protocols::forge::remodel Namespace Reference

Classes
struct	LineObject
class	RemodelAccumulator
class	RemodelConstraintGenerator
	pure virtual base class More...
class	RemodelData
class	RemodelDesignMover
class	RemodelEnzdesCstModule
class	RemodelGlobalFrame
class	RemodelLoopMover
	Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++. More...
class	RemodelLoopMoverCreator
class	RemodelMover
class	RemodelMoverCreator
class	RemodelRotamerLinks
class	RemodelRotamerLinksCreator
class	RemodelWorkingSet
class	ResidueVicinityCstGeneratorCreator
class	ResidueVicinityInfo
	small helper class for the ResidueVicinityRCG More...
class	ResidueVicinityRCG
	a RemodelConstraintGenerator that creates AmbiguousMultiConstraints for all positions More...
class	Segment

Typedefs
typedef utility::pointer::owning_ptr < RemodelConstraintGenerator >	RemodelConstraintGeneratorOP
typedef utility::pointer::owning_ptr < RemodelConstraintGenerator const >	RemodelConstraintGeneratorCOP
typedef utility::pointer::access_ptr < RemodelConstraintGenerator >	RemodelConstraintGeneratorAP
typedef utility::pointer::access_ptr < RemodelConstraintGenerator const >	RemodelConstraintGeneratorCAP
typedef utility::pointer::owning_ptr < RemodelEnzdesCstModule >	RemodelEnzdesCstModuleOP
typedef utility::pointer::owning_ptr < RemodelGlobalFrame >	RemodelGlobalFrame_OP
	RemodelGlobalFrame owning pointer. More...
typedef utility::pointer::owning_ptr < RemodelGlobalFrame const >	RemodelGlobalFrame_COP
	RemodelGlobalFrame const owning pointer. More...
typedef utility::pointer::access_ptr < RemodelGlobalFrame >	RemodelGlobalFrame_AP
	RemodelGlobalFrame access pointer. More...
typedef utility::pointer::access_ptr < RemodelGlobalFrame const >	RemodelGlobalFrame_CAP
	RemodelGlobalFrame const access pointer. More...
typedef utility::pointer::access_ptr < RemodelLoopMover >	RemodelLoopMoverAP
	access pointer for RemodelLoopMover More...
typedef utility::pointer::access_ptr < RemodelLoopMover const >	RemodelLoopMoverCAP
	const access pointer for RemodelLoopMover More...
typedef utility::pointer::owning_ptr < RemodelLoopMover >	RemodelLoopMoverOP
	owning pointer for RemodelLoopMover More...
typedef utility::pointer::owning_ptr < RemodelLoopMover const >	RemodelLoopMoverCOP
	const owning pointer for RemodelLoopMover More...
typedef utility::pointer::owning_ptr < RemodelMover >	RemodelMover_OP
	RemodelMover owning pointer. More...
typedef utility::pointer::owning_ptr < RemodelMover const >	RemodelMover_COP
	RemodelMover const owning pointer. More...
typedef utility::pointer::access_ptr < RemodelMover >	RemodelMover_AP
	RemodelMover access pointer. More...
typedef utility::pointer::access_ptr < RemodelMover const >	RemodelMover_CAP
	RemodelMover const access pointer. More...
typedef utility::pointer::owning_ptr < RemodelRotamerLinks >	RemodelRotamerLinksOP
typedef utility::pointer::owning_ptr < ResidueVicinityRCG >	ResidueVicinityRCGOP
typedef utility::pointer::access_ptr < ResidueVicinityRCG const >	ResidueVicinityRCGCAP
typedef utility::pointer::owning_ptr < ResidueVicinityInfo >	ResidueVicinityInfoOP
typedef utility::pointer::owning_ptr < ResidueVicinityInfo const >	ResidueVicinityInfoCOP

Functions
numeric::xyzVector< core::Real >	compute_center_of_mass (core::pose::Pose const &pose, core::Size range_start, core::Size range_stop)
Matrix3f	rot_mat (MatrixXf &A, MatrixXf &B)
MatrixXf	ideal_COMs (double rise, double radius, double omega, int unitn)
double	get_RMSD (MatrixXf &A, MatrixXf &B)
bool	fast_clash_check (core::pose::Pose const &pose, utility::vector1< core::id::AtomID > const check_atids, core::Real const clash_dist_cut)
utility::vector1 < utility::vector1< std::pair < Size, Size > > >	recursive_multiple_disulfide_former (utility::vector1< std::pair< Size, Size > > &disulfides_formed, utility::vector1< std::pair< Size, Size > > &disulfides_possible, Size const &max_disulfides)
	Function for recursively creating multiple disulfides. More...

