protocols::comparative_modeling Namespace Reference

Namespaces
	features

Classes
class	Align_RmsdEvaluator
class	Align_RotamerEvaluator
class	AlignmentCluster
class	AlignmentClustering
class	AlignmentSet
class	AlignRmsdTargetEvaluatorCreator
	creator for the AlignRmsdTargetEvaluatorCreator class More...
class	ExtraThreadingMover
class	GenericJobInputter
class	GenericJobInputterCreator
class	IgnoreSubsetConstraintSet
class	LoopRelaxThreadingMover
class	MultiThreadingMover
class	PartialThreadingMover
class	RecoverSideChainsMover
class	StealLigandMover
class	StealSideChainsMover
class	ThreadingJob
class	ThreadingJobInputter
class	ThreadingJobInputterCreator
class	ThreadingMover

Typedefs
typedef utility::pointer::shared_ptr< Align_RmsdEvaluator >	Align_RmsdEvaluatorOP
typedef utility::pointer::shared_ptr< Align_RmsdEvaluator const >	Align_RmsdEvaluatorCOP
typedef utility::pointer::shared_ptr< Align_RotamerEvaluator >	Align_RotamerEvaluatorOP
typedef utility::pointer::shared_ptr< Align_RotamerEvaluator const >	Align_RotamerEvaluatorCOP
typedef utility::pointer::shared_ptr< AlignmentCluster >	AlignmentClusterOP
typedef utility::pointer::shared_ptr< AlignmentCluster const >	AlignmentClusterCOP
typedef utility::pointer::shared_ptr< AlignmentClustering >	AlignmentClusteringOP
typedef utility::pointer::shared_ptr< AlignmentClustering const >	AlignmentClusteringCOP
typedef utility::pointer::shared_ptr< AlignmentSet >	AlignmentSetOP
typedef utility::pointer::shared_ptr< AlignmentSet const >	AlignmentSetCOP
typedef utility::pointer::shared_ptr< IgnoreSubsetConstraintSet >	IgnoreSubsetConstraintSetOP
typedef utility::pointer::shared_ptr< IgnoreSubsetConstraintSet const >	IgnoreSubsetConstraintSetCOP
typedef utility::pointer::shared_ptr< LoopRelaxThreadingMover >	LoopRelaxThreadingMoverOP
typedef utility::pointer::shared_ptr< LoopRelaxThreadingMover const >	LoopRelaxThreadingMoverCOP
typedef utility::pointer::shared_ptr< RecoverSideChainsMover >	RecoverSideChainsMoverOP
typedef utility::pointer::shared_ptr< RecoverSideChainsMover const >	RecoverSideChainsMoverCOP
typedef utility::pointer::shared_ptr< StealLigandMover >	StealLigandMoverOP
typedef utility::pointer::shared_ptr< StealLigandMover const >	StealLigandMoverCOP
typedef utility::pointer::shared_ptr< StealSideChainsMover >	StealSideChainsMoverOP
typedef utility::pointer::shared_ptr< StealSideChainsMover const >	StealSideChainsMoverCOP
typedef utility::pointer::shared_ptr< ThreadingJob >	ThreadingJobOP
typedef utility::pointer::shared_ptr< ThreadingJob const >	ThreadingJobCOP
typedef utility::pointer::shared_ptr< ThreadingJobInputter >	ThreadingJobInputterOP
typedef utility::pointer::shared_ptr< ThreadingJobInputter const >	ThreadingJobInputterCOP

