protocols::simple_ddg::ddG Class Reference

#include <ddG.hh>

Inheritance diagram for protocols::simple_ddg::ddG:

Public Types
typedef core::Real	Real
typedef core::scoring::ScoreType	ScoreType
typedef core::pose::Pose	Pose
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP
typedef core::pose::Pose	Pose
typedef core::pose::PoseCOP	PoseCOP
typedef std::list< std::string >	Strings

Public Member Functions
	ddG ()
	ddG (core::scoring::ScoreFunctionCOP scorefxn_in, core::Size const jump=1)
	ddG (core::scoring::ScoreFunctionCOP scorefxn_in, core::Size const jump, utility::vector1< core::Size > const &chain_ids)
void	apply (Pose &pose) override
	Main Method. More...
void	clean_pose (Pose &pose_copy)
	removed water and virtual residues from pose to hopefully make its size match that of an input native More...
void	compute_rmsd_with_super (Pose const &pose, Real &input_rmsd_super, Real &input_rmsd)
	compute the rmsd of a pose to an input native with superposition More...
virtual void	calculate (Pose const &pose_in)
	compute the energy of the repacked complex in the bound and unbound states More...
virtual void	report_ddG (std::ostream &out) const
virtual Real	sum_bound () const
virtual Real	sum_unbound () const
virtual Real	sum_ddG () const
core::Size	rb_jump () const
void	rb_jump (core::Size j)
core::Size	repeats () const
void	repeats (core::Size repeats)
core::Real	translate_by () const
void	translate_by (core::Real translate_by)
utility::vector1< core::Size >	chain_ids () const
	Get the hard-set chain ids. Note these are not necessarily the only chains to be moved. More...
std::set< core::Size >	get_movable_jumps (core::pose::Pose const &pose) const
	~ddG () override
protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...
protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...
void	parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
protocols::moves::MoverOP	relax_mover () const
void	relax_mover (protocols::moves::MoverOP m)
protocols::filters::FilterOP	filter () const
void	filter (protocols::filters::FilterOP f)
void	task_factory (core::pack::task::TaskFactoryOP task_factory)
core::pack::task::TaskFactoryOP	task_factory () const
void	use_custom_task (bool uct)
bool	use_custom_task () const
void	repack_unbound (bool rpu)
bool	repack_unbound () const
void	repack_bound (bool rpb)
bool	repack_bound () const
void	relax_bound (bool rlb)
bool	relax_bound () const
void	relax_unbound (bool const rlu)
bool	relax_unbound () const
void	compute_rmsd (bool const crms)
bool	compute_rmsd () const
virtual void	scorefxn (core::scoring::ScoreFunctionCOP scorefxn_in)
void	dump_pdbs (bool dp)
bool	dump_pdbs () const
std::string	get_name () const override
	Each derived class must specify its name. The class name. More...
Public Member Functions inherited from protocols::moves::Mover
	Mover ()
virtual MoverOP	create ()
MoverCOP	get_self_ptr () const
MoverOP	get_self_ptr ()
MoverCAP	get_self_weak_ptr () const
MoverAP	get_self_weak_ptr ()
	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...
virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...
void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...
void	set_type (std::string const &setting)
	Set the 'type' string. More...
std::string	get_type () const
void	type (const std::string &type_in)
	Set the 'type' string. More...
std::string const &	type () const
	Get the set 'type' string. More...
virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...
virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
PoseCOP	get_input_pose () const
PoseCOP	get_native_pose () const
void	set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP	get_current_job () const
virtual void	set_current_tag (std::string const &new_tag)
std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...
virtual core::Real	last_proposal_density_ratio ()
virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
virtual Strings &	info ()
	non-const accessor More...
virtual Strings const &	info () const
	const accessor More...
virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static std::string	mover_name ()
static utility::tag::XMLSchemaComplexTypeGeneratorOP	define_ddG_schema ()
static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()
static void	register_options ()
	Overload this static method if you access options within the mover. More...