Variables
static basic::Tracer	TR ("protocols.forge.remodel.RemodelAccumulator")
static basic::Tracer	TR ("protocols.forge.remodel.RemodelDesignMover")
static numeric::random::RandomGenerator	RG (2342342)
static basic::Tracer	TR ("protocols.forge.remodel.RemodelEnzdesCstModule")
static basic::Tracer	TR ("protocols.forge.remodel.RemodelGlobalFrame")
static basic::Tracer	TR ("protocols.forge.remodel.RemodelLoopMover")
static numeric::random::RandomGenerator	RG (9788221)
static basic::Tracer	TR ("protocols.forge.remodel.RemodelMover")
static basic::Tracer	TR ("protocols.forge.remodel.RemodelRotamerLinks", t_info)
static basic::Tracer	TR ("protocols.forge.remodel.RemodelWorkingSet")

Typedef Documentation

typedef utility::pointer::access_ptr< RemodelConstraintGenerator > protocols::forge::remodel::RemodelConstraintGeneratorAP

typedef utility::pointer::access_ptr< RemodelConstraintGenerator const > protocols::forge::remodel::RemodelConstraintGeneratorCAP

typedef utility::pointer::owning_ptr< RemodelConstraintGenerator const > protocols::forge::remodel::RemodelConstraintGeneratorCOP

typedef utility::pointer::owning_ptr< RemodelConstraintGenerator > protocols::forge::remodel::RemodelConstraintGeneratorOP

typedef utility::pointer::owning_ptr< RemodelEnzdesCstModule > protocols::forge::remodel::RemodelEnzdesCstModuleOP

typedef utility::pointer::access_ptr< RemodelGlobalFrame > protocols::forge::remodel::RemodelGlobalFrame_AP

RemodelGlobalFrame access pointer.

typedef utility::pointer::access_ptr< RemodelGlobalFrame const > protocols::forge::remodel::RemodelGlobalFrame_CAP

RemodelGlobalFrame const access pointer.

typedef utility::pointer::owning_ptr< RemodelGlobalFrame const > protocols::forge::remodel::RemodelGlobalFrame_COP

RemodelGlobalFrame const owning pointer.

typedef utility::pointer::owning_ptr< RemodelGlobalFrame > protocols::forge::remodel::RemodelGlobalFrame_OP

RemodelGlobalFrame owning pointer.

typedef utility::pointer::access_ptr< RemodelLoopMover > protocols::forge::remodel::RemodelLoopMoverAP

access pointer for RemodelLoopMover

typedef utility::pointer::access_ptr< RemodelLoopMover const > protocols::forge::remodel::RemodelLoopMoverCAP

const access pointer for RemodelLoopMover

typedef utility::pointer::owning_ptr< RemodelLoopMover const > protocols::forge::remodel::RemodelLoopMoverCOP

const owning pointer for RemodelLoopMover

typedef utility::pointer::owning_ptr< RemodelLoopMover > protocols::forge::remodel::RemodelLoopMoverOP

owning pointer for RemodelLoopMover

typedef utility::pointer::access_ptr< RemodelMover > protocols::forge::remodel::RemodelMover_AP

RemodelMover access pointer.

typedef utility::pointer::access_ptr< RemodelMover const > protocols::forge::remodel::RemodelMover_CAP

RemodelMover const access pointer.

typedef utility::pointer::owning_ptr< RemodelMover const > protocols::forge::remodel::RemodelMover_COP

RemodelMover const owning pointer.

typedef utility::pointer::owning_ptr< RemodelMover > protocols::forge::remodel::RemodelMover_OP

RemodelMover owning pointer.

typedef utility::pointer::owning_ptr< RemodelRotamerLinks > protocols::forge::remodel::RemodelRotamerLinksOP

typedef utility::pointer::owning_ptr< ResidueVicinityInfo const > protocols::forge::remodel::ResidueVicinityInfoCOP

typedef utility::pointer::owning_ptr< ResidueVicinityInfo > protocols::forge::remodel::ResidueVicinityInfoOP

typedef utility::pointer::access_ptr< ResidueVicinityRCG const > protocols::forge::remodel::ResidueVicinityRCGCAP

typedef utility::pointer::owning_ptr< ResidueVicinityRCG > protocols::forge::remodel::ResidueVicinityRCGOP