Functions
utility::vector1< core::pack::dunbrack::RotVector >	rots_from_pose (core::pose::Pose const &pose)
utility::vector1< utility::vector1< core::Real > >	chis_from_pose (core::pose::Pose const &pose)
void	cm_main ()
	Initiates LoopRelaxThreadingMover using the job distributor (jd2) More...
void	gather_coords (core::pose::Pose const &model, core::pose::Pose const &native, core::sequence::SequenceAlignment const &aln, int &natoms, ObjexxFCL::FArray2D< core::Real > &p1a, ObjexxFCL::FArray2D< core::Real > &p2a, std::string const &atom_name="CA")
static basic::Tracer	tr ("protocols.comparative_modeling.extra_threading")
static basic::Tracer	tr ("protocols.threading")
static basic::Tracer	tr ("protocols.comparative_modeling.threading")
static basic::Tracer	tr ("protocols.comparative_modeling.ThreadingJob")
static basic::Tracer	tr ("protocols.comparative_modeling.ThreadingJobInputter")
std::map< std::string, utility::vector1< core::Size > >	read_extra_residues (utility::vector1< std::string > const &fns)
static basic::Tracer	tr ("protocols.comparative_modeling.threading")
static basic::Tracer	tr ("protocols.comparative_modeling.util")
core::id::SequenceMapping	get_qt_mapping_general (core::pose::Pose const &query_pose, core::sequence::SequenceAlignment const &align, core::pose::Pose const &template_pose, core::Size const query_index, core::Size const template_index)
void	bounded_loops_from_alignment (const core::Size num_residues, const core::Size min_size, const core::sequence::SequenceAlignment &alignment, protocols::loops::LoopsOP &unaligned_regions)
	Identifies consecutive stretches of unaligned residues by scanning the alignment. Each unaligned region is guaranteed to have length at least <min_size>. Aligned regions share this property as well, and can be obtained by calling the invert() method on the output parameter <unaligned_regions>. More...
protocols::loops::LoopsOP	loops_from_alignment (core::Size nres, core::sequence::SequenceAlignment const &aln, core::Size const min_loop_size)
protocols::loops::LoopsOP	loops_from_transitive_alignments (core::Size nres1, core::sequence::SequenceAlignment const &aln1, core::Size nres2, core::sequence::SequenceAlignment const &aln2, core::Size const min_loop_size)
void	rebuild_loops_until_closed (core::pose::Pose &query_pose, core::Size const min_loop_size, core::Size const max_rebuild, std::string const &loop_mover_name)
void	steal_ligands (core::pose::Pose &dest_pose, core::pose::Pose const &source_pose_in, core::id::NamedAtomID const &anchor_atom_dest, core::id::NamedAtomID const &anchor_atom_source, utility::vector1< core::id::NamedAtomID > const &ligand_indices)
	Function for stealing ligands from a given Pose and adding them to source_pose. More...
void	initialize_ss (core::pose::Pose &pose)
utility::vector1< core::pose::Pose >	templates_from_cmd_line ()
bool	loops_are_closed (core::pose::Pose &pose)
std::map< std::string, core::pose::Pose >	poses_from_cmd_line (utility::vector1< std::string > const &fn_list)
AlignmentSet	alignments_from_cmd_line ()
void	randomize_selected_atoms (core::pose::Pose &query_pose, core::id::AtomID_Mask const &selected)

Typedef Documentation

Align_RmsdEvaluatorCOP

typedef utility::pointer::shared_ptr< Align_RmsdEvaluator const > protocols::comparative_modeling::Align_RmsdEvaluatorCOP

Align_RmsdEvaluatorOP

typedef utility::pointer::shared_ptr< Align_RmsdEvaluator > protocols::comparative_modeling::Align_RmsdEvaluatorOP

Align_RotamerEvaluatorCOP

typedef utility::pointer::shared_ptr< Align_RotamerEvaluator const > protocols::comparative_modeling::Align_RotamerEvaluatorCOP

Align_RotamerEvaluatorOP

typedef utility::pointer::shared_ptr< Align_RotamerEvaluator > protocols::comparative_modeling::Align_RotamerEvaluatorOP

AlignmentClusterCOP

typedef utility::pointer::shared_ptr< AlignmentCluster const > protocols::comparative_modeling::AlignmentClusterCOP

AlignmentClusteringCOP

typedef utility::pointer::shared_ptr< AlignmentClustering const > protocols::comparative_modeling::AlignmentClusteringCOP

AlignmentClusteringOP

typedef utility::pointer::shared_ptr< AlignmentClustering > protocols::comparative_modeling::AlignmentClusteringOP

AlignmentClusterOP

typedef utility::pointer::shared_ptr< AlignmentCluster > protocols::comparative_modeling::AlignmentClusterOP

AlignmentSetCOP

typedef utility::pointer::shared_ptr< AlignmentSet const > protocols::comparative_modeling::AlignmentSetCOP

AlignmentSetOP

typedef utility::pointer::shared_ptr< AlignmentSet > protocols::comparative_modeling::AlignmentSetOP

