protocols::forge::remodel Namespace Reference

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

Typedefs
typedef utility::pointer::shared_ptr< RemodelConstraintGenerator >	RemodelConstraintGeneratorOP
typedef utility::pointer::shared_ptr< RemodelConstraintGenerator const >	RemodelConstraintGeneratorCOP
typedef utility::pointer::weak_ptr< RemodelConstraintGenerator >	RemodelConstraintGeneratorAP
typedef utility::pointer::weak_ptr< RemodelConstraintGenerator const >	RemodelConstraintGeneratorCAP
typedef utility::pointer::shared_ptr< GenericRemodelConstraintGenerator >	GenericRemodelConstraintGeneratorOP
typedef utility::pointer::shared_ptr< GenericRemodelConstraintGenerator const >	GenericRemodelConstraintGeneratorCOP
typedef utility::pointer::shared_ptr< RemodelEnzdesCstModule >	RemodelEnzdesCstModuleOP
typedef utility::pointer::shared_ptr< RemodelGlobalFrame >	RemodelGlobalFrame_OP
	RemodelGlobalFrame owning pointer. More...
typedef utility::pointer::shared_ptr< RemodelGlobalFrame const >	RemodelGlobalFrame_COP
	RemodelGlobalFrame const owning pointer. More...
typedef utility::pointer::weak_ptr< RemodelGlobalFrame >	RemodelGlobalFrame_AP
	RemodelGlobalFrame access pointer. More...
typedef utility::pointer::weak_ptr< RemodelGlobalFrame const >	RemodelGlobalFrame_CAP
	RemodelGlobalFrame const access pointer. More...
typedef utility::pointer::shared_ptr< RemodelLigandHandler >	RemodelLigandHandler_OP
	RemodelLigandHandler owning pointer. More...
typedef utility::pointer::shared_ptr< RemodelLigandHandler const >	RemodelLigandHandler_COP
	RemodelLigandHandler const owning pointer. More...
typedef utility::pointer::weak_ptr< RemodelLigandHandler >	RemodelLigandHandler_AP
	RemodelLigandHandler access pointer. More...
typedef utility::pointer::weak_ptr< RemodelLigandHandler const >	RemodelLigandHandler_CAP
	RemodelLigandHandler const access pointer. More...
typedef utility::pointer::weak_ptr< RemodelLoopMover >	RemodelLoopMoverAP
	access pointer for RemodelLoopMover More...
typedef utility::pointer::weak_ptr< RemodelLoopMover const >	RemodelLoopMoverCAP
	const access pointer for RemodelLoopMover More...
typedef utility::pointer::shared_ptr< RemodelLoopMover >	RemodelLoopMoverOP
	owning pointer for RemodelLoopMover More...
typedef utility::pointer::shared_ptr< RemodelLoopMover const >	RemodelLoopMoverCOP
	const owning pointer for RemodelLoopMover More...
typedef utility::pointer::shared_ptr< RemodelMover >	RemodelMover_OP
	RemodelMover owning pointer. More...
typedef utility::pointer::shared_ptr< RemodelMover const >	RemodelMover_COP
	RemodelMover const owning pointer. More...
typedef utility::pointer::weak_ptr< RemodelMover >	RemodelMover_AP
	RemodelMover access pointer. More...
typedef utility::pointer::weak_ptr< RemodelMover const >	RemodelMover_CAP
	RemodelMover const access pointer. More...
typedef utility::pointer::shared_ptr< RemodelRotamerLinks >	RemodelRotamerLinksOP
typedef utility::pointer::shared_ptr< ResidueVicinityRCG >	ResidueVicinityRCGOP
typedef utility::pointer::weak_ptr< ResidueVicinityRCG const >	ResidueVicinityRCGCAP
typedef utility::pointer::shared_ptr< ResidueVicinityInfo >	ResidueVicinityInfoOP
typedef utility::pointer::shared_ptr< ResidueVicinityInfo const >	ResidueVicinityInfoCOP

