protocols::matdes Namespace Reference

Classes
class	BuildingBlockInterfaceOperation
class	BuildingBlockInterfaceOperationCreator
class	ClashCheckFilter
class	ClashCheckFilterCreator
class	ExtractSubposeMover
class	ExtractSubposeMoverCreator
class	GetRBDOFValues
	WARNING WARNING WARNING THIS CLASS USES THE THREAD UNSAFE SymDofMoverSampler AND MAKES ANY PROTOCOL THAT USES THIS CLASS THREAD UNSAFE. More...
class	GetRBDOFValuesCreator
class	InterfacePackingFilter
class	InterfacePackingFilterCreator
class	MatDesGreedyOptMutationMover
class	MatDesGreedyOptMutationMoverCreator
class	MatDesPointMutationCalculator
class	OligomericAverageDegreeFilter
class	OligomericAverageDegreeFilterCreator
class	SchemePlaceMotifsMover
class	SchemePlaceMotifsMoverCreator
class	SymDofMover
class	SymDofMoverCreator
class	SymDofMoverSampler
	WARNING WARNING WARNING THIS SINGLETON CLASS HOLDS NON-CONST, JOB SPECIFIC DATA AND MAKES EVERY CLASS THAT USES THIS DATA THREAD UNSAFE. THIS IS NOT HOW SINGLETONS SHOULD BE USED. More...
class	SymUnsatHbondFilter
	filters based on an upper bound # of buried unsatisfied polar residues More...
class	SymUnsatHbondFilterCreator

Typedefs
typedef utility::pointer::shared_ptr < BuildingBlockInterfaceOperation >	BuildingBlockInterfaceOperationOP
typedef utility::pointer::shared_ptr < BuildingBlockInterfaceOperation const >	BuildingBlockInterfaceOperationCOP
typedef utility::pointer::shared_ptr < ClashCheckFilter >	ClashCheckFilterOP
typedef utility::pointer::shared_ptr < ClashCheckFilter const >	ClashCheckFilterCOP
typedef utility::pointer::shared_ptr < ExtractSubposeMover >	ExtractSubposeMoverOP
typedef utility::pointer::shared_ptr < ExtractSubposeMover const >	ExtractSubposeMoverCOP
typedef utility::pointer::shared_ptr < GetRBDOFValues >	GetRBDOFValuesOP
typedef utility::pointer::shared_ptr < GetRBDOFValues const >	GetRBDOFValuesCOP
typedef utility::pointer::shared_ptr < InterfacePackingFilter >	InterfacePackingFilterOP
typedef utility::pointer::shared_ptr < InterfacePackingFilter const >	InterfacePackingFilterCOP
typedef utility::pointer::shared_ptr < MatDesGreedyOptMutationMover >	MatDesGreedyOptMutationMoverOP
typedef utility::pointer::shared_ptr < MatDesGreedyOptMutationMover const >	MatDesGreedyOptMutationMoverCOP
typedef utility::pointer::shared_ptr < MatDesPointMutationCalculator >	MatDesPointMutationCalculatorOP
typedef utility::pointer::shared_ptr < MatDesPointMutationCalculator const >	MatDesPointMutationCalculatorCOP
typedef utility::pointer::shared_ptr < OligomericAverageDegreeFilter >	OligomericAverageDegreeFilterOP
typedef utility::pointer::shared_ptr < OligomericAverageDegreeFilter const >	OligomericAverageDegreeFilterCOP
typedef utility::pointer::shared_ptr < SchemePlaceMotifsMover >	SchemePlaceMotifsMoverOP
typedef utility::pointer::shared_ptr < SchemePlaceMotifsMover const >	SchemePlaceMotifsMoverCOP
typedef numeric::xyzVector< Real >	Vec
typedef numeric::xyzMatrix< Real >	Mat
typedef utility::pointer::shared_ptr < SymDofMover >	SymDofMoverOP
typedef utility::pointer::shared_ptr < SymDofMover const >	SymDofMoverCOP
typedef utility::pointer::shared_ptr < SymUnsatHbondFilter >	SymUnsatHbondFilterOP
typedef utility::pointer::shared_ptr < SymUnsatHbondFilter const >	SymUnsatHbondFilterCOP

