Inheritance diagram for MPInterfaceStatistics:

Public Member Functions
	MPInterfaceStatistics ()
	Constructors ///. More...

	MPInterfaceStatistics (MPInterfaceStatistics const &src)
	Copy Constructor. More...

MPInterfaceStatistics &	operator= (MPInterfaceStatistics const &src)
	Assignment Operator. More...

	~MPInterfaceStatistics () override
	Destructor. More...

std::string	get_name () const override
	Mover Methods ///. More...

void	apply (Pose &pose) override
	Get Membrane protein interface statistics. More...

Private Member Functions
void	register_options ()
	Rosetta Scripts Methods ///. More...

void	init_from_cmd ()
	Initialize Mover options from the comandline. More...

utility::vector1< bool >	get_chains_from_cmd (Pose &pose)
	Get the chains from the commandline. More...

void	calculate_interfaces (Pose &pose)
	calculate interfaces More...

void	fill_vectors_with_data (Pose &pose)
	fill vectors with data More...

void	add_to_scorefile (Pose &pose)
	Add output to scorefile. More...

void	print_aa_statistics (Pose &pose)
	Print amino acid statistics. More...

Real	get_size (Pose &pose)
	Get size of the interface. More...

utility::vector1< SSize >	get_charge (Pose &pose)
	Get charge for all states. More...

utility::vector1< Real >	get_avg_charge (Pose &pose)
	Get avg charge for all states. More...

utility::vector1< Size >	get_number_charges (Pose &pose)
	Get number of charged residues for all states. More...

utility::vector1< Real >	get_avg_number_charges (Pose &pose)
	Get avg number of charged residues for all states. More...

utility::vector1< Real >	get_hydrophobicity (Pose &pose)
	Get hydrophobicity for all states (UHS, Koehler & Meiler, Proteins, 2008) More...

utility::vector1< Real >	get_avg_hydrophobicity (Pose &pose)
	Get avg hydrophobicity for all states (UHS, Koehler & Meiler, Proteins, 2008) More...

utility::vector1< Size >	get_number_of_residues (Pose &pose)
	Get number of residues in each state, this is what we are normalizing with. More...

Real	get_surface_complementarity (Pose &pose)
	Get surface complementarity. More...

utility::vector1< Real >	get_residue_size (Pose &pose)
	Get avg residue size (in number of atoms) for all states. More...

Size	get_number_hbonds (Pose &pose)
	Get number of Hbonds across interface. More...

Size	get_number_pi_stacking (Pose &pose)
	Get number of pi-stacking across interface. More...

Real	get_inout_orientation (Pose &pose)
	Get in/out orientation. More...

utility::vector1< utility::vector1< Size > >	get_aa_statistics (Pose &pose)
	Get AA statistics. More...

Private Attributes
bool	membrane_ {}
	Membrane protein? More...

core::scoring::ScoreFunctionOP	sfxn_
	scorefunction More...

std::string	partner_
	Partners;. More...

utility::vector1< std::string >	partners_
	Partners split up. More...

utility::vector1< core::Size >	jumps_
	jumps More...

utility::vector1< Interface >	interfaces_
	Interfaces. More...

std::string	chains_
	Chains to consider for computing statistics. More...

utility::vector1< bool >	uniq_
	Unique chains to minimize bias from multiple counts. More...

utility::vector1< bool >	in_mem_
	Are residues in the membrane? More...

utility::vector1< bool >	intf_
	Are the residues in the interface? More...

utility::vector1< bool >	exposed_
	Are the residues exposed? More...

Constructor & Destructor Documentation

◆ MPInterfaceStatistics() [1/2]

MPInterfaceStatistics::MPInterfaceStatistics ( )

Constructors ///.

Construct a Default Membrane Position Mover

Referenced by main(), and operator=().

◆ MPInterfaceStatistics() [2/2]

MPInterfaceStatistics::MPInterfaceStatistics ( MPInterfaceStatistics const & src )

default

Copy Constructor.

Make a deep copy of this mover object

◆ ~MPInterfaceStatistics()

MPInterfaceStatistics::~MPInterfaceStatistics ( )

overridedefault

Destructor.

Member Function Documentation

◆ add_to_scorefile()

void MPInterfaceStatistics::add_to_scorefile ( Pose & pose )

private

Add output to scorefile.

