protocols::motifs::LigandMotifSearch Class Reference

#include <LigandMotifSearch.hh>

Public Types
typedef core::Real	Real
typedef core::Size	Size
typedef utility::vector1< Size >	Sizes
typedef core::pose::Pose	Pose
typedef protocols::dna::DnaDesignDefOP	DnaDesignDefOP
typedef protocols::dna::DnaDesignDefOPs	DnaDesignDefOPs
typedef core::pack::task::PackerTask	PackerTask

Public Member Functions
	LigandMotifSearch ()
virtual	~LigandMotifSearch ()
	LigandMotifSearch (LigandMotifSearch const &src)
LigandMotifSearch const &	operator= (LigandMotifSearch const &src)
void	run (Pose const &pose, utility::vector1< Size > &input_BPs)
void	run (Pose const &pose, PackerTask &task)
void	run (Pose const &pose, core::Real &ligand_motif_sphere)
void	initialize (Pose const &pose)
void	initialize (Pose const &pose, utility::vector1< Size > &input_BPs)
void	incorporate_motifs (Pose const &pose)
core::pack::rotamer_set::Rotamers	bp_rotamers (Size const seqpos)
core::pack::rotamer_set::Rotamers	get_rotamers ()
bool	protein_dna_motif ()
void	position_vector_setup (Pose const &pose)
void	identify_motif_build_positions (Pose const &pose, Sizes &build_positions)
utility::vector1< Size >	get_sphere_aa (Pose const &pose, core::Real cut1)
void	identify_motif_BuildPositions (Pose const &pose)
void	BuildPosition_from_Size (Pose const &pose, Size const input_BP)
void	defs2BuildPositions (Pose const &pose, protocols::dna::DnaDesignDefOPs const &defs)
void	defs2BuildPositions_findts (Pose const &pose, protocols::dna::DnaDesignDefOPs const &defs)
utility::vector1< Size >	map2keyvector (std::map< Size, std::set< std::string > > mappositions)
utility::vector1< Size >	shorten_target_list (Pose const &pose, Size const bp, Sizes &full_tl)
void	protein_DNA_motif_build_positions_JA (Pose const &pose, Sizes &build_positions, Sizes &target_positions)
void	protein_DNA_motif_target_positions_JA (Pose const &pose, Sizes &build_positions, Sizes &target_positions, Sizes &short_tl)
void	override_option_input (Real const &r1, Real const &z1, Real const &r2, Real const &z2, Real const &d1, Size const &rlevel)
void	reset_option_input ()
void	set_motif_library (MotifLibrary &motiflibrary)
MotifCOPs const &	motif_library () const
Sizes const &	dna_positions () const
Sizes const &	protein_positions () const
std::map< Size, std::set < std::string > > const &	target_positions () const
BuildPositionOPs const &	build_positionOPs () const
std::map< std::string, core::conformation::ResidueOPs > const &	target_conformers_map () const
Real const &	ztest_cutoff_1 () const
Real const &	ztest_cutoff_2 () const
Real const &	rmsd_cutoff_1 () const
Real const &	rmsd_cutoff_2 () const
Real const &	dtest_cutoff () const
Size const &	rot_level () const
bool const &	minimize () const

Private Member Functions
void	init_options ()

Private Attributes
MotifCOPs	motif_library_
Sizes	dna_positions_
Sizes	protein_positions_
std::map< Size, std::set < std::string > >	target_positions_
BuildPositionOPs	build_positionOPs_
std::map< std::string, core::conformation::ResidueOPs >	target_conformers_map_
Real	ztest_cutoff_1_
Real	ztest_cutoff_2_
Real	rmsd_cutoff_1_
Real	rmsd_cutoff_2_
Real	dtest_cutoff_
Size	rot_level_
bool	minimize_
bool	bpdata_
std::string	bpdata_filename_
bool	output_
std::string	output_filename_
bool	data_
std::string	data_filename_
bool	quick_and_dirty_
bool	dump_motifs_
bool	clear_bprots_
Size	rots2add_

Member Typedef Documentation

typedef protocols::dna::DnaDesignDefOP protocols::motifs::LigandMotifSearch::DnaDesignDefOP

typedef protocols::dna::DnaDesignDefOPs protocols::motifs::LigandMotifSearch::DnaDesignDefOPs

typedef core::pack::task::PackerTask protocols::motifs::LigandMotifSearch::PackerTask

typedef core::pose::Pose protocols::motifs::LigandMotifSearch::Pose

typedef core::Real protocols::motifs::LigandMotifSearch::Real

typedef core::Size protocols::motifs::LigandMotifSearch::Size

typedef utility::vector1< Size > protocols::motifs::LigandMotifSearch::Sizes

Constructor & Destructor Documentation

protocols::motifs::LigandMotifSearch::LigandMotifSearch

(

)

