#include <InterfaceAnalyzerMover.hh>

Inheritance diagram for protocols::analysis::InterfaceAnalyzerMover:

Collaboration diagram for protocols::analysis::InterfaceAnalyzerMover:

Public Types
typedef std::set< core::Size >	one_group

typedef std::pair< one_group, one_group >	group_pair

typedef utility::vector1 < group_pair >	group_set

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Public Member Functions
	InterfaceAnalyzerMover (core::Size interface_jump=1, bool const tracer=false, core::scoring::ScoreFunctionCOP sf=NULL, bool compute_packstat=false, bool pack_input=false, bool pack_separated=false, bool use_jobname=true)

	InterfaceAnalyzerMover (std::set< int > fixed_chains, bool const tracer=false, core::scoring::ScoreFunctionCOP sf=NULL, bool compute_packstat=false, bool pack_input=false, bool pack_separated=false, bool use_jobname=true)

virtual	~InterfaceAnalyzerMover ()

virtual protocols::moves::MoverOP	clone () const
	required in the context of the parser/scripting scheme More...

virtual protocols::moves::MoverOP	fresh_instance () const
	required in the context of the parser/scripting scheme More...

virtual void	parse_my_tag (utility::tag::TagPtr const, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

virtual void	apply (core::pose::Pose &pose)
	apply function will calculate data about the input pose. It is not intended to modify the pose itself (conformation and energies objects) although it may toss data into the DataCache or a Job object. More...

virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...

void	set_pose_info (core::pose::Pose const &pose)

void	use_tracer (bool const tracer)

virtual void	make_multichain_interface_set (core::pose::Pose &Pose, std::set< int > &fixed_chains)
	funtions to make interface sets needed More...

virtual void	make_interface_set (core::pose::Pose &pose)

virtual core::pose::Pose	make_separated_pose (core::pose::Pose &pose)
	assigns the complexed and separated poses for the entire mover More...

virtual core::Size	reorder_foldtree_find_jump (core::pose::Pose &pose, std::set< int > &fixed_chains)
	reorder the fold tree to allow multichain interfaces to be evaluated returns the jump number to use to define the interface More...

virtual void	compute_separated_sasa (core::pose::Pose &complexed_pose, core::pose::Pose &separated_pose)

virtual void	compute_interface_energy (core::pose::Pose &complexed_pose, core::pose::Pose &separated_pose)

virtual void	compute_interface_packstat (core::pose::Pose &pose)

virtual void	compute_interface_delta_hbond_unsat (core::pose::Pose &complexed_pose, core::pose::Pose &separated_pose)

virtual void	score_separated_chains (core::pose::Pose &complexed_pose, core::pose::Pose &separated_pose)

virtual void	report_data ()

void	set_use_resfile (bool const use_resfile)
	setters for the various parameters used by the analyze More...

bool	get_use_resfile () const

void	set_use_centroid_dG (bool const use_centroid)

bool	get_use_centroid_dG () const

void	set_compute_packstat (bool const compute_packstat)
	setters for various computations - each of these are expensive, so you can turn them off if desired More...

void	set_compute_interface_sc (bool const compute_interface_sc)

void	set_compute_separated_sasa (bool const compute_separated_sasa)

void	set_compute_interface_energy (bool const iface_en)

void	set_calc_hbond_sasaE (bool const calc_hbond_sasaE)

void	set_compute_interface_delta_hbond_unsat (bool const IDHU)

void	set_pack_input (bool const pack_input)

void	set_pack_separated (bool const pack_separated)

void	set_interface_jump (core::Size const interface_jump)

void	set_skip_reporting (bool const skip_reporting)

void	set_tracer (bool const tracer)

void	set_use_jobname (bool const use_jobname)

core::Real	get_total_sasa ()
	getters for the various parameters used by the analyzer More...

core::Real	get_interface_delta_sasa ()

core::Size	get_num_interface_residues ()

core::Real	get_complex_energy ()

core::Real	get_per_residue_energy ()

core::Real	get_separated_interface_energy ()

core::Real	get_crossterm_interface_energy ()

core::Real	get_separated_interface_energy_ratio ()

core::Real	get_crossterm_interface_energy_ratio ()

core::Real	get_interface_packstat ()

core::Size	get_interface_delta_hbond_unsat ()

core::Real	get_side1_score ()

core::Real	get_side2_score ()

core::Size	get_side1_nres ()

core::Size	get_side2_nres ()

std::string	get_pymol_sel_interface ()

std::string	get_pymol_sel_hbond_unsat ()

std::string	get_pymol_sel_packing ()

core::Real	get_interface_ddG () const

bool	get_multichain_constructor ()

std::set< int >	get_fixed_chains ()

std::set< core::Size >	get_interface_set ()

group_set	get_chain_groups ()

bool	get_pack_input ()

core::pack::task::PackerTaskOP	get_packer_task ()

core::Real	get_gly_interface_energy ()
	return the interface energy of an all glycine interface (like bb-bb energies) More...

core::Real	get_centroid_dG ()

core::Real	get_total_Hbond_E ()
	the exposure/possible ratio avg for hbonds in the interface More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

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...

void	set_current_tag (std::string const &new_tag)

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

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...

void	type (const std::string &type_in)

std::string	get_type () const

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...

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 bool	reinitialize_for_each_job () const
	this function informs 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
	this function informs 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...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
void	register_calculators ()
	registers the posemetric calculators More...

void	register_intergroup_calculator ()
	register calculator for multichain poses More...

void	setup_task (core::pose::Pose &pose)
	sets up the packer task within the mover More...

void	print_pymol_selection_of_interface_residues (core::pose::Pose const &pose, std::set< core::Size > const interface_set)

void	print_pymol_selection_of_hbond_unsat (core::pose::Pose &pose, utility::vector1< core::id::AtomID > delta_unsat_hbond_atid_vector)

void	print_pymol_selection_of_packing (core::pose::Pose const &pose, utility::vector1< core::Real > interface_pack_scores)

void	calc_per_residue_energy (core::pose::Pose pose)
	calculate the average energy per residue in the interface More...

void	mut_to_gly (core::pose::Pose complex_pose, core::pose::Pose separated_pose)
	mutate all residue in the interface to Gly and recalc the energy - not used right now More...

void	calc_centroid_dG (core::pose::Pose complex_pose, core::pose::Pose separated_pose)
	report the dG of a centroid pose with score3 More...

void	calc_hbond_sasaE (core::pose::Pose pose)
	fill in later More...

void	compute_interface_sc (core::Size &interface_jump, core::pose::Pose const &complexed_pose)
	find the interface shape compementarity value between the chains More...