Private Member Functions
bool	unbind (Pose &pose) const
	Helper method to appropriately form unbound complex. Returns false if monomer. More...
void	setup_task (Pose const &pose)
void	duplicate_waters_across_jump (Pose &pose, core::Size jumpnum) const
void	setup_solvated_task (Pose const &pose, bool bound)
void	do_minimize (Pose &pose) const
void	fill_energy_vector (Pose const &pose, std::map< ScoreType, Real > &energy_map)
void	fill_per_residue_energy_vector (Pose const &pose, std::map< core::Size, Real > &energy_map)

Private Attributes
std::map< ScoreType, Real >	bound_energies_
std::map< ScoreType, Real >	unbound_energies_
std::map< core::Size, Real >	bound_per_residue_energies_
std::map< core::Size, Real >	unbound_per_residue_energies_
core::Size	repeats_
core::scoring::ScoreFunctionOP	scorefxn_
core::Size	rb_jump_
utility::vector1< core::Size >	chain_ids_
utility::vector1< std::string >	chain_names_
bool	per_residue_ddg_
bool	repack_unbound_
protocols::moves::MoverOP	relax_mover_
protocols::filters::FilterOP	filter_
core::pack::task::TaskFactoryOP	task_factory_
core::pack::task::PackerTaskOP	task_
bool	use_custom_task_
bool	repack_bound_
bool	relax_bound_
bool	relax_unbound_
bool	solvate_
bool	solvate_unbound_
bool	solvate_rbmin_
bool	min_water_jump_
core::energy_methods::PBLifetimeCacheOP	pb_cached_data_
	info carrier for poisson-boltzmann potential energy computation More...
bool	pb_enabled_
	true when PB potential is part of scorefxn More...
core::Real	translate_by_
	distance in A to separate moledules More...
core::pose::PoseOP	native_
core::Size	bound_HOH_
core::Size	bound_HOH_V_
core::Size	unbound_HOH_
core::Size	unbound_HOH_V_
bool	compute_rmsd_
core::Real	bound_rmsd_
core::Real	bound_rmsd_super_
bool	dump_pdbs_

Additional Inherited Members
Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Member Typedef Documentation

Pose

typedef core::pose::Pose protocols::simple_ddg::ddG::Pose

Real

typedef core::Real protocols::simple_ddg::ddG::Real

ScoreType

typedef core::scoring::ScoreType protocols::simple_ddg::ddG::ScoreType

Constructor & Destructor Documentation

ddG() [1/3]

protocols::simple_ddg::ddG::ddG

(

)

References bound_energies_, bound_per_residue_energies_, unbound_energies_, and unbound_per_residue_energies_.

ddG() [2/3]

protocols::simple_ddg::ddG::ddG	(	core::scoring::ScoreFunctionCOP	scorefxn_in,
		core::Size const	jump = 1
	)

References bound_energies_, bound_per_residue_energies_, core::scoring::PB_elec, pb_enabled_, scorefxn_, protocols::simple_ddg::TR(), unbound_energies_, and unbound_per_residue_energies_.

ddG() [3/3]

protocols::simple_ddg::ddG::ddG	(	core::scoring::ScoreFunctionCOP	scorefxn_in,
		core::Size const	jump,
		utility::vector1< core::Size > const &	chain_ids
	)

References bound_energies_, bound_per_residue_energies_, chain_ids(), chain_ids_, core::scoring::PB_elec, pb_enabled_, scorefxn_, protocols::simple_ddg::TR(), unbound_energies_, and unbound_per_residue_energies_.

~ddG()

protocols::simple_ddg::ddG::~ddG ( )

overridedefault

Member Function Documentation

apply()

void protocols::simple_ddg::ddG::apply ( Pose &  )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References bound_HOH_, bound_HOH_V_, bound_per_residue_energies_, bound_rmsd_, bound_rmsd_super_, calculate(), compute_rmsd(), core::pose::Pose::data(), core::pose::Pose::fold_tree(), native_, core::kinematics::FoldTree::num_jump(), pb_cached_data_, per_residue_ddg_, rb_jump(), repeats_, report_ddG(), scorefxn_, core::pose::setPoseExtraScore(), core::pose::Pose::size(), solvate_, sum_ddG(), protocols::simple_ddg::TR(), unbound_HOH_, unbound_HOH_V_, and unbound_per_residue_energies_.

calculate()

void protocols::simple_ddg::ddG::calculate ( pose::Pose const &  pose_original )

virtual

compute the energy of the repacked complex in the bound and unbound states

Parameters

pose_in

The base pose.