References dtest, init_options(), motifs, option, options, r1, r2, rotlevel, z1, and z2.

protocols::motifs::LigandMotifSearch::~LigandMotifSearch ( )

virtual

protocols::motifs::LigandMotifSearch::LigandMotifSearch

(

LigandMotifSearch const &

src

)

Member Function Documentation

core::pack::rotamer_set::Rotamers protocols::motifs::LigandMotifSearch::bp_rotamers

(

Size const

seqpos

)

References build_positionOPs_, empty, and protocols::motifs::ms_tr.

Referenced by run().

BuildPositionOPs const& protocols::motifs::LigandMotifSearch::build_positionOPs ( ) const

inline

References build_positionOPs_.

void protocols::motifs::LigandMotifSearch::BuildPosition_from_Size	(	Pose const &	pose,
		Size const	input_BP
	)

References build_positionOPs_, map2keyvector(), shorten_target_list(), target_positions(), and target_positions_.

Referenced by initialize().

void protocols::motifs::LigandMotifSearch::defs2BuildPositions	(	Pose const &	pose,
		protocols::dna::DnaDesignDefOPs const &	defs
	)

References build_positionOPs_, protocols::motifs::defs2map(), end, map2keyvector(), protocols::motifs::ms_tr, protein_dna_motif(), and target_positions_.

void protocols::motifs::LigandMotifSearch::defs2BuildPositions_findts	(	Pose const &	pose,
		protocols::dna::DnaDesignDefOPs const &	defs
	)

References build_positionOPs_, protocols::motifs::defs2map(), end, map2keyvector(), protocols::motifs::ms_tr, protein_dna_motif(), shorten_target_list(), and target_positions_.

Sizes const& protocols::motifs::LigandMotifSearch::dna_positions ( ) const

inline

References dna_positions_.

Real const& protocols::motifs::LigandMotifSearch::dtest_cutoff ( ) const

inline

References dtest_cutoff_.

Referenced by incorporate_motifs().

core::pack::rotamer_set::Rotamers protocols::motifs::LigandMotifSearch::get_rotamers

(

)

References build_positionOPs_, and empty.

utility::vector1< core::Size > protocols::motifs::LigandMotifSearch::get_sphere_aa	(	Pose const &	pose,
		core::Real	cut1
	)

References chemical, cut2, cut3, cut4, numeric::xyzVector< class >::distance_squared(), core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), protocols::motifs::ms_tr, core::conformation::Residue::nheavyatoms(), nres, optimization, core::pose::Pose::residue(), core::pose::Pose::residue_type(), scoring, core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by run().

void protocols::motifs::LigandMotifSearch::identify_motif_build_positions	(	Pose const &	pose,
		Sizes &	build_positions
	)

References dna_positions_, protocols::motifs::ms_tr, protein_dna_motif(), and protein_DNA_motif_build_positions_JA().

void protocols::motifs::LigandMotifSearch::identify_motif_BuildPositions

(

Pose const &

pose

)

References build_positionOPs_, end, map2keyvector(), protocols::motifs::ms_tr, protein_dna_motif(), protein_DNA_motif_build_positions_JA(), shorten_target_list(), target_positions(), and target_positions_.

void protocols::motifs::LigandMotifSearch::incorporate_motifs

(

Pose const &

pose

)

References core::chemical::aa_from_name(), protocols::motifs::add_motif_sc_constraints(), core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::atom(), core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::atom_name(), protocols::motifs::atom_specific_rms(), core::conformation::Residue::atom_type(), core::chemical::AtomType::atom_type_name(), core::chemical::ChemicalManager::atom_type_set(), core::conformation::Residue::bonded_neighbor(), build_positionOPs_, protocols::motifs::build_rotamers_lite(), chemical, core::conformation::Residue::clone(), clone(), utility::io::ozstream::close(), core::pose::Pose::constraint_set(), contacts, coordinate_constraint, core::conformation::ResidueFactory::create_residue(), core::pack::rotamer_set::RotamerSetFactory::create_rotamer_set(), data_, data_filename_, protocols::dna::dna_full_name3(), dtest_cutoff(), dtest_cutoff_, dump_motifs_, core::io::pdb::dump_pdb(), empty, end, core::pose::Pose::energies(), FA_STANDARD, core::chemical::ChemicalManager::get_instance(), get_score_function_legacy(), protocols::motifs::make_base_pair_mutation(), minimize_, motif_filename, motif_library(), motif_library_, movemap, protocols::motifs::ms_tr, core::conformation::Residue::name3(), core::chemical::name_from_aa(), core::conformation::Residue::natoms(), nres, core::chemical::num_canonical_aas, utility::io::ozstream::open_append(), optimization, options, output_, output_filename_, core::pose::Pose::pdb_info(), core::scoring::PRE_TALARIS_2013_STANDARD_WTS, quick_and_dirty_, core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), rmsd_cutoff_1(), rmsd_cutoff_1_, rmsd_cutoff_2(), rmsd_cutoff_2_, rot_level_, rots2add_, scoring, target_conformers_map_, target_positions(), core::scoring::Energies::total_energies(), core::pose::Pose::total_residue(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by run().

