core::pack::dunbrack::RotamerLibraryScratchSpace Class Reference

#include <RotamerLibraryScratchSpace.hh>

Inheritance diagram for core::pack::dunbrack::RotamerLibraryScratchSpace:

Public Member Functions
	RotamerLibraryScratchSpace ()
	~RotamerLibraryScratchSpace () override
Real4 const &	chidev () const
Real4 const &	chidevpen () const
Real5 const &	dchidevpen_dbb () const
Real4 const &	dchidevpen_dchi () const
Real5 const &	dE_dbb () const
Real5 const &	dE_dbb_dev () const
Real5 const &	dE_dbb_semi () const
Real4 const &	dE_dchi () const
Real4 const &	dE_dchi_dev () const
Real4 const &	dE_dchi_semi () const
FiveReal4 const &	dE_dbb_dev_perchi () const
Real	fa_dun_tot () const
Real	fa_dun_rot () const
Real	fa_dun_semi () const
Real	fa_dun_dev () const
Real4 &	chidev ()
Real4 &	chidevpen ()
Real5 &	dchidevpen_dbb ()
Real4 &	dchidevpen_dchi ()
Real5 &	dE_dbb ()
Real5 &	dE_dbb_dev ()
Real5 &	dE_dbb_rot ()
Real5 &	dE_dbb_semi ()
Real4 &	dE_dchi ()
Real4 &	dE_dchi_dev ()
Real4 &	dE_dchi_semi ()
FiveReal4 &	dE_dbb_dev_perchi ()
Real &	fa_dun_tot ()
Real &	fa_dun_rot ()
Real &	fa_dun_semi ()
Real &	fa_dun_dev ()
void	extract_torsion_deriv (id::TorsionID const &tor_id, core::conformation::Residue const &rsd, core::pose::Pose const &pose, rotamers::TorsionEnergy &tderiv) const
Real4 const &	dchimean_domg () const
Real4 const &	dchisd_domg () const
Real4 &	dchimean_domg ()
Real4 &	dchisd_domg ()
Public Member Functions inherited from core::pack::dunbrack::RotamerLibraryInterpolationScratch
Real	rotprob () const
Real	negln_rotprob () const
Real4 const &	chimean () const
Real4 const &	chisd () const
Real5 const &	drotprob_dbb () const
Real5 const &	dneglnrotprob_dbb () const
FiveReal4 const &	dchimean_dbb () const
FiveReal4 const &	dchisd_dbb () const
Real &	rotprob ()
Real &	negln_rotprob ()
Real4 &	chimean ()
Real4 &	chisd ()
Real5 &	drotprob_dbb ()
Real5 &	dneglnrotprob_dbb ()
FiveReal4 &	dchimean_dbb ()
FiveReal4 &	dchisd_dbb ()
Real	entropy () const
Real5	dentropy_dbb () const
Real &	entropy ()
Real5 &	dentropy_dbb ()

Static Public Attributes
static Size const	AA_OMG_INDEX = 3
static Size const	AA_PHI_INDEX = 1
static Size const	AA_PSI_INDEX = 2

Protected Member Functions
core::Size	get_scratch_index (core::id::TorsionID const &torid, core::conformation::Residue const &rsd, core::pose::Pose const &pose) const
	Given a mainchain torsion index and a ResidueType, get the index of the corresponding torsion in the data stored in the Dunbrack scratch space. More...

Private Attributes
Real4	chidev_
Real4	chidevpen_
Real5	dchidevpen_dbb_
Real4	dchidevpen_dchi_
Real5	dE_dbb_
Real5	dE_dbb_dev_
Real5	dE_dbb_rot_
Real5	dE_dbb_semi_
Real4	dE_dchi_
Real4	dE_dchi_dev_
Real4	dE_dchi_semi_
FiveReal4	dE_dbb_dev_perchi_
Real	fa_dun_tot_
Real	fa_dun_rot_
Real	fa_dun_semi_
Real	fa_dun_dev_
Real4	dchimean_domg_
Real4	dchisd_domg_

Constructor & Destructor Documentation

RotamerLibraryScratchSpace()

core::pack::dunbrack::RotamerLibraryScratchSpace::RotamerLibraryScratchSpace

(

)