Returns

Nothing, but the base pose's cache be augmented with extra cached data if the scorefunction contains non-zero PB_elec term.

References protocols::simple_moves::DumpPdb::apply(), protocols::simple_moves::ExplicitWaterMover::apply(), core::scoring::automorphic_rmsd(), bound_energies_, bound_HOH_, bound_HOH_V_, bound_per_residue_energies_, bound_rmsd_, bound_rmsd_super_, compute_rmsd(), compute_rmsd_with_super(), core::pack::task::TaskFactory::create_packer_task(), protocols::jd2::current_output_name(), core::pose::Pose::data(), do_minimize(), core::kinematics::FoldTree::downstream_jump_residue(), dump_pdbs_, fill_energy_vector(), fill_per_residue_energy_vector(), core::pose::Pose::fold_tree(), get_movable_jumps(), core::conformation::Residue::is_ligand(), core::conformation::Residue::is_water(), protocols::moves::Mover::name(), core::conformation::Residue::name(), native_, core::pack::pack_rotamers(), core::scoring::methods::EnergyMethodOptions::pb_bound_tag(), pb_cached_data_, pb_enabled_, core::scoring::methods::EnergyMethodOptions::pb_unbound_tag(), core::import_pose::PDB_file, per_residue_ddg_, core::scoring::pointwater, core::import_pose::pose_from_file(), relax_bound(), relax_mover(), relax_unbound(), repack_bound(), repack_bound_, repack_unbound_, core::pose::Pose::residue(), scorefxn_, protocols::simple_moves::ExplicitWaterMover::set_gen_fixed(), protocols::simple_moves::ExplicitWaterMover::set_mode(), protocols::simple_moves::ExplicitWaterMover::set_taskop(), core::pose::setPoseExtraScore(), setup_solvated_task(), setup_task(), solvate_, solvate_unbound_, task_, core::pose::Pose::total_residue(), protocols::simple_ddg::TR(), unbind(), unbound_energies_, unbound_HOH_, unbound_HOH_V_, unbound_per_residue_energies_, and core::pose::Pose::update_residue_neighbors().

Referenced by apply(), protocols::simple_ddg::DdgFilter::compute(), and protocols::protein_interface_design::ddG_cycles().

chain_ids()

utility::vector1<core::Size> protocols::simple_ddg::ddG::chain_ids ( ) const

inline

Get the hard-set chain ids. Note these are not necessarily the only chains to be moved.

References chain_ids_.

Referenced by ddG(), and get_movable_jumps().

clean_pose()

void protocols::simple_ddg::ddG::clean_pose

(

pose::Pose &

pose_copy

)

removed water and virtual residues from pose to hopefully make its size match that of an input native

References core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_slow(), core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::is_water(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by compute_rmsd_with_super().

clone()

protocols::moves::MoverOP protocols::simple_ddg::ddG::clone ( ) const

overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

compute_rmsd() [1/2]

bool protocols::simple_ddg::ddG::compute_rmsd ( ) const

inline

References compute_rmsd_.

Referenced by apply(), and calculate().

compute_rmsd() [2/2]

void protocols::simple_ddg::ddG::compute_rmsd ( bool const  crms )

inline

References compute_rmsd_.

compute_rmsd_with_super()

void protocols::simple_ddg::ddG::compute_rmsd_with_super	(	pose::Pose const &	pose,
		core::Real &	input_rmsd_super,
		core::Real &	input_rmsd
	)

compute the rmsd of a pose to an input native with superposition

References clean_pose(), core::pose::Pose::fold_tree(), get_movable_jumps(), core::scoring::is_protein_CA(), native_, core::scoring::native_CA_rmsd(), core::kinematics::FoldTree::partition_by_jump(), core::scoring::rmsd_with_super_subset(), and core::pose::Pose::size().

Referenced by calculate().

define_ddG_schema()

utility::tag::XMLSchemaComplexTypeGeneratorOP protocols::simple_ddg::ddG::define_ddG_schema ( )

static

References core::scoring::attributes_for_parse_score_function(), core::pack::task::attributes_for_parse_task_operations(), protocols::moves::complex_type_name_for_mover(), and mover_name().