void protocols::motifs::LigandMotifSearch::init_options ( )

private

References basic::options::OptionKeys::motifs::BPData, bpdata_, bpdata_filename_, basic::options::OptionKeys::motifs::clear_bprots, clear_bprots_, data_, basic::options::OptionKeys::motifs::data_file, data_filename_, basic::options::OptionKeys::motifs::dump_motifs, dump_motifs_, basic::options::option, output_, basic::options::OptionKeys::motifs::output_file, output_filename_, basic::options::OptionKeys::motifs::quick_and_dirty, quick_and_dirty_, basic::options::OptionKeys::motifs::rots2add, rots2add_, and user.

Referenced by LigandMotifSearch().

void protocols::motifs::LigandMotifSearch::initialize

(

Pose const &

pose

)

References protocols::motifs::get_LigandMotifLibrary_user(), protocols::motifs::get_targetconformers_user(), protocols::motifs::MotifLibrary::library(), motif_library_, motifs, position_vector_setup(), protocols::motifs::setup_conformer_map(), and target_conformers_map_.

Referenced by run().

void protocols::motifs::LigandMotifSearch::initialize	(	Pose const &	pose,
		utility::vector1< Size > &	input_BPs
	)

References BuildPosition_from_Size(), protocols::motifs::get_LigandMotifLibrary_user(), protocols::motifs::get_targetconformers_user(), protocols::motifs::MotifLibrary::library(), motif_library_, motifs, protocols::motifs::ms_tr, position_vector_setup(), protocols::motifs::setup_conformer_map(), and target_conformers_map_.

utility::vector1< core::Size > protocols::motifs::LigandMotifSearch::map2keyvector

(

std::map< Size, std::set< std::string > >

mappositions

)

References end.

Referenced by BuildPosition_from_Size(), defs2BuildPositions(), defs2BuildPositions_findts(), and identify_motif_BuildPositions().

bool const& protocols::motifs::LigandMotifSearch::minimize ( ) const

inline

References minimize_.

MotifCOPs const& protocols::motifs::LigandMotifSearch::motif_library ( ) const

inline

References motif_library_.

Referenced by incorporate_motifs().

LigandMotifSearch const & protocols::motifs::LigandMotifSearch::operator=

(

LigandMotifSearch const &

src

)

References bpdata_, bpdata_filename_, build_positionOPs_, clear_bprots_, data_, data_filename_, dtest_cutoff_, dump_motifs_, minimize_, motif_library_, output_, output_filename_, quick_and_dirty_, rmsd_cutoff_1_, rmsd_cutoff_2_, rot_level_, rots2add_, target_conformers_map_, target_positions_, ztest_cutoff_1_, and ztest_cutoff_2_.

void protocols::motifs::LigandMotifSearch::override_option_input	(	Real const &	r1,
		Real const &	z1,
		Real const &	r2,
		Real const &	z2,
		Real const &	d1,
		Size const &	rlevel
	)

References dtest_cutoff_, rmsd_cutoff_1_, rmsd_cutoff_2_, rot_level_, ztest_cutoff_1_, and ztest_cutoff_2_.

void protocols::motifs::LigandMotifSearch::position_vector_setup

(

Pose const &

pose

)

References dna_positions_, end, core::chemical::ResidueType::is_DNA(), core::chemical::ResidueType::is_protein(), protein_positions_, core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by initialize().

bool protocols::motifs::LigandMotifSearch::protein_dna_motif

(

)

References core::conformation::ResidueFactory::create_residue(), protocols::dna::dna_full_name3(), FA_STANDARD, core::chemical::ChemicalManager::get_instance(), core::conformation::Residue::is_DNA(), core::conformation::Residue::is_protein(), motif_library_, protocols::motifs::ms_tr, and residue_type_set.