References get_avg_charge(), get_avg_hydrophobicity(), get_avg_number_charges(), get_charge(), get_hydrophobicity(), get_inout_orientation(), get_number_charges(), get_number_hbonds(), get_number_of_residues(), get_number_pi_stacking(), get_residue_size(), get_size(), get_surface_complementarity(), bin_torsions::job, beta_nonlocal::pose, subloop_histogram::size, and TR.

Referenced by apply().

◆ apply()

void MPInterfaceStatistics::apply ( Pose & pose )

override

Get Membrane protein interface statistics.

References add_to_scorefile(), calculate_interfaces(), chains, chains_, pyrosetta::create_score_function, basic::options::OptionKeys::docking::docking, fill_vectors_with_data(), get_chains_from_cmd(), create_a3b_hbs::i, init_from_cmd(), docking::jumps, jumps_, basic::options::OptionKeys::abinitio::membrane, membrane_, partner_, beta_nonlocal::pose, print_aa_statistics(), register_options(), sfxn_, TR, and uniq_.

Referenced by pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

◆ calculate_interfaces()

void MPInterfaceStatistics::calculate_interfaces ( Pose & pose )

private

calculate interfaces

Calculate interfaces @detail This is for 2-body docking.

References create_a3b_hbs::i, interfaces_, intf_, jumps_, partner_, partners_, beta_nonlocal::pose, create_a3b_hbs::r, and utility::string_split().

Referenced by apply().

◆ fill_vectors_with_data()

void MPInterfaceStatistics::fill_vectors_with_data ( Pose & pose )

private

fill vectors with data

Fill vectors with data.

References exposed_, create_a3b_hbs::i, in_mem_, intf_, membrane_, beta_nonlocal::pose, basic::options::OptionKeys::AnchoredDesign::filters::sasa, TR, and uniq_.

Referenced by apply().

◆ get_aa_statistics()

utility::vector1< utility::vector1< Size > > MPInterfaceStatistics::get_aa_statistics ( Pose & pose )

private

Get AA statistics.

These are counts, outer vector is over 6 bins, inner vector over 20 AAs

References exposed_, create_a3b_hbs::i, in_mem_, intf_, beta_nonlocal::pose, and uniq_.

Referenced by print_aa_statistics().

◆ get_avg_charge()

utility::vector1< Real > MPInterfaceStatistics::get_avg_charge ( Pose & pose )

private

Get avg charge for all states.

Get average charge of the interface, meaning averaged over the number of residues.

References get_charge(), get_number_of_residues(), create_a3b_hbs::i, create_a3b_hbs::nres, and beta_nonlocal::pose.

Referenced by add_to_scorefile().

◆ get_avg_hydrophobicity()

utility::vector1< Real > MPInterfaceStatistics::get_avg_hydrophobicity ( Pose & pose )

private

Get avg hydrophobicity for all states (UHS, Koehler & Meiler, Proteins, 2008)

References get_hydrophobicity(), get_number_of_residues(), create_a3b_hbs::i, create_a3b_hbs::nres, and beta_nonlocal::pose.

Referenced by add_to_scorefile().

◆ get_avg_number_charges()

utility::vector1< Real > MPInterfaceStatistics::get_avg_number_charges ( Pose & pose )

private

Get avg number of charged residues for all states.

Get average number of charges, meaning averaged over the number of residues.

References get_number_charges(), get_number_of_residues(), create_a3b_hbs::i, create_a3b_hbs::nres, and beta_nonlocal::pose.

Referenced by add_to_scorefile().

◆ get_chains_from_cmd()

utility::vector1< bool > MPInterfaceStatistics::get_chains_from_cmd ( Pose & pose )

private

Get the chains from the commandline.

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, predPRE::chain, chains_, beta_nonlocal::pose, and create_a3b_hbs::r.

Referenced by apply().

◆ get_charge()

utility::vector1< SSize > MPInterfaceStatistics::get_charge ( Pose & pose )

private

Get charge for all states.

Get charge of the interface.

References exposed_, create_a3b_hbs::i, in_mem_, intf_, make_symmdef_file_denovo::pos, beta_nonlocal::pose, res, and uniq_.

Referenced by add_to_scorefile(), and get_avg_charge().

