protocols::design_opt Namespace Reference

Classes
class	GreedyOptMutationMover
class	GreedyOptMutationMoverCreator
class	PointMutationCalculator
class	Supercharge
	Adds charged residues to a protein surface. More...

Typedefs
typedef utility::pointer::shared_ptr< GreedyOptMutationMover >	GreedyOptMutationMoverOP
typedef utility::pointer::shared_ptr< GreedyOptMutationMover const >	GreedyOptMutationMoverCOP
typedef utility::pointer::shared_ptr< ParetoOptMutationMover >	ParetoOptMutationMoverOP
typedef utility::pointer::shared_ptr< ParetoOptMutationMover const >	ParetoOptMutationMoverCOP
typedef utility::pointer::shared_ptr< PointMutationCalculator >	PointMutationCalculatorOP
typedef utility::pointer::shared_ptr< PointMutationCalculator const >	PointMutationCalculatorCOP
using	Pose = core::pose::Pose
typedef utility::pointer::shared_ptr< Supercharge >	SuperchargeOP
typedef utility::pointer::shared_ptr< Supercharge const >	SuperchargeCOP

Functions
static basic::Tracer	TR ("protocols.design_opt.GreedyOptMutationMover")
bool	cmp_pair_by_second (pair< core::Size, Real > const pair1, pair< core::Size, Real > const pair2)
bool	cmp_pair_by_first_vec_val (pair< AA, vector1< Real > > const pair1, pair< AA, vector1< Real > > const pair2)
bool	cmp_pair_vec_by_first_vec_val (pair< core::Size, vector1< pair< AA, vector1< Real > > > > const pair1, pair< core::Size, vector1< pair< AA, vector1< Real > > > > const pair2)
void	calc_pareto_front_nbrs (vector1< vector1< Real > > coords, vector1< bool > const &is_pfront, vector1< bool > &is_pfront_nbr, vector1< Real > const &nbr_dist)
void	calc_pareto_front (vector1< vector1< Real > > coords, vector1< bool > &is_pfront, vector1< Real > const &coord_perts, bool const div, bool const incl_nbrs)
static basic::Tracer	TR ("protocols.design_opt.PointMutationCalculator")
void	insert_point_mut_filter_vals (core::Size const seqpos, chemical::AA const aa, vector1< Real > const vals, vector1< pair< core::Size, vector1< pair< AA, vector1< Real > > > > > &seqpos_aa_vals_vec)
static basic::Tracer	TR ("protocols.design_opt.Supercharge")

Typedef Documentation

GreedyOptMutationMoverCOP

typedef utility::pointer::shared_ptr< GreedyOptMutationMover const > protocols::design_opt::GreedyOptMutationMoverCOP

GreedyOptMutationMoverOP

typedef utility::pointer::shared_ptr< GreedyOptMutationMover > protocols::design_opt::GreedyOptMutationMoverOP

ParetoOptMutationMoverCOP

typedef utility::pointer::shared_ptr< ParetoOptMutationMover const > protocols::design_opt::ParetoOptMutationMoverCOP

ParetoOptMutationMoverOP

typedef utility::pointer::shared_ptr< ParetoOptMutationMover > protocols::design_opt::ParetoOptMutationMoverOP

PointMutationCalculatorCOP

typedef utility::pointer::shared_ptr< PointMutationCalculator const > protocols::design_opt::PointMutationCalculatorCOP

PointMutationCalculatorOP

typedef utility::pointer::shared_ptr< PointMutationCalculator > protocols::design_opt::PointMutationCalculatorOP

Pose

using protocols::design_opt::Pose = typedef core::pose::Pose

SuperchargeCOP

typedef utility::pointer::shared_ptr< Supercharge const > protocols::design_opt::SuperchargeCOP

SuperchargeOP

typedef utility::pointer::shared_ptr< Supercharge > protocols::design_opt::SuperchargeOP

Function Documentation

calc_pareto_front()

void protocols::design_opt::calc_pareto_front	(	vector1< vector1< Real > >	coords,
		vector1< bool > &	is_pfront,
		vector1< Real > const &	coord_perts,
		bool const	div,
		bool const	incl_nbrs
	)

References calc_pareto_front_nbrs(), protocols::simple_filters::coords(), and core::scoring::rg.

