Class for analyzing interfaces of a pose. Many metrics are calculated and accessible after the apply method. More...

#include <InterfaceAnalyzerMover.hh>

Inheritance 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::TagCOP	TagCOP

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=nullptr, bool compute_packstat=false, bool pack_input=false, bool pack_separated=false, bool use_jobname=true)
	Constructor for 2 chain poses, separates them by jump number. More...

	InterfaceAnalyzerMover (std::set< int > const &fixed_chains, bool const tracer=false, core::scoring::ScoreFunctionCOP sf=nullptr, bool compute_packstat=false, bool pack_input=false, bool pack_separated=false, bool use_jobname=true)
	Constructor for poses with >= 1 jump, keeps defined chains together. More...

	InterfaceAnalyzerMover (std::string dock_chains, bool const tracer=false, core::scoring::ScoreFunctionCOP sf=nullptr, bool compute_packstat=false, bool pack_input=false, bool pack_separated=false, bool use_jobname=true)
	Constructor for any interface in a pose. Uses string designation (ex LH_A) to keep the left chain/chains fixed ALA docking. More...

	~InterfaceAnalyzerMover () override

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

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

void	init_on_new_input (const core::pose::Pose &pose)
	Explicitly initialize settings on apply - not at the constructor, since this can hold state, and some protocols use apply multiple times. More...

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

void	apply (core::pose::Pose &pose) override
	apply function will calculate data about the input pose. It is not intended to modify the pose itself (conformation and energies objects). It will add data to the pose for output into a scorefile. More...

virtual void	apply_const (core::pose::Pose const &pose)
	Apply method for const pose. Used by InterfaceFeatures reporter. More...

virtual void	report_data ()
	Print data to tracer or scorefile if tracer is not set (default). More...

void	add_score_info_to_pose (core::pose::Pose &pose)
	Add all the scoring data normally output via job to the pose instead. Can't add this to method due to const apply. Use after you have used the apply for the class. More...

bool	reinitialize_for_each_job () const override
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

bool	reinitialize_for_new_input () const override
	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...

void	set_defaults ()

void	set_scorefunction (core::scoring::ScoreFunctionCOP sf)

void	set_use_centroid_dG (bool const use_centroid)

bool	get_use_centroid_dG () const

void	set_compute_packstat (bool const compute_packstat)

void	set_compute_interface_sc (bool const compute_interface_sc)
	Compute the Lawrence and Coleman Shape Complementarity score? More...

void	set_compute_separated_sasa (bool const compute_separated_sasa)

void	set_calc_dSASA (bool calc_dSASA)

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)
	Repack the interface of the complex before separation. More...

void	set_pack_separated (bool const pack_separated)
	Repack the interface of the complex after separation. More...

void	set_pack_rounds (core::Size pack_rounds)
	If pack separated or together is set, this controls how many rounds of packing we do. Default is 1, but that certainly may not be enough... More...

void	set_interface_jump (core::Size const interface_jump)
	Repack any interface between ignored chains and others. Used by dock_chains constructor if the dock_chains interface is less than the total number of pose chains. More...

void	set_interface (std::string const &interface)

void	set_skip_reporting (bool const skip_reporting)

void	set_use_tracer (bool const tracer)

void	set_use_jobname (bool const use_jobname)

void	set_use_resfile (bool const use_resfile)

InterfaceData	get_all_data ()
	Get all interface data. More...

PerResidueInterfaceData	get_all_per_residue_data ()
	Get all per residue interface data. More...

core::Size	get_num_interface_residues ()

core::Real	get_complexed_sasa ()

core::Real	get_interface_delta_sasa ()

core::Real	get_complex_energy ()

core::Real	get_per_residue_energy ()
	return the average per residue interface energy More...

core::Real	get_total_Hbond_E ()

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_gly_interface_energy ()
	Return the interface energy of an all glycine interface (like bb-bb energies) More...

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_dG () const

bool	get_multichain_constructor ()
	Return boolean if a multichain (fixedchain) constructor was used. More...

std::set< int >	get_fixed_chains ()

std::set< core::Size >	get_interface_set ()
	Get the residues at the interface in question. More...

group_set	get_chain_groups ()

bool	get_pack_input ()

core::Real	get_centroid_dG ()

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 ()

	~Mover () override

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...

	Mover (Mover const &other)

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

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

void	set_type (std::string const &setting)

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	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...

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

Static Public Member Functions
static std::string	mover_name ()

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
void	register_calculators ()
	the exposure/possible ratio avg for hbonds in the interface More...

core::pack::task::PackerTaskOP	setup_task (core::pose::Pose &pose)
	sets up the packer task. Used for both sep and tog pose More...

