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	MotifHitsRotamersOperation
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< MotifHitsRotamersOperation >	MotifHitsRotamersOperationOP
typedef utility::pointer::shared_ptr< MotifHitsRotamersOperation const >	MotifHitsRotamersOperationCOP
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
using	Vec = numeric::xyzVector< Real >
using	Mat = numeric::xyzMatrix< Real >
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
utility::vector1< core::Size >	get_matching_subunits (core::pose::Pose const &pose, core::pose::Pose const &subpose)
static basic::Tracer	TR ("protocols.matdes.InterfacePackingFilter")
static basic::Tracer	TR ("protocols.matdes.MatDesGreedyOptMutationMover")
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.matdes.MatDesPointMutationCalculator")
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.matdes.MotifHitsRotamersOperation")
core::conformation::ResidueOP	dup_residue (core::conformation::Residue const &existing, core::conformation::Residue const &conformer)
	Helper function, combines existing's metadata with conformer's conformation. More...
static void	trans_pose (Pose &pose, Vec const &trans, core::Size start, core::Size end)
static void	rot_pose (Pose &pose, Mat const &rot, core::Size start, core::Size end)
static void	rot_pose (Pose &pose, Mat const &rot, Vec const &cen, core::Size start, core::Size end)
static void	rot_pose (Pose &pose, Vec const &axis, core::Real const &ang, core::Size start, core::Size end)
static void	rot_pose (Pose &pose, Vec const &axis, core::Real const &ang, Vec const &cen, core::Size start, core::Size end)
static void	alignaxis (core::pose::Pose &pose, Vec newaxis, Vec oldaxis, Vec cen, core::Size start, core::Size end)
numeric::Real	get_intra_contacts (Pose const &pose)
void	maximize_sub1_contact (Pose &pose, core::Size const &nf1, core::Size const &nf2, Vec const &ax1, Vec const &ax2)
static basic::Tracer	TR ("protocols.matdes.SymUnsatHbondFilter")

Typedef Documentation

BuildingBlockInterfaceOperationCOP

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

BuildingBlockInterfaceOperationOP

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

ClashCheckFilterCOP

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

ClashCheckFilterOP

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

ExtractSubposeMoverCOP

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

ExtractSubposeMoverOP

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

GetRBDOFValuesCOP

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

GetRBDOFValuesOP

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

InterfacePackingFilterCOP

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

InterfacePackingFilterOP

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

Mat

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

MatDesGreedyOptMutationMoverCOP

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

MatDesGreedyOptMutationMoverOP

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

MatDesPointMutationCalculatorCOP

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

MatDesPointMutationCalculatorOP

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

MotifHitsRotamersOperationCOP

typedef utility::pointer::shared_ptr< MotifHitsRotamersOperation const > protocols::matdes::MotifHitsRotamersOperationCOP

MotifHitsRotamersOperationOP

typedef utility::pointer::shared_ptr< MotifHitsRotamersOperation > protocols::matdes::MotifHitsRotamersOperationOP

OligomericAverageDegreeFilterCOP

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

OligomericAverageDegreeFilterOP

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

SchemePlaceMotifsMoverCOP

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

SchemePlaceMotifsMoverOP

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

SymDofMoverCOP

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

SymDofMoverOP

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

SymUnsatHbondFilterCOP

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

SymUnsatHbondFilterOP

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

Vec

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

Function Documentation

alignaxis()

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

static

References core::sequence::end, protocols::mean_field::max(), protocols::mean_field::min(), rot_pose(), and protocols::loops::start.

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

calc_pareto_front()

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(), and core::scoring::rg.

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

calc_pareto_front_nbrs()

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().

Referenced by calc_pareto_front().

cmp_pair_by_first_vec_val()

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().

cmp_pair_by_second()

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

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

cmp_pair_vec_by_first_vec_val()

bool protocols::matdes::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::matdes::MatDesGreedyOptMutationMover::apply().

dup_residue()

core::conformation::ResidueOP protocols::matdes::dup_residue	(	core::conformation::Residue const &	existing,
		core::conformation::Residue const &	conformer
	)

Helper function, combines existing's metadata with conformer's conformation.