Functions
static thread_local basic::Tracer	TR ("protocols.matdes.InterfacePackingFilter")
static thread_local basic::Tracer	TR ("protocols.matdes.MatDesGreedyOptMutationMover")
bool	cmp_pair_by_second (pair< Size, Real > const pair1, pair< 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< Size, vector1< pair< AA, vector1< Real > > > > const pair1, pair< 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 thread_local basic::Tracer	TR ("protocols.matdes.MatDesPointMutationCalculator")
void	insert_point_mut_filter_vals (Size const seqpos, chemical::AA const aa, vector1< Real > const vals, vector1< pair< Size, vector1< pair< AA, vector1< Real > > > > > &seqpos_aa_vals_vec)
static void	trans_pose (Pose &pose, Vec const &trans, Size start, Size end)
static void	rot_pose (Pose &pose, Mat const &rot, Size start, Size end)
static void	rot_pose (Pose &pose, Mat const &rot, Vec const &cen, Size start, Size end)
static void	rot_pose (Pose &pose, Vec const &axis, double const &ang, Size start, Size end)
static void	rot_pose (Pose &pose, Vec const &axis, double const &ang, Vec const &cen, Size start, Size end)
static void	alignaxis (core::pose::Pose &pose, Vec newaxis, Vec oldaxis, Vec cen, Size start, Size end)
numeric::Real	get_intra_contacts (Pose const &pose)
void	maximize_sub1_contact (Pose &pose, Size const &nf1, Size const &nf2, Vec const &ax1, Vec const &ax2)
static thread_local basic::Tracer	TR ("protocols.matdes.SymUnsatHbondFilter")

Typedef Documentation

typedef utility::pointer::shared_ptr< BuildingBlockInterfaceOperation const > protocols::matdes::BuildingBlockInterfaceOperationCOP

typedef utility::pointer::shared_ptr< BuildingBlockInterfaceOperation > protocols::matdes::BuildingBlockInterfaceOperationOP

typedef utility::pointer::shared_ptr< ClashCheckFilter const > protocols::matdes::ClashCheckFilterCOP

typedef utility::pointer::shared_ptr< ClashCheckFilter > protocols::matdes::ClashCheckFilterOP

typedef utility::pointer::shared_ptr< ExtractSubposeMover const > protocols::matdes::ExtractSubposeMoverCOP

typedef utility::pointer::shared_ptr< ExtractSubposeMover > protocols::matdes::ExtractSubposeMoverOP

typedef utility::pointer::shared_ptr< GetRBDOFValues const > protocols::matdes::GetRBDOFValuesCOP

typedef utility::pointer::shared_ptr< GetRBDOFValues > protocols::matdes::GetRBDOFValuesOP

typedef utility::pointer::shared_ptr< InterfacePackingFilter const > protocols::matdes::InterfacePackingFilterCOP

typedef utility::pointer::shared_ptr< InterfacePackingFilter > protocols::matdes::InterfacePackingFilterOP

typedef numeric::xyzMatrix<Real> protocols::matdes::Mat

typedef utility::pointer::shared_ptr< MatDesGreedyOptMutationMover const > protocols::matdes::MatDesGreedyOptMutationMoverCOP

typedef utility::pointer::shared_ptr< MatDesGreedyOptMutationMover > protocols::matdes::MatDesGreedyOptMutationMoverOP

typedef utility::pointer::shared_ptr< MatDesPointMutationCalculator const > protocols::matdes::MatDesPointMutationCalculatorCOP

typedef utility::pointer::shared_ptr< MatDesPointMutationCalculator > protocols::matdes::MatDesPointMutationCalculatorOP

typedef utility::pointer::shared_ptr< OligomericAverageDegreeFilter const > protocols::matdes::OligomericAverageDegreeFilterCOP

typedef utility::pointer::shared_ptr< OligomericAverageDegreeFilter > protocols::matdes::OligomericAverageDegreeFilterOP

typedef utility::pointer::shared_ptr< SchemePlaceMotifsMover const > protocols::matdes::SchemePlaceMotifsMoverCOP

typedef utility::pointer::shared_ptr< SchemePlaceMotifsMover > protocols::matdes::SchemePlaceMotifsMoverOP

typedef utility::pointer::shared_ptr< SymDofMover const > protocols::matdes::SymDofMoverCOP

typedef utility::pointer::shared_ptr< SymDofMover > protocols::matdes::SymDofMoverOP

typedef utility::pointer::shared_ptr< SymUnsatHbondFilter const > protocols::matdes::SymUnsatHbondFilterCOP

typedef utility::pointer::shared_ptr< SymUnsatHbondFilter > protocols::matdes::SymUnsatHbondFilterOP

typedef numeric::xyzVector<Real> protocols::matdes::Vec

Function Documentation

static void protocols::matdes::alignaxis ( core::pose::Pose &  pose, Vec  newaxis, Vec  oldaxis, Vec  cen, Size  start, Size  end  )

static

References numeric::xyzVector< class >::cross(), numeric::xyzVector< class >::dot(), numeric::max(), numeric::min(), numeric::xyzVector< class >::normalize(), numeric::xyzVector< class >::normalized(), numeric::constants::d::pi, and rot_pose().

