protocols::simple_filters::RotamerBoltzmannWeight Class Reference

#include <RotamerBoltzmannWeight.hh>

Public Member Functions
	RotamerBoltzmannWeight ()
	default ctor More...
virtual bool	apply (core::pose::Pose const &pose) const
	Constructor with a single target residue. More...
virtual void	report (std::ostream &out, core::pose::Pose const &pose) const
virtual core::Real	report_sm (core::pose::Pose const &pose) const
	used to report filter internals through a score or silent file More...
virtual protocols::filters::FilterOP	clone () const
virtual protocols::filters::FilterOP	fresh_instance () const
core::Real	compute (core::pose::Pose const &pose) const
virtual	~RotamerBoltzmannWeight ()
core::pack::task::TaskFactoryOP	task_factory () const
void	task_factory (core::pack::task::TaskFactoryOP task_factory)
void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks)
utility::vector1< core::Size >	first_pass_ala_scan (core::pose::Pose const &pose) const
core::Real	compute_Boltzmann_weight (core::pose::Pose const &pose, core::Size const resi) const
void	rb_jump (core::Size const jump)
core::Size	rb_jump () const
void	sym_dof_names (std::string const dof_names)
std::string	sym_dof_names () const
void	repacking_radius (core::Real const rad)
core::Real	repacking_radius () const
core::Real	ddG_threshold () const
void	ddG_threshold (core::Real const ddG)
void	scorefxn (core::scoring::ScoreFunctionOP scorefxn)
core::scoring::ScoreFunctionOP	scorefxn () const
core::Real	temperature () const
void	temperature (core::Real const temp)
bool	unbound () const
void	unbound (bool const u)
void	threshold_probability (core::chemical::AA const aa_type, core::Real const probability)
core::Real	threshold_probability (core::chemical::AA const aa_type) const
void	energy_reduction_factor (core::Real const factor)
core::Real	energy_reduction_factor () const
core::Real	interface_interaction_energy (core::pose::Pose const &pose, core::Size const res) const
bool	compute_entropy_reduction () const
void	compute_entropy_reduction (bool const cer)
void	repack (bool const repack)
bool	repack () const
bool	skip_ala_scan () const
void	skip_ala_scan (bool const s)
std::string	type () const
void	type (std::string const &s)
bool	write2pdb () const
void	write2pdb (bool const write)
core::Real	compute_modified_ddG (core::pose::Pose const &pose, std::ostream &out) const
	Note that compute( pose ) needs to have been run first. This merely sums over the probabilities. More...
void	write_to_pdb (core::Size const residue, std::string const residue_name, core::Real const boltzmann_weight) const
	Output per-residue Boltzmann weights to the output pdb file if desired. More...
Public Member Functions inherited from protocols::filters::Filter
	Filter ()
	Filter (std::string const &)
	Filter (Filter const &)
virtual	~Filter ()
virtual std::string	get_type () const
std::string	get_user_defined_name () const
void	set_user_defined_name (std::string const &name)
virtual void	clear ()
	used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More...
virtual void	apply (core::io::serialization::PipeMap &pmap)
virtual void	score (core::io::serialization::PipeMap &pmap)
virtual core::Real	score (core::pose::Pose &pose)
virtual std::string	name () const

Private Types
typedef protocols::filters::Filter	parent

Private Attributes
core::pack::task::TaskFactoryOP	task_factory_
core::Size	rb_jump_
std::string	sym_dof_names_
bool	unbound_
core::scoring::ScoreFunctionOP	scorefxn_
core::Real	temperature_
core::Real	ddG_threshold_
core::Real	repacking_radius_
utility::vector1< core::Real >	threshold_probabilities_per_residue_
core::Real	energy_reduction_factor_
bool	compute_entropy_reduction_
bool	repack_
std::map< core::Size, core::Real >	ddGs_
std::map< core::Size, core::Real >	rotamer_probabilities_
std::string	type_
bool	skip_ala_scan_
bool	fast_calc_
bool	no_modified_ddG_
std::string	target_residues_
bool	write2pdb_

Additional Inherited Members
Protected Attributes inherited from protocols::filters::Filter
std::string	scorename_

Member Typedef Documentation

typedef protocols::filters::Filter protocols::simple_filters::RotamerBoltzmannWeight::parent

private

Constructor & Destructor Documentation

protocols::simple_filters::RotamerBoltzmannWeight::RotamerBoltzmannWeight

(

)

default ctor

References core::chemical::num_canonical_aas, and threshold_probabilities_per_residue_.

