protocols::motifs::LigandMotifSearch Class Reference

#include <LigandMotifSearch.hh>

Inheritance diagram for protocols::motifs::LigandMotifSearch:

Public Types
typedef core::Real	Real
typedef core::Size	Size
typedef utility::vector1< core::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 ()
	~LigandMotifSearch () override
	LigandMotifSearch (LigandMotifSearch const &src)
LigandMotifSearch &	operator= (LigandMotifSearch const &src)
void	run (Pose const &pose, utility::vector1< core::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, utility::vector1< core::Size > &input_BPs)
void	incorporate_motifs (Pose const &pose)
core::pack::rotamer_set::Rotamers	bp_rotamers (core::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< core::Size >	get_sphere_aa (Pose const &pose, core::Real cut1)
void	identify_motif_BuildPositions (Pose const &pose)
void	BuildPosition_from_Size (Pose const &pose, core::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< core::Size >	map2keyvector (std::map< core::Size, std::set< std::string > > mappositions)
utility::vector1< core::Size >	shorten_target_list (Pose const &pose, core::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, core::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< core::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
core::Size const &	rot_level () const
bool const &	minimize () const
bool const &	output_build_positions_only () const
core::Size const &	specific_build_position () const

Private Member Functions
void	init_options ()

Private Attributes
MotifCOPs	motif_library_
Sizes	dna_positions_
Sizes	protein_positions_
std::map< core::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_
core::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_
core::Size	rots2add_
bool	output_build_positions_only_
core::Size	specific_build_position_

Member Typedef Documentation

DnaDesignDefOP

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

DnaDesignDefOPs

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

PackerTask

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

Pose

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

Real

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

Size

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

Sizes

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

Constructor & Destructor Documentation

LigandMotifSearch() [1/2]

protocols::motifs::LigandMotifSearch::LigandMotifSearch

(

)

References init_options().

~LigandMotifSearch()

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

overridedefault

LigandMotifSearch() [2/2]

protocols::motifs::LigandMotifSearch::LigandMotifSearch

(

LigandMotifSearch const &

src

)

Member Function Documentation

bp_rotamers()

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

(

core::Size const

seqpos

)

References build_positionOPs_, and protocols::motifs::ms_tr().

Referenced by run().

build_positionOPs()

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

inline

References build_positionOPs_.

BuildPosition_from_Size()

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

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

Referenced by initialize().

defs2BuildPositions()

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

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

defs2BuildPositions_findts()

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

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

dna_positions()

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

inline

References dna_positions_.

dtest_cutoff()

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

inline

References dtest_cutoff_.

Referenced by incorporate_motifs().

get_rotamers()

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

(

)

References build_positionOPs_.

get_sphere_aa()

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

References core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::has(), core::chemical::ResidueType::is_ligand(), core::conformation::Residue::is_protein(), protocols::motifs::ms_tr(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by run().

identify_motif_build_positions()

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().

identify_motif_BuildPositions()

void protocols::motifs::LigandMotifSearch::identify_motif_BuildPositions

(

Pose const &

pose

)

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

incorporate_motifs()

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(), protocols::motifs::atom_specific_rms(), core::chemical::