protocols::loop_grower::LoopPartialSolution Class Reference

#include <LoopGrower.hh>

Public Member Functions
	LoopPartialSolution (core::pose::Pose const &pose, int reslow, int reshigh, core::Real score)
	LoopPartialSolution ()
void	store_coordinates (core::pose::Pose const &pose, int reslow, int reshigh, core::Size lower_fasta)
void	set_centerofmass ()
void	set_coordinates (core::pose::Pose &pose)
void	store_sheetpositions (core::pose::Pose &pose, core::Size rangelo, core::Size rangehi, core::Size jumpid, core::Size basres)
void	write_beam_lps (std::ostream &lpsfile)
void	write_beam (std::ostream &outbeam)
void	apply (core::pose::Pose &pose, int range1lo, int range1hi, int range2lo, int range2hi)
void	apply_sheets (core::pose::Pose &pose)
void	add_sheets (core::pose::Pose &pose, core::Size takeoffres, core::Size totalres)
void	set_rms (core::Real RMS)
void	set_gdt (core::Real GDT)
void	set_bonus_score (core::Real bonus)
core::Real	get_bonus_score () const
core::Real	get_rms () const
core::Real	get_gdt () const
void	apply (core::pose::Pose &pose, int range1lo, int range1hi)
void	set_id (std::string id)
std::string	get_id ()
core::Real	size ()
void	push_back_restorsions (ResTorsions restorsions)
void	push_back_backbone (utility::vector1< core::Vector > backbone)
void	push_back_sheet (SheetPositions sheet)
void	set_positions (utility::vector1< numeric::xyzVector< core::Real > > positions)
void	set_ids (utility::vector1< core::id::AtomID > ids)
void	set_score (core::Real score)
void	set_history (utility::vector1< std::pair< core::Size, core::Size > > history, std::pair< core::Size, core::Size > newfrag)
void	set_history (utility::vector1< std::pair< core::Size, core::Size > > history)
utility::vector1< std::pair< core::Size, core::Size > >	get_history ()
utility::vector1< core::Vector >	get_calphas () const
utility::vector1< utility::vector1< core::Vector > >	get_backbone () const
core::Real	get_score () const
core::Real	partialrms (const LoopPartialSolution &, int fragmelt, int total_lower, bool takeoffonly, int rmswindow) const
core::Real	max_calpha_distance (const LoopPartialSolution &, core::Size fragmelt, core::Size total_lower, bool takeoffonly, bool full_loop, bool lower) const
bool	operator< (const LoopPartialSolution &lps1) const

Private Attributes
utility::vector1< ResTorsions >	residues_
utility::vector1< SheetPositions >	sheets_
utility::vector1< core::Vector >	calphas_
utility::vector1< core::id::AtomID >	ids_
utility::vector1< numeric::xyzVector< core::Real > >	positions_
utility::vector1< utility::vector1< core::Vector > >	backbones_
utility::vector1< std::pair< core::Size, core::Size > >	fragmenthistory_
numeric::xyzVector< core::Real >	centerofmass_
core::Real	score_
core::Real	bonus_score_ = 0
core::Real	RMS_ = 0
core::Real	GDT_ = 0
std::string	id_

Constructor & Destructor Documentation

LoopPartialSolution() [1/2]

protocols::loop_grower::LoopPartialSolution::LoopPartialSolution ( core::pose::Pose const &  pose, int  reslow, int  reshigh, core::Real  score  )

inline

References core::conformation::Residue::atom(), backbones_, bonus_score_, calphas_, core::conformation::Residue::name3(), core::pose::Pose::residue(), residues_, protocols::hybridization::score, score_, set_centerofmass(), and core::conformation::Atom::xyz().

