vector1< Vectore_
 
utility::vector1< Vectors_
 
utility::vector1< Vectortau_
 
utility::vector1< Vectorxyz_
 
utility::vector1< Realimportance_
 
utility::vector1< id::AtomIDatomID_
 
utility::vector1< id::TorsionIDtorID_
 
utility::vector1< Realeigval_
 
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 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
void protocols::normalmode::NormalMode::clear_torsions_using ( )
inline
utility::vector1< utility::vector1< Real > > protocols::normalmode::NormalMode::convert_to_torsion_crd ( utility::vector1< utility::vector1< Real > > const &  U)
private
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
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
utility::vector1< Real > protocols::normalmode::NormalMode::get_eigvec_tor ( Size const  imode) const
inline
utility::vector1< Real > protocols::normalmode::NormalMode::get_importance ( ) const
inline
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
Size protocols::normalmode::NormalMode::i_to_a ( Size const  i) const
inline
utility::vector1< utility::vector1< Real > > protocols::normalmode::NormalMode::make_Hessian_ANM ( )
private
utility::vector1< utility::vector1< Real > > protocols::normalmode::NormalMode::make_Hessian_TNM ( )
private
std::string protocols::normalmode::NormalMode::mode ( ) const
inline
Size protocols::normalmode::NormalMode::natm ( ) const
inline
Size protocols::normalmode::NormalMode::nmode ( ) const
inline

References torsion().

Size protocols::normalmode::NormalMode::ntor ( ) const
inline
void protocols::normalmode::NormalMode::prepare_coord ( pose::Pose const &  pose)
private
Real protocols::normalmode::NormalMode::pythag ( Real  a,
Real  b 
)
private
void protocols::normalmode::NormalMode::set_harmonic_constant_map ( pose::Pose const &  pose)
private
void protocols::normalmode::NormalMode::set_harmonic_constants ( Real const &  k_uniform)
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
Real protocols::normalmode::NormalMode::sign ( Real  a,
Real  b 
)
inlineprivate
void protocols::normalmode::NormalMode::solve ( core::pose::Pose const &  pose)
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, 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 
)
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, 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

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