Private Attributes
core::Size	interface_jump_
	jump to define which interface is interesting More...

std::set< int >	fixed_chains_

core::scoring::ScoreFunctionCOP	sf_
	scorefunction More...

utility::file::FileName	posename_

std::string	posename_base_

core::Size	chain1_

core::Size	chain2_

std::string	chain1_char_

std::string	chain2_char_

std::set< core::Size >	upstream_chains_

std::set< core::Size >	downstream_chains_

bool	tracer_
	output to tracer or PDB/silent file More...

bool	calcs_ready_
	are calculators ready? More...

bool	compute_packstat_
	bother with computing packstat More...

bool	compute_interface_sc_
	bother with computing interface sc More...

bool	compute_separated_sasa_
	skip this expensive calculation More...

bool	compute_interface_energy_
	skip this expensive calculation More...

bool	calc_hbond_sasaE_
	skip this expensive calculation More...

bool	compute_interface_delta_hbond_unsat_
	skip this expensive calculation More...

bool	skip_reporting_
	hush! be quiet! silence! More...

bool	multichain_constructor_
	which constructor are we using More...

bool	pack_input_
	pack the input pose More...

bool	pack_separated_
	pack the separated poses default is false More...

bool	use_jobname_
	just the jobname (true value) or the pose name (flase value) More...

bool	use_resfile_
	use a resfile during the pack_input and pack_separated operations More...

bool	use_centroid_
	skip the centroid_dG step, for incoming poses not centroid convertible More...

core::Real	ddG_
	interface energy More...

core::Real	total_sasa_

core::Real	interface_delta_sasa_

core::Real	interface_hsasa_

core::Real	interface_polar_sasa_

core::Size	n_interface_res_

core::Real	per_residue_energy_

core::Real	complex_energy_

core::Real	separated_interface_energy_

core::Real	crossterm_interface_energy_

core::Real	separated_interface_energy_ratio_

core::Real	crossterm_interface_energy_ratio_

core::Real	interface_packstat_

core::Real	gly_dG_
	Energy of a all Gly interface. More...

core::Real	centroid_dG_
	centroid_dG of interface More...

core::Size	delta_unsat_hbond_counter_
	number of unsat hbonds in complex More...

std::string	pymol_sel_interface_
	pymol style selections More...

std::string	pymol_sel_hbond_unsat_

std::string	pymol_sel_packing_

core::Real	side1_score_

core::Real	side2_score_

core::Size	nres_

core::Size	side1_nres_

core::Size	side2_nres_

core::Real	total_hb_E_
	avg hbond exposure ratio More...

core::Real	sc_value_
	shape complementarity values More...

std::set< core::Size >	interface_set_
	set of residues at the interface in question More...

group_set	chain_groups_
	group of residue ids of fixed chains and mobile chains (see typedef) More...

core::pack::task::PackerTaskOP	task_
	packer task used to repack pulled apart chains More...

std::string	Sasa_
	Sasa calculator name string. More...

std::string	InterfaceNeighborDefinition_
	InterfaceNeighborDefinition calculator name string. More...

std::string	InterfaceSasaDefinition_
	InterfaceSasaDefinition calculator name string. More...

std::string	InterfaceDeltaEnergetics_
	InterfaceDeltaEnergetics calculator name string. More...

std::string	NumberHBonds_
	NumberHBonds calculator name string. More...

std::string	BuriedUnsatisfiedPolars_
	BuriedUnsatisfiedPolars calculator name string. More...

std::string	InterGroupNeighborsCalculator_
	InterGroupNeighborsCalculator calculator name string. More...

Additional Inherited Members
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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...

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...

Detailed Description

Definition at line 41 of file InterfaceAnalyzerMover.hh.

Member Typedef Documentation

typedef std::pair< one_group, one_group > protocols::analysis::InterfaceAnalyzerMover::group_pair

Definition at line 46 of file InterfaceAnalyzerMover.hh.

typedef utility::vector1< group_pair > protocols::analysis::InterfaceAnalyzerMover::group_set

Definition at line 47 of file InterfaceAnalyzerMover.hh.

typedef std::set< core::Size > protocols::analysis::InterfaceAnalyzerMover::one_group

Definition at line 45 of file InterfaceAnalyzerMover.hh.

Constructor & Destructor Documentation

protocols::analysis::InterfaceAnalyzerMover::InterfaceAnalyzerMover	(	core::Size	interface_jump = `1`,
		bool const	tracer = `false`,
		core::scoring::ScoreFunctionCOP	sf = `NULL`,
		bool	compute_packstat = `false`,
		bool	pack_input = `false`,
		bool	pack_separated = `false`,
		bool	use_jobname = `true`
	)

Definition at line 140 of file InterfaceAnalyzerMover.cc.

References downstream_chains_, protocols::moves::Mover::type(), and upstream_chains_.

Referenced by clone(), and fresh_instance().

protocols::analysis::InterfaceAnalyzerMover::InterfaceAnalyzerMover	(	std::set< int >	fixed_chains,
		bool const	tracer = `false`,
		core::scoring::ScoreFunctionCOP	sf = `NULL`,
		bool	compute_packstat = `false`,
		bool	pack_input = `false`,
		bool	pack_separated = `false`,
		bool	use_jobname = `true`
	)

Definition at line 204 of file InterfaceAnalyzerMover.cc.

References downstream_chains_, protocols::moves::Mover::type(), and upstream_chains_.

protocols::analysis::InterfaceAnalyzerMover::~InterfaceAnalyzerMover ( )

virtual

Definition at line 281 of file InterfaceAnalyzerMover.cc.

Member Function Documentation

void protocols::analysis::InterfaceAnalyzerMover::apply ( core::pose::Pose & pose)

virtual

apply function will calculate data about the input pose. It is not intended to modify the pose itself (conformation and energies objects) although it may toss data into the DataCache or a Job object.

InterfaceAnalyzerMover computes various interface statistics and makes them available through getters

Implements protocols::moves::Mover.

Definition at line 328 of file InterfaceAnalyzerMover.cc.

References calc_centroid_dG(), calc_hbond_sasaE(), calc_hbond_sasaE_, calcs_ready_, compute_interface_delta_hbond_unsat(), compute_interface_delta_hbond_unsat_, compute_interface_energy(), compute_interface_energy_, compute_interface_packstat(), compute_interface_sc(), compute_interface_sc_, compute_packstat_, compute_separated_sasa(), compute_separated_sasa_, core::pose::Pose::conformation(), get_fixed_chains(), interface_jump_, interface_set_, make_interface_set(), make_separated_pose(), multichain_constructor_, core::conformation::Conformation::num_chains(), print_pymol_selection_of_interface_residues(), register_calculators(), reorder_foldtree_find_jump(), report_data(), set_pose_info(), setup_task(), skip_reporting_, protocols::TR(), and use_centroid_.

void protocols::analysis::InterfaceAnalyzerMover::calc_centroid_dG	(	core::pose::Pose	complex_pose,
		core::pose::Pose	separated_pose
	)

private

report the dG of a centroid pose with score3

Definition at line 1382 of file InterfaceAnalyzerMover.cc.