LoopPartialSolution() [2/2]

protocols::loop_grower::LoopPartialSolution::LoopPartialSolution ( )

inline

Member Function Documentation

add_sheets()

void protocols::loop_grower::LoopPartialSolution::add_sheets	(	core::pose::Pose &	pose,
		core::Size	takeoffres,
		core::Size	totalres
	)

References core::conformation::Conformation::append_residue_by_jump(), core::chemical::CENTROID, core::chemical::CENTROID_ROT, core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::chemical::FA_STANDARD, core::pose::Pose::is_centroid(), core::pose::Pose::is_fullatom(), core::conformation::Conformation::safely_append_polymer_residue_after_seqpos(), core::conformation::Conformation::safely_prepend_polymer_residue_before_seqpos(), and core::pose::Pose::total_residue().

apply() [1/2]

void protocols::loop_grower::LoopPartialSolution::apply ( core::pose::Pose &  pose, int  range1lo, int  range1hi  )

inline

References apply().

apply() [2/2]

void protocols::loop_grower::LoopPartialSolution::apply	(	core::pose::Pose &	pose,
		int	range1lo,
		int	range1hi,
		int	range2lo,
		int	range2hi
	)

References core::chemical::CENTROID_ROT_t, protocols::loop_grower::ResTorsions::chi1_, protocols::loop_grower::ResTorsions::chi2_, protocols::loop_grower::ResTorsions::chi3_, protocols::loop_grower::ResTorsions::chi4_, core::pose::Pose::conformation(), core::pose::Pose::is_centroid(), protocols::loop_grower::ResTorsions::nchi_, protocols::loop_grower::ResTorsions::omega_, protocols::loop_grower::ResTorsions::phi_, protocols::loop_grower::ResTorsions::psi_, core::conformation::Conformation::residue_typeset_mode(), core::pose::Pose::set_chi(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and protocols::loop_grower::TR().

Referenced by protocols::loop_grower::LoopGrower::apply(), apply(), protocols::loop_grower::LoopPartialSolutionStore::cluster_check(), protocols::loop_grower::LoopGrower::coordinate_filter(), protocols::loop_grower::LoopGrower::fafilter(), protocols::loop_grower::LoopPartialSolutionStore::filter(), protocols::loop_grower::LoopGrower::full_atom_beam(), protocols::loop_grower::LoopPartialSolutionStore::parametercheck_filter(), protocols::loop_grower::LoopPartialSolutionStore::push(), protocols::loop_grower::LoopGrower::refine_cycle(), protocols::loop_grower::LoopGrower::rescoresolutionset(), protocols::loop_grower::LoopGrower::single_grow(), protocols::loop_grower::LoopPartialSolutionStore::skeleton_filter(), and protocols::loop_grower::LoopGrower::update_and_writelps().

apply_sheets()

void protocols::loop_grower::LoopPartialSolution::apply_sheets

(

core::pose::Pose &

pose

)

References core::chemical::CENTROID_ROT_t, protocols::loop_grower::ResTorsions::chi1_, protocols::loop_grower::ResTorsions::chi2_, protocols::loop_grower::ResTorsions::chi3_, protocols::loop_grower::ResTorsions::chi4_, core::pose::Pose::conformation(), core::pose::Pose::is_centroid(), core::pose::Pose::jump(), protocols::loop_grower::ResTorsions::nchi_, core::pose::Pose::num_jump(), protocols::loop_grower::ResTorsions::omega_, protocols::loop_grower::ResTorsions::phi_, protocols::loop_grower::ResTorsions::psi_, core::conformation::Conformation::residue_typeset_mode(), core::pose::Pose::set_chi(), core::pose::Pose::set_jump(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::kinematics::Jump::set_rotation(), core::kinematics::Jump::set_translation(), and core::pose::Pose::total_residue().

Referenced by protocols::loop_grower::LoopPartialSolutionStore::filter(), protocols::loop_grower::LoopGrower::refine_cycle(), and protocols::loop_grower::LoopGrower::rescoresolutionset().

get_backbone()

utility::vector1< utility::vector1< core::Vector > > protocols::loop_grower::LoopPartialSolution::get_backbone ( ) const

inline

References backbones_.

Referenced by max_calpha_distance(), and partialrms().

get_bonus_score()

core::Real protocols::loop_grower::LoopPartialSolution::get_bonus_score ( ) const

inline

References bonus_score_.