Referenced by clone(), protocols::simple_filters::RotamerBoltzmannWeightFilterCreator::create_filter(), and fresh_instance().

protocols::simple_filters::RotamerBoltzmannWeight::~RotamerBoltzmannWeight ( )

virtual

Member Function Documentation

bool protocols::simple_filters::RotamerBoltzmannWeight::apply ( core::pose::Pose const &  pose ) const

virtual

Constructor with a single target residue.

Implements protocols::filters::Filter.

protocols::filters::FilterOP protocols::simple_filters::RotamerBoltzmannWeight::clone ( ) const

virtual

Implements protocols::filters::Filter.

References RotamerBoltzmannWeight().

Referenced by parse_def().

core::Real protocols::simple_filters::RotamerBoltzmannWeight::compute

(

core::pose::Pose const &

pose

)

const

References core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_phe, core::chemical::aa_trp, core::chemical::aa_tyr, protocols::rigid::RigidBodyTransMover::apply(), protocols::toolbox::SelectResiduesByLayer::compute(), compute_Boltzmann_weight(), protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator::computeBoltzWeight(), ddGs_, fast_calc_, first_pass_ala_scan(), core::pose::get_resnum_list_ordered(), core::pose::symmetry::get_sym_aware_jump_num(), core::conformation::Residue::name3(), rb_jump(), repacking_radius(), core::pose::Pose::residue(), protocols::toolbox::SelectResiduesByLayer::restrict_aatypes_for_selection(), rotamer_probabilities_, scorefxn(), protocols::rigid::RigidBodyTransMover::step_size(), utility::string_split(), core::pose::symmetry::sym_dof_jump_num(), sym_dof_names(), target_residues_, temperature(), protocols::simple_filters::TR, protocols::stepwise::sampler::rigid_body::translate(), type_, unbound(), write2pdb(), and write_to_pdb().

Referenced by report(), and report_sm().

core::Real protocols::simple_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight	(	core::pose::Pose const &	pose,
		core::Size const	resi
	)		const

References protocols::simple_filters::ScoreTypeFilter::compute(), protocols::toolbox::task_operations::DesignAroundOperation::design_shell(), core::pose::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_movemap(), core::pack::make_symmetric_PackerTask_by_truncation(), core::pack::pack_rotamers(), core::pack::task::TaskFactory::push_back(), rb_jump(), repacking_radius(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pack::task::ResidueLevelTask::restrict_to_repacking(), protocols::filters::Filter::score(), scorefxn(), scorefxn_, core::pack::rotamer_set::RotamerSet::set_resid(), temperature(), core::pose::Pose::total_residue(), core::scoring::total_score, protocols::simple_filters::TR, and unbound().

Referenced by compute().

bool protocols::simple_filters::RotamerBoltzmannWeight::compute_entropy_reduction

(

)

const

References compute_entropy_reduction_.

Referenced by parse_def(), and parse_my_tag().

void protocols::simple_filters::RotamerBoltzmannWeight::compute_entropy_reduction

(

bool const

cer

)

References compute_entropy_reduction_.

core::Real protocols::simple_filters::RotamerBoltzmannWeight::compute_modified_ddG	(	core::pose::Pose const &	pose,
		std::ostream &	out
	)		const

Note that compute( pose ) needs to have been run first. This merely sums over the probabilities.

References core::conformation::Residue::aa(), protocols::simple_filters::DdgFilter::compute(), ddGs_, energy_reduction_factor(), log(), core::conformation::Residue::name3(), no_modified_ddG_, core::pose::Pose::pdb_info(), rb_jump(), protocols::simple_filters::DdgFilter::repack(), repack(), core::pose::Pose::residue(), rot(), rotamer_probabilities_, scorefxn(), temperature(), and threshold_probability().

Referenced by report(), and report_sm().

core::Real protocols::simple_filters::RotamerBoltzmannWeight::ddG_threshold

(

)

const

References ddG_threshold_.