References core::chemical::CENTROID, centroid_dG_, core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::rg, core::util::switch_to_residue_type_set(), protocols::TR(), and use_centroid_.

Referenced by apply().

void protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE ( core::pose::Pose pose)

private

fill in later

calculate the hbond energy and dampen it by exposure

Definition at line 1127 of file InterfaceAnalyzerMover.cc.

References core::pose::Pose::chain(), core::id::AtomID_Map< T >::clear(), core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies(), core::scoring::hbonds::HBond::don_res(), fixed_chains_, core::scoring::getScoreFunction(), core::scoring::methods::EnergyMethodOptions::hbond_options(), multichain_constructor_, core::pose::Pose::n_residue(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nheavyatoms(), core::pose::Pose::residue_type(), total_hb_E_, protocols::TR(), and core::pose::Pose::update_residue_neighbors().

Referenced by apply(), and set_calc_hbond_sasaE().

void protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_energy ( core::pose::Pose pose)

private

calculate the average energy per residue in the interface

Definition at line 1111 of file InterfaceAnalyzerMover.cc.

References core::sequence::end, core::pose::Pose::energies(), interface_set_, n_interface_res_, per_residue_energy_, core::scoring::Energies::residue_total_energies(), and core::scoring::total_score.

Referenced by compute_interface_energy().

protocols::moves::MoverOP protocols::analysis::InterfaceAnalyzerMover::clone ( ) const

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

Definition at line 1500 of file InterfaceAnalyzerMover.cc.

References InterfaceAnalyzerMover().

void protocols::analysis::InterfaceAnalyzerMover::compute_interface_delta_hbond_unsat	(	core::pose::Pose &	complexed_pose,
		core::pose::Pose &	separated_pose
	)

virtual

If a polar atom at the interface is also "buried unsat" in the monomer, we don't count this one

Definition at line 804 of file InterfaceAnalyzerMover.cc.

References BuriedUnsatisfiedPolars_, delta_unsat_hbond_counter_, core::sequence::end, interface_set_, make_interface_set(), core::pose::Pose::metric(), print_pymol_selection_of_hbond_unsat(), core::pose::Pose::residue_type(), and protocols::TR().

Referenced by apply().

void protocols::analysis::InterfaceAnalyzerMover::compute_interface_energy	(	core::pose::Pose &	complexed_pose,
		core::pose::Pose &	separated_pose
	)

virtual

computes the interface energy of the interface

Definition at line 624 of file InterfaceAnalyzerMover.cc.

References calc_per_residue_energy(), crossterm_interface_energy_, crossterm_interface_energy_ratio_, core::pose::Pose::energies(), interface_delta_sasa_, InterfaceDeltaEnergetics_, InterfaceNeighborDefinition_, core::pose::Pose::metric(), nres_, core::scoring::Energies::residue_total_energy(), score_separated_chains(), separated_interface_energy_, separated_interface_energy_ratio_, side1_nres_, side1_score_, side2_nres_, side2_score_, and core::pose::Pose::total_residue().

Referenced by apply().

void protocols::analysis::InterfaceAnalyzerMover::compute_interface_packstat ( core::pose::Pose & pose)

virtual

Averaged packstat of interface residues only

Definition at line 777 of file InterfaceAnalyzerMover.cc.

References core::scoring::packstat::compute_residue_packing_scores(), core::sequence::end, interface_packstat_, interface_set_, make_interface_set(), print_pymol_selection_of_packing(), and protocols::TR().

Referenced by apply().

void protocols::analysis::InterfaceAnalyzerMover::compute_interface_sc	(	core::Size &	interface_jump,
		core::pose::Pose const &	complexed_pose
	)

private

find the interface shape compementarity value between the chains

Definition at line 1311 of file InterfaceAnalyzerMover.cc.

References core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::scoring::sc::ShapeComplementarityCalculator::Calc(), core::pose::Pose::chain(), downstream_chains_, core::sequence::end, core::scoring::sc::MolecularSurfaceCalculator::GetResults(), core::pose::Pose::n_residue(), core::pose::Pose::residue(), core::scoring::sc::_RESULTS::sc, sc_value_, protocols::TR(), and upstream_chains_.

Referenced by apply(), and set_compute_interface_sc().

void protocols::analysis::InterfaceAnalyzerMover::compute_separated_sasa	(	core::pose::Pose &	complexed_pose,
		core::pose::Pose &	separated_pose
	)

virtual

computes the SASA by finding difference between complex and separated SASA also does the same thing for hydrophobic/polar SASA

Definition at line 590 of file InterfaceAnalyzerMover.cc.

References core::scoring::calc_per_res_hydrophobic_sasa(), interface_delta_sasa_, interface_hsasa_, interface_polar_sasa_, core::pose::Pose::metric(), Sasa_, core::pose::Pose::total_residue(), and total_sasa_.

Referenced by apply(), and set_compute_separated_sasa().

protocols::moves::MoverOP protocols::analysis::InterfaceAnalyzerMover::fresh_instance ( ) const

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

Definition at line 1493 of file InterfaceAnalyzerMover.cc.

References InterfaceAnalyzerMover().

core::Real protocols::analysis::InterfaceAnalyzerMover::get_centroid_dG ( )

Definition at line 307 of file InterfaceAnalyzerMover.cc.

References centroid_dG_.

InterfaceAnalyzerMover::group_set protocols::analysis::InterfaceAnalyzerMover::get_chain_groups ( )

Definition at line 303 of file InterfaceAnalyzerMover.cc.

References chain_groups_.

core::Real protocols::analysis::InterfaceAnalyzerMover::get_complex_energy ( )

Definition at line 290 of file InterfaceAnalyzerMover.cc.

References complex_energy_.

core::Real protocols::analysis::InterfaceAnalyzerMover::get_crossterm_interface_energy ( )

Definition at line 292 of file InterfaceAnalyzerMover.cc.

References crossterm_interface_energy_.

core::Real protocols::analysis::InterfaceAnalyzerMover::get_crossterm_interface_energy_ratio ( )

Definition at line 294 of file InterfaceAnalyzerMover.cc.

References crossterm_interface_energy_ratio_.

std::set< int > protocols::analysis::InterfaceAnalyzerMover::get_fixed_chains ( )

Definition at line 301 of file InterfaceAnalyzerMover.cc.

References fixed_chains_.