Referenced by protocols::loop_grower::LoopGrower::rescoresolutionset(), and protocols::loop_grower::LoopGrower::single_grow().

get_calphas()

utility::vector1< core::Vector > protocols::loop_grower::LoopPartialSolution::get_calphas ( ) const

inline

References calphas_.

Referenced by max_calpha_distance(), and partialrms().

get_gdt()

core::Real protocols::loop_grower::LoopPartialSolution::get_gdt ( ) const

inline

References GDT_.

Referenced by protocols::loop_grower::LoopGrower::rescoresolutionset().

get_history()

utility::vector1< std::pair<core::Size,core::Size> > protocols::loop_grower::LoopPartialSolution::get_history ( )

inline

References fragmenthistory_.

Referenced by protocols::loop_grower::LoopGrower::rescoresolutionset(), and protocols::loop_grower::LoopGrower::single_grow().

get_id()

std::string protocols::loop_grower::LoopPartialSolution::get_id ( )

inline

References id_.

Referenced by protocols::loop_grower::LoopPartialSolutionStore::filter(), protocols::loop_grower::LoopPartialSolutionStore::parametercheck_filter(), and protocols::loop_grower::LoopGrower::rescoresolutionset().

get_rms()

core::Real protocols::loop_grower::LoopPartialSolution::get_rms ( ) const

inline

References RMS_.

Referenced by protocols::loop_grower::LoopPartialSolutionStore::cluster_check(), protocols::loop_grower::LoopPartialSolutionStore::diversityfilter(), protocols::loop_grower::LoopPartialSolutionStore::filter(), protocols::loop_grower::RMSComparator::operator()(), protocols::loop_grower::LoopPartialSolutionStore::parametercheck_filter(), protocols::loop_grower::LoopGrower::rescoresolutionset(), and protocols::loop_grower::LoopGrower::single_grow().

get_score()

core::Real protocols::loop_grower::LoopPartialSolution::get_score ( ) const

inline

References score_.

Referenced by protocols::loop_grower::LoopPartialSolutionStore::cluster_check(), protocols::loop_grower::LoopPartialSolutionStore::diversityfilter(), protocols::loop_grower::LoopPartialSolutionStore::filter(), protocols::loop_grower::LoopPartialSolutionStore::filterprevious(), protocols::loop_grower::LoopGrower::full_atom_beam(), protocols::loop_grower::LoopPartialSolutionStore::parametercheck_filter(), protocols::loop_grower::LoopPartialSolutionStore::push(), protocols::loop_grower::LoopGrower::rescoresolutionset(), protocols::loop_grower::LoopComparator::set_scores(), and protocols::loop_grower::LoopGrower::single_grow().

max_calpha_distance()

Real protocols::loop_grower::LoopPartialSolution::max_calpha_distance	(	const LoopPartialSolution &	newlps,
		core::Size	fragmelt,
		core::Size	total_lower,
		bool	takeoffonly,
		bool	full_loop,
		bool	lower
	)		const

References get_backbone(), and get_calphas().

Referenced by protocols::loop_grower::LoopPartialSolutionStore::push().

operator<()

bool protocols::loop_grower::LoopPartialSolution::operator< ( const LoopPartialSolution &  lps1 ) const

inline

References score_.

partialrms()

Real protocols::loop_grower::LoopPartialSolution::partialrms	(	const LoopPartialSolution &	newlps,
		int	fragmelt,
		int	total_lower,
		bool	takeoffonly,
		int	rmswindow
	)		const

References get_backbone(), and get_calphas().

Referenced by protocols::loop_grower::LoopPartialSolutionStore::cluster_check(), protocols::loop_grower::LoopPartialSolutionStore::diversityfilter(), protocols::loop_grower::LoopPartialSolutionStore::filterprevious(), and protocols::loop_grower::LoopPartialSolutionStore::parametercheck_filter().

push_back_backbone()

void protocols::loop_grower::LoopPartialSolution::push_back_backbone ( utility::vector1< core::Vector >  backbone )

inline

References backbones_.

Referenced by protocols::loop_grower::LoopGrower::read_from_disk().

push_back_restorsions()

void protocols::loop_grower::LoopPartialSolution::push_back_restorsions ( ResTorsions  restorsions )

inline

References residues_.