◆ get_hydrophobicity()

utility::vector1< Real > MPInterfaceStatistics::get_hydrophobicity ( Pose & pose )

private

Get hydrophobicity for all states (UHS, Koehler & Meiler, Proteins, 2008)

Get hydrophobicity of the interface (UHS, Koehler & Meiler, Proteins, 2008)

References exposed_, create_a3b_hbs::i, in_mem_, intf_, beta_nonlocal::pose, and uniq_.

Referenced by add_to_scorefile(), and get_avg_hydrophobicity().

◆ get_inout_orientation()

Real MPInterfaceStatistics::get_inout_orientation ( Pose & pose )

private

Get in/out orientation.

References val2thr::atom, beta_nonlocal::pose, basic::options::OptionKeys::in::file::xyz, and predPRE::z.

Referenced by add_to_scorefile().

◆ get_name()

std::string MPInterfaceStatistics::get_name ( ) const

override

Mover Methods ///.

Get the name of this mover

◆ get_number_charges()

utility::vector1< Size > MPInterfaceStatistics::get_number_charges ( Pose & pose )

private

Get number of charged residues for all states.

Get number of charged residues in the interface.

References exposed_, create_a3b_hbs::i, in_mem_, intf_, beta_nonlocal::pose, res, and uniq_.

Referenced by add_to_scorefile(), and get_avg_number_charges().

◆ get_number_hbonds()

Size MPInterfaceStatistics::get_number_hbonds ( Pose & pose )

private

Get number of Hbonds across interface.

References basic::options::OptionKeys::mp::scoring::hbond, create_a3b_hbs::i, create_a3b_hbs::j, devel::metal_interface::partner1, devel::metal_interface::partner2, partner_, basic::options::OptionKeys::docking::partners, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, utility::split(), and utility::string_split().

Referenced by add_to_scorefile().

◆ get_number_of_residues()

utility::vector1< Size > MPInterfaceStatistics::get_number_of_residues ( Pose & pose )

private

Get number of residues in each state, this is what we are normalizing with.

Get number of residues in each bin, this is what we are normalizing by.

References exposed_, create_a3b_hbs::i, in_mem_, intf_, beta_nonlocal::pose, and uniq_.

Referenced by add_to_scorefile(), get_avg_charge(), get_avg_hydrophobicity(), get_avg_number_charges(), and get_residue_size().

◆ get_number_pi_stacking()

Size MPInterfaceStatistics::get_number_pi_stacking ( Pose & pose )

private

Get number of pi-stacking across interface.

References beta_nonlocal::pose, utility::string2Size(), TR, and basic::Tracer::Warning.

Referenced by add_to_scorefile().

◆ get_residue_size()

utility::vector1< Real > MPInterfaceStatistics::get_residue_size ( Pose & pose )

private

Get avg residue size (in number of atoms) for all states.

Get avg residue in the interface.

References exposed_, get_number_of_residues(), create_a3b_hbs::i, in_mem_, intf_, create_a3b_hbs::nres, beta_nonlocal::pose, TR, and uniq_.

Referenced by add_to_scorefile().

◆ get_size()

Real MPInterfaceStatistics::get_size ( Pose & pose )

private

Get size of the interface.

Get size of the interface in square Angstrom.

Supports multiple partners; the interface is sum of all interfaces, independent of uniq partners

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, clean_pdb_keep_ligand::chainid, chains, create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, partners_, beta_nonlocal::pose, basic::options::OptionKeys::AnchoredDesign::filters::sasa, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by add_to_scorefile().

◆ get_surface_complementarity()

Real MPInterfaceStatistics::get_surface_complementarity ( Pose & pose )

private

Get surface complementarity.

References jumps_, beta_nonlocal::pose, and basic::options::OptionKeys::canonical_sampling::probabilities::sc.

Referenced by add_to_scorefile().

◆ init_from_cmd()

void MPInterfaceStatistics::init_from_cmd ( )

private

Initialize Mover options from the comandline.

References chains, chains_, membrane_, option, partner_, basic::options::OptionKeys::docking::partners, basic::options::OptionKeys::mp::setup::spanfiles, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by apply().

◆ operator=()

MPInterfaceStatistics & MPInterfaceStatistics::operator= ( MPInterfaceStatistics const & src )

Assignment Operator.

Make a deep copy of this mover object, overriding the assignment operator

References MPInterfaceStatistics().