Referenced by apply().

core::Real protocols::analysis::InterfaceAnalyzerMover::get_gly_interface_energy ( )

return the interface energy of an all glycine interface (like bb-bb energies)

Definition at line 306 of file InterfaceAnalyzerMover.cc.

References gly_dG_.

core::Real protocols::analysis::InterfaceAnalyzerMover::get_interface_ddG ( ) const

Definition at line 283 of file InterfaceAnalyzerMover.cc.

References ddG_.

core::Size protocols::analysis::InterfaceAnalyzerMover::get_interface_delta_hbond_unsat ( )

Definition at line 296 of file InterfaceAnalyzerMover.cc.

References delta_unsat_hbond_counter_.

core::Real protocols::analysis::InterfaceAnalyzerMover::get_interface_delta_sasa ( )

Definition at line 287 of file InterfaceAnalyzerMover.cc.

References interface_delta_sasa_.

core::Real protocols::analysis::InterfaceAnalyzerMover::get_interface_packstat ( )

Definition at line 295 of file InterfaceAnalyzerMover.cc.

References interface_packstat_.

std::set< core::Size > protocols::analysis::InterfaceAnalyzerMover::get_interface_set ( )

Definition at line 302 of file InterfaceAnalyzerMover.cc.

References interface_set_.

bool protocols::analysis::InterfaceAnalyzerMover::get_multichain_constructor ( )

Definition at line 300 of file InterfaceAnalyzerMover.cc.

References multichain_constructor_.

std::string protocols::analysis::InterfaceAnalyzerMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 417 of file InterfaceAnalyzerMover.cc.

core::Size protocols::analysis::InterfaceAnalyzerMover::get_num_interface_residues ( )

Definition at line 289 of file InterfaceAnalyzerMover.cc.

References n_interface_res_.

bool protocols::analysis::InterfaceAnalyzerMover::get_pack_input ( )

Definition at line 304 of file InterfaceAnalyzerMover.cc.

References pack_input_.

core::pack::task::PackerTaskOP protocols::analysis::InterfaceAnalyzerMover::get_packer_task ( )

Definition at line 305 of file InterfaceAnalyzerMover.cc.

References task_.

core::Real protocols::analysis::InterfaceAnalyzerMover::get_per_residue_energy ( )

Definition at line 291 of file InterfaceAnalyzerMover.cc.

References per_residue_energy_.

std::string protocols::analysis::InterfaceAnalyzerMover::get_pymol_sel_hbond_unsat ( )

Definition at line 298 of file InterfaceAnalyzerMover.cc.

References pymol_sel_hbond_unsat_.

std::string protocols::analysis::InterfaceAnalyzerMover::get_pymol_sel_interface ( )

Definition at line 297 of file InterfaceAnalyzerMover.cc.

References pymol_sel_interface_.

std::string protocols::analysis::InterfaceAnalyzerMover::get_pymol_sel_packing ( )

Definition at line 299 of file InterfaceAnalyzerMover.cc.

References pymol_sel_packing_.

core::Real protocols::analysis::InterfaceAnalyzerMover::get_separated_interface_energy ( )

Definition at line 288 of file InterfaceAnalyzerMover.cc.

References separated_interface_energy_.

core::Real protocols::analysis::InterfaceAnalyzerMover::get_separated_interface_energy_ratio ( )

Definition at line 293 of file InterfaceAnalyzerMover.cc.

References separated_interface_energy_ratio_.

core::Size protocols::analysis::InterfaceAnalyzerMover::get_side1_nres ( )

inline

Definition at line 157 of file InterfaceAnalyzerMover.hh.

References side1_nres_.

core::Real protocols::analysis::InterfaceAnalyzerMover::get_side1_score ( )

inline

Definition at line 155 of file InterfaceAnalyzerMover.hh.

References side1_score_.

core::Size protocols::analysis::InterfaceAnalyzerMover::get_side2_nres ( )

inline

Definition at line 158 of file InterfaceAnalyzerMover.hh.

References side2_nres_.

core::Real protocols::analysis::InterfaceAnalyzerMover::get_side2_score ( )

inline

Definition at line 156 of file InterfaceAnalyzerMover.hh.

References side2_score_.

core::Real protocols::analysis::InterfaceAnalyzerMover::get_total_Hbond_E ( )

the exposure/possible ratio avg for hbonds in the interface

total hbond energy for pose

Definition at line 310 of file InterfaceAnalyzerMover.cc.

References total_hb_E_.

core::Real protocols::analysis::InterfaceAnalyzerMover::get_total_sasa ( )

getters for the various parameters used by the analyzer

getters

Definition at line 286 of file InterfaceAnalyzerMover.cc.

References total_sasa_.

bool protocols::analysis::InterfaceAnalyzerMover::get_use_centroid_dG ( ) const

Definition at line 313 of file InterfaceAnalyzerMover.cc.

References use_centroid_.

bool protocols::analysis::InterfaceAnalyzerMover::get_use_resfile ( ) const

Definition at line 312 of file InterfaceAnalyzerMover.cc.

References use_resfile_.

void protocols::analysis::InterfaceAnalyzerMover::make_interface_set ( core::pose::Pose & pose)

virtual

makes the interface sets for either constructor

Definition at line 445 of file InterfaceAnalyzerMover.cc.

References fixed_chains_, interface_set_, InterfaceNeighborDefinition_, make_multichain_interface_set(), core::pose::Pose::metric(), multichain_constructor_, posename_base_, and protocols::TR().

Referenced by apply(), compute_interface_delta_hbond_unsat(), and compute_interface_packstat().

void protocols::analysis::InterfaceAnalyzerMover::make_multichain_interface_set	(	core::pose::Pose &	Pose,
		std::set< int > &	fixed_chains
	)

virtual

funtions to make interface sets needed

Definition at line 519 of file InterfaceAnalyzerMover.cc.

References core::pose::Pose::chain(), chain_groups_, downstream_chains_, interface_set_, InterGroupNeighborsCalculator_, core::pose::Pose::metric(), register_intergroup_calculator(), core::pose::Pose::total_residue(), and upstream_chains_.

Referenced by make_interface_set().

core::pose::Pose protocols::analysis::InterfaceAnalyzerMover::make_separated_pose ( core::pose::Pose & pose)

virtual

assigns the complexed and separated poses for the entire mover

makes the complexed and separated poses for the mover

Definition at line 567 of file InterfaceAnalyzerMover.cc.

References core::scoring::getScoreFunction(), interface_jump_, sf_, protocols::TR(), and protocols::swa::translate().