Referenced by protocols::loop_grower::LoopGrower::read_from_disk().

push_back_sheet()

void protocols::loop_grower::LoopPartialSolution::push_back_sheet ( SheetPositions  sheet )

inline

References core::scoring::sheet, and sheets_.

Referenced by protocols::loop_grower::LoopGrower::read_from_disk().

set_bonus_score()

void protocols::loop_grower::LoopPartialSolution::set_bonus_score ( core::Real  bonus )

inline

References bonus_score_.

Referenced by protocols::loop_grower::LoopGrower::apply(), protocols::loop_grower::LoopGrower::full_atom_beam(), protocols::loop_grower::LoopGrower::read_from_disk(), protocols::loop_grower::LoopGrower::rescoresolutionset(), and protocols::loop_grower::LoopGrower::single_grow().

set_centerofmass()

void protocols::loop_grower::LoopPartialSolution::set_centerofmass

(

)

Referenced by LoopPartialSolution().

set_coordinates()

void protocols::loop_grower::LoopPartialSolution::set_coordinates ( core::pose::Pose &  pose )

inline

References core::pose::Pose::batch_set_xyz(), ids_, and positions_.

Referenced by protocols::loop_grower::LoopComparator::apply(), and protocols::loop_grower::LoopComparator::set_scores().

set_gdt()

void protocols::loop_grower::LoopPartialSolution::set_gdt ( core::Real  GDT )

inline

References GDT_.

Referenced by protocols::loop_grower::LoopGrower::addnativesolution(), protocols::loop_grower::LoopGrower::fafilter(), protocols::loop_grower::LoopGrower::read_from_disk(), protocols::loop_grower::LoopGrower::rescoresolutionset(), and protocols::loop_grower::LoopGrower::single_grow().

set_history() [1/2]

void protocols::loop_grower::LoopPartialSolution::set_history ( utility::vector1< std::pair< core::Size, core::Size > >  history )

inline

References fragmenthistory_.

set_history() [2/2]

void protocols::loop_grower::LoopPartialSolution::set_history ( utility::vector1< std::pair< core::Size, core::Size > >  history, std::pair< core::Size, core::Size >  newfrag  )

inline

References fragmenthistory_.

Referenced by protocols::loop_grower::LoopGrower::rescoresolutionset(), and protocols::loop_grower::LoopGrower::single_grow().

set_id()

void protocols::loop_grower::LoopPartialSolution::set_id ( std::string  id )

inline

References id_.

Referenced by protocols::loop_grower::LoopGrower::single_grow().

set_ids()

void protocols::loop_grower::LoopPartialSolution::set_ids ( utility::vector1< core::id::AtomID >  ids )

inline

References ids_.

Referenced by protocols::loop_grower::LoopComparator::read_from_file().

set_positions()

void protocols::loop_grower::LoopPartialSolution::set_positions ( utility::vector1< numeric::xyzVector< core::Real > >  positions )

inline

References positions_.

Referenced by protocols::loop_grower::LoopComparator::read_from_file().

set_rms()

void protocols::loop_grower::LoopPartialSolution::set_rms ( core::Real  RMS )

inline

References RMS_.

Referenced by protocols::loop_grower::LoopGrower::addnativesolution(), protocols::loop_grower::LoopGrower::fafilter(), protocols::loop_grower::LoopPartialSolutionStore::push(), protocols::loop_grower::LoopGrower::read_from_disk(), protocols::loop_grower::LoopGrower::rescoresolutionset(), and protocols::loop_grower::LoopGrower::single_grow().

set_score()

void protocols::loop_grower::LoopPartialSolution::set_score ( core::Real  score )

inline

References protocols::hybridization::score, and score_.

Referenced by protocols::loop_grower::LoopGrower::full_atom_beam(), protocols::loop_grower::LoopGrower::read_from_disk(), protocols::loop_grower::LoopComparator::read_from_file(), and protocols::loop_grower::LoopGrower::rescoresolutionset().

size()

core::Real protocols::loop_grower::LoopPartialSolution::size ( )

inline

References residues_.