Referenced by protocols::pb_potential::SetupPoissonBoltzmannPotential::provide_xml_schema(), and provide_xml_schema().

do_minimize()

void protocols::simple_ddg::ddG::do_minimize ( Pose &  pose ) const

private

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_jump_that_builds_residue(), get_movable_jumps(), core::conformation::Residue::is_water(), min_water_jump_, core::pose::Pose::residue(), scorefxn_, solvate_rbmin_, and task_.

Referenced by calculate().

dump_pdbs() [1/2]

bool protocols::simple_ddg::ddG::dump_pdbs ( ) const

inline

References dump_pdbs_.

dump_pdbs() [2/2]

void protocols::simple_ddg::ddG::dump_pdbs ( bool  dp )

inline

References dump_pdbs_.

Referenced by protocols::simple_ddg::DdgFilter::compute().

duplicate_waters_across_jump()

void protocols::simple_ddg::ddG::duplicate_waters_across_jump ( Pose &  pose, core::Size  jumpnum  ) const

private

References core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::atom(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::fold_tree(), core::chemical::FULL_ATOM_t, core::conformation::Residue::is_water(), core::conformation::Residue::nbr_atom(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), core::pose::Pose::total_residue(), protocols::simple_ddg::TR(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

Referenced by unbind().

fill_energy_vector()

void protocols::simple_ddg::ddG::fill_energy_vector ( pose::Pose const &  pose, std::map< ScoreType, Real > &  energy_map  )

private

a private function for storing energy values

References core::pose::Pose::energies(), filter_, core::scoring::n_score_types, core::scoring::pro_close, scorefxn_, core::scoring::Energies::total_energies(), core::scoring::total_score, and protocols::simple_ddg::TR().

Referenced by calculate().

fill_per_residue_energy_vector()

void protocols::simple_ddg::ddG::fill_per_residue_energy_vector ( pose::Pose const &  pose, std::map< core::Size, Real > &  energy_map  )

private

References core::pose::Pose::energies(), protocols::buns::energy, filter_, core::scoring::n_score_types, core::scoring::pro_close, core::scoring::Energies::residue_total_energies(), scorefxn_, and core::pose::Pose::size().

Referenced by calculate().

filter() [1/2]

protocols::filters::FilterOP protocols::simple_ddg::ddG::filter

(

)

const

References filter_.

Referenced by protocols::simple_ddg::DdgFilter::compute(), and parse_my_tag().

filter() [2/2]

void protocols::simple_ddg::ddG::filter

(

protocols::filters::FilterOP

f

)

References filter_.

fresh_instance()

protocols::moves::MoverOP protocols::simple_ddg::ddG::fresh_instance ( ) const

inlineoverridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

get_movable_jumps()

std::set< core::Size > protocols::simple_ddg::ddG::get_movable_jumps

(

core::pose::Pose const &

pose

)

const

References chain_ids(), chain_ids_, chain_names_, core::pose::Pose::conformation(), core::pose::get_chain_ids_from_chain(), core::pose::get_jump_id_from_chain_id(), core::conformation::Conformation::num_chains(), core::pose::Pose::num_chains(), and rb_jump_.

Referenced by calculate(), compute_rmsd_with_super(), do_minimize(), setup_task(), and unbind().

get_name()

std::string protocols::simple_ddg::ddG::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

mover_name()

std::string protocols::simple_ddg::ddG::mover_name ( )

static

Referenced by define_ddG_schema(), get_name(), and protocols::simple_ddg::ddGCreator::keyname().

parse_my_tag()

void protocols::simple_ddg::ddG::parse_my_tag ( utility::tag::TagCOP  tag, basic::datacache::DataMap &  data  )

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References chain_ids_, chain_names_, compute_rmsd_, dump_pdbs_, filter(), min_water_jump_, protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_mover(), core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), core::scoring::PB_elec, pb_enabled_, per_residue_ddg_, rb_jump_, relax_bound_, relax_mover(), relax_unbound_, repack_bound_, repack_unbound_, repeats_, scorefxn_, solvate_, solvate_rbmin_, solvate_unbound_, task_factory(), protocols::simple_ddg::TR(), translate_by_, and use_custom_task().

provide_xml_schema()

void protocols::simple_ddg::ddG::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

References define_ddG_schema().