Referenced by apply().

void protocols::analysis::InterfaceAnalyzerMover::mut_to_gly	(	core::pose::Pose	complex_pose,
		core::pose::Pose	separated_pose
	)

private

mutate all residue in the interface to Gly and recalc the energy - not used right now

Mutate all residues to GlY rescore complex energy and separated energy

Definition at line 1348 of file InterfaceAnalyzerMover.cc.

References core::chemical::aa_from_oneletter_code(), core::pack::task::TaskFactory::create_packer_task(), core::sequence::end, gly_dG_, interface_set_, core::chemical::num_canonical_aas, sf_, core::pose::Pose::total_residue(), and protocols::TR().

void protocols::analysis::InterfaceAnalyzerMover::parse_my_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::DataMap &	datamap,
		protocols::filters::Filters_map const &	,
		protocols::moves::Movers_map const &	,
		core::pose::Pose const &	pose
	)

virtual

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

parse XML (specifically in the context of the parser/scripting scheme)

Reimplemented from protocols::moves::Mover.

Definition at line 1432 of file InterfaceAnalyzerMover.cc.

References core::pose::Pose::chain(), fixed_chains_, multichain_constructor_, protocols::rosetta_scripts::parse_score_function(), core::pose::Pose::pdb_info(), set_compute_interface_sc(), set_compute_packstat(), set_interface_jump(), set_pack_input(), set_pack_separated(), set_tracer(), set_use_jobname(), set_use_resfile(), sf_, core::pose::Pose::total_residue(), and protocols::TR().

void protocols::analysis::InterfaceAnalyzerMover::print_pymol_selection_of_hbond_unsat	(	core::pose::Pose &	pose,
		utility::vector1< core::id::AtomID >	delta_unsat_hbond_atid_vector
	)

private

This function reports a few things: a pymol sytle selection of the unstat atoms and reports to the tracer or job what these atoms are. The app InterfaceAnalyzer gets the multi-line string to write a file or print the selection. Unsat hbonds to be shown as Spheres

Definition at line 934 of file InterfaceAnalyzerMover.cc.

References core::conformation::Residue::atom_name(), protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), core::pose::Pose::pdb_info(), posename_base_, pymol_sel_hbond_unsat_, core::pose::Pose::residue(), core::pack::interaction_graph::T(), tracer_, TRhbonds(), and protocols::analysis::which_ostream().

Referenced by compute_interface_delta_hbond_unsat().

void protocols::analysis::InterfaceAnalyzerMover::print_pymol_selection_of_interface_residues	(	core::pose::Pose const &	pose,
		std::set< core::Size > const	interface_set
	)

private

prints tracer output of pymol selction of interface residues, also builds a pymol selection that can be used from a file.

Definition at line 871 of file InterfaceAnalyzerMover.cc.

References compute_packstat_, protocols::nonlocal::current_job(), core::sequence::end, protocols::jd2::JobDistributor::get_instance(), core::pose::Pose::pdb_info(), posename_base_, pymol_sel_interface_, tracer_, TRinterface(), and protocols::analysis::which_ostream().

Referenced by apply().

void protocols::analysis::InterfaceAnalyzerMover::print_pymol_selection_of_packing	(	core::pose::Pose const &	pose,
		utility::vector1< core::Real >	interface_pack_scores
	)

private

This function doesn't do the printing itself. The app InterfaceAnalyzer gets the multi-line string to write a file or print the selection

From best packing to worse packing, colors go as Blue, Purple, Pink, Red

Definition at line 1002 of file InterfaceAnalyzerMover.cc.

References core::pose::Pose::pdb_info(), posename_base_, pymol_sel_packing_, and core::pose::Pose::total_residue().

Referenced by compute_interface_packstat().

void protocols::analysis::InterfaceAnalyzerMover::register_calculators ( )

private

registers the posemetric calculators

Only want to register the calculators once, thus the 'if' statement in apply

Definition at line 1031 of file InterfaceAnalyzerMover.cc.

References BuriedUnsatisfiedPolars_, chain1_, chain2_, interface_jump_, InterfaceDeltaEnergetics_, InterfaceNeighborDefinition_, InterfaceSasaDefinition_, NumberHBonds_, and Sasa_.

Referenced by apply().

void protocols::analysis::InterfaceAnalyzerMover::register_intergroup_calculator ( )

private

register calculator for multichain poses

Definition at line 1098 of file InterfaceAnalyzerMover.cc.

References chain_groups_, InterGroupNeighborsCalculator_, and posename_base_.

Referenced by make_multichain_interface_set().

core::Size protocols::analysis::InterfaceAnalyzerMover::reorder_foldtree_find_jump	(	core::pose::Pose &	pose,
		std::set< int > &	fixed_chains
	)

virtual

reorder the fold tree to allow multichain interfaces to be evaluated returns the jump number to use to define the interface

reorder the fold tree to allow multichain interfaces to be evaluated returns the new chain for the jump

Definition at line 462 of file InterfaceAnalyzerMover.cc.

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), and core::conformation::Conformation::num_chains().

Referenced by apply().

void protocols::analysis::InterfaceAnalyzerMover::report_data ( )

virtual

reports all the cool stuff we calculate to tracer output OR puts it into the job object.

Definition at line 706 of file InterfaceAnalyzerMover.cc.

References centroid_dG_, complex_energy_, compute_interface_sc_, compute_packstat_, crossterm_interface_energy_, crossterm_interface_energy_ratio_, protocols::nonlocal::current_job(), delta_unsat_hbond_counter_, protocols::jd2::JobDistributor::get_instance(), interface_delta_sasa_, interface_hsasa_, interface_packstat_, interface_polar_sasa_, n_interface_res_, nres_, per_residue_energy_, posename_base_, sc_value_, separated_interface_energy_, separated_interface_energy_ratio_, side1_nres_, side1_score_, side2_nres_, side2_score_, core::pack::interaction_graph::T(), total_hb_E_, total_sasa_, tracer_, and use_centroid_.

Referenced by apply().

void protocols::analysis::InterfaceAnalyzerMover::score_separated_chains	(	core::pose::Pose &	complexed_pose,
		core::pose::Pose &	separated_pose
	)

virtual

actual function to separate the chains based on the chosen jump and score

Definition at line 665 of file InterfaceAnalyzerMover.cc.

References complex_energy_, ddG_, pack_input_, pack_separated_, separated_interface_energy_, sf_, and task_.

Referenced by compute_interface_energy().

void protocols::analysis::InterfaceAnalyzerMover::set_calc_hbond_sasaE ( bool const calc_hbond_sasaE)

inline

Definition at line 129 of file InterfaceAnalyzerMover.hh.

References calc_hbond_sasaE(), and calc_hbond_sasaE_.

void protocols::analysis::InterfaceAnalyzerMover::set_compute_interface_delta_hbond_unsat ( bool const IDHU)

inline

Definition at line 130 of file InterfaceAnalyzerMover.hh.