Referenced by protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::apply(), first_pass_ala_scan(), parse_def(), and parse_my_tag().

void protocols::simple_filters::RotamerBoltzmannWeight::ddG_threshold

(

core::Real const

ddG

)

References ddG_threshold_.

void protocols::simple_filters::RotamerBoltzmannWeight::energy_reduction_factor

(

core::Real const

factor

)

References energy_reduction_factor_.

core::Real protocols::simple_filters::RotamerBoltzmannWeight::energy_reduction_factor

(

)

const

References energy_reduction_factor_.

Referenced by compute_modified_ddG(), parse_def(), and parse_my_tag().

utility::vector1< core::Size > protocols::simple_filters::RotamerBoltzmannWeight::first_pass_ala_scan

(

core::pose::Pose const &

pose

)

const

iterate over all packable residues according to the task factory and for each determine whether it contributes to binding at least ddG_threshold R.e.u. (using alanine scanning This list will later be used to do the Boltzmann weight calculations.

References ala_scan, protocols::simple_filters::DdgFilter::compute(), protocols::simple_filters::AlaScan::ddG_for_single_residue(), ddG_threshold(), ddGs_, core::conformation::Residue::is_protein(), protocols::simple_filters::AlaScan::jump(), core::conformation::Residue::name3(), rb_jump(), protocols::simple_filters::DdgFilter::repack(), protocols::simple_filters::AlaScan::repack(), repack(), protocols::simple_filters::AlaScan::repeats(), resi, core::pose::Pose::residue(), runtime_assert, protocols::simple_filters::AlaScan::scorefxn(), scorefxn(), skip_ala_scan(), task_factory(), core::pose::Pose::total_residue(), and protocols::simple_filters::TR.

Referenced by protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::apply(), and compute().

protocols::filters::FilterOP protocols::simple_filters::RotamerBoltzmannWeight::fresh_instance ( ) const

virtual

Implements protocols::filters::Filter.

References RotamerBoltzmannWeight().

core::Real protocols::simple_filters::RotamerBoltzmannWeight::interface_interaction_energy	(	core::pose::Pose const &	pose,
		core::Size const	res
	)		const

References core::conformation::Residue::chain(), core::scoring::EnergyEdge::dot(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::pose::Pose::residue(), scorefxn(), and core::scoring::Energies::weights().

void protocols::simple_filters::RotamerBoltzmannWeight::parse_def ( utility::lua::LuaObject const &  def, utility::lua::LuaObject const &  score_fxns, utility::lua::LuaObject const &  tasks  )

virtual

Reimplemented from protocols::filters::Filter.

References core::chemical::aa_from_name(), begin, clone(), compute_entropy_reduction(), ddG_threshold(), end, energy_reduction_factor(), fast_calc_, no_modified_ddG_, protocols::elscripts::parse_scoredef(), protocols::elscripts::parse_taskdef(), rb_jump(), repack(), repacking_radius(), scorefxn_, skip_ala_scan(), target_residues_, task_factory(), temperature(), threshold_probability(), utility::lua::LuaObject::to(), protocols::simple_filters::TR, type_, unbound(), and write2pdb().

void protocols::simple_filters::RotamerBoltzmannWeight::parse_my_tag ( utility::tag::TagCOP  tag, basic::datacache::DataMap &  data, protocols::filters::Filters_map const &  , protocols::moves::Movers_map const &  , core::pose::Pose const &    )

virtual

Reimplemented from protocols::filters::Filter.

References aa_from_name(), compute_entropy_reduction(), ddG_threshold(), energy_reduction_factor(), fast_calc_, no_modified_ddG_, protocols::rosetta_scripts::parse_score_function(), protocols::rosetta_scripts::parse_task_operations(), rb_jump(), repack(), repacking_radius(), scorefxn(), skip_ala_scan(), sym_dof_names(), target_residues_, task_factory(), temperature(), threshold_probability(), protocols::simple_filters::TR, type_, unbound(), and write2pdb().

void protocols::simple_filters::RotamerBoltzmannWeight::rb_jump

(

core::Size const

jump

)

References rb_jump_, and runtime_assert.

core::Size protocols::simple_filters::RotamerBoltzmannWeight::rb_jump

(

)

const

References rb_jump_.