Referenced by defs2BuildPositions(), defs2BuildPositions_findts(), identify_motif_build_positions(), and identify_motif_BuildPositions().

void protocols::motifs::LigandMotifSearch::protein_DNA_motif_build_positions_JA	(	Pose const &	pose,
		Sizes &	build_positions,
		Sizes &	target_positions
	)

References protocols::dna::DnaInterfaceFinder::determine_protein_interface(), end, protocols::motifs::ms_tr, and protein_positions_.

Referenced by identify_motif_build_positions(), and identify_motif_BuildPositions().

void protocols::motifs::LigandMotifSearch::protein_DNA_motif_target_positions_JA	(	Pose const &	pose,
		Sizes &	build_positions,
		Sizes &	target_positions,
		Sizes &	short_tl
	)

References protocols::dna::DnaInterfaceFinder::determine_dna_interface(), end, and protocols::motifs::ms_tr.

Referenced by shorten_target_list().

Sizes const& protocols::motifs::LigandMotifSearch::protein_positions ( ) const

inline

References protein_positions_.

void protocols::motifs::LigandMotifSearch::reset_option_input

(

)

References basic::options::OptionKeys::motifs::dtest, dtest_cutoff_, basic::options::option, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, rmsd_cutoff_1_, rmsd_cutoff_2_, rot_level_, basic::options::OptionKeys::motifs::rotlevel, basic::options::OptionKeys::motifs::z1, basic::options::OptionKeys::motifs::z2, ztest_cutoff_1_, and ztest_cutoff_2_.

Real const& protocols::motifs::LigandMotifSearch::rmsd_cutoff_1 ( ) const

inline

References rmsd_cutoff_1_.

Referenced by incorporate_motifs().

Real const& protocols::motifs::LigandMotifSearch::rmsd_cutoff_2 ( ) const

inline

References rmsd_cutoff_2_.

Referenced by incorporate_motifs().

Size const& protocols::motifs::LigandMotifSearch::rot_level ( ) const

inline

References rot_level_.

void protocols::motifs::LigandMotifSearch::run	(	Pose const &	pose,
		utility::vector1< Size > &	input_BPs
	)

References incorporate_motifs(), initialize(), and protocols::motifs::ms_tr.

void protocols::motifs::LigandMotifSearch::run	(	Pose const &	pose,
		PackerTask &	task
	)

References core::pose::add_variant_type_to_residue(), core::pack::task::ResidueLevelTask::append_rotamerset_operation(), core::pack::task::PackerTask::being_designed(), bp_rotamers(), build_positionOPs_, clear_bprots_, file_exists(), utility::file::file_exists(), incorporate_motifs(), initialize(), core::conformation::Residue::is_protein(), protocols::motifs::load_build_position_data(), motif_library_, protocols::motifs::ms_tr, core::pack::task::PackerTask::nonconst_residue_task(), utility::io::ozstream::open_append(), output_, output_filename_, core::pose::Pose::residue(), rot(), core::chemical::SPECIAL_ROT, target_positions(), and core::pose::Pose::total_residue().

void protocols::motifs::LigandMotifSearch::run	(	Pose const &	pose,
		core::Real &	ligand_motif_sphere
	)

References build_positionOPs_, clear_bprots_, file_exists(), utility::file::file_exists(), get_sphere_aa(), incorporate_motifs(), initialize(), protocols::motifs::load_build_position_data(), motif_library_, protocols::motifs::ms_tr, utility::io::ozstream::open_append(), output_, and output_filename_.

void protocols::motifs::LigandMotifSearch::set_motif_library

(

MotifLibrary &

motiflibrary

)

References protocols::motifs::MotifLibrary::begin(), protocols::motifs::MotifLibrary::end(), and motif_library_.

utility::vector1< core::Size > protocols::motifs::LigandMotifSearch::shorten_target_list	(	Pose const &	pose,
		Size const	bp,
		Sizes &	full_tl
	)

References protein_DNA_motif_target_positions_JA().

Referenced by BuildPosition_from_Size(), defs2BuildPositions_findts(), and identify_motif_BuildPositions().

std::map< std::string, core::conformation::ResidueOPs > const& protocols::motifs::LigandMotifSearch::target_conformers_map ( ) const

inline

References target_conformers_map_.

std::map< Size, std::set< std::string > > const& protocols::motifs::LigandMotifSearch::target_positions ( ) const

inline

References target_positions_.

Referenced by BuildPosition_from_Size(), identify_motif_BuildPositions(), incorporate_motifs(), and run().