All the fixedsizearrays are allocated and initialized to 0

~RotamerLibraryScratchSpace()

core::pack::dunbrack::RotamerLibraryScratchSpace::~RotamerLibraryScratchSpace ( )

overridedefault

Member Function Documentation

chidev() [1/2]

Real4& core::pack::dunbrack::RotamerLibraryScratchSpace::chidev ( )

inline

References chidev_.

chidev() [2/2]

Real4 const& core::pack::dunbrack::RotamerLibraryScratchSpace::chidev ( ) const

inline

References chidev_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::eval_rotameric_deriv().

chidevpen() [1/2]

Real4& core::pack::dunbrack::RotamerLibraryScratchSpace::chidevpen ( )

inline

References chidevpen_.

chidevpen() [2/2]

Real4 const& core::pack::dunbrack::RotamerLibraryScratchSpace::chidevpen ( ) const

inline

References chidevpen_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::eval_rotameric_deriv().

dchidevpen_dbb() [1/2]

Real5& core::pack::dunbrack::RotamerLibraryScratchSpace::dchidevpen_dbb ( )

inline

References dchidevpen_dbb_.

dchidevpen_dbb() [2/2]

Real5 const& core::pack::dunbrack::RotamerLibraryScratchSpace::dchidevpen_dbb ( ) const

inline

References dchidevpen_dbb_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::eval_rotameric_deriv(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::rotamer_deriv_bbdep(), and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv().

dchidevpen_dchi() [1/2]

Real4& core::pack::dunbrack::RotamerLibraryScratchSpace::dchidevpen_dchi ( )

inline

References dchidevpen_dchi_.

dchidevpen_dchi() [2/2]

Real4 const& core::pack::dunbrack::RotamerLibraryScratchSpace::dchidevpen_dchi ( ) const

inline

References dchidevpen_dchi_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::eval_rotameric_deriv(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::rotamer_deriv_bbdep(), and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv().

dchimean_domg() [1/2]

Real4& core::pack::dunbrack::RotamerLibraryScratchSpace::dchimean_domg ( )

inline

References dchimean_domg_.

dchimean_domg() [2/2]

Real4 const& core::pack::dunbrack::RotamerLibraryScratchSpace::dchimean_domg ( ) const

inline

References dchimean_domg_.

dchisd_domg() [1/2]

Real4& core::pack::dunbrack::RotamerLibraryScratchSpace::dchisd_domg ( )

inline

References dchisd_domg_.

dchisd_domg() [2/2]

Real4 const& core::pack::dunbrack::RotamerLibraryScratchSpace::dchisd_domg ( ) const

inline

References dchisd_domg_.

dE_dbb() [1/2]

Real5& core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb ( )

inline

References dE_dbb_.

dE_dbb() [2/2]

Real5 const& core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb ( ) const

inline

References dE_dbb_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::correct_termini_derivatives(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::rotamer_deriv_bbdep(), and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv().

dE_dbb_dev() [1/2]

Real5& core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb_dev ( )

inline

References dE_dbb_dev_.

dE_dbb_dev() [2/2]

Real5 const& core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb_dev ( ) const

inline

References dE_dbb_dev_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::correct_termini_derivatives(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::rotamer_deriv_bbdep(), and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv().

dE_dbb_dev_perchi() [1/2]

FiveReal4& core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb_dev_perchi ( )

inline

References dE_dbb_dev_perchi_.

dE_dbb_dev_perchi() [2/2]

FiveReal4 const& core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb_dev_perchi ( ) const

inline

References dE_dbb_dev_perchi_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::eval_rotameric_deriv().

dE_dbb_rot()

Real5& core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb_rot ( )

inline

References dE_dbb_rot_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::correct_termini_derivatives(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::rotamer_deriv_bbdep(), and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv().

dE_dbb_semi() [1/2]

Real5& core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb_semi ( )

inline

References dE_dbb_semi_.

dE_dbb_semi() [2/2]

Real5 const& core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb_semi ( ) const

inline

References dE_dbb_semi_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::correct_termini_derivatives(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::rotamer_deriv_bbdep().

dE_dchi() [1/2]

Real4& core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dchi ( )

inline

References dE_dchi_.

dE_dchi() [2/2]

Real4 const& core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dchi ( ) const

inline

References dE_dchi_.