Functions
static basic::Tracer	TR ("protocols.forge.remodel.RemodelAccumulator")
static basic::Tracer	TR ("protocols.forge.remodel.RemodelDesignMover")
core::Real	build_and_score_disulfide (core::pose::Pose &blank_pose, core::scoring::ScoreFunctionOP sfxn, const bool relax_bb, core::Size const res1, core::Size const res2)
static basic::Tracer	TR ("protocols.forge.remodel.RemodelEnzdesCstModule")
static basic::Tracer	TR ("protocols.forge.remodel.RemodelGlobalFrame")
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 (core::Real rise, core::Real radius, core::Real omega, int unitn)
core::Real	get_RMSD (MatrixXf &A, MatrixXf &B)
core::Real	get_RMSD (Eigen::MatrixXf &A, Eigen::MatrixXf &B)
Eigen::Matrix3f	rot_mat (Eigen::MatrixXf &A, Eigen::MatrixXf &B)
static basic::Tracer	TR ("protocols.forge.remodel.RemodelLigandHandler")
static basic::Tracer	TR ("protocols.forge.remodel.RemodelMover")
bool	fast_clash_check (core::pose::Pose const &pose, utility::vector1< core::id::AtomID > const check_atids, core::Real const clash_dist_cut)
static basic::Tracer	TR ("protocols.forge.remodel.RemodelMover")
utility::vector1< utility::vector1< std::pair< core::Size, Size > > >	recursive_multiple_disulfide_former (utility::vector1< std::pair< core::Size, Size > > &disulfides_formed, utility::vector1< std::pair< core::Size, Size > > &disulfides_possible, core::Size const &max_disulfides)
	Function for recursively creating multiple disulfides. More...
static basic::Tracer	TR ("protocols.forge.remodel.RemodelRotamerLinks", t_info)
static basic::Tracer	TR ("protocols.forge.remodel.RemodelWorkingSet")

Typedef Documentation

GenericRemodelConstraintGeneratorCOP

typedef utility::pointer::shared_ptr< GenericRemodelConstraintGenerator const > protocols::forge::remodel::GenericRemodelConstraintGeneratorCOP

GenericRemodelConstraintGeneratorOP

typedef utility::pointer::shared_ptr< GenericRemodelConstraintGenerator > protocols::forge::remodel::GenericRemodelConstraintGeneratorOP

RemodelConstraintGeneratorAP

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

RemodelConstraintGeneratorCAP

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

RemodelConstraintGeneratorCOP

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

RemodelConstraintGeneratorOP

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

RemodelEnzdesCstModuleOP

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

RemodelGlobalFrame_AP

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

RemodelGlobalFrame access pointer.

RemodelGlobalFrame_CAP

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

RemodelGlobalFrame const access pointer.

RemodelGlobalFrame_COP

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

RemodelGlobalFrame const owning pointer.

RemodelGlobalFrame_OP

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

RemodelGlobalFrame owning pointer.

RemodelLigandHandler_AP

typedef utility::pointer::weak_ptr< RemodelLigandHandler > protocols::forge::remodel::RemodelLigandHandler_AP

RemodelLigandHandler access pointer.

RemodelLigandHandler_CAP

typedef utility::pointer::weak_ptr< RemodelLigandHandler const > protocols::forge::remodel::RemodelLigandHandler_CAP

RemodelLigandHandler const access pointer.

RemodelLigandHandler_COP

typedef utility::pointer::shared_ptr< RemodelLigandHandler const > protocols::forge::remodel::RemodelLigandHandler_COP

RemodelLigandHandler const owning pointer.

RemodelLigandHandler_OP

typedef utility::pointer::shared_ptr< RemodelLigandHandler > protocols::forge::remodel::RemodelLigandHandler_OP

RemodelLigandHandler owning pointer.

RemodelLoopMoverAP

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

access pointer for RemodelLoopMover

RemodelLoopMoverCAP

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

const access pointer for RemodelLoopMover

RemodelLoopMoverCOP

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

const owning pointer for RemodelLoopMover

RemodelLoopMoverOP

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

owning pointer for RemodelLoopMover

RemodelMover_AP

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

RemodelMover access pointer.

RemodelMover_CAP

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

RemodelMover const access pointer.

RemodelMover_COP

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

RemodelMover const owning pointer.

RemodelMover_OP

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

RemodelMover owning pointer.