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

virtual void	make_interface_set (core::pose::Pose &pose)
	makes the interface sets for either constructor and sets up any other basic interface info. (chains, upstream chains, etc.) More...

virtual core::pose::Pose	make_separated_pose (core::pose::Pose &pose, core::Size interface_jump, core::Size step_size=1000)
	Creates a single pose that is separated structurally at the interface. More...

virtual core::pose::Pose	make_separated_pose (core::pose::Pose &pose, std::set< Size > const &moving_chains, core::Size step_size=1000)
	Creates a single pose that is separated structurally at the interface. 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...

void	compute_interface_sc (core::Size &interface_jump, core::pose::Pose const &complexed_pose)
	find the interface shape compementarity value between the chains using old fortran SC score. 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)

void	calc_per_residue_and_regional_data (core::pose::Pose &complexed_pose, core::pose::Pose &separated_pose)
	Calculate the average energy per residue in the interface as well as other data. More...

utility::vector1< core::Real >	calc_per_residue_dSASA (const core::pose::Pose &complexed_pose, const utility::vector1< core::Real > &separated_sasa, const utility::vector1< core::Real > &complexed_sasa)
	calculates dSASA for each residue More...

core::Real	calc_per_residue_dSASA_general (const core::Size resnum, const core::pose::Pose &complexed_pose, const core::Real separated_sasa, const core::Real complexed_sasa, utility::vector1< core::Real > &regional)

utility::vector1< core::Real >	calc_per_residue_dG (core::pose::Pose &complexed_pose, const utility::vector1< core::Real > &separated_energy, const utility::vector1< core::Real > &complexed_energy)

void	calc_hbond_sasaE (core::pose::Pose &pose)

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

void	calc_interface_to_surface_fraction (core::pose::Pose const &separated_pose, const utility::vector1< core::Real > &separated_sasa)
	Calculate the number of residues in the interface vs the surface based on SASA cutoff (40A^2 as per LayerDesign and selection operations). 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	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	set_pose_info (core::pose::Pose const &pose)
	sets up the pose information such as the name and chain ids More...

void	init_per_residue_data (core::pose::Pose const &pose)
	Initialize the per residue data structure. More...

void	init_data (const core::pose::Pose &pose)
	Initialize the data structure. More...

void	setup_scorefxn ()
	Setup the scorefunction to include hbond energies in the EnergyGraph. Yay forums and Rocco for this bug fix! More...

void	setup_for_dock_chains (core::pose::Pose &pose, std::string dock_chains)
	Setup for the dock_chains constructor. More...

void	setup_score_data ()

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

std::set< int >	fixed_chains_
	what chains are fixed in an interface More...

std::string	ligand_chain_
	the ligand chain that will be moved in an interface In this scheme, everything else is fixed More...

core::scoring::ScoreFunctionOP	sf_
	scorefunction More...

utility::file::FileName	posename_

std::string	posename_base_

core::Size	chain1_ = 1

core::Size	chain2_ = 2

std::string	dock_chains_

std::set< core::Size >	upstream_chains_

std::set< core::Size >	downstream_chains_

std::set< core::Size >	ignored_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	explicit_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...

InterfaceData	data_

PerResidueInterfaceData	per_residue_data_

core::Size	included_nres_
	avg hbond exposure ratio More...

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

utility::vector1< bool >	include_residue_

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

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

std::string	InterfaceNeighborDefinition_
	InterfaceNeighborDefinition 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::map< std::string, core::Real >	score_data_

core::Size	pack_rounds_ = 1

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...

Detailed Description

Class for analyzing interfaces of a pose. Many metrics are calculated and accessible after the apply method.

Member Typedef Documentation

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

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

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

Constructor & Destructor Documentation

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

Constructor for 2 chain poses, separates them by jump number.

pack_separated and pack_input only pack the detected interface residues.

References set_defaults(), sf_, and protocols::moves::Mover::type().

Referenced by clone().

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

Constructor for poses with >= 1 jump, keeps defined chains together.

pack_separated and pack_input only pack the detected interface residues.

References set_defaults(), sf_, and protocols::moves::Mover::type().

protocols::analysis::InterfaceAnalyzerMover::InterfaceAnalyzerMover	(	std::string	dock_chains,
		bool const	tracer = `false`,
		core::scoring::ScoreFunctionCOP	sf = `nullptr`,
		bool	compute_packstat = `false`,
		bool	pack_input = `false`,
		bool	pack_separated = `false`,
		bool	use_jobname = `true`
	)

Constructor for any interface in a pose. Uses string designation (ex LH_A) to keep the left chain/chains fixed ALA docking.