Referenced by core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::rotamer_deriv_bbdep(), and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv().

dE_dchi_dev() [1/2]

Real4& core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dchi_dev ( )

inline

References dE_dchi_dev_.

dE_dchi_dev() [2/2]

Real4 const& core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dchi_dev ( ) const

inline

References dE_dchi_dev_.

Referenced by core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::rotamer_deriv_bbdep(), and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv().

dE_dchi_semi() [1/2]

Real4& core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dchi_semi ( )

inline

References dE_dchi_semi_.

dE_dchi_semi() [2/2]

Real4 const& core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dchi_semi ( ) const

inline

References dE_dchi_semi_.

Referenced by core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::rotamer_deriv_bbdep().

extract_torsion_deriv()

void core::pack::dunbrack::RotamerLibraryScratchSpace::extract_torsion_deriv	(	id::TorsionID const &	tor_id,
		core::conformation::Residue const &	rsd,
		core::pose::Pose const &	pose,
		rotamers::TorsionEnergy &	tderiv
	)		const

References core::id::BB, core::id::CHI, dE_dbb_, dE_dbb_dev_, dE_dbb_rot_, dE_dbb_semi_, dE_dchi_, dE_dchi_dev_, dE_dchi_semi_, core::pack::rotamers::TorsionEnergy::dev, core::pack::dunbrack::DUNBRACK_MAX_BBTOR, core::pack::dunbrack::DUNBRACK_MAX_SCTOR, get_scratch_index(), core::pack::rotamers::TorsionEnergy::rot, core::pack::rotamers::TorsionEnergy::semi, core::id::TorsionID::torsion(), core::pack::rotamers::TorsionEnergy::tot, and core::id::TorsionID::type().

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv().

fa_dun_dev() [1/2]

Real& core::pack::dunbrack::RotamerLibraryScratchSpace::fa_dun_dev ( )

inline

References fa_dun_dev_.

fa_dun_dev() [2/2]

Real core::pack::dunbrack::RotamerLibraryScratchSpace::fa_dun_dev ( ) const

inline

References fa_dun_dev_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::eval_rotameric_deriv(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::rotamer_deriv_bbdep().

fa_dun_rot() [1/2]

Real& core::pack::dunbrack::RotamerLibraryScratchSpace::fa_dun_rot ( )

inline

References fa_dun_rot_.

fa_dun_rot() [2/2]

Real core::pack::dunbrack::RotamerLibraryScratchSpace::fa_dun_rot ( ) const

inline

References fa_dun_rot_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::eval_rotameric_deriv(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::rotamer_deriv_bbdep().

fa_dun_semi() [1/2]

Real& core::pack::dunbrack::RotamerLibraryScratchSpace::fa_dun_semi ( )

inline

References fa_dun_semi_.

fa_dun_semi() [2/2]

Real core::pack::dunbrack::RotamerLibraryScratchSpace::fa_dun_semi ( ) const

inline

References fa_dun_semi_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::eval_rotameric_deriv(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::rotamer_deriv_bbdep().

fa_dun_tot() [1/2]

Real& core::pack::dunbrack::RotamerLibraryScratchSpace::fa_dun_tot ( )

inline

References fa_dun_tot_.

fa_dun_tot() [2/2]

Real core::pack::dunbrack::RotamerLibraryScratchSpace::fa_dun_tot ( ) const

inline

References fa_dun_tot_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::eval_rotameric_deriv(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::rotamer_deriv_bbdep().

get_scratch_index()

core::Size core::pack::dunbrack::RotamerLibraryScratchSpace::get_scratch_index ( core::id::TorsionID const &  torid, core::conformation::Residue const &  rsd, core::pose::Pose const &  pose  ) const

protected

Given a mainchain torsion index and a ResidueType, get the index of the corresponding torsion in the data stored in the Dunbrack scratch space.