References core::conformation::Residue::chain(), core::conformation::Residue::clone(), and core::conformation::Residue::seqpos().

Referenced by protocols::matdes::MotifHitsRotamersOperation::alter_rotamer_set().

get_intra_contacts()

numeric::Real protocols::matdes::get_intra_contacts

(

Pose const &

pose

)

References core::pose::symmetry::get_component_lower_bound(), core::pose::symmetry::get_component_upper_bound(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), and core::pose::symmetry::symmetric_components().

Referenced by maximize_sub1_contact().

get_matching_subunits()

utility::vector1< core::Size > protocols::matdes::get_matching_subunits	(	core::pose::Pose const &	pose,
		core::pose::Pose const &	subpose
	)

References core::conformation::Residue::atom(), core::pose::Pose::conformation(), core::conformation::symmetry::SymmetricConformation::get_transformation(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::scoring::rms, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), TR(), and core::conformation::Atom::xyz().

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

insert_point_mut_filter_vals()

void protocols::matdes::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.

maximize_sub1_contact()

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

References core::pose::symmetry::get_component_lower_bound(), core::pose::symmetry::get_component_upper_bound(), get_intra_contacts(), rot_pose(), and core::pose::symmetry::symmetric_components().

rot_pose() [1/4]

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

static

References core::sequence::end, core::pose::Pose::residue_type(), rot(), core::pose::Pose::set_xyz(), protocols::loops::start, and core::pose::Pose::xyz().

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

rot_pose() [2/4]

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

static

References core::sequence::end, rot(), rot_pose(), protocols::loops::start, and trans_pose().

rot_pose() [3/4]

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

static

References core::sequence::end, rot_pose(), and protocols::loops::start.

rot_pose() [4/4]

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

static

References core::sequence::end, rot_pose(), and protocols::loops::start.

TR() [1/5]

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

static

Referenced by protocols::matdes::SymDofMover::add_components_to_pose_if_necessary(), protocols::matdes::MotifHitsRotamersOperation::alter_rotamer_set(), protocols::matdes::ExtractSubposeMover::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::matdes::ClashCheckFilter::apply(), protocols::matdes::InterfacePackingFilter::apply(), protocols::matdes::SymUnsatHbondFilter::apply(), protocols::matdes::MatDesGreedyOptMutationMover::apply(), protocols::matdes::SchemePlaceMotifsMover::apply(), protocols::matdes::SymDofMover::apply(), protocols::matdes::InterfacePackingFilter::compute(), protocols::matdes::ClashCheckFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), protocols::matdes::GetRBDOFValues::compute(), protocols::matdes::MatDesGreedyOptMutationMover::dump_scoring_table(), protocols::matdes::MatDesPointMutationCalculator::eval_filters(), get_matching_subunits(), protocols::matdes::MatDesPointMutationCalculator::MatDesPointMutationCalculator(), protocols::matdes::MatDesPointMutationCalculator::mutate_and_relax(), protocols::matdes::OligomericAverageDegreeFilter::parse_my_tag(), protocols::matdes::SymUnsatHbondFilter::parse_my_tag(), protocols::matdes::SymDofMover::parse_my_tag(), protocols::matdes::InterfacePackingFilter::parse_my_tag(), protocols::matdes::MatDesGreedyOptMutationMover::parse_my_tag(), protocols::matdes::SchemePlaceMotifsMover::parse_my_tag(), protocols::matdes::MatDesGreedyOptMutationMover::reset_delta_filter_baselines(), protocols::matdes::SymDofMoverSampler::set_angle_ranges(), protocols::matdes::SymDofMoverSampler::set_radial_disp_ranges(), and protocols::matdes::SymDofMoverSampler::step().

TR() [2/5]

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

static

TR() [3/5]

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

static

TR() [4/5]

static basic::Tracer protocols::matdes::TR ( "protocols.matdes.MotifHitsRotamersOperation"  )

static

TR() [5/5]

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

static

trans_pose()

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

static

References core::sequence::end, core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), protocols::loops::start, trans(), and core::pose::Pose::xyz().

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