Can be used for subsets of interfaces, for example L_H in a LHA pose. pack_separated and pack_input only pack the detected interface residues.

References dock_chains_, set_defaults(), sf_, and protocols::moves::Mover::type().

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

overridedefault

Member Function Documentation

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

Add all the scoring data normally output via job to the pose instead. Can't add this to method due to const apply. Use after you have used the apply for the class.

References score_data_, core::pose::setPoseExtraScore(), and protocols::TR().

Referenced by apply().

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

overridevirtual

apply function will calculate data about the input pose. It is not intended to modify the pose itself (conformation and energies objects). It will add data to the pose for output into a scorefile.

InterfaceAnalyzerMover computes various interface statistics and makes them available through getters

Implements protocols::moves::Mover.

References add_score_info_to_pose(), and apply_const().

Referenced by protocols::antibody::AntibodyModelerProtocol::apply(), and protocols::antibody::snugdock::SnugDockProtocol::apply().

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

virtual

Apply method for const pose. Used by InterfaceFeatures reporter.

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(), dock_chains_, downstream_chains_, explicit_constructor_, fixed_chains_, core::pose::get_chain_id_from_chain(), init_on_new_input(), interface_jump_, interface_set_, ligand_chain_, make_interface_set(), make_separated_pose(), core::conformation::Conformation::num_chains(), print_pymol_selection_of_interface_residues(), register_calculators(), report_data(), set_pose_info(), setup_for_dock_chains(), setup_score_data(), setup_scorefxn(), skip_reporting_, protocols::TR(), and use_centroid_.

Referenced by apply().

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

private

report the dG of a centroid pose with score3

References protocols::analysis::InterfaceData::centroid_dG, core::chemical::CENTROID_t, core::scoring::ScoreFunctionFactory::create_score_function(), data_, core::scoring::rg, core::util::switch_to_residue_type_set(), protocols::TR(), and use_centroid_.

Referenced by apply_const().

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

private

calculate the hbond energy and dampen it by exposure

References core::pose::Pose::chain(), core::id::AtomID_Map< T >::clear(), data_, core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies(), protocols::analysis::InterfaceData::dG, explicit_constructor_, fixed_chains_, core::scoring::get_score_function(), core::scoring::hbond, protocols::analysis::InterfaceData::hbond_E_fraction, core::scoring::methods::EnergyMethodOptions::hbond_options(), protocols::analysis::InterfaceData::interface_hbonds, core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nheavyatoms(), core::pose::Pose::residue_type(), core::pose::Pose::size(), protocols::analysis::total, protocols::analysis::InterfaceData::total_hb_E, protocols::TR(), and core::pose::Pose::update_residue_neighbors().

Referenced by apply_const(), and set_calc_hbond_sasaE().

void protocols::analysis::InterfaceAnalyzerMover::calc_interface_to_surface_fraction	(	core::pose::Pose const &	separated_pose,
		const utility::vector1< core::Real > &	separated_sasa
	)

private

Calculate the number of residues in the interface vs the surface based on SASA cutoff (40A^2 as per LayerDesign and selection operations).

Correct way to calculate this though is through % maximal SASA buried, but calculations will need to be done later to find these values.

References core::pose::Pose::chain(), data_, include_residue_, protocols::analysis::InterfaceData::interface_nres, protocols::analysis::InterfaceData::interface_to_surface_fraction, protocols::analysis::side1, protocols::analysis::side2, protocols::analysis::total, and upstream_chains_.

Referenced by compute_separated_sasa().

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

private

Calculate the average energy per residue in the interface as well as other data.

calculate the average energy per residue in the interface as well as other data

Referenced by compute_interface_energy().

vector1< core::Real > protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_dG	(	core::pose::Pose &	complexed_pose,
		const utility::vector1< core::Real > &	separated_energy,
		const utility::vector1< core::Real > &	complexed_energy
	)

private

References core::pose::Pose::chain(), protocols::analysis::PerResidueInterfaceData::interface_residues, interface_set_, per_residue_data_, protocols::analysis::PerResidueInterfaceData::regional_avg_per_residue_dG, protocols::analysis::PerResidueInterfaceData::regional_avg_per_residue_energy_int, protocols::analysis::PerResidueInterfaceData::regional_avg_per_residue_energy_sep, protocols::analysis::side1, protocols::analysis::side2, protocols::analysis::total, and upstream_chains_.

Referenced by calc_per_residue_and_regional_data().

vector1< core::Real > protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_dSASA	(	const core::pose::Pose &	complexed_pose,
		const utility::vector1< core::Real > &	separated_sasa,
		const utility::vector1< core::Real > &	complexed_sasa
	)

private

calculates dSASA for each residue

Referenced by compute_separated_sasa().