IgnoreSubsetConstraintSetCOP

typedef utility::pointer::shared_ptr< IgnoreSubsetConstraintSet const> protocols::comparative_modeling::IgnoreSubsetConstraintSetCOP

IgnoreSubsetConstraintSetOP

typedef utility::pointer::shared_ptr< IgnoreSubsetConstraintSet > protocols::comparative_modeling::IgnoreSubsetConstraintSetOP

LoopRelaxThreadingMoverCOP

typedef utility::pointer::shared_ptr< LoopRelaxThreadingMover const > protocols::comparative_modeling::LoopRelaxThreadingMoverCOP

LoopRelaxThreadingMoverOP

typedef utility::pointer::shared_ptr< LoopRelaxThreadingMover > protocols::comparative_modeling::LoopRelaxThreadingMoverOP

RecoverSideChainsMoverCOP

typedef utility::pointer::shared_ptr< RecoverSideChainsMover const > protocols::comparative_modeling::RecoverSideChainsMoverCOP

RecoverSideChainsMoverOP

typedef utility::pointer::shared_ptr< RecoverSideChainsMover > protocols::comparative_modeling::RecoverSideChainsMoverOP

StealLigandMoverCOP

typedef utility::pointer::shared_ptr< StealLigandMover const > protocols::comparative_modeling::StealLigandMoverCOP

StealLigandMoverOP

typedef utility::pointer::shared_ptr< StealLigandMover > protocols::comparative_modeling::StealLigandMoverOP

StealSideChainsMoverCOP

typedef utility::pointer::shared_ptr< StealSideChainsMover const > protocols::comparative_modeling::StealSideChainsMoverCOP

StealSideChainsMoverOP

typedef utility::pointer::shared_ptr< StealSideChainsMover > protocols::comparative_modeling::StealSideChainsMoverOP

ThreadingJobCOP

typedef utility::pointer::shared_ptr< ThreadingJob const > protocols::comparative_modeling::ThreadingJobCOP

ThreadingJobInputterCOP

typedef utility::pointer::shared_ptr< ThreadingJobInputter const > protocols::comparative_modeling::ThreadingJobInputterCOP

ThreadingJobInputterOP

typedef utility::pointer::shared_ptr< ThreadingJobInputter > protocols::comparative_modeling::ThreadingJobInputterOP

ThreadingJobOP

typedef utility::pointer::shared_ptr< ThreadingJob > protocols::comparative_modeling::ThreadingJobOP

Function Documentation

alignments_from_cmd_line()

AlignmentSet protocols::comparative_modeling::alignments_from_cmd_line

(

)

References core::sequence::AlignerFactory::get_aligner(), and core::sequence::ScoringSchemeFactory::get_scoring_scheme().

bounded_loops_from_alignment()

void protocols::comparative_modeling::bounded_loops_from_alignment	(	const core::Size	num_residues,
		const core::Size	min_size,
		const core::sequence::SequenceAlignment &	alignment,
		protocols::loops::LoopsOP &	unaligned_regions
	)

Identifies consecutive stretches of unaligned residues by scanning the alignment. Each unaligned region is guaranteed to have length at least <min_size>. Aligned regions share this property as well, and can be obtained by calling the invert() method on the output parameter <unaligned_regions>.

@detail The premise underlying this tortuous method is simple– identify aligned/unaligned regions in a sequence alignment with the constraint that each region has a certain minimum length.

The current implementation achieves this goal in a roundabout manner by making use of existing, less specialized utility functions.

References core::scoring::alignment, NO_LOOP_SIZE_CST, and protocols::loops::pick_loops_unaligned().

Referenced by protocols::nonlocal::find_regions_with_minimum_size().

chis_from_pose()

utility::vector1< utility::vector1< core::Real > > protocols::comparative_modeling::chis_from_pose

(

core::pose::Pose const &

pose

)

References core::pose::Pose::chi(), core::chemical::ResidueType::nchi(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

cm_main()

void protocols::comparative_modeling::cm_main

(

)

Initiates LoopRelaxThreadingMover using the job distributor (jd2)

References protocols::jd2::JobDistributor::get_instance(), and protocols::jd2::JobDistributor::go().

gather_coords()

void protocols::comparative_modeling::gather_coords	(	core::pose::Pose const &	model,
		core::pose::Pose const &	native,
		core::sequence::SequenceAlignment const &	aln,
		int &	natoms,
		ObjexxFCL::FArray2D< core::Real > &	p1a,
		ObjexxFCL::FArray2D< core::Real > &	p2a,
		std::string const &	atom_name = "CA"
	)

