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	LoopRelaxMover
class	LoopRelaxMoverCreator
class	LoopRelaxThreadingMover
class	MultiThreadingMover
class	PartialThreadingMover
class	RecoverSideChainsMover
class	StealLigandMover
class	StealSideChainsMover
class	ThreadingJob
class	ThreadingJobInputter
class	ThreadingJobInputterCreator
class	ThreadingMover

Typedefs
typedef utility::pointer::owning_ptr < Align_RmsdEvaluator >	Align_RmsdEvaluatorOP
typedef utility::pointer::owning_ptr < Align_RmsdEvaluator const >	Align_RmsdEvaluatorCOP
typedef utility::pointer::owning_ptr < Align_RotamerEvaluator >	Align_RotamerEvaluatorOP
typedef utility::pointer::owning_ptr < Align_RotamerEvaluator const >	Align_RotamerEvaluatorCOP
typedef utility::pointer::owning_ptr < AlignmentCluster >	AlignmentClusterOP
typedef utility::pointer::owning_ptr < AlignmentCluster const >	AlignmentClusterCOP
typedef utility::pointer::owning_ptr < AlignmentClustering >	AlignmentClusteringOP
typedef utility::pointer::owning_ptr < AlignmentClustering const >	AlignmentClusteringCOP
typedef utility::pointer::owning_ptr < AlignmentSet >	AlignmentSetOP
typedef utility::pointer::owning_ptr < AlignmentSet const >	AlignmentSetCOP
typedef utility::pointer::owning_ptr < IgnoreSubsetConstraintSet >	IgnoreSubsetConstraintSetOP
typedef utility::pointer::owning_ptr < IgnoreSubsetConstraintSet const >	IgnoreSubsetConstraintSetCOP
typedef utility::pointer::owning_ptr < LoopRelaxMover >	LoopRelaxMoverOP
typedef utility::pointer::owning_ptr < LoopRelaxMover const >	LoopRelaxMoverCOP
typedef utility::pointer::owning_ptr < LoopRelaxThreadingMover >	LoopRelaxThreadingMoverOP
typedef utility::pointer::owning_ptr < LoopRelaxThreadingMover const >	LoopRelaxThreadingMoverCOP
typedef utility::pointer::owning_ptr < RecoverSideChainsMover >	RecoverSideChainsMoverOP
typedef utility::pointer::owning_ptr < RecoverSideChainsMover const >	RecoverSideChainsMoverCOP
typedef utility::pointer::owning_ptr < StealLigandMover >	StealLigandMoverOP
typedef utility::pointer::owning_ptr < StealLigandMover const >	StealLigandMoverCOP
typedef utility::pointer::owning_ptr < StealSideChainsMover >	StealSideChainsMoverOP
typedef utility::pointer::owning_ptr < StealSideChainsMover const >	StealSideChainsMoverCOP
typedef utility::pointer::owning_ptr < ThreadingJob >	ThreadingJobOP
typedef utility::pointer::owning_ptr < ThreadingJob const >	ThreadingJobCOP
typedef utility::pointer::owning_ptr < ThreadingJobInputter >	ThreadingJobInputterOP
typedef utility::pointer::owning_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.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 numeric::random::RandomGenerator	RG (298211)
static basic::Tracer	tr ("protocols.comparative_modeling.util")
core::sequence::SequenceAlignment	alignment_from_cmd_line ()
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)
protocols::loops::LoopsOP	pick_loops_unaligned (core::Size nres, utility::vector1< core::Size > const &unaligned_residues, core::Size min_loop_size)
protocols::loops::LoopsOP	pick_loops_chainbreak (core::pose::Pose &query_pose, core::Size 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

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

Definition at line 24 of file Align_RmsdEvaluator.fwd.hh.

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

Definition at line 22 of file Align_RmsdEvaluator.fwd.hh.

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

Definition at line 24 of file Align_RotamerEvaluator.fwd.hh.

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

Definition at line 22 of file Align_RotamerEvaluator.fwd.hh.

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

Definition at line 25 of file AlignmentClustering.fwd.hh.

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

Definition at line 29 of file AlignmentClustering.fwd.hh.

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

Definition at line 27 of file AlignmentClustering.fwd.hh.

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

Definition at line 23 of file AlignmentClustering.fwd.hh.

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

Definition at line 24 of file AlignmentSet.fwd.hh.

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

Definition at line 22 of file AlignmentSet.fwd.hh.

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

Definition at line 27 of file IgnoreSubsetConstraintSet.fwd.hh.

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

Definition at line 25 of file IgnoreSubsetConstraintSet.fwd.hh.

typedef utility::pointer::owning_ptr< LoopRelaxMover const > protocols::comparative_modeling::LoopRelaxMoverCOP

Definition at line 22 of file LoopRelaxMover.fwd.hh.

typedef utility::pointer::owning_ptr< LoopRelaxMover > protocols::comparative_modeling::LoopRelaxMoverOP

Definition at line 19 of file LoopRelaxMover.fwd.hh.

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

Definition at line 29 of file LoopRelaxMover.fwd.hh.

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

Definition at line 26 of file LoopRelaxMover.fwd.hh.

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

Definition at line 24 of file RecoverSideChainsMover.fwd.hh.

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

Definition at line 22 of file RecoverSideChainsMover.fwd.hh.

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

Definition at line 24 of file StealLigandMover.fwd.hh.

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

Definition at line 22 of file StealLigandMover.fwd.hh.

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

Definition at line 24 of file StealSideChainsMover.fwd.hh.

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

Definition at line 22 of file StealSideChainsMover.fwd.hh.

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

Definition at line 25 of file ThreadingJob.fwd.hh.