Real protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_dSASA_general	(	const core::Size	resnum,
		const core::pose::Pose &	complexed_pose,
		const core::Real	separated_sasa,
		const core::Real	complexed_sasa,
		utility::vector1< core::Real > &	regional
	)

private

References core::pose::Pose::chain(), protocols::analysis::PerResidueInterfaceData::interface_residues, per_residue_data_, protocols::analysis::side1, protocols::analysis::side2, protocols::analysis::total, and upstream_chains_.

Referenced by compute_separated_sasa().

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

References InterfaceAnalyzerMover().

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

privatevirtual

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

References BuriedUnsatisfiedPolars_, data_, protocols::analysis::InterfaceData::delta_unsat_hbonds, interface_set_, core::pose::Pose::metric(), print_pymol_selection_of_hbond_unsat(), core::pose::Pose::residue_type(), and protocols::TR().

Referenced by apply_const().

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

privatevirtual

computes the interface energy of the interface

References calc_per_residue_and_regional_data(), core::pose::Pose::conformation(), protocols::analysis::InterfaceData::crossterm_interface_energy, protocols::analysis::InterfaceData::crossterm_interface_energy_dSASA_ratio, data_, protocols::analysis::InterfaceData::dG, protocols::analysis::InterfaceData::dG_dSASA_ratio, protocols::analysis::InterfaceData::dSASA, InterfaceDeltaEnergetics_, core::pose::Pose::metric(), core::conformation::Conformation::num_chains(), score_separated_chains(), and protocols::analysis::total.

Referenced by apply_const().

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

privatevirtual

References core::scoring::packstat::compute_residue_packing_scores(), data_, interface_set_, protocols::analysis::InterfaceData::packstat, print_pymol_selection_of_packing(), core::pose::Pose::size(), and protocols::TR().

Referenced by apply_const().

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 using old fortran SC score.

(From the wiki) Calculates the Lawrence & Coleman shape complementarity using a port of the original Fortran code from CCP4's sc.

References core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::scoring::sc::ShapeComplementarityCalculator::Calc(), core::pose::Pose::chain(), data_, downstream_chains_, core::scoring::sc::MolecularSurfaceCalculator::GetResults(), include_residue_, core::pose::Pose::residue(), core::scoring::sc::_RESULTS::sc, protocols::analysis::InterfaceData::sc_value, core::pose::Pose::size(), protocols::TR(), and upstream_chains_.

Referenced by apply_const(), and set_compute_interface_sc().

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

privatevirtual

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

Referenced by apply_const(), and set_compute_separated_sasa().

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

InterfaceData protocols::analysis::InterfaceAnalyzerMover::get_all_data ( )

inline

Get all interface data.

References data_.

PerResidueInterfaceData protocols::analysis::InterfaceAnalyzerMover::get_all_per_residue_data ( )

inline

Get all per residue interface data.

References per_residue_data_.

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

References protocols::analysis::InterfaceData::centroid_dG, and data_.

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

References chain_groups_.

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

References protocols::analysis::InterfaceData::complex_total_energy, data_, and protocols::analysis::total.

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

getters

References protocols::analysis::InterfaceData::complexed_SASA, and data_.

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

References protocols::analysis::InterfaceData::crossterm_interface_energy, and data_.

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

References protocols::analysis::InterfaceData::crossterm_interface_energy_dSASA_ratio, and data_.

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

References fixed_chains_.

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

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

References data_, and protocols::analysis::InterfaceData::gly_dG.

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

References data_, and protocols::analysis::InterfaceData::delta_unsat_hbonds.

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

References data_, protocols::analysis::InterfaceData::dSASA, and protocols::analysis::total.

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

References data_, protocols::analysis::InterfaceData::dG, and protocols::analysis::total.

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

References data_, and protocols::analysis::InterfaceData::packstat.

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

Get the residues at the interface in question.

References interface_set_.

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

Return boolean if a multichain (fixedchain) constructor was used.

References explicit_constructor_.

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

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

References data_, protocols::analysis::InterfaceData::interface_nres, and protocols::analysis::total.

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

References pack_input_.

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

return the average per residue interface energy

References per_residue_data_, protocols::analysis::PerResidueInterfaceData::regional_avg_per_residue_energy_int, and protocols::analysis::total.

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

References data_, and protocols::analysis::InterfaceData::pymol_sel_hbond_unsat.

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

References data_, and protocols::analysis::InterfaceData::pymol_sel_interface.