Referenced by compute(), compute_Boltzmann_weight(), compute_modified_ddG(), first_pass_ala_scan(), parse_def(), and parse_my_tag().

void protocols::simple_filters::RotamerBoltzmannWeight::repack

(

bool const

repack

)

References repack(), and repack_.

bool protocols::simple_filters::RotamerBoltzmannWeight::repack

(

)

const

References repack_.

Referenced by compute_modified_ddG(), first_pass_ala_scan(), parse_def(), parse_my_tag(), and repack().

void protocols::simple_filters::RotamerBoltzmannWeight::repacking_radius

(

core::Real const

rad

)

References repacking_radius_.

Referenced by protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::apply().

core::Real protocols::simple_filters::RotamerBoltzmannWeight::repacking_radius

(

)

const

References repacking_radius_.

Referenced by compute(), compute_Boltzmann_weight(), parse_def(), and parse_my_tag().

void protocols::simple_filters::RotamerBoltzmannWeight::report ( std::ostream &  out, core::pose::Pose const &  pose  ) const

virtual

Reimplemented from protocols::filters::Filter.

References compute(), compute_modified_ddG(), core::conformation::Residue::name3(), no_modified_ddG_, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), rot(), rotamer_probabilities_, and type_.

core::Real protocols::simple_filters::RotamerBoltzmannWeight::report_sm ( core::pose::Pose const &  ) const

virtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute(), compute_modified_ddG(), no_modified_ddG_, rotamer_probabilities_, and protocols::simple_filters::TR.

void protocols::simple_filters::RotamerBoltzmannWeight::scorefxn

(

core::scoring::ScoreFunctionOP

scorefxn

)

References scorefxn(), and scorefxn_.

Referenced by protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::apply().

core::scoring::ScoreFunctionOP protocols::simple_filters::RotamerBoltzmannWeight::scorefxn

(

)

const

References scorefxn_.

Referenced by compute(), compute_Boltzmann_weight(), compute_modified_ddG(), first_pass_ala_scan(), interface_interaction_energy(), parse_my_tag(), and scorefxn().

bool protocols::simple_filters::RotamerBoltzmannWeight::skip_ala_scan

(

)

const

References skip_ala_scan_.

Referenced by first_pass_ala_scan(), parse_def(), and parse_my_tag().

void protocols::simple_filters::RotamerBoltzmannWeight::skip_ala_scan

(

bool const

s

)

References skip_ala_scan_.

void protocols::simple_filters::RotamerBoltzmannWeight::sym_dof_names

(

std::string const

dof_names

)

References sym_dof_names_.

std::string protocols::simple_filters::RotamerBoltzmannWeight::sym_dof_names

(

)

const

References sym_dof_names_.

Referenced by compute(), and parse_my_tag().

core::pack::task::TaskFactoryOP protocols::simple_filters::RotamerBoltzmannWeight::task_factory

(

)

const

References task_factory_.

Referenced by protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::apply(), first_pass_ala_scan(), parse_def(), parse_my_tag(), and task_factory().

void protocols::simple_filters::RotamerBoltzmannWeight::task_factory

(

core::pack::task::TaskFactoryOP

task_factory

)

References task_factory(), and task_factory_.

core::Real protocols::simple_filters::RotamerBoltzmannWeight::temperature

(

)

const

References temperature_.

Referenced by compute(), compute_Boltzmann_weight(), compute_modified_ddG(), parse_def(), and parse_my_tag().

void protocols::simple_filters::RotamerBoltzmannWeight::temperature

(

core::Real const

temp

)

References temperature_.

void protocols::simple_filters::RotamerBoltzmannWeight::threshold_probability	(	core::chemical::AA const	aa_type,
		core::Real const	probability
	)

References threshold_probabilities_per_residue_.

Referenced by compute_modified_ddG(), parse_def(), and parse_my_tag().

core::Real protocols::simple_filters::RotamerBoltzmannWeight::threshold_probability

(

core::chemical::AA const

aa_type

)

const

References threshold_probabilities_per_residue_.

std::string protocols::simple_filters::RotamerBoltzmannWeight::type

(

)

const

References type_.

void protocols::simple_filters::RotamerBoltzmannWeight::type

(

std::string const &

s

)

References type_.

bool protocols::simple_filters::RotamerBoltzmannWeight::unbound

(

)

const

References unbound_.