References compute_interface_delta_hbond_unsat_.

void protocols::analysis::InterfaceAnalyzerMover::set_compute_interface_energy ( bool const iface_en)

inline

Definition at line 128 of file InterfaceAnalyzerMover.hh.

References compute_interface_energy_.

void protocols::analysis::InterfaceAnalyzerMover::set_compute_interface_sc ( bool const compute_interface_sc)

inline

Definition at line 126 of file InterfaceAnalyzerMover.hh.

References compute_interface_sc(), and compute_interface_sc_.

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::set_compute_packstat ( bool const compute_packstat)

setters for various computations - each of these are expensive, so you can turn them off if desired

Definition at line 318 of file InterfaceAnalyzerMover.cc.

References compute_packstat_.

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::set_compute_separated_sasa ( bool const compute_separated_sasa)

inline

Definition at line 127 of file InterfaceAnalyzerMover.hh.

References compute_separated_sasa(), and compute_separated_sasa_.

void protocols::analysis::InterfaceAnalyzerMover::set_interface_jump ( core::Size const interface_jump)

Definition at line 320 of file InterfaceAnalyzerMover.cc.

References interface_jump_.

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::set_pack_input ( bool const pack_input)

Definition at line 319 of file InterfaceAnalyzerMover.cc.

References pack_input_.

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::set_pack_separated ( bool const pack_separated)

Definition at line 324 of file InterfaceAnalyzerMover.cc.

References pack_separated_.

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::set_pose_info ( core::pose::Pose const & pose)

sets up the pose information such as the name and chain ids

Definition at line 422 of file InterfaceAnalyzerMover.cc.

References chain1_, chain1_char_, chain2_, chain2_char_, core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), protocols::nonlocal::current_job(), downstream_chains_, core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), protocols::jd2::JobDistributor::get_instance(), interface_jump_, protocols::jd2::JobDistributor::job_outputter(), core::pose::Pose::pdb_info(), posename_, posename_base_, core::pose::Pose::residue(), upstream_chains_, core::kinematics::FoldTree::upstream_jump_residue(), and use_jobname_.

Referenced by apply().

void protocols::analysis::InterfaceAnalyzerMover::set_skip_reporting ( bool const skip_reporting)

inline

Definition at line 137 of file InterfaceAnalyzerMover.hh.

References skip_reporting_.

void protocols::analysis::InterfaceAnalyzerMover::set_tracer ( bool const tracer)

Definition at line 321 of file InterfaceAnalyzerMover.cc.

References protocols::frag_picker::tracer(), and tracer_.

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::set_use_centroid_dG ( bool const use_centroid)

Definition at line 317 of file InterfaceAnalyzerMover.cc.

References use_centroid_.

void protocols::analysis::InterfaceAnalyzerMover::set_use_jobname ( bool const use_jobname)

Definition at line 323 of file InterfaceAnalyzerMover.cc.

References use_jobname_.

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::set_use_resfile ( bool const use_resfile)

setters for the various parameters used by the analyze

setters

Definition at line 316 of file InterfaceAnalyzerMover.cc.

References use_resfile_.

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::setup_task ( core::pose::Pose & pose)

private

sets up the packer task within the mover

sets up the packer task for the interface

Definition at line 1403 of file InterfaceAnalyzerMover.cc.

References InterfaceNeighborDefinition_, InterGroupNeighborsCalculator_, multichain_constructor_, task_, and use_resfile_.

Referenced by apply().

void protocols::analysis::InterfaceAnalyzerMover::use_tracer ( bool const tracer)

inline

Definition at line 89 of file InterfaceAnalyzerMover.hh.

References protocols::frag_picker::tracer(), and tracer_.

Member Data Documentation

std::string protocols::analysis::InterfaceAnalyzerMover::BuriedUnsatisfiedPolars_

private

BuriedUnsatisfiedPolars calculator name string.

Definition at line 314 of file InterfaceAnalyzerMover.hh.

Referenced by compute_interface_delta_hbond_unsat(), and register_calculators().

bool protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE_

private

skip this expensive calculation

Definition at line 233 of file InterfaceAnalyzerMover.hh.

Referenced by apply(), and set_calc_hbond_sasaE().

bool protocols::analysis::InterfaceAnalyzerMover::calcs_ready_

private

are calculators ready?

Definition at line 221 of file InterfaceAnalyzerMover.hh.

Referenced by apply().

core::Real protocols::analysis::InterfaceAnalyzerMover::centroid_dG_

private

centroid_dG of interface

Definition at line 273 of file InterfaceAnalyzerMover.hh.

Referenced by calc_centroid_dG(), get_centroid_dG(), and report_data().

core::Size protocols::analysis::InterfaceAnalyzerMover::chain1_

private

Definition at line 211 of file InterfaceAnalyzerMover.hh.

Referenced by register_calculators(), and set_pose_info().

std::string protocols::analysis::InterfaceAnalyzerMover::chain1_char_

private

Definition at line 213 of file InterfaceAnalyzerMover.hh.

Referenced by set_pose_info().

core::Size protocols::analysis::InterfaceAnalyzerMover::chain2_

private

Definition at line 212 of file InterfaceAnalyzerMover.hh.

Referenced by register_calculators(), and set_pose_info().

std::string protocols::analysis::InterfaceAnalyzerMover::chain2_char_

private

Definition at line 214 of file InterfaceAnalyzerMover.hh.

Referenced by set_pose_info().

group_set protocols::analysis::InterfaceAnalyzerMover::chain_groups_

private

group of residue ids of fixed chains and mobile chains (see typedef)

Definition at line 299 of file InterfaceAnalyzerMover.hh.

Referenced by get_chain_groups(), make_multichain_interface_set(), and register_intergroup_calculator().

core::Real protocols::analysis::InterfaceAnalyzerMover::complex_energy_

private

Definition at line 264 of file InterfaceAnalyzerMover.hh.

Referenced by get_complex_energy(), report_data(), and score_separated_chains().

bool protocols::analysis::InterfaceAnalyzerMover::compute_interface_delta_hbond_unsat_

private

skip this expensive calculation

Definition at line 235 of file InterfaceAnalyzerMover.hh.

Referenced by apply(), and set_compute_interface_delta_hbond_unsat().

bool protocols::analysis::InterfaceAnalyzerMover::compute_interface_energy_

private

skip this expensive calculation

Definition at line 231 of file InterfaceAnalyzerMover.hh.

Referenced by apply(), and set_compute_interface_energy().

bool protocols::analysis::InterfaceAnalyzerMover::compute_interface_sc_

private

bother with computing interface sc

Definition at line 226 of file InterfaceAnalyzerMover.hh.