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

References data_, and protocols::analysis::InterfaceData::pymol_sel_packing.

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

References data_, protocols::analysis::InterfaceData::dG, and protocols::analysis::total.

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

References data_, and protocols::analysis::InterfaceData::dG_dSASA_ratio.

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

inline

References data_, protocols::analysis::InterfaceData::interface_nres, and protocols::analysis::side1.

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

inline

References protocols::analysis::InterfaceData::complexed_interface_score, data_, and protocols::analysis::side1.

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

inline

References data_, protocols::analysis::InterfaceData::interface_nres, and protocols::analysis::side2.

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

inline

References protocols::analysis::InterfaceData::complexed_interface_score, data_, and protocols::analysis::side2.

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

References data_, and protocols::analysis::InterfaceData::total_hb_E.

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

References use_centroid_.

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

private

Initialize the data structure.

Referenced by init_on_new_input().

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

Explicitly initialize settings on apply - not at the constructor, since this can hold state, and some protocols use apply multiple times.

References downstream_chains_, include_residue_, included_nres_, init_data(), init_per_residue_data(), interface_set_, score_data_, core::pose::Pose::size(), and upstream_chains_.

Referenced by apply_const().

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

private

Initialize the per residue data structure.

Referenced by init_on_new_input().

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

privatevirtual

makes the interface sets for either constructor and sets up any other basic interface info. (chains, upstream chains, etc.)

makes the interface sets for either constructor

References core::conformation::Residue::chain(), chain1_, chain2_, data_, downstream_chains_, explicit_constructor_, fixed_chains_, protocols::analysis::InterfaceData::interface_nres, protocols::analysis::PerResidueInterfaceData::interface_residues, protocols::analysis::InterfaceData::interface_residues, interface_set_, InterfaceNeighborDefinition_, make_multichain_interface_set(), core::pose::Pose::metric(), per_residue_data_, posename_base_, core::pose::Pose::residue(), protocols::analysis::side1, protocols::analysis::side2, core::pose::Pose::size(), protocols::analysis::total, protocols::TR(), and upstream_chains_.

Referenced by apply_const().

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

privatevirtual

functions to make interface sets needed

References core::pose::Pose::chain(), chain_groups_, downstream_chains_, ignored_chains_, include_residue_, interface_set_, core::pose::Pose::size(), protocols::TR(), and upstream_chains_.

Referenced by make_interface_set().

core::pose::Pose protocols::analysis::InterfaceAnalyzerMover::make_separated_pose	(	core::pose::Pose &	pose,
		core::Size	interface_jump,
		core::Size	step_size = `1000`
	)

privatevirtual

Creates a single pose that is separated structurally at the interface.

Uses the jump number to find downstream residues and move them in the Z axis in cartesian space according to step_size (A)

References core::pose::Pose::fold_tree(), core::kinematics::residues_downstream_of_jump(), and protocols::toolbox::rigid_body::translate().

Referenced by apply_const(), and setup_for_dock_chains().

core::pose::Pose protocols::analysis::InterfaceAnalyzerMover::make_separated_pose	(	core::pose::Pose &	pose,
		std::set< Size > const &	chain_nums,
		core::Size	step_size = `1000`
	)

privatevirtual

Creates a single pose that is separated structurally at the interface.

Moves the moving_chains in cartesian space a distance according to step_size (A) in the Z axis

References core::conformation::Residue::chain(), core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::toolbox::rigid_body::translate().

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

static

Referenced by get_name(), protocols::analysis::InterfaceAnalyzerMoverCreator::keyname(), and provide_xml_schema().

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

References core::chemical::aa_from_oneletter_code(), core::pack::task::TaskFactory::create_packer_task(), data_, protocols::analysis::InterfaceData::gly_dG, interface_set_, core::chemical::num_canonical_aas, sf_, core::pose::Pose::size(), and protocols::TR().

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

overridevirtual

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.

References core::pose::Pose::chain(), dock_chains_, explicit_constructor_, fixed_chains_, ligand_chain_, core::scoring::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_use_jobname(), set_use_resfile(), set_use_tracer(), sf_, core::pose::Pose::size(), 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

References protocols::jd2::add_string_to_current_job(), core::conformation::Residue::atom_name(), data_, core::pose::Pose::pdb_info(), posename_base_, protocols::analysis::InterfaceData::pymol_sel_hbond_unsat, core::pose::Pose::residue(), 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.

References protocols::jd2::add_string_to_current_job(), compute_packstat_, data_, core::pose::Pose::pdb_info(), posename_base_, protocols::analysis::InterfaceData::pymol_sel_interface, tracer_, TRinterface(), and protocols::analysis::which_ostream().