References core::conformation::Residue::is_protein(), core::pose::Pose::residue(), core::sequence::SequenceAlignment::sequence_mapping(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), protocols::comparative_modeling::Align_RmsdEvaluator::apply(), and protocols::hybridization::get_gdtmm().

get_qt_mapping_general()

core::id::SequenceMapping protocols::comparative_modeling::get_qt_mapping_general	(	core::pose::Pose const &	query_pose,
		core::sequence::SequenceAlignment const &	align,
		core::pose::Pose const &	template_pose,
		core::Size const	query_index,
		core::Size const	template_index
	)

References core::sequence::SWAligner::align(), core::sequence::SequenceAlignment::identities(), core::sequence::SequenceAlignment::length(), core::pose::Pose::sequence(), core::sequence::SequenceAlignment::sequence(), core::sequence::SequenceAlignment::sequence_mapping(), core::id::SequenceMapping::show(), tr(), and core::sequence::transitive_map().

Referenced by protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::comparative_modeling::ExtraThreadingMover::get_qt_mapping(), and protocols::comparative_modeling::ThreadingMover::get_qt_mapping().

initialize_ss()

void protocols::comparative_modeling::initialize_ss

(

core::pose::Pose &

pose

)

References protocols::simple_filters::dssp(), protocols::loops::set_secstruct_from_dssp(), protocols::loops::set_secstruct_from_psipred_ss2(), and core::pose::set_ss_from_phipsi().

loops_are_closed()

bool protocols::comparative_modeling::loops_are_closed

(

core::pose::Pose &

pose

)

References protocols::loops::pick_loops_chainbreak().

loops_from_alignment()

protocols::loops::LoopsOP protocols::comparative_modeling::loops_from_alignment	(	core::Size	nres,
		core::sequence::SequenceAlignment const &	aln,
		core::Size const	min_loop_size
	)

References protocols::loops::pick_loops_unaligned(), core::sequence::SequenceAlignment::sequence_mapping(), core::id::SequenceMapping::show(), and tr().

Referenced by protocols::comparative_modeling::ThreadingMover::apply(), and protocols::topology_broker::generate_rigid_from_alignment().

loops_from_transitive_alignments()

protocols::loops::LoopsOP protocols::comparative_modeling::loops_from_transitive_alignments	(	core::Size	nres1,
		core::sequence::SequenceAlignment const &	aln1,
		core::Size	nres2,
		core::sequence::SequenceAlignment const &	aln2,
		core::Size const	min_loop_size
	)

References protocols::loops::pick_loops_unaligned(), core::id::SequenceMapping::push_back(), core::sequence::SequenceAlignment::sequence_mapping(), core::id::SequenceMapping::show(), and tr().

Referenced by protocols::comparative_modeling::ThreadingJob::loops().

poses_from_cmd_line()

std::map< std::string, core::pose::Pose > protocols::comparative_modeling::poses_from_cmd_line

(

utility::vector1< std::string > const &

fn_list

)

References core::import_pose::PDB_file, core::import_pose::pose_from_file(), and core::chemical::rsd_set_from_cmd_line().

Referenced by protocols::comparative_modeling::AlignmentClustering::AlignmentClustering().

randomize_selected_atoms()

void protocols::comparative_modeling::randomize_selected_atoms	(	core::pose::Pose &	query_pose,
		core::id::AtomID_Mask const &	selected
	)

References core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::attached_H_begin(), core::conformation::Residue::attached_H_end(), core::sequence::end, core::pose::Pose::residue(), core::scoring::rg, core::pose::Pose::set_xyz(), and core::pose::Pose::size().