Real const& protocols::motifs::LigandMotifSearch::ztest_cutoff_1 ( ) const

inline

References ztest_cutoff_1_.

Real const& protocols::motifs::LigandMotifSearch::ztest_cutoff_2 ( ) const

inline

References ztest_cutoff_2_.

Member Data Documentation

bool protocols::motifs::LigandMotifSearch::bpdata_

private

Referenced by init_options(), and operator=().

std::string protocols::motifs::LigandMotifSearch::bpdata_filename_

private

Referenced by init_options(), and operator=().

BuildPositionOPs protocols::motifs::LigandMotifSearch::build_positionOPs_

private

Referenced by bp_rotamers(), build_positionOPs(), BuildPosition_from_Size(), defs2BuildPositions(), defs2BuildPositions_findts(), get_rotamers(), identify_motif_BuildPositions(), incorporate_motifs(), operator=(), and run().

bool protocols::motifs::LigandMotifSearch::clear_bprots_

private

Referenced by init_options(), operator=(), and run().

bool protocols::motifs::LigandMotifSearch::data_

private

Referenced by incorporate_motifs(), init_options(), and operator=().

std::string protocols::motifs::LigandMotifSearch::data_filename_

private

Referenced by incorporate_motifs(), init_options(), and operator=().

Sizes protocols::motifs::LigandMotifSearch::dna_positions_

private

Referenced by dna_positions(), identify_motif_build_positions(), and position_vector_setup().

Real protocols::motifs::LigandMotifSearch::dtest_cutoff_

private

Referenced by dtest_cutoff(), incorporate_motifs(), operator=(), override_option_input(), and reset_option_input().

bool protocols::motifs::LigandMotifSearch::dump_motifs_

private

Referenced by incorporate_motifs(), init_options(), and operator=().

bool protocols::motifs::LigandMotifSearch::minimize_

private

Referenced by incorporate_motifs(), minimize(), and operator=().

MotifCOPs protocols::motifs::LigandMotifSearch::motif_library_

private

Referenced by incorporate_motifs(), initialize(), motif_library(), operator=(), protein_dna_motif(), run(), and set_motif_library().

bool protocols::motifs::LigandMotifSearch::output_

private

Referenced by incorporate_motifs(), init_options(), operator=(), and run().

std::string protocols::motifs::LigandMotifSearch::output_filename_

private

Referenced by incorporate_motifs(), init_options(), operator=(), and run().

Sizes protocols::motifs::LigandMotifSearch::protein_positions_

private

Referenced by position_vector_setup(), protein_DNA_motif_build_positions_JA(), and protein_positions().

bool protocols::motifs::LigandMotifSearch::quick_and_dirty_

private

Referenced by incorporate_motifs(), init_options(), and operator=().

Real protocols::motifs::LigandMotifSearch::rmsd_cutoff_1_

private

Referenced by incorporate_motifs(), operator=(), override_option_input(), reset_option_input(), and rmsd_cutoff_1().

Real protocols::motifs::LigandMotifSearch::rmsd_cutoff_2_

private

Referenced by incorporate_motifs(), operator=(), override_option_input(), reset_option_input(), and rmsd_cutoff_2().

Size protocols::motifs::LigandMotifSearch::rot_level_

private

Referenced by incorporate_motifs(), operator=(), override_option_input(), reset_option_input(), and rot_level().

Size protocols::motifs::LigandMotifSearch::rots2add_

private

Referenced by incorporate_motifs(), init_options(), and operator=().

std::map< std::string, core::conformation::ResidueOPs > protocols::motifs::LigandMotifSearch::target_conformers_map_

private

Referenced by incorporate_motifs(), initialize(), operator=(), and target_conformers_map().

std::map< Size, std::set< std::string > > protocols::motifs::LigandMotifSearch::target_positions_

private

Referenced by BuildPosition_from_Size(), defs2BuildPositions(), defs2BuildPositions_findts(), identify_motif_BuildPositions(), operator=(), and target_positions().

Real protocols::motifs::LigandMotifSearch::ztest_cutoff_1_

private

Referenced by operator=(), override_option_input(), reset_option_input(), and ztest_cutoff_1().

Real protocols::motifs::LigandMotifSearch::ztest_cutoff_2_

private

Referenced by operator=(), override_option_input(), reset_option_input(), and ztest_cutoff_2().

---

The documentation for this class was generated from the following files:

• src/protocols/motifs/LigandMotifSearch.hh
• src/protocols/motifs/LigandMotifSearch.cc