Referenced by apply_const().

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

References data_, include_residue_, core::pose::Pose::pdb_info(), posename_base_, protocols::analysis::InterfaceData::pymol_sel_packing, core::pose::Pose::size(), and protocols::TR().

Referenced by compute_interface_packstat().

void protocols::analysis::InterfaceAnalyzerMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_parse_score_function(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::analysis::InterfaceAnalyzerMoverCreator::provide_xml_schema().

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

private

the exposure/possible ratio avg for hbonds in the interface

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

total hbond energy for pose registers the posemetric calculators

References BuriedUnsatisfiedPolars_, chain1_, chain2_, interface_jump_, InterfaceDeltaEnergetics_, InterfaceNeighborDefinition_, NumberHBonds_, Sasa_, and protocols::TR().

Referenced by apply_const().

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

inlineoverridevirtual

Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use.

Movers default to not regenerating

Reimplemented from protocols::moves::Mover.

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

inlineoverridevirtual

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).

Movers default to not regenerating

Reimplemented from protocols::moves::Mover.

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

privatevirtual

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

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::pose::get_chain_id_from_chain(), core::pose::get_jump_id_from_chain_id(), ligand_chain_, core::conformation::Conformation::num_chains(), and protocols::make_rot_lib::PEPTIDE.

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

virtual

Print data to tracer or scorefile if tracer is not set (default).

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

Referenced by apply_const().

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

privatevirtual

void protocols::analysis::InterfaceAnalyzerMover::set_calc_dSASA ( bool calc_dSASA )

inline

References compute_separated_sasa_.

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

inline

References calc_hbond_sasaE(), and calc_hbond_sasaE_.

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

inline

References compute_interface_delta_hbond_unsat_.

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

inline

References compute_interface_energy_.

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

inline

Compute the Lawrence and Coleman Shape Complementarity score?

References compute_interface_sc(), and compute_interface_sc_.

Referenced by parse_my_tag().

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

References compute_packstat_.

Referenced by parse_my_tag().

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

inline

References compute_separated_sasa(), and compute_separated_sasa_.

void protocols::analysis::InterfaceAnalyzerMover::set_defaults ( )

References calc_hbond_sasaE_, calcs_ready_, compute_interface_delta_hbond_unsat_, compute_interface_energy_, compute_interface_sc_, compute_separated_sasa_, skip_reporting_, use_centroid_, and use_resfile_.

Referenced by InterfaceAnalyzerMover().

void protocols::analysis::InterfaceAnalyzerMover::set_interface ( std::string const & interface )

References dock_chains_, and explicit_constructor_.

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

Repack any interface between ignored chains and others. Used by dock_chains constructor if the dock_chains interface is less than the total number of pose chains.

Ex: LHA pose, pass L_H dock_chains to get the interface between L and H. A will be translated away from the L H interface to do the calculation. If this option is set - it will repack any SC that would make an LH_A interface after separation

References explicit_constructor_, and interface_jump_.

Referenced by parse_my_tag().

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

Repack the interface of the complex before separation.

References pack_input_.

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::set_pack_rounds ( core::Size pack_rounds )

inline

If pack separated or together is set, this controls how many rounds of packing we do. Default is 1, but that certainly may not be enough...

References pack_rounds_.

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

Repack the interface of the complex after separation.

References pack_separated_.

Referenced by parse_my_tag().

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

private

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

References chain1_, chain2_, protocols::jd2::current_output_name(), core::kinematics::FoldTree::downstream_jump_residue(), explicit_constructor_, core::pose::Pose::fold_tree(), interface_jump_, core::pose::Pose::pdb_info(), posename_, posename_base_, core::pose::Pose::residue(), core::kinematics::FoldTree::upstream_jump_residue(), and use_jobname_.

Referenced by apply_const().

void protocols::analysis::InterfaceAnalyzerMover::set_scorefunction ( core::scoring::ScoreFunctionCOP sf )

References sf_.

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

inline

References skip_reporting_.

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

References use_centroid_.

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

References use_jobname_.

Referenced by parse_my_tag().

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

setters

References use_resfile_.

Referenced by parse_my_tag().

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

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

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::setup_for_dock_chains	(	core::pose::Pose &	pose,
		std::string	dock_chains
	)

private

Setup for the dock_chains constructor.

References core::pose::Pose::conformation(), dock_chains_, fixed_chains_, core::pose::get_chain_from_chain_id(), core::pose::get_chain_id_from_chain(), ignored_chains_, make_separated_pose(), core::conformation::Conformation::num_chains(), core::pose::set_reasonable_fold_tree(), and protocols::TR().