◆ print_aa_statistics()

void MPInterfaceStatistics::print_aa_statistics ( Pose & pose )

private

Print amino acid statistics.

Doesn't print to scorefile, too many columns; prints to out

References aa, get_aa_statistics(), create_a3b_hbs::i, test.T110_numeric::I, beta_nonlocal::pose, and TR.

Referenced by apply().

◆ register_options()

void MPInterfaceStatistics::register_options ( )

private

Rosetta Scripts Methods ///.

Register Options with JD2.

Register Options with JD2

References chains, option, basic::options::OptionKeys::docking::partners, and basic::options::OptionKeys::mp::setup::spanfiles.

Referenced by apply().

Member Data Documentation

◆ chains_

std::string MPInterfaceStatistics::chains_

private

Chains to consider for computing statistics.

Referenced by apply(), get_chains_from_cmd(), and init_from_cmd().

◆ exposed_

utility::vector1< bool > MPInterfaceStatistics::exposed_

private

Are the residues exposed?

Referenced by fill_vectors_with_data(), get_aa_statistics(), get_charge(), get_hydrophobicity(), get_number_charges(), get_number_of_residues(), and get_residue_size().

◆ in_mem_

utility::vector1< bool > MPInterfaceStatistics::in_mem_

private

Are residues in the membrane?

Referenced by fill_vectors_with_data(), get_aa_statistics(), get_charge(), get_hydrophobicity(), get_number_charges(), get_number_of_residues(), and get_residue_size().

◆ interfaces_

utility::vector1< Interface > MPInterfaceStatistics::interfaces_

private

Interfaces.

Referenced by calculate_interfaces().

◆ intf_

utility::vector1< bool > MPInterfaceStatistics::intf_

private

Are the residues in the interface?

Referenced by calculate_interfaces(), fill_vectors_with_data(), get_aa_statistics(), get_charge(), get_hydrophobicity(), get_number_charges(), get_number_of_residues(), and get_residue_size().

◆ jumps_

utility::vector1< core::Size > MPInterfaceStatistics::jumps_

private

jumps

Referenced by apply(), calculate_interfaces(), and get_surface_complementarity().

◆ membrane_

bool MPInterfaceStatistics::membrane_ {}

private

Membrane protein?

Referenced by apply(), fill_vectors_with_data(), and init_from_cmd().

◆ partner_

std::string MPInterfaceStatistics::partner_

private

Partners;.

Referenced by apply(), calculate_interfaces(), get_number_hbonds(), and init_from_cmd().

◆ partners_

utility::vector1< std::string > MPInterfaceStatistics::partners_

private

Partners split up.

Referenced by calculate_interfaces(), and get_size().

◆ sfxn_

core::scoring::ScoreFunctionOP MPInterfaceStatistics::sfxn_

private

scorefunction

Referenced by apply().

◆ uniq_

utility::vector1< bool > MPInterfaceStatistics::uniq_

private

Unique chains to minimize bias from multiple counts.

Referenced by apply(), fill_vectors_with_data(), get_aa_statistics(), get_charge(), get_hydrophobicity(), get_number_charges(), get_number_of_residues(), and get_residue_size().

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

src/apps/pilot/jkleman/interface_statistics.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ MPInterfaceStatistics() [1/2]

◆ MPInterfaceStatistics() [2/2]

◆ ~MPInterfaceStatistics()

Member Function Documentation

◆ add_to_scorefile()

◆ apply()

◆ calculate_interfaces()

◆ fill_vectors_with_data()

◆ get_aa_statistics()

◆ get_avg_charge()

◆ get_avg_hydrophobicity()

◆ get_avg_number_charges()

◆ get_chains_from_cmd()

◆ get_charge()

◆ get_hydrophobicity()

◆ get_inout_orientation()

◆ get_name()

◆ get_number_charges()

◆ get_number_hbonds()

◆ get_number_of_residues()

◆ get_number_pi_stacking()

◆ get_residue_size()

◆ get_size()

◆ get_surface_complementarity()

◆ init_from_cmd()

◆ operator=()

◆ print_aa_statistics()

◆ register_options()

Member Data Documentation

◆ chains_

◆ exposed_

◆ in_mem_

◆ interfaces_

◆ intf_

◆ jumps_

◆ membrane_

◆ partner_

◆ partners_

◆ sfxn_

◆ uniq_