Referenced by protocols::design_opt::GreedyOptMutationMover::filter_pareto_opt_poses(), and protocols::design_opt::GreedyOptMutationMover::filter_seqpos_pareto_opt_ptmuts().

calc_pareto_front_nbrs()

void protocols::design_opt::calc_pareto_front_nbrs	(	vector1< vector1< Real > >	coords,
		vector1< bool > const &	is_pfront,
		vector1< bool > &	is_pfront_nbr,
		vector1< Real > const &	nbr_dist
	)

References protocols::simple_filters::coords().

Referenced by calc_pareto_front().

cmp_pair_by_first_vec_val()

bool protocols::design_opt::cmp_pair_by_first_vec_val	(	pair< AA, vector1< Real > > const	pair1,
		pair< AA, vector1< Real > > const	pair2
	)

Referenced by protocols::design_opt::GreedyOptMutationMover::apply().

cmp_pair_by_second()

bool protocols::design_opt::cmp_pair_by_second	(	pair< core::Size, Real > const	pair1,
		pair< core::Size, Real > const	pair2
	)

Referenced by protocols::design_opt::GreedyOptMutationMover::calc_pfront_poses_filter_ranks().

cmp_pair_vec_by_first_vec_val()

bool protocols::design_opt::cmp_pair_vec_by_first_vec_val	(	pair< core::Size, vector1< pair< AA, vector1< Real > > > > const	pair1,
		pair< core::Size, vector1< pair< AA, vector1< Real > > > > const	pair2
	)

Referenced by protocols::design_opt::GreedyOptMutationMover::apply().

insert_point_mut_filter_vals()

void protocols::design_opt::insert_point_mut_filter_vals	(	core::Size const	seqpos,
		chemical::AA const	aa,
		vector1< Real > const	vals,
		vector1< pair< core::Size, vector1< pair< AA, vector1< Real > > > > > &	seqpos_aa_vals_vec
	)

References protocols::cluster::calibur::aa, core::chemical::oneletter_code_from_aa(), and core::scoring::pair.

TR() [1/3]

static basic::Tracer protocols::design_opt::TR ( "protocols.design_opt.GreedyOptMutationMover"  )

static

Referenced by protocols::design_opt::GreedyOptMutationMover::apply(), protocols::design_opt::Supercharge::apply(), protocols::design_opt::Supercharge::AvNAPSA_values(), protocols::design_opt::Supercharge::design_supercharge(), protocols::design_opt::Supercharge::design_supercharge_AvNAPSA(), protocols::design_opt::GreedyOptMutationMover::dump_scoring_table(), protocols::design_opt::Supercharge::energy_comparison(), protocols::design_opt::PointMutationCalculator::eval_filters(), protocols::design_opt::PointMutationCalculator::mutate_and_relax(), protocols::design_opt::GreedyOptMutationMover::parse_my_tag(), protocols::design_opt::PointMutationCalculator::PointMutationCalculator(), protocols::design_opt::Supercharge::prepack_input_structure(), protocols::design_opt::Supercharge::print_netcharge_and_mutations(), protocols::design_opt::Supercharge::set_resfile(), protocols::design_opt::Supercharge::set_resfile_AvNAPSA(), and protocols::design_opt::Supercharge::set_surface().

TR() [2/3]

static basic::Tracer protocols::design_opt::TR ( "protocols.design_opt.PointMutationCalculator"  )

static

TR() [3/3]

static basic::Tracer protocols::design_opt::TR ( "protocols.design_opt.Supercharge"  )

static