Referenced by apply_const().

void protocols::analysis::InterfaceAnalyzerMover::setup_score_data ( )

private

Referenced by apply_const().

void protocols::analysis::InterfaceAnalyzerMover::setup_scorefxn ( )

private

Setup the scorefunction to include hbond energies in the EnergyGraph. Yay forums and Rocco for this bug fix!

References core::scoring::get_score_function(), sf_, and protocols::TR().

Referenced by apply_const().

core::pack::task::PackerTaskOP protocols::analysis::InterfaceAnalyzerMover::setup_task ( core::pose::Pose & pose )

private

sets up the packer task. Used for both sep and tog pose

sets up the packer task for the interface

References data_, protocols::analysis::InterfaceData::interface_residues, protocols::analysis::total, and use_resfile_.

Referenced by score_separated_chains().

Member Data Documentation

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

private

BuriedUnsatisfiedPolars calculator name string.

Referenced by compute_interface_delta_hbond_unsat(), and register_calculators().

bool protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE_

private

skip this expensive calculation

Referenced by apply_const(), set_calc_hbond_sasaE(), and set_defaults().

bool protocols::analysis::InterfaceAnalyzerMover::calcs_ready_

private

are calculators ready?

Referenced by apply_const(), and set_defaults().

core::Size protocols::analysis::InterfaceAnalyzerMover::chain1_ = 1

private

Referenced by make_interface_set(), register_calculators(), and set_pose_info().

core::Size protocols::analysis::InterfaceAnalyzerMover::chain2_ = 2

private

Referenced by make_interface_set(), register_calculators(), and set_pose_info().

group_set protocols::analysis::InterfaceAnalyzerMover::chain_groups_

private

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

Referenced by get_chain_groups(), and make_multichain_interface_set().

bool protocols::analysis::InterfaceAnalyzerMover::compute_interface_delta_hbond_unsat_

private

skip this expensive calculation

Referenced by apply_const(), set_compute_interface_delta_hbond_unsat(), and set_defaults().

bool protocols::analysis::InterfaceAnalyzerMover::compute_interface_energy_

private

skip this expensive calculation

Referenced by apply_const(), set_compute_interface_energy(), and set_defaults().

bool protocols::analysis::InterfaceAnalyzerMover::compute_interface_sc_

private

bother with computing interface sc

Referenced by apply_const(), report_data(), set_compute_interface_sc(), and set_defaults().

bool protocols::analysis::InterfaceAnalyzerMover::compute_packstat_

private

bother with computing packstat

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

bool protocols::analysis::InterfaceAnalyzerMover::compute_separated_sasa_

private

skip this expensive calculation

Referenced by apply_const(), compute_separated_sasa(), set_calc_dSASA(), set_compute_separated_sasa(), and set_defaults().

InterfaceData protocols::analysis::InterfaceAnalyzerMover::data_

private

Referenced by calc_centroid_dG(), calc_hbond_sasaE(), calc_interface_to_surface_fraction(), calc_per_residue_and_regional_data(), calc_per_residue_dSASA(), compute_interface_delta_hbond_unsat(), compute_interface_energy(), compute_interface_packstat(), compute_interface_sc(), compute_separated_sasa(), get_all_data(), get_centroid_dG(), get_complex_energy(), get_complexed_sasa(), get_crossterm_interface_energy(), get_crossterm_interface_energy_ratio(), get_gly_interface_energy(), get_interface_delta_hbond_unsat(), get_interface_delta_sasa(), get_interface_dG(), get_interface_packstat(), get_num_interface_residues(), get_pymol_sel_hbond_unsat(), get_pymol_sel_interface(), get_pymol_sel_packing(), get_separated_interface_energy(), get_separated_interface_energy_ratio(), get_side1_nres(), get_side1_score(), get_side2_nres(), get_side2_score(), get_total_Hbond_E(), init_data(), make_interface_set(), mut_to_gly(), print_pymol_selection_of_hbond_unsat(), print_pymol_selection_of_interface_residues(), print_pymol_selection_of_packing(), report_data(), score_separated_chains(), setup_score_data(), and setup_task().

std::string protocols::analysis::InterfaceAnalyzerMover::dock_chains_

private

Referenced by apply_const(), InterfaceAnalyzerMover(), parse_my_tag(), set_interface(), and setup_for_dock_chains().

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

private

Referenced by apply_const(), compute_interface_sc(), init_on_new_input(), make_interface_set(), and make_multichain_interface_set().

bool protocols::analysis::InterfaceAnalyzerMover::explicit_constructor_

private

which constructor are we using

Referenced by apply_const(), calc_hbond_sasaE(), get_multichain_constructor(), make_interface_set(), parse_my_tag(), set_interface(), set_interface_jump(), and set_pose_info().