Function Documentation

numeric::xyzVector< core::Real > protocols::forge::remodel::compute_center_of_mass	(	core::pose::Pose const &	pose,
		core::Size	range_start,
		core::Size	range_stop
	)

References core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by protocols::forge::remodel::RemodelGlobalFrame::setup_CM_helical_constraint().

bool protocols::forge::remodel::fast_clash_check	(	core::pose::Pose const &	pose,
		utility::vector1< core::id::AtomID > const	check_atids,
		core::Real const	clash_dist_cut
	)

References core::conformation::Residue::atom_type(), core::chemical::AtomType::lj_wdepth(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

double protocols::forge::remodel::get_RMSD	(	MatrixXf &	A,
		MatrixXf &	B
	)

References rmsd.

MatrixXf protocols::forge::remodel::ideal_COMs	(	double	rise,
		double	radius,
		double	omega,
		int	unitn
	)

Referenced by protocols::forge::remodel::RemodelGlobalFrame::setup_CM_helical_constraint().

utility::vector1< utility::vector1< std::pair<Size,Size> > > protocols::forge::remodel::recursive_multiple_disulfide_former	(	utility::vector1< std::pair< Size, Size > > &	disulfides_formed,
		utility::vector1< std::pair< Size, Size > > &	disulfides_possible,
		Size const &	max_disulfides
	)

Function for recursively creating multiple disulfides.

Referenced by protocols::forge::remodel::RemodelMover::apply().

Matrix3f protocols::forge::remodel::rot_mat	(	MatrixXf &	A,
		MatrixXf &	B
	)

References cov(), and H.

Referenced by protocols::pockets::PocketGrid::move_pose_to_standard_orie(), and protocols::forge::remodel::RemodelGlobalFrame::setup_CM_helical_constraint().

Variable Documentation

numeric::random::RandomGenerator protocols::forge::remodel::RG(2342342)

static

Referenced by protocols::forge::remodel::RemodelLoopMover::abinitio_stage(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::forge::remodel::RemodelLoopMover::determine_loops_to_model(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), and protocols::forge::remodel::RemodelLoopMover::simultaneous_stage().

numeric::random::RandomGenerator protocols::forge::remodel::RG(9788221)

static

basic::Tracer protocols::forge::remodel::TR("protocols.forge.remodel.RemodelRotamerLinks", t_info)

static

basic::Tracer protocols::forge::remodel::TR("protocols.forge.remodel.RemodelEnzdesCstModule")

static

basic::Tracer protocols::forge::remodel::TR("protocols.forge.remodel.RemodelDesignMover")

static

basic::Tracer protocols::forge::remodel::TR("protocols.forge.remodel.RemodelAccumulator")

static

Referenced by protocols::forge::remodel::RemodelLoopMover::abinitio_stage(), protocols::forge::remodel::RemodelEnzdesCstModule::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), protocols::forge::remodel::RemodelEnzdesCstModule::blueprint_cst_definition(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::forge::remodel::RemodelMover::centroid_build(), protocols::forge::remodel::RemodelLoopMover::check_closure_criteria(), protocols::forge::remodel::RemodelConstraintGenerator::clear_stored_constraints(), protocols::forge::remodel::RemodelMover::confirm_sequence(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::forge::remodel::RemodelMover::design_refine_cart_relax(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), protocols::forge::remodel::RemodelEnzdesCstModule::enable_constraint_scoreterms(), protocols::forge::remodel::RemodelLoopMover::fa_relax_stage(), protocols::forge::remodel::RemodelLoopMover::generate_ncs_csts(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::forge::remodel::RemodelConstraintGenerator::parse_my_tag(), protocols::forge::remodel::RemodelMover::parse_my_tag(), protocols::forge::remodel::RemodelLoopMover::randomize_stage(), protocols::forge::remodel::RemodelMover::register_user_options(), protocols::forge::remodel::RemodelMover::RemodelMover(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_sync(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), protocols::forge::remodel::RemodelLoopMover::small_move_stage(), and protocols::forge::remodel::RemodelWorkingSet::workingSetGen().

basic::Tracer protocols::forge::remodel::TR("protocols.forge.remodel.RemodelWorkingSet")

static

basic::Tracer protocols::forge::remodel::TR("protocols.forge.remodel.RemodelGlobalFrame")

static

basic::Tracer protocols::forge::remodel::TR("protocols.forge.remodel.RemodelLoopMover")

static

basic::Tracer protocols::forge::remodel::TR("protocols.forge.remodel.RemodelMover")

static