RemodelRotamerLinksOP

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

ResidueVicinityInfoCOP

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

ResidueVicinityInfoOP

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

ResidueVicinityRCGCAP

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

ResidueVicinityRCGOP

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

Function Documentation

build_and_score_disulfide()

core::Real protocols::forge::remodel::build_and_score_disulfide	(	core::pose::Pose &	blank_pose,
		core::scoring::ScoreFunctionOP	sfxn,
		const bool	relax_bb,
		core::Size const	res1,
		core::Size const	res2
	)

References core::pose::Pose::conformation(), core::conformation::form_disulfide(), core::util::rebuild_disulfide(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), and protocols::hybridization::score.

Referenced by protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood().

compute_center_of_mass()

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 protocols::membrane::com(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

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

fast_clash_check()

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::pose::Pose::residue(), core::pose::Pose::size(), and core::pose::Pose::xyz().

get_RMSD() [1/2]

core::Real protocols::forge::remodel::get_RMSD	(	Eigen::MatrixXf &	A,
		Eigen::MatrixXf &	B
	)

get_RMSD() [2/2]

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

References protocols::comparative_modeling::features::A, and core::chemical::element::B.

ideal_COMs()

Eigen::MatrixXf protocols::forge::remodel::ideal_COMs	(	core::Real	rise,
		core::Real	radius,
		core::Real	omega,
		int	unitn
	)

References core::scoring::omega.

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

recursive_multiple_disulfide_former()

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

Function for recursively creating multiple disulfides.

References core::sequence::end.

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

rot_mat() [1/2]

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

rot_mat() [2/2]

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

References protocols::comparative_modeling::features::A, core::chemical::element::B, and core::chemical::element::H.

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

TR() [1/9]

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::RemodelLoopMover::apply(), protocols::forge::remodel::RemodelMover::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::RemodelAccumulator::cluster_loop(), 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::RemodelMover::parse_my_tag(), protocols::forge::remodel::RemodelConstraintGenerator::parse_my_tag(), protocols::forge::remodel::RemodelLoopMover::randomize_stage(), protocols::forge::remodel::RemodelMover::register_user_options(), protocols::forge::remodel::RemodelMover::RemodelMover(), protocols::forge::remodel::RemodelConstraintGenerator::remove_remodel_constraints_from_pose(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_sync(), protocols::forge::remodel::RemodelLoopMover::set_ideal_helices(), protocols::forge::remodel::RemodelLoopMover::set_segment_stage(), protocols::forge::remodel::RemodelMover::setup_remodel_data_for_loop_btw_parametric_components(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), protocols::forge::remodel::RemodelLoopMover::small_move_stage(), and protocols::forge::remodel::RemodelWorkingSet::workingSetGen().

TR() [2/9]

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

static

Referenced by protocols::forge::remodel::RemodelDesignMover::apply(), protocols::forge::remodel::RemodelDesignMover::check_state(), protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), protocols::forge::remodel::RemodelDesignMover::make_disulfide(), protocols::forge::remodel::RemodelDesignMover::make_disulfide_fast(), protocols::forge::remodel::RemodelDesignMover::mode1_1_packertask(), protocols::forge::remodel::RemodelDesignMover::mode1_packertask(), protocols::forge::remodel::RemodelDesignMover::mode2_packertask(), protocols::forge::remodel::RemodelDesignMover::mode3_packertask(), protocols::forge::remodel::RemodelDesignMover::mode4_packertask(), protocols::forge::remodel::RemodelDesignMover::mode5_packertask(), protocols::forge::remodel::RemodelDesignMover::mode6_packertask(), protocols::forge::remodel::RemodelDesignMover::reduce_task(), and protocols::forge::remodel::RemodelDesignMover::RemodelDesignMover().

TR() [3/9]

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

static

TR() [4/9]

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

static

Referenced by protocols::forge::remodel::RemodelGlobalFrame::align_segment(), protocols::forge::remodel::RemodelGlobalFrame::get_helical_params(), protocols::forge::remodel::RemodelGlobalFrame::restore_original_cst(), protocols::forge::remodel::RemodelGlobalFrame::setup_CM_helical_constraint(), and protocols::forge::remodel::RemodelGlobalFrame::setup_helical_constraint().

TR() [5/9]

static basic::Tracer protocols::forge::remodel::TR ( "protocols.forge.remodel.RemodelLigandHandler"  )

static

Referenced by protocols::forge::remodel::RemodelLigandHandler::minimize().

TR() [6/9]

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

static

TR() [7/9]

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

static

TR() [8/9]

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

static

TR() [9/9]

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

static