Referenced by protocols::simple_ddg::ddGCreator::provide_xml_schema().

rb_jump() [1/2]

core::Size protocols::simple_ddg::ddG::rb_jump ( ) const

inline

References rb_jump_.

Referenced by apply().

rb_jump() [2/2]

void protocols::simple_ddg::ddG::rb_jump ( core::Size  j )

inline

References rb_jump_.

relax_bound() [1/2]

bool protocols::simple_ddg::ddG::relax_bound ( ) const

inline

References relax_bound_.

Referenced by calculate().

relax_bound() [2/2]

void protocols::simple_ddg::ddG::relax_bound ( bool  rlb )

inline

References relax_bound_.

Referenced by protocols::simple_ddg::DdgFilter::compute().

relax_mover() [1/2]

protocols::moves::MoverOP protocols::simple_ddg::ddG::relax_mover ( ) const

inline

References relax_mover_.

Referenced by calculate(), protocols::simple_ddg::DdgFilter::compute(), and parse_my_tag().

relax_mover() [2/2]

void protocols::simple_ddg::ddG::relax_mover ( protocols::moves::MoverOP  m )

inline

References relax_mover_.

relax_unbound() [1/2]

bool protocols::simple_ddg::ddG::relax_unbound ( ) const

inline

References relax_unbound_.

Referenced by calculate().

relax_unbound() [2/2]

void protocols::simple_ddg::ddG::relax_unbound ( bool const  rlu )

inline

References relax_unbound_.

Referenced by protocols::simple_ddg::DdgFilter::compute().

repack_bound() [1/2]

bool protocols::simple_ddg::ddG::repack_bound ( ) const

inline

References repack_bound_.

Referenced by calculate().

repack_bound() [2/2]

void protocols::simple_ddg::ddG::repack_bound ( bool  rpb )

inline

References repack_bound_.

Referenced by protocols::simple_ddg::DdgFilter::compute().

repack_unbound() [1/2]

bool protocols::simple_ddg::ddG::repack_unbound ( ) const

inline

References repack_unbound_.

repack_unbound() [2/2]

void protocols::simple_ddg::ddG::repack_unbound ( bool  rpu )

inline

References repack_unbound_.

repeats() [1/2]

core::Size protocols::simple_ddg::ddG::repeats ( ) const

inline

References repeats_.

repeats() [2/2]

void protocols::simple_ddg::ddG::repeats ( core::Size  repeats )

inline

References repeats(), and repeats_.

Referenced by repeats().

report_ddG()

void protocols::simple_ddg::ddG::report_ddG ( std::ostream &  out ) const

virtual

output the ddG values

References bound_energies_, core::chemical::element::F, core::scoring::sasa::LJ, core::conformation::membrane::out, sum_bound(), sum_ddG(), sum_unbound(), and unbound_energies_.

Referenced by apply(), and protocols::simple_ddg::DdgFilter::compute().

scorefxn()

void protocols::simple_ddg::ddG::scorefxn ( core::scoring::ScoreFunctionCOP  scorefxn_in )

virtual

References scorefxn_.

setup_solvated_task()

void protocols::simple_ddg::ddG::setup_solvated_task ( Pose const &  pose, bool  bound  )

private

References core::pack::task::TaskFactory::create_packer_task(), core::conformation::Residue::is_water(), repack_bound_, repack_unbound_, core::pose::Pose::residue(), task_, and core::pack::task::ResidueLevelTask_::update_commutative().

Referenced by calculate().

setup_task()

void protocols::simple_ddg::ddG::setup_task ( pose::Pose const &  pose )

private

References protocols::simple_task_operations::RestrictToInterface::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), core::pack::task::operation::RestrictToRepacking::apply(), chain_ids_, chain_names_, core::pack::task::TaskFactory::create_packer_task(), protocols::simple_task_operations::RestrictToInterface::distance(), get_movable_jumps(), core::pose::symmetry::is_symmetric(), core::pack::make_symmetric_PackerTask_by_truncation(), protocols::simple_task_operations::InterfaceTaskOperation::set_movable_jumps(), task_, task_factory_, protocols::simple_ddg::TR(), and use_custom_task().