Referenced by protocols::matdes::SymDofMover::apply().

void protocols::matdes::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(), numeric::random::rg(), size(), and numeric::random::RandomGenerator::uniform().

Referenced by protocols::matdes::MatDesGreedyOptMutationMover::filter_pareto_opt_poses(), and protocols::matdes::MatDesGreedyOptMutationMover::filter_seqpos_pareto_opt_ptmuts().

void protocols::matdes::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(), and size().

Referenced by calc_pareto_front().

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

Referenced by protocols::matdes::MatDesGreedyOptMutationMover::apply().

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

Referenced by protocols::matdes::MatDesGreedyOptMutationMover::calc_pfront_poses_filter_ranks().

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

Referenced by protocols::matdes::MatDesGreedyOptMutationMover::apply().

numeric::Real protocols::matdes::get_intra_contacts

(

Pose const &

pose

)

References numeric::xyzVector< class >::distance_squared(), get_component_lower_bound(), get_component_upper_bound(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), runtime_assert, size(), and symmetric_components().

Referenced by maximize_sub1_contact().

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

References pair.

void protocols::matdes::maximize_sub1_contact	(	Pose &	pose,
		Size const &	nf1,
		Size const &	nf2,
		Vec const &	ax1,
		Vec const &	ax2
	)

References get_component_lower_bound(), get_component_upper_bound(), get_intra_contacts(), rot_pose(), runtime_assert, size(), and symmetric_components().

static void protocols::matdes::rot_pose ( Pose &  pose, Mat const &  rot, Size  start, Size  end  )

static

References core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), and core::pose::Pose::xyz().

Referenced by alignaxis(), protocols::matdes::SymDofMover::apply(), maximize_sub1_contact(), and rot_pose().

static void protocols::matdes::rot_pose ( Pose &  pose, Mat const &  rot, Vec const &  cen, Size  start, Size  end  )

static

References rot_pose(), and trans_pose().

static void protocols::matdes::rot_pose ( Pose &  pose, Vec const &  axis, double const &  ang, Size  start, Size  end  )

static

References rot_pose(), and rotation_matrix_degrees().

static void protocols::matdes::rot_pose ( Pose &  pose, Vec const &  axis, double const &  ang, Vec const &  cen, Size  start, Size  end  )

static

References rot_pose(), and rotation_matrix_degrees().

static thread_local basic::Tracer protocols::matdes::TR ( "protocols.matdes.InterfacePackingFilter"  )

static

Referenced by protocols::matdes::SymDofMover::add_components_to_pose_if_necessary(), protocols::matdes::SchemePlaceMotifsMover::apply(), protocols::matdes::InterfacePackingFilter::apply(), protocols::matdes::ExtractSubposeMover::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::matdes::SymDofMover::apply(), protocols::matdes::SymUnsatHbondFilter::apply(), protocols::matdes::ClashCheckFilter::apply(), protocols::matdes::InterfacePackingFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::matdes::ClashCheckFilter::compute(), protocols::matdes::GetRBDOFValues::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), protocols::matdes::InterfacePackingFilter::parse_def(), protocols::matdes::SymUnsatHbondFilter::parse_def(), protocols::matdes::OligomericAverageDegreeFilter::parse_def(), protocols::matdes::SchemePlaceMotifsMover::parse_my_tag(), protocols::matdes::InterfacePackingFilter::parse_my_tag(), protocols::matdes::SymDofMover::parse_my_tag(), protocols::matdes::SymUnsatHbondFilter::parse_my_tag(), protocols::matdes::OligomericAverageDegreeFilter::parse_my_tag(), protocols::matdes::SymDofMoverSampler::set_angle_ranges(), protocols::matdes::SymDofMoverSampler::set_radial_disp_ranges(), and protocols::matdes::SymDofMoverSampler::step().

static thread_local basic::Tracer protocols::matdes::TR ( "protocols.matdes.MatDesGreedyOptMutationMover"  )

static

static thread_local basic::Tracer protocols::matdes::TR ( "protocols.matdes.SymUnsatHbondFilter"  )

static

static thread_local basic::Tracer protocols::matdes::TR ( "protocols.matdes.MatDesPointMutationCalculator"  )

static

static void protocols::matdes::trans_pose ( Pose &  pose, Vec const &  trans, Size  start, Size  end  )

static

References core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), and core::pose::Pose::xyz().

Referenced by protocols::matdes::SymDofMover::apply(), and rot_pose().