Referenced by apply(), report_data(), and set_compute_interface_sc().

bool protocols::analysis::InterfaceAnalyzerMover::compute_packstat_

private

bother with computing packstat

Definition at line 224 of file InterfaceAnalyzerMover.hh.

Referenced by apply(), print_pymol_selection_of_interface_residues(), report_data(), and set_compute_packstat().

bool protocols::analysis::InterfaceAnalyzerMover::compute_separated_sasa_

private

skip this expensive calculation

Definition at line 229 of file InterfaceAnalyzerMover.hh.

Referenced by apply(), and set_compute_separated_sasa().

core::Real protocols::analysis::InterfaceAnalyzerMover::crossterm_interface_energy_

private

Definition at line 266 of file InterfaceAnalyzerMover.hh.

Referenced by compute_interface_energy(), get_crossterm_interface_energy(), and report_data().

core::Real protocols::analysis::InterfaceAnalyzerMover::crossterm_interface_energy_ratio_

private

Definition at line 268 of file InterfaceAnalyzerMover.hh.

Referenced by compute_interface_energy(), get_crossterm_interface_energy_ratio(), and report_data().

core::Real protocols::analysis::InterfaceAnalyzerMover::ddG_

private

interface energy

Definition at line 255 of file InterfaceAnalyzerMover.hh.

Referenced by get_interface_ddG(), and score_separated_chains().

core::Size protocols::analysis::InterfaceAnalyzerMover::delta_unsat_hbond_counter_

private

number of unsat hbonds in complex

Definition at line 275 of file InterfaceAnalyzerMover.hh.

Referenced by compute_interface_delta_hbond_unsat(), get_interface_delta_hbond_unsat(), and report_data().

std::set<core::Size> protocols::analysis::InterfaceAnalyzerMover::downstream_chains_

private

Definition at line 216 of file InterfaceAnalyzerMover.hh.

Referenced by compute_interface_sc(), InterfaceAnalyzerMover(), make_multichain_interface_set(), and set_pose_info().

std::set<int> protocols::analysis::InterfaceAnalyzerMover::fixed_chains_

private

Definition at line 204 of file InterfaceAnalyzerMover.hh.

Referenced by calc_hbond_sasaE(), get_fixed_chains(), make_interface_set(), and parse_my_tag().

core::Real protocols::analysis::InterfaceAnalyzerMover::gly_dG_

private

Energy of a all Gly interface.

Definition at line 271 of file InterfaceAnalyzerMover.hh.

Referenced by get_gly_interface_energy(), and mut_to_gly().

core::Real protocols::analysis::InterfaceAnalyzerMover::interface_delta_sasa_

private

Definition at line 257 of file InterfaceAnalyzerMover.hh.

Referenced by compute_interface_energy(), compute_separated_sasa(), get_interface_delta_sasa(), and report_data().

core::Real protocols::analysis::InterfaceAnalyzerMover::interface_hsasa_

private

Definition at line 258 of file InterfaceAnalyzerMover.hh.

Referenced by compute_separated_sasa(), and report_data().

core::Size protocols::analysis::InterfaceAnalyzerMover::interface_jump_

private

jump to define which interface is interesting

Definition at line 202 of file InterfaceAnalyzerMover.hh.

Referenced by apply(), make_separated_pose(), register_calculators(), set_interface_jump(), and set_pose_info().

core::Real protocols::analysis::InterfaceAnalyzerMover::interface_packstat_

private

Definition at line 269 of file InterfaceAnalyzerMover.hh.

Referenced by compute_interface_packstat(), get_interface_packstat(), and report_data().

core::Real protocols::analysis::InterfaceAnalyzerMover::interface_polar_sasa_

private

Definition at line 259 of file InterfaceAnalyzerMover.hh.

Referenced by compute_separated_sasa(), and report_data().

std::set< core::Size > protocols::analysis::InterfaceAnalyzerMover::interface_set_

private

set of residues at the interface in question

Definition at line 297 of file InterfaceAnalyzerMover.hh.

Referenced by apply(), calc_per_residue_energy(), compute_interface_delta_hbond_unsat(), compute_interface_packstat(), get_interface_set(), make_interface_set(), make_multichain_interface_set(), and mut_to_gly().

std::string protocols::analysis::InterfaceAnalyzerMover::InterfaceDeltaEnergetics_

private

InterfaceDeltaEnergetics calculator name string.

Definition at line 310 of file InterfaceAnalyzerMover.hh.

Referenced by compute_interface_energy(), and register_calculators().

std::string protocols::analysis::InterfaceAnalyzerMover::InterfaceNeighborDefinition_

private

InterfaceNeighborDefinition calculator name string.

Definition at line 306 of file InterfaceAnalyzerMover.hh.

Referenced by compute_interface_energy(), make_interface_set(), register_calculators(), and setup_task().

std::string protocols::analysis::InterfaceAnalyzerMover::InterfaceSasaDefinition_

private

InterfaceSasaDefinition calculator name string.

Definition at line 308 of file InterfaceAnalyzerMover.hh.

Referenced by register_calculators().

std::string protocols::analysis::InterfaceAnalyzerMover::InterGroupNeighborsCalculator_

private

InterGroupNeighborsCalculator calculator name string.

Definition at line 316 of file InterfaceAnalyzerMover.hh.

Referenced by make_multichain_interface_set(), register_intergroup_calculator(), and setup_task().

bool protocols::analysis::InterfaceAnalyzerMover::multichain_constructor_

private

which constructor are we using

Definition at line 242 of file InterfaceAnalyzerMover.hh.

Referenced by apply(), calc_hbond_sasaE(), get_multichain_constructor(), make_interface_set(), parse_my_tag(), and setup_task().

core::Size protocols::analysis::InterfaceAnalyzerMover::n_interface_res_

private

Definition at line 261 of file InterfaceAnalyzerMover.hh.

Referenced by calc_per_residue_energy(), get_num_interface_residues(), and report_data().

core::Size protocols::analysis::InterfaceAnalyzerMover::nres_

private

Definition at line 283 of file InterfaceAnalyzerMover.hh.

Referenced by compute_interface_energy(), and report_data().

std::string protocols::analysis::InterfaceAnalyzerMover::NumberHBonds_

private

NumberHBonds calculator name string.

Definition at line 312 of file InterfaceAnalyzerMover.hh.

Referenced by register_calculators().

bool protocols::analysis::InterfaceAnalyzerMover::pack_input_

private

pack the input pose

Definition at line 244 of file InterfaceAnalyzerMover.hh.

Referenced by get_pack_input(), score_separated_chains(), and set_pack_input().

bool protocols::analysis::InterfaceAnalyzerMover::pack_separated_

private

pack the separated poses default is false

Definition at line 246 of file InterfaceAnalyzerMover.hh.