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

Definition at line 24 of file ThreadingJobInputter.fwd.hh.

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

Definition at line 22 of file ThreadingJobInputter.fwd.hh.

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

Definition at line 23 of file ThreadingJob.fwd.hh.

Function Documentation

core::sequence::SequenceAlignment protocols::comparative_modeling::alignment_from_cmd_line

(

)

Definition at line 82 of file util.cc.

References core::sequence::read_general_aln_file(), and core::sequence::read_grishin_aln_file().

AlignmentSet protocols::comparative_modeling::alignments_from_cmd_line

(

)

Definition at line 560 of file util.cc.

References core::sequence::AlignerFactory::get_aligner().

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>.

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.

Definition at line 113 of file util.cc.

References NO_LOOP_SIZE_CST, pick_loops_unaligned(), core::sequence::SequenceAlignment::sequence_mapping(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

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

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

(

core::pose::Pose const &

pose)

Definition at line 69 of file Align_RotamerEvaluator.cc.

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

void protocols::comparative_modeling::cm_main

(

)

Initiates LoopRelaxThreadingMover using the job distributor (jd2)

Definition at line 25 of file cm_main.cc.

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

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"
	)

Definition at line 30 of file coord_util.cc.

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

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

void protocols::comparative_modeling::initialize_ss

(

core::pose::Pose &

pose)

Definition at line 497 of file util.cc.

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

bool protocols::comparative_modeling::loops_are_closed

(

core::pose::Pose &

pose)

Definition at line 527 of file util.cc.

References pick_loops_chainbreak(), and core::io::serialization::size().

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

Definition at line 173 of file util.cc.

References pick_loops_unaligned(), core::sequence::SequenceAlignment::sequence_mapping(), and tr().

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

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
	)

Definition at line 214 of file util.cc.

References pick_loops_unaligned(), core::sequence::SequenceAlignment::sequence_mapping(), and tr().

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

protocols::loops::LoopsOP protocols::comparative_modeling::pick_loops_chainbreak	(	core::pose::Pose &	query_pose,
		core::Size	min_loop_size
	)

Definition at line 324 of file util.cc.

References core::pose::Pose::conformation(), core::chemical::ResidueType::is_protein(), core::pose::symmetry::is_symmetric(), pick_loops_unaligned(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), tr(), and core::conformation::Residue::xyz().

Referenced by protocols::comparative_modeling::LoopRelaxThreadingMover::apply(), protocols::domain_assembly::AssembleLinkerMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), loops_are_closed(), and rebuild_loops_until_closed().

protocols::loops::LoopsOP protocols::comparative_modeling::pick_loops_unaligned	(	core::Size	nres,
		utility::vector1< core::Size > const &	unaligned_residues,
		core::Size	min_loop_size
	)

Definition at line 268 of file util.cc.

References core::sequence::end, and tr().

Referenced by bounded_loops_from_alignment(), protocols::star::Extender::Extender(), loops_from_alignment(), loops_from_transitive_alignments(), and pick_loops_chainbreak().

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

(

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

fn_list)

Definition at line 532 of file util.cc.

References core::sequence::end, protocols::swa::rna::file_exists(), core::import_pose::pose_from_pdb(), and core::chemical::rsd_set_from_cmd_line().

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

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

Definition at line 620 of file util.cc.

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(), RG(), core::pose::Pose::set_xyz(), and core::pose::Pose::total_residue().

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

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

(

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

fns)

Definition at line 53 of file ThreadingJobInputter.cc.

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

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
	)

Definition at line 368 of file util.cc.

References core::chemical::CENTROID, protocols::loops::LoopMoverFactory::create_loop_mover(), protocols::loops::LoopMoverFactory::get_instance(), core::chemical::ResidueTypeSet::name(), pick_loops_chainbreak(), core::pose::Pose::residue_type(), core::chemical::ResidueType::residue_type_set(), core::util::switch_to_residue_type_set(), and tr().

static numeric::random::RandomGenerator protocols::comparative_modeling::RG ( 298211  )

static

Referenced by randomize_selected_atoms().

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

(

core::pose::Pose const &

pose)

Definition at line 53 of file Align_RotamerEvaluator.cc.

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

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.

Detailed:: 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.

Definition at line 416 of file util.cc.

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::total_residue(), tr(), and core::id::NamedAtomID::valid().

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

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

(

)

Definition at line 512 of file util.cc.

References core::import_pose::poses_from_pdbs().

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

static

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

static

Referenced by protocols::comparative_modeling::LoopRelaxThreadingMover::apply(), protocols::comparative_modeling::Align_RotamerEvaluator::apply(), protocols::comparative_modeling::Align_RmsdEvaluator::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::comparative_modeling::MultiThreadingMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::comparative_modeling::GenericJobInputter::fill_jobs(), protocols::comparative_modeling::ThreadingJobInputter::fill_jobs(), protocols::comparative_modeling::GenericJobInputter::GenericJobInputter(), protocols::comparative_modeling::ExtraThreadingMover::get_qt_mapping(), protocols::comparative_modeling::ThreadingMover::get_qt_mapping(), loops_from_alignment(), loops_from_transitive_alignments(), pick_loops_chainbreak(), pick_loops_unaligned(), protocols::comparative_modeling::GenericJobInputter::pose_from_job(), protocols::comparative_modeling::ThreadingJobInputter::pose_from_job(), rebuild_loops_until_closed(), steal_ligands(), protocols::comparative_modeling::ThreadingJob::ThreadingJob(), and protocols::comparative_modeling::ThreadingJobInputter::ThreadingJobInputter().

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

static

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

static