Referenced by protocols::comparative_modeling::MultiThreadingMover::apply(), and protocols::comparative_modeling::ThreadingMover::apply().

read_extra_residues()

std::map< std::string, utility::vector1< core::Size > > protocols::comparative_modeling::read_extra_residues

(

utility::vector1< std::string > const &

fns

)

Referenced by protocols::comparative_modeling::ThreadingJobInputter::ThreadingJobInputter().

rebuild_loops_until_closed()

void protocols::comparative_modeling::rebuild_loops_until_closed	(	core::pose::Pose &	query_pose,
		core::Size const	min_loop_size,
		core::Size const	max_rebuild,
		std::string const &	loop_mover_name
	)

References core::chemical::CENTROID_t, core::pose::Pose::conformation(), protocols::loops::pick_loops_chainbreak(), core::conformation::Conformation::residue_typeset_mode(), core::util::switch_to_residue_type_set(), and tr().

rots_from_pose()

utility::vector1< core::pack::dunbrack::RotVector > protocols::comparative_modeling::rots_from_pose

(

core::pose::Pose const &

pose

)

References core::pose::Pose::residue(), rot(), core::pack::dunbrack::rotamer_from_chi(), and core::pose::Pose::size().

steal_ligands()

void protocols::comparative_modeling::steal_ligands	(	core::pose::Pose &	dest_pose,
		core::pose::Pose const &	source_pose_in,
		core::id::NamedAtomID const &	anchor_atom_dest,
		core::id::NamedAtomID const &	anchor_atom_source,
		utility::vector1< core::id::NamedAtomID > const &	ligand_indices
	)

Function for stealing ligands from a given Pose and adding them to source_pose.

: The parameters are:

• dest_pose Pose to which ligands are added.
• source_pose_in Pose from which ligands and orientations are taken.
• anchor_atom_dest anchor atom providing reference in dest_pose for ligand orientation.
• anchor_atom_source anchor atom providing reference in source_pose for ligand orientation.
• ligand_indices list of AtomID entries for ligand, one per ligand. Ligand orientation is determined by orientation between anchor_atom_source and each ligand AtomID.

References core::kinematics::FoldTree::add_edge(), core::pose::Pose::append_residue_by_jump(), core::id::NamedAtomID::atom(), core::pose::Pose::fold_tree(), core::pose::Pose::jump(), core::kinematics::Edge::PEPTIDE, core::pose::Pose::residue(), core::id::NamedAtomID::rsd(), core::pose::Pose::set_jump(), core::pose::Pose::size(), tr(), and core::id::NamedAtomID::valid().

Referenced by protocols::comparative_modeling::StealLigandMover::apply().

templates_from_cmd_line()

utility::vector1< core::pose::Pose > protocols::comparative_modeling::templates_from_cmd_line

(

)

References core::import_pose::PDB_file, and core::import_pose::poses_from_files().

tr() [1/7]

static basic::Tracer protocols::comparative_modeling::tr ( "protocols.comparative_modeling.extra_threading"  )

static

Referenced by protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), protocols::comparative_modeling::LoopRelaxThreadingMover::apply(), protocols::comparative_modeling::Align_RmsdEvaluator::apply(), protocols::comparative_modeling::Align_RotamerEvaluator::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::comparative_modeling::GenericJobInputter::fill_jobs(), protocols::comparative_modeling::ThreadingJobInputter::fill_jobs(), protocols::comparative_modeling::AlignmentClustering::generateRankedAlignments(), protocols::comparative_modeling::GenericJobInputter::GenericJobInputter(), get_qt_mapping_general(), loops_from_alignment(), loops_from_transitive_alignments(), protocols::comparative_modeling::AlignmentCluster::output(), protocols::comparative_modeling::GenericJobInputter::pose_from_job(), protocols::comparative_modeling::ThreadingJobInputter::pose_from_job(), rebuild_loops_until_closed(), steal_ligands(), and protocols::comparative_modeling::ThreadingJobInputter::ThreadingJobInputter().

tr() [2/7]

static basic::Tracer protocols::comparative_modeling::tr ( "protocols.comparative_modeling.threading"  )

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tr() [3/7]

static basic::Tracer protocols::comparative_modeling::tr ( "protocols.comparative_modeling.threading"  )

static

tr() [4/7]

static basic::Tracer protocols::comparative_modeling::tr ( "protocols.comparative_modeling.ThreadingJob"  )

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tr() [5/7]

static basic::Tracer protocols::comparative_modeling::tr ( "protocols.comparative_modeling.ThreadingJobInputter"  )

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tr() [6/7]

static basic::Tracer protocols::comparative_modeling::tr ( "protocols.comparative_modeling.util"  )

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tr() [7/7]

static basic::Tracer protocols::comparative_modeling::tr ( "protocols.threading"  )

static