Referenced by compute(), compute_Boltzmann_weight(), parse_def(), and parse_my_tag().

void protocols::simple_filters::RotamerBoltzmannWeight::unbound

(

bool const

u

)

References unbound_.

bool protocols::simple_filters::RotamerBoltzmannWeight::write2pdb

(

)

const

References write2pdb_.

Referenced by compute(), parse_def(), and parse_my_tag().

void protocols::simple_filters::RotamerBoltzmannWeight::write2pdb

(

bool const

write

)

References write2pdb_.

void protocols::simple_filters::RotamerBoltzmannWeight::write_to_pdb	(	core::Size const	residue,
		std::string const	residue_name,
		core::Real const	boltzmann_weight
	)		const

Output per-residue Boltzmann weights to the output pdb file if desired.

References protocols::jd2::Job::add_string(), protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), and protocols::filters::Filter::get_user_defined_name().

Referenced by compute().

Member Data Documentation

bool protocols::simple_filters::RotamerBoltzmannWeight::compute_entropy_reduction_

private

Referenced by compute_entropy_reduction().

core::Real protocols::simple_filters::RotamerBoltzmannWeight::ddG_threshold_

private

Referenced by ddG_threshold().

std::map< core::Size, core::Real > protocols::simple_filters::RotamerBoltzmannWeight::ddGs_

mutableprivate

the following are mutable b/c they only sum up data in the filter. They do not affect how the filter is run (so the filter will remain logically constant, despite these variables) Mutability here allows the variables to be changed even in const methods.

Referenced by compute(), compute_modified_ddG(), and first_pass_ala_scan().

core::Real protocols::simple_filters::RotamerBoltzmannWeight::energy_reduction_factor_

private

Referenced by energy_reduction_factor().

bool protocols::simple_filters::RotamerBoltzmannWeight::fast_calc_

private

Referenced by compute(), parse_def(), and parse_my_tag().

bool protocols::simple_filters::RotamerBoltzmannWeight::no_modified_ddG_

private

Referenced by compute_modified_ddG(), parse_def(), parse_my_tag(), report(), and report_sm().

core::Size protocols::simple_filters::RotamerBoltzmannWeight::rb_jump_

private

Referenced by rb_jump().

bool protocols::simple_filters::RotamerBoltzmannWeight::repack_

private

Referenced by repack().

core::Real protocols::simple_filters::RotamerBoltzmannWeight::repacking_radius_

private

Referenced by repacking_radius().

std::map< core::Size, core::Real > protocols::simple_filters::RotamerBoltzmannWeight::rotamer_probabilities_

mutableprivate

Referenced by compute(), compute_modified_ddG(), report(), and report_sm().

core::scoring::ScoreFunctionOP protocols::simple_filters::RotamerBoltzmannWeight::scorefxn_

private

Referenced by compute_Boltzmann_weight(), parse_def(), and scorefxn().

bool protocols::simple_filters::RotamerBoltzmannWeight::skip_ala_scan_

private

Referenced by skip_ala_scan().

std::string protocols::simple_filters::RotamerBoltzmannWeight::sym_dof_names_

private

Referenced by sym_dof_names().

std::string protocols::simple_filters::RotamerBoltzmannWeight::target_residues_

private

Referenced by compute(), parse_def(), and parse_my_tag().

core::pack::task::TaskFactoryOP protocols::simple_filters::RotamerBoltzmannWeight::task_factory_

private

Referenced by task_factory().

core::Real protocols::simple_filters::RotamerBoltzmannWeight::temperature_

private

Referenced by temperature().

utility::vector1< core::Real > protocols::simple_filters::RotamerBoltzmannWeight::threshold_probabilities_per_residue_

private

Referenced by RotamerBoltzmannWeight(), and threshold_probability().

std::string protocols::simple_filters::RotamerBoltzmannWeight::type_

private

Referenced by compute(), parse_def(), parse_my_tag(), report(), and type().

bool protocols::simple_filters::RotamerBoltzmannWeight::unbound_

private

Referenced by unbound().

bool protocols::simple_filters::RotamerBoltzmannWeight::write2pdb_

private

Referenced by write2pdb().

---

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

• src/protocols/simple_filters/RotamerBoltzmannWeight.hh
• src/protocols/simple_filters/RotamerBoltzmannWeight.cc