For most residue types, this just returns torsion_index. The index is only different in cases in which a residue type has rotamers that depend on a subset of mainchain torsions. For example, if a residue's rotamers depended on mainchain torsions 2, 3, and 4, then the scratch indices 1, 2, and 3 would correspond to mainchain torsions 2, 3, and 4, respectively. This function returns 0 if torsion_index is a torsion on which rotamers do not depend.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::conformation::Residue::connected_residue_at_lower(), core::conformation::Residue::is_peptoid(), core::conformation::Residue::mainchain_torsions(), core::pose::Pose::residue(), core::chemical::ResidueTypeBase::rotamer_library_specification(), core::id::TorsionID::rsd(), core::conformation::Residue::seqpos(), core::id::TorsionID::torsion(), and core::conformation::Residue::type().

Referenced by extract_torsion_deriv().

Member Data Documentation

AA_OMG_INDEX

Size const core::pack::dunbrack::RotamerLibraryScratchSpace::AA_OMG_INDEX = 3

static

AA_PHI_INDEX

Size const core::pack::dunbrack::RotamerLibraryScratchSpace::AA_PHI_INDEX = 1

static

AA_PSI_INDEX

Size const core::pack::dunbrack::RotamerLibraryScratchSpace::AA_PSI_INDEX = 2

static

chidev_

Real4 core::pack::dunbrack::RotamerLibraryScratchSpace::chidev_

private

Referenced by chidev().

chidevpen_

Real4 core::pack::dunbrack::RotamerLibraryScratchSpace::chidevpen_

private

Referenced by chidevpen().

dchidevpen_dbb_

Real5 core::pack::dunbrack::RotamerLibraryScratchSpace::dchidevpen_dbb_

private

Referenced by dchidevpen_dbb().

dchidevpen_dchi_

Real4 core::pack::dunbrack::RotamerLibraryScratchSpace::dchidevpen_dchi_

private

Referenced by dchidevpen_dchi().

dchimean_domg_

Real4 core::pack::dunbrack::RotamerLibraryScratchSpace::dchimean_domg_

private

Referenced by dchimean_domg().

dchisd_domg_

Real4 core::pack::dunbrack::RotamerLibraryScratchSpace::dchisd_domg_

private

Referenced by dchisd_domg().

dE_dbb_

Real5 core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb_

private

Referenced by dE_dbb(), and extract_torsion_deriv().

dE_dbb_dev_

Real5 core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb_dev_

private

Referenced by dE_dbb_dev(), and extract_torsion_deriv().

dE_dbb_dev_perchi_

FiveReal4 core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb_dev_perchi_

private

Referenced by dE_dbb_dev_perchi().

dE_dbb_rot_

Real5 core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb_rot_

private

Referenced by dE_dbb_rot(), and extract_torsion_deriv().

dE_dbb_semi_

Real5 core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb_semi_

private

Referenced by dE_dbb_semi(), and extract_torsion_deriv().

dE_dchi_

Real4 core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dchi_

private

Referenced by dE_dchi(), and extract_torsion_deriv().

dE_dchi_dev_

Real4 core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dchi_dev_

private

Referenced by dE_dchi_dev(), and extract_torsion_deriv().

dE_dchi_semi_

Real4 core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dchi_semi_

private

Referenced by dE_dchi_semi(), and extract_torsion_deriv().

fa_dun_dev_

Real core::pack::dunbrack::RotamerLibraryScratchSpace::fa_dun_dev_

private

Referenced by fa_dun_dev().

fa_dun_rot_

Real core::pack::dunbrack::RotamerLibraryScratchSpace::fa_dun_rot_

private

Referenced by fa_dun_rot().

fa_dun_semi_

Real core::pack::dunbrack::RotamerLibraryScratchSpace::fa_dun_semi_

private

Referenced by fa_dun_semi().

fa_dun_tot_

Real core::pack::dunbrack::RotamerLibraryScratchSpace::fa_dun_tot_

private

Referenced by fa_dun_tot().

---

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

• src/core/pack/dunbrack/RotamerLibraryScratchSpace.hh
• src/core/pack/dunbrack/RotamerLibraryScratchSpace.cc