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Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::pmut_scan::AlterSpecDisruptionDriver Class Reference

#include <AlterSpecDisruptionDriver.hh>

Inheritance diagram for protocols::pmut_scan::AlterSpecDisruptionDriver:
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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::Sizeinterface_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

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_.

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

Destructor.

Member Function Documentation

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().

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

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().

Member Data Documentation

protocols::analysis::InterfaceAnalyzerMoverOP protocols::pmut_scan::AlterSpecDisruptionDriver::IAM_
private
std::set<core::Size> protocols::pmut_scan::AlterSpecDisruptionDriver::interface_set_
private

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