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

private

what chains are fixed in an interface

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

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

private

Referenced by make_multichain_interface_set(), and setup_for_dock_chains().

utility::vector1< bool > protocols::analysis::InterfaceAnalyzerMover::include_residue_

private

Referenced by calc_interface_to_surface_fraction(), compute_interface_sc(), init_on_new_input(), make_multichain_interface_set(), print_pymol_selection_of_packing(), and score_separated_chains().

core::Size protocols::analysis::InterfaceAnalyzerMover::included_nres_

private

avg hbond exposure ratio

Referenced by init_on_new_input(), score_separated_chains(), and setup_score_data().

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

private

jump to define which interface is interesting

Referenced by apply_const(), register_calculators(), set_interface_jump(), and set_pose_info().

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

private

set of residues at the interface in question

Referenced by apply_const(), calc_per_residue_and_regional_data(), calc_per_residue_dG(), calc_per_residue_dSASA(), compute_interface_delta_hbond_unsat(), compute_interface_packstat(), get_interface_set(), init_on_new_input(), make_interface_set(), make_multichain_interface_set(), and mut_to_gly().

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

private

InterfaceDeltaEnergetics calculator name string.

Referenced by compute_interface_energy(), and register_calculators().

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

private

InterfaceNeighborDefinition calculator name string.

Referenced by make_interface_set(), and register_calculators().

std::string protocols::analysis::InterfaceAnalyzerMover::ligand_chain_

private

the ligand chain that will be moved in an interface In this scheme, everything else is fixed

Referenced by apply_const(), parse_my_tag(), and reorder_foldtree_find_jump().

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

private

NumberHBonds calculator name string.

Referenced by register_calculators().

bool protocols::analysis::InterfaceAnalyzerMover::pack_input_

private

pack the input pose

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

core::Size protocols::analysis::InterfaceAnalyzerMover::pack_rounds_ = 1

private

Referenced by score_separated_chains(), and set_pack_rounds().

bool protocols::analysis::InterfaceAnalyzerMover::pack_separated_

private

pack the separated poses default is false

Referenced by score_separated_chains(), and set_pack_separated().

PerResidueInterfaceData protocols::analysis::InterfaceAnalyzerMover::per_residue_data_

private

Referenced by calc_per_residue_and_regional_data(), calc_per_residue_dG(), calc_per_residue_dSASA(), calc_per_residue_dSASA_general(), compute_separated_sasa(), get_all_per_residue_data(), get_per_residue_energy(), init_per_residue_data(), make_interface_set(), report_data(), score_separated_chains(), and setup_score_data().

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

private

Referenced by set_pose_info().

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

private

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

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

private

Sasa calculator name string.

Referenced by compute_separated_sasa(), and register_calculators().

std::map< std::string, core::Real > protocols::analysis::InterfaceAnalyzerMover::score_data_

private

Referenced by add_score_info_to_pose(), init_on_new_input(), report_data(), and setup_score_data().

core::scoring::ScoreFunctionOP protocols::analysis::InterfaceAnalyzerMover::sf_

private

scorefunction

Referenced by InterfaceAnalyzerMover(), mut_to_gly(), parse_my_tag(), score_separated_chains(), set_scorefunction(), and setup_scorefxn().

bool protocols::analysis::InterfaceAnalyzerMover::skip_reporting_

private

hush! be quiet! silence!

Referenced by apply_const(), set_defaults(), and set_skip_reporting().

bool protocols::analysis::InterfaceAnalyzerMover::tracer_

private

output to tracer or PDB/silent file

Referenced by print_pymol_selection_of_hbond_unsat(), print_pymol_selection_of_interface_residues(), report_data(), and set_use_tracer().

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

private

Referenced by calc_interface_to_surface_fraction(), calc_per_residue_and_regional_data(), calc_per_residue_dG(), calc_per_residue_dSASA(), calc_per_residue_dSASA_general(), compute_interface_sc(), init_on_new_input(), make_interface_set(), make_multichain_interface_set(), and score_separated_chains().

bool protocols::analysis::InterfaceAnalyzerMover::use_centroid_

private

skip the centroid_dG step, for incoming poses not centroid convertible

Referenced by apply_const(), calc_centroid_dG(), get_use_centroid_dG(), report_data(), set_defaults(), set_use_centroid_dG(), and setup_score_data().

bool protocols::analysis::InterfaceAnalyzerMover::use_jobname_

private

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

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

Referenced by set_defaults(), 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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