#include <AlterSpecDisruptionDriver.hh>

Inheritance diagram for protocols::pmut_scan::AlterSpecDisruptionDriver:

Public Member Functions
	AlterSpecDisruptionDriver (utility::vector1< std::string > &pdb_file_names, bool double_mutant_scan, std::string list_file, bool output_mutant_structures)
	Main constructor for the class. More...

	~AlterSpecDisruptionDriver () override
	Destructor. More...

core::Energy	score (core::pose::Pose &pose) override
	return a score that is a ddG of binding, rather than a ddG of the interface. It returns a reversed value because this class wants to find DEstabilizing mutations. More...

bool	reject_mutant (Mutant const &mutant, core::pose::Pose const &pose) override
	offers a chance for child classes to inject mutant selection logic More...

Public Member Functions inherited from protocols::pmut_scan::PointMutScanDriver
	PointMutScanDriver (utility::vector1< std::string > &pdb_file_names, bool double_mutant_scan, std::string const &list_file, bool output_mutant_structures)
	Main constructor for the class. What all does it do? More...

virtual	~PointMutScanDriver ()
	Destructor. What all needs to be done here? More...

void	go ()
	Entry point for the pmut_scan protocol. This is function the app calls to do the scan. More...

void	read_in_structures ()
	Reads in the structure (or list of structures) specified on the command line to a class member variable. Create Pose objects for all of the structures because we'll pass these out to the slave nodes later. More...

void	fill_mutations_list ()
	Determines whether the user specified a list of mutants or just wants to do a scan over all possible combinations. More...

void	calculate_neighbor_table (core::pose::Pose &pose, utility::vector1< utility::vector1< bool > > &neighbors)
	Calculates the 10A neighbor graph using the given pose object and then sets values in a 2D array to indicate which resids are neighbors. More...

void	make_specific_mutant (utility::vector1< core::pose::Pose > &mutant_poses, utility::vector1< core::pose::Pose > &native_poses, protocols::pmut_scan::Mutant &m, std::string mutation_string="", std::string mutation_string_PDB_numbering="")
	Function which takes in a mutation to make (either single, double or more) and calls itself recursively until the desired structure is created. Useful for testing certain combinations of mutations (like putting two double mutants together) without having to run an entire scan protocol that would cover those mutations. More...

core::scoring::ScoreFunctionCOP	get_scorefxn () const
	accessor for scorefxn_ now that it is private member data More...

void	set_ddG_cutoff (core::Real threshold)

utility::vector1< Mutant >::const_iterator	mutants_begin () const
	returns a const iterator to the beginning of the Mutant data member variable vector More...

utility::vector1< Mutant >::const_iterator	mutants_end () const
	returns a const iterator to the end of the Mutant data member variable vector More...

core::Size	n_mutants () const
	returns the size of the Mutant data member variable vector More...

Private Member Functions
bool	reject_on_chains (Mutant const &mutant)
	reject Mutant based on chain IDs of constituent mutations More...

bool	reject_on_interface (Mutant const &mutant, core::pose::Pose const &pose)
	reject Mutant based on interface-ness of constituent mutations More...

Private Attributes
protocols::analysis::InterfaceAnalyzerMoverOP	IAM_

std::set< core::Size >	interface_set_

Detailed Description

this subclass of Ron's PointMutScanDriver exists to tweak one aspect of his code: instead of looking for total-energy-stabilizing mutations, it looks for binding-energy-DEstabilizing point & pair mutations.

Constructor & Destructor Documentation

◆ AlterSpecDisruptionDriver()

protocols::pmut_scan::AlterSpecDisruptionDriver::AlterSpecDisruptionDriver	(	utility::vector1< std::string > &	pdb_file_names,
		bool	double_mutant_scan,
		std::string	list_file,
		bool	output_mutant_structures
	)

Main constructor for the class.

References protocols::pmut_scan::PointMutScanDriver::get_scorefxn(), IAM_, and interface_set_.

◆ ~AlterSpecDisruptionDriver()

protocols::pmut_scan::AlterSpecDisruptionDriver::~AlterSpecDisruptionDriver ( )

overridedefault

Destructor.

Member Function Documentation

◆ reject_mutant()

bool protocols::pmut_scan::AlterSpecDisruptionDriver::reject_mutant	(	Mutant const &	mutant,
		core::pose::Pose const &	pose
	)

overridevirtual

offers a chance for child classes to inject mutant selection logic

Reimplemented from protocols::pmut_scan::PointMutScanDriver.

References reject_on_chains(), and reject_on_interface().

◆ reject_on_chains()

bool protocols::pmut_scan::AlterSpecDisruptionDriver::reject_on_chains ( Mutant const & mutant )

private

reject Mutant based on chain IDs of constituent mutations

References core::sequence::end, protocols::pmut_scan::Mutant::mutations_begin(), protocols::pmut_scan::Mutant::mutations_end(), and protocols::pmut_scan::Mutant::n_mutations().

Referenced by reject_mutant().

◆ reject_on_interface()

bool protocols::pmut_scan::AlterSpecDisruptionDriver::reject_on_interface	(	Mutant const &	mutant,
		core::pose::Pose const &	pose
	)

private

reject Mutant based on interface-ness of constituent mutations

reject Mutant based on interface-ness of constituent mutations. This function accumulates state - on first call it determines what the interface is, and assumes that interface is the same for all subsequent calls! If you are trying to use different Poses this may cause problems.

References core::sequence::end, IAM_, interface_set_, protocols::pmut_scan::Mutant::mutations_begin(), and protocols::pmut_scan::Mutant::mutations_end().

Referenced by reject_mutant().

◆ score()

core::Energy protocols::pmut_scan::AlterSpecDisruptionDriver::score ( core::pose::Pose & pose )

overridevirtual

return a score that is a ddG of binding, rather than a ddG of the interface. It returns a reversed value because this class wants to find DEstabilizing mutations.

calculate dG of binding by scoring, separating, repacking, and rescoring

Reimplemented from protocols::pmut_scan::PointMutScanDriver.

References core::pose::Pose::conformation(), IAM_, and core::conformation::Conformation::num_chains().