Referenced by protocols::loop_grower::LoopGrower::write_to_disk().

store_coordinates()

void protocols::loop_grower::LoopPartialSolution::store_coordinates ( core::pose::Pose const &  pose, int  reslow, int  reshigh, core::Size  lower_fasta  )

inline

References ids_, positions_, core::pose::Pose::residue_type(), and core::pose::Pose::xyz().

Referenced by protocols::loop_grower::LoopGrower::apply(), and protocols::loop_grower::LoopGrower::update_and_writelps().

store_sheetpositions()

void protocols::loop_grower::LoopPartialSolution::store_sheetpositions ( core::pose::Pose &  pose, core::Size  rangelo, core::Size  rangehi, core::Size  jumpid, core::Size  basres  )

inline

References sheets_.

Referenced by protocols::loop_grower::LoopGrower::store_sheets().

write_beam()

void protocols::loop_grower::LoopPartialSolution::write_beam

(

std::ostream &

outbeam

)

References protocols::loop_grower::ResTorsions::chi1_, protocols::loop_grower::ResTorsions::chi2_, protocols::loop_grower::ResTorsions::chi3_, protocols::loop_grower::ResTorsions::chi4_, protocols::loop_grower::ResTorsions::nchi_, protocols::loop_grower::ResTorsions::omega_, protocols::loop_grower::ResTorsions::phi_, and protocols::loop_grower::ResTorsions::psi_.

Referenced by protocols::loop_grower::LoopGrower::write_to_disk().

write_beam_lps()

void protocols::loop_grower::LoopPartialSolution::write_beam_lps

(

std::ostream &

lpsfile

)

Referenced by protocols::loop_grower::LoopPartialSolutionStore::writelpsstore().

Member Data Documentation

backbones_

utility::vector1< utility::vector1< core::Vector > > protocols::loop_grower::LoopPartialSolution::backbones_

private

Referenced by get_backbone(), LoopPartialSolution(), and push_back_backbone().

bonus_score_

core::Real protocols::loop_grower::LoopPartialSolution::bonus_score_ = 0

private

Referenced by get_bonus_score(), LoopPartialSolution(), and set_bonus_score().

calphas_

utility::vector1< core::Vector > protocols::loop_grower::LoopPartialSolution::calphas_

private

Referenced by get_calphas(), and LoopPartialSolution().

centerofmass_

numeric::xyzVector<core::Real> protocols::loop_grower::LoopPartialSolution::centerofmass_

private

fragmenthistory_

utility::vector1< std::pair<core::Size,core::Size> > protocols::loop_grower::LoopPartialSolution::fragmenthistory_

private

Referenced by get_history(), and set_history().

GDT_

core::Real protocols::loop_grower::LoopPartialSolution::GDT_ = 0

private

Referenced by get_gdt(), and set_gdt().

id_

std::string protocols::loop_grower::LoopPartialSolution::id_

private

Referenced by get_id(), and set_id().

ids_

utility::vector1< core::id::AtomID > protocols::loop_grower::LoopPartialSolution::ids_

private

Referenced by set_coordinates(), set_ids(), and store_coordinates().

positions_

utility::vector1< numeric::xyzVector<core::Real> > protocols::loop_grower::LoopPartialSolution::positions_

private

Referenced by set_coordinates(), set_positions(), and store_coordinates().

residues_

utility::vector1< ResTorsions > protocols::loop_grower::LoopPartialSolution::residues_

private

Referenced by LoopPartialSolution(), push_back_restorsions(), and size().

RMS_

core::Real protocols::loop_grower::LoopPartialSolution::RMS_ = 0

private

Referenced by get_rms(), and set_rms().

score_

core::Real protocols::loop_grower::LoopPartialSolution::score_

private

Referenced by get_score(), LoopPartialSolution(), operator<(), and set_score().

sheets_

utility::vector1< SheetPositions > protocols::loop_grower::LoopPartialSolution::sheets_

private

Referenced by push_back_sheet(), and store_sheetpositions().

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

• src/protocols/loop_grower/LoopGrower.hh
• src/protocols/loop_grower/LoopGrower.cc