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")
std::map< std::string, utility::vector1< core::Size > >	read_extra_residues (utility::vector1< std::string > const &fns)
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)

Variables
static basic::Tracer	tr ("protocols.comparative_modeling.extra_threading")
static basic::Tracer	tr ("protocols.comparative_modeling.ThreadingJobInputter")
static basic::Tracer	tr ("protocols.comparative_modeling.threading")
static numeric::random::RandomGenerator	RG (298211)
static basic::Tracer	tr ("protocols.comparative_modeling.util")

Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Function Documentation

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

(

)

References in::file::alignment, cm::aln_format, option, read_general_aln_file(), read_grishin_aln_file(), runtime_assert, and utility_exit_with_message.

AlignmentSet protocols::comparative_modeling::alignments_from_cmd_line

(

)

References cm::aligner, aligner, core::sequence::AlignerFactory::get_aligner(), cm::max_gap_extend, max_gap_extend, max_gap_open, cm::max_gap_open, min_gap_extend, cm::min_gap_extend, min_gap_open, cm::min_gap_open, o, option, in::file::pssm, core::sequence::SequenceProfile::read_from_file(), runtime_assert, seq_score, cm::seq_score, and ss.

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.

References j, NO_LOOP_SIZE_CST, pick_loops_unaligned(), resi, 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

)

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)

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"
	)

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

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

void protocols::comparative_modeling::initialize_ss

(

core::pose::Pose &

pose

)

References in::file::dssp, option, protocols::loops::set_secstruct_from_dssp(), protocols::loops::set_secstruct_from_psipred_ss2(), and set_ss_from_phipsi().

bool protocols::comparative_modeling::loops_are_closed

(

core::pose::Pose &

pose

)

References pick_loops_chainbreak(), and size().

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

References pick_loops_unaligned(), resi, 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
	)

References pick_loops_unaligned(), resi, 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
	)

References core::pose::Pose::conformation(), numeric::xyzVector< class >::distance(), core::chemical::ResidueType::is_protein(), core::pose::symmetry::is_symmetric(), nres, 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
	)

References 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

)

References end, utility::file_basename(), file_exists(), utility::file::file_exists(), core::import_pose::pose_from_pdb(), and 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
	)

References core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::attached_H_begin(), core::conformation::Residue::attached_H_end(), begin, end, core::pose::Pose::residue(), RG, core::pose::Pose::set_xyz(), core::pose::Pose::total_residue(), and numeric::random::RandomGenerator::uniform().

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

)

References utility::io::izstream::close(), getline(), utility::io::izstream::good(), ss, and utility_exit_with_message.

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
	)

References core::chemical::CENTROID, protocols::loops::LoopMoverFactory::create_loop_mover(), protocols::loops::LoopMoverFactory::get_instance(), loop_mover, 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.

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

(

core::pose::Pose const &

pose

)

References core::pose::Pose::residue(), rot(), rotamer_from_chi(), rots, 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.

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

(

)

References option, core::import_pose::poses_from_pdbs(), and in::file::template_pdb.

Variable Documentation

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

static

Referenced by randomize_selected_atoms().

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

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().

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

static

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

static