Referenced by score_separated_chains(), and set_pack_separated().

core::Real protocols::analysis::InterfaceAnalyzerMover::per_residue_energy_

private

Definition at line 263 of file InterfaceAnalyzerMover.hh.

Referenced by calc_per_residue_energy(), get_per_residue_energy(), and report_data().

utility::file::FileName protocols::analysis::InterfaceAnalyzerMover::posename_

private

Definition at line 208 of file InterfaceAnalyzerMover.hh.

Referenced by set_pose_info().

std::string protocols::analysis::InterfaceAnalyzerMover::posename_base_

private

Definition at line 209 of file InterfaceAnalyzerMover.hh.

Referenced by make_interface_set(), print_pymol_selection_of_hbond_unsat(), print_pymol_selection_of_interface_residues(), print_pymol_selection_of_packing(), register_intergroup_calculator(), report_data(), and set_pose_info().

std::string protocols::analysis::InterfaceAnalyzerMover::pymol_sel_hbond_unsat_

private

Definition at line 278 of file InterfaceAnalyzerMover.hh.

Referenced by get_pymol_sel_hbond_unsat(), and print_pymol_selection_of_hbond_unsat().

std::string protocols::analysis::InterfaceAnalyzerMover::pymol_sel_interface_

private

pymol style selections

Definition at line 277 of file InterfaceAnalyzerMover.hh.

Referenced by get_pymol_sel_interface(), and print_pymol_selection_of_interface_residues().

std::string protocols::analysis::InterfaceAnalyzerMover::pymol_sel_packing_

private

Definition at line 279 of file InterfaceAnalyzerMover.hh.

Referenced by get_pymol_sel_packing(), and print_pymol_selection_of_packing().

std::string protocols::analysis::InterfaceAnalyzerMover::Sasa_

private

Sasa calculator name string.

Definition at line 304 of file InterfaceAnalyzerMover.hh.

Referenced by compute_separated_sasa(), and register_calculators().

core::Real protocols::analysis::InterfaceAnalyzerMover::sc_value_

private

shape complementarity values

Definition at line 294 of file InterfaceAnalyzerMover.hh.

Referenced by compute_interface_sc(), and report_data().

core::Real protocols::analysis::InterfaceAnalyzerMover::separated_interface_energy_

private

Definition at line 265 of file InterfaceAnalyzerMover.hh.

Referenced by compute_interface_energy(), get_separated_interface_energy(), report_data(), and score_separated_chains().

core::Real protocols::analysis::InterfaceAnalyzerMover::separated_interface_energy_ratio_

private

Definition at line 267 of file InterfaceAnalyzerMover.hh.

Referenced by compute_interface_energy(), get_separated_interface_energy_ratio(), and report_data().

core::scoring::ScoreFunctionCOP protocols::analysis::InterfaceAnalyzerMover::sf_

private

scorefunction

Definition at line 206 of file InterfaceAnalyzerMover.hh.

Referenced by make_separated_pose(), mut_to_gly(), parse_my_tag(), and score_separated_chains().

core::Size protocols::analysis::InterfaceAnalyzerMover::side1_nres_

private

Definition at line 284 of file InterfaceAnalyzerMover.hh.

Referenced by compute_interface_energy(), get_side1_nres(), and report_data().

core::Real protocols::analysis::InterfaceAnalyzerMover::side1_score_

private

Definition at line 281 of file InterfaceAnalyzerMover.hh.

Referenced by compute_interface_energy(), get_side1_score(), and report_data().

core::Size protocols::analysis::InterfaceAnalyzerMover::side2_nres_

private

Definition at line 285 of file InterfaceAnalyzerMover.hh.

Referenced by compute_interface_energy(), get_side2_nres(), and report_data().

core::Real protocols::analysis::InterfaceAnalyzerMover::side2_score_

private

Definition at line 282 of file InterfaceAnalyzerMover.hh.

Referenced by compute_interface_energy(), get_side2_score(), and report_data().

bool protocols::analysis::InterfaceAnalyzerMover::skip_reporting_

private

hush! be quiet! silence!

Definition at line 238 of file InterfaceAnalyzerMover.hh.

Referenced by apply(), and set_skip_reporting().

core::pack::task::PackerTaskOP protocols::analysis::InterfaceAnalyzerMover::task_

private

packer task used to repack pulled apart chains

Definition at line 301 of file InterfaceAnalyzerMover.hh.

Referenced by get_packer_task(), score_separated_chains(), and setup_task().

core::Real protocols::analysis::InterfaceAnalyzerMover::total_hb_E_

private

avg hbond exposure ratio

total energy of interface Hbonds

Definition at line 291 of file InterfaceAnalyzerMover.hh.

Referenced by calc_hbond_sasaE(), get_total_Hbond_E(), and report_data().

core::Real protocols::analysis::InterfaceAnalyzerMover::total_sasa_

private

Definition at line 256 of file InterfaceAnalyzerMover.hh.

Referenced by compute_separated_sasa(), get_total_sasa(), and report_data().

bool protocols::analysis::InterfaceAnalyzerMover::tracer_

private

output to tracer or PDB/silent file

Definition at line 219 of file InterfaceAnalyzerMover.hh.

Referenced by print_pymol_selection_of_hbond_unsat(), print_pymol_selection_of_interface_residues(), report_data(), set_tracer(), and use_tracer().

std::set<core::Size> protocols::analysis::InterfaceAnalyzerMover::upstream_chains_

private

Definition at line 215 of file InterfaceAnalyzerMover.hh.

Referenced by compute_interface_sc(), InterfaceAnalyzerMover(), make_multichain_interface_set(), and set_pose_info().

bool protocols::analysis::InterfaceAnalyzerMover::use_centroid_

private

skip the centroid_dG step, for incoming poses not centroid convertible

Definition at line 252 of file InterfaceAnalyzerMover.hh.

Referenced by apply(), calc_centroid_dG(), get_use_centroid_dG(), report_data(), and set_use_centroid_dG().

bool protocols::analysis::InterfaceAnalyzerMover::use_jobname_

private

just the jobname (true value) or the pose name (flase value)

Definition at line 248 of file InterfaceAnalyzerMover.hh.

Referenced by set_pose_info(), and set_use_jobname().

bool protocols::analysis::InterfaceAnalyzerMover::use_resfile_

private

use a resfile during the pack_input and pack_separated operations

Definition at line 250 of file InterfaceAnalyzerMover.hh.

Referenced by get_use_resfile(), set_use_resfile(), and setup_task().

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

src/protocols/analysis/InterfaceAnalyzerMover.hh
src/protocols/analysis/InterfaceAnalyzerMover.cc

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