protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers Class Reference

implementation of rosetta 2.x style rotamer explosion builds a whole bunch of extra rotamers, but only adds them to the set if they score better than a cutoff with a given set of target residues More...

#include <AddGood2BPairEnergyRotamers.hh>

Inheritance diagram for protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers:

Public Types
typedef core::pack::rotamer_set::RotamerSetOperation	parent
typedef core::Real	Real
typedef core::Size	Size

Public Member Functions
	AddGood2BPairEnergyRotamers (core::Size seqpos, core::Size ex_level, utility::vector1< core::Size > const &target_seqpos, Real score_cutoff, bool drop_rots_above_cutoff)
	~AddGood2BPairEnergyRotamers () override
core::pack::rotamer_set::RotamerSetOperationOP	clone () const override
void	alter_rotamer_set (core::pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn, core::pack::task::PackerTask const &ptask, utility::graph::GraphCOP packer_neighbor_graph, core::pack::rotamer_set::RotamerSet &rotamer_set) override
Real	get_res_res_score (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2, core::pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn) const
	helper function More...
void	set_debug (bool setting)
bool	rotamer_set_contains_rotamer (core::pack::rotamer_set::RotamerSet const &rotamer_set, core::conformation::Residue const &candidte_rot) const
	helper function to check if the passed in candi More...
Public Member Functions inherited from core::pack::rotamer_set::RotamerSetOperation
	RotamerSetOperation ()
	~RotamerSetOperation () override
virtual Real	increase_packer_residue_radius (pose::Pose const &pose, task::PackerTaskCOP the_task, core::Size residue_in) const

Private Attributes
core::Size	seqpos_
core::Size	ex_level_
utility::vector1< core::Size >	target_seqpos_
core::Real	score_cutoff_
bool	debug_
bool	disabled_

Detailed Description

implementation of rosetta 2.x style rotamer explosion builds a whole bunch of extra rotamers, but only adds them to the set if they score better than a cutoff with a given set of target residues

Member Typedef Documentation

parent

typedef core::pack::rotamer_set::RotamerSetOperation protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::parent

Real

typedef core::Real protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::Real

Size

typedef core::Size protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::Size

Constructor & Destructor Documentation

AddGood2BPairEnergyRotamers()

protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::AddGood2BPairEnergyRotamers	(	core::Size	seqpos,
		core::Size	ex_level,
		utility::vector1< core::Size > const &	target_seqpos,
		Real	score_cutoff,
		bool	drop_rots_above_cutoff
	)

~AddGood2BPairEnergyRotamers()

protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::~AddGood2BPairEnergyRotamers ( )

overridedefault

Member Function Documentation

alter_rotamer_set()

void protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::alter_rotamer_set ( core::pose::Pose const &  pose, core::scoring::ScoreFunction const &  sfxn, core::pack::task::PackerTask const &  ptask, utility::graph::GraphCOP  packer_neighbor_graph, core::pack::rotamer_set::RotamerSet &  rotamer_set  )

overridevirtual

strategy: 1. note energy of existing rotamer towards target seqpos

1. build extra rotamers as specified by ex-flag
2. evaluate score towards target, keep rotamers that have score below cutoff
3. little tricky: check against existing rotamer set to make sure that no rotamers get added twice
4. in case of demand, output rotamers that were kept to a file

Implements core::pack::rotamer_set::RotamerSetOperation.

References core::pack::rotamer_set::RotamerSet::add_rotamer_into_existing_group(), core::pack::task::PackerTask::clone(), core::pack::rotamer_set::RotamerSetFactory::create_rotamer_set(), debug_, disabled_, core::io::pdb::dump_pdb_residue(), ex_level_, protocols::abinitio::filename(), core::pack::rotamer_set::RotamerSet::get_n_residue_groups(), get_res_res_score(), core::pack::rotamer_set::RotamerSet::num_rotamers(), core::scoring::pair, protocols::toolbox::rotamer_set_operations::pair_first_sort_helper(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), rotamer_set_contains_rotamer(), score_cutoff_, core::conformation::Residue::seqpos(), seqpos_, target_seqpos_, core::id::to_string(), and protocols::toolbox::rotamer_set_operations::tr().

clone()

core::pack::rotamer_set::RotamerSetOperationOP protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::clone ( ) const

overridevirtual

Implements core::pack::rotamer_set::RotamerSetOperation.

get_res_res_score()

AddGood2BPairEnergyRotamers::Real protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::get_res_res_score	(	core::conformation::Residue const &	rsd1,
		core::conformation::Residue const &	rsd2,
		core::pose::Pose const &	pose,
		core::scoring::ScoreFunction const &	sfxn
	)		const

helper function

two things need to be done

1. easy: short range interactions
2. more cumbersome: long range stuff, need to duplicate some code from the scorefunction

References core::scoring::ScoreFunction::cd_lr_2b_methods_begin(), core::scoring::ScoreFunction::cd_lr_2b_methods_end(), core::scoring::ScoreFunction::ci_lr_2b_methods_begin(), core::scoring::ScoreFunction::ci_lr_2b_methods_end(), core::scoring::EMapVector::dot(), core::scoring::ScoreFunction::eval_cd_2b(), core::scoring::ScoreFunction::eval_ci_2b(), and core::scoring::ScoreFunction::weights().

Referenced by alter_rotamer_set().

rotamer_set_contains_rotamer()

bool protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::rotamer_set_contains_rotamer	(	core::pack::rotamer_set::RotamerSet const &	rotamer_set,
		core::conformation::Residue const &	candidte_rot
	)		const

helper function to check if the passed in candi

References core::conformation::Residue::chi(), core::pack::rotamer_set::RotamerSet::get_n_residue_groups(), core::pack::rotamer_set::RotamerSet::get_residue_group_begin(), core::conformation::Residue::name3(), core::conformation::Residue::nchi(), core::pack::rotamer_set::RotamerSet::num_rotamers(), and core::pack::rotamer_set::RotamerSet::rotamer().

Referenced by alter_rotamer_set().

set_debug()

void protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::set_debug ( bool  setting )

inline

References debug_.

Member Data Documentation

debug_

bool protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::debug_

private

Referenced by alter_rotamer_set(), and set_debug().

disabled_

bool protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::disabled_

private

Referenced by alter_rotamer_set().

ex_level_

core::Size protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::ex_level_

private

Referenced by alter_rotamer_set().

score_cutoff_

core::Real protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::score_cutoff_

private

Referenced by alter_rotamer_set().

seqpos_

core::Size protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::seqpos_

private

Referenced by alter_rotamer_set().

target_seqpos_

utility::vector1< core::Size > protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::target_seqpos_

private

Referenced by alter_rotamer_set().

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

• src/protocols/toolbox/rotamer_set_operations/AddGood2BPairEnergyRotamers.hh
• src/protocols/toolbox/rotamer_set_operations/AddGood2BPairEnergyRotamers.cc