Referenced by calculate().

sum_bound()

Real protocols::simple_ddg::ddG::sum_bound ( ) const

virtual

returns energy sum of bound pose

References bound_energies_.

Referenced by report_ddG().

sum_ddG()

Real protocols::simple_ddg::ddG::sum_ddG ( ) const

virtual

returns the total ddG

References bound_energies_, and unbound_energies_.

Referenced by apply(), protocols::simple_ddg::DdgFilter::compute(), protocols::protein_interface_design::ddG_cycles(), and report_ddG().

sum_unbound()

Real protocols::simple_ddg::ddG::sum_unbound ( ) const

virtual

returns energy sum of unbound pose

References unbound_energies_.

Referenced by report_ddG().

task_factory() [1/2]

core::pack::task::TaskFactoryOP protocols::simple_ddg::ddG::task_factory ( ) const

inline

References task_factory_.

Referenced by parse_my_tag().

task_factory() [2/2]

void protocols::simple_ddg::ddG::task_factory ( core::pack::task::TaskFactoryOP  task_factory )

inline

References task_factory(), and task_factory_.

Referenced by protocols::simple_ddg::DdgFilter::compute(), and task_factory().

translate_by() [1/2]

core::Real protocols::simple_ddg::ddG::translate_by ( ) const

inline

References translate_by_.

Referenced by protocols::simple_ddg::DdgFilter::compute().

translate_by() [2/2]

void protocols::simple_ddg::ddG::translate_by ( core::Real  translate_by )

inline

References translate_by(), and translate_by_.

Referenced by translate_by().

unbind()

bool protocols::simple_ddg::ddG::unbind ( pose::Pose &  pose ) const

private

Helper method to appropriately form unbound complex. Returns false if monomer.

References core::pose::Pose::conformation(), duplicate_waters_across_jump(), get_movable_jumps(), core::pose::symmetry::is_symmetric(), solvate_, protocols::toolbox::rigid_body::translate(), and translate_by_.

Referenced by calculate().

use_custom_task() [1/2]

bool protocols::simple_ddg::ddG::use_custom_task ( ) const

inline

References use_custom_task_.

Referenced by parse_my_tag(), and setup_task().

use_custom_task() [2/2]

void protocols::simple_ddg::ddG::use_custom_task ( bool  uct )

inline

References use_custom_task_.

Referenced by protocols::simple_ddg::DdgFilter::compute().

Member Data Documentation

bound_energies_

std::map< ScoreType, Real > protocols::simple_ddg::ddG::bound_energies_

private

Referenced by calculate(), ddG(), report_ddG(), sum_bound(), and sum_ddG().

bound_HOH_

core::Size protocols::simple_ddg::ddG::bound_HOH_

private

Referenced by apply(), and calculate().

bound_HOH_V_

core::Size protocols::simple_ddg::ddG::bound_HOH_V_

private

Referenced by apply(), and calculate().

bound_per_residue_energies_

std::map< core::Size, Real > protocols::simple_ddg::ddG::bound_per_residue_energies_

private

Referenced by apply(), calculate(), and ddG().

bound_rmsd_

core::Real protocols::simple_ddg::ddG::bound_rmsd_

private

Referenced by apply(), and calculate().

bound_rmsd_super_

core::Real protocols::simple_ddg::ddG::bound_rmsd_super_

private

Referenced by apply(), and calculate().

chain_ids_

utility::vector1<core::Size> protocols::simple_ddg::ddG::chain_ids_

private

Referenced by chain_ids(), ddG(), get_movable_jumps(), parse_my_tag(), and setup_task().

chain_names_

utility::vector1<std::string> protocols::simple_ddg::ddG::chain_names_

private

Referenced by get_movable_jumps(), parse_my_tag(), and setup_task().

compute_rmsd_

bool protocols::simple_ddg::ddG::compute_rmsd_

private

Referenced by compute_rmsd(), and parse_my_tag().

dump_pdbs_

bool protocols::simple_ddg::ddG::dump_pdbs_

private

Referenced by calculate(), dump_pdbs(), and parse_my_tag().

filter_

protocols::filters::FilterOP protocols::simple_ddg::ddG::filter_

private

Referenced by fill_energy_vector(), fill_per_residue_energy_vector(), and filter().

min_water_jump_

bool protocols::simple_ddg::ddG::min_water_jump_

private

Referenced by do_minimize(), and parse_my_tag().

native_

core::pose::PoseOP protocols::simple_ddg::ddG::native_

private

Referenced by apply(), calculate(), and compute_rmsd_with_super().

pb_cached_data_

core::energy_methods::PBLifetimeCacheOP protocols::simple_ddg::ddG::pb_cached_data_

private

info carrier for poisson-boltzmann potential energy computation

Referenced by apply(), and calculate().

pb_enabled_

bool protocols::simple_ddg::ddG::pb_enabled_

private

true when PB potential is part of scorefxn

Referenced by calculate(), ddG(), and parse_my_tag().

per_residue_ddg_

bool protocols::simple_ddg::ddG::per_residue_ddg_

private

Referenced by apply(), calculate(), and parse_my_tag().

rb_jump_

core::Size protocols::simple_ddg::ddG::rb_jump_

private

Referenced by get_movable_jumps(), parse_my_tag(), and rb_jump().

relax_bound_

bool protocols::simple_ddg::ddG::relax_bound_

private

Referenced by parse_my_tag(), and relax_bound().

relax_mover_

protocols::moves::MoverOP protocols::simple_ddg::ddG::relax_mover_

private

Referenced by relax_mover().

relax_unbound_

bool protocols::simple_ddg::ddG::relax_unbound_

private

Referenced by parse_my_tag(), and relax_unbound().

repack_bound_

bool protocols::simple_ddg::ddG::repack_bound_

private

Referenced by calculate(), parse_my_tag(), repack_bound(), and setup_solvated_task().

repack_unbound_

bool protocols::simple_ddg::ddG::repack_unbound_

private

Referenced by calculate(), parse_my_tag(), repack_unbound(), and setup_solvated_task().

repeats_

core::Size protocols::simple_ddg::ddG::repeats_

private

Referenced by apply(), parse_my_tag(), and repeats().

scorefxn_

core::scoring::ScoreFunctionOP protocols::simple_ddg::ddG::scorefxn_

private

Referenced by apply(), calculate(), ddG(), do_minimize(), fill_energy_vector(), fill_per_residue_energy_vector(), parse_my_tag(), and scorefxn().

solvate_

bool protocols::simple_ddg::ddG::solvate_

private

Referenced by apply(), calculate(), parse_my_tag(), and unbind().

solvate_rbmin_

bool protocols::simple_ddg::ddG::solvate_rbmin_

private

Referenced by do_minimize(), and parse_my_tag().

solvate_unbound_

bool protocols::simple_ddg::ddG::solvate_unbound_

private

Referenced by calculate(), and parse_my_tag().

task_

core::pack::task::PackerTaskOP protocols::simple_ddg::ddG::task_

private

Referenced by calculate(), do_minimize(), setup_solvated_task(), and setup_task().

task_factory_

core::pack::task::TaskFactoryOP protocols::simple_ddg::ddG::task_factory_

private

Referenced by setup_task(), and task_factory().

translate_by_

core::Real protocols::simple_ddg::ddG::translate_by_

private

distance in A to separate moledules

Referenced by parse_my_tag(), translate_by(), and unbind().

unbound_energies_

std::map< ScoreType, Real > protocols::simple_ddg::ddG::unbound_energies_

private

Referenced by calculate(), ddG(), report_ddG(), sum_ddG(), and sum_unbound().

unbound_HOH_

core::Size protocols::simple_ddg::ddG::unbound_HOH_

private

Referenced by apply(), and calculate().

unbound_HOH_V_

core::Size protocols::simple_ddg::ddG::unbound_HOH_V_

private

Referenced by apply(), and calculate().

unbound_per_residue_energies_

std::map< core::Size, Real > protocols::simple_ddg::ddG::unbound_per_residue_energies_

private

Referenced by apply(), calculate(), and ddG().

use_custom_task_

bool protocols::simple_ddg::ddG::use_custom_task_

private

Referenced by use_custom_task().

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

• src/protocols/simple_ddg/ddG.hh
• src/protocols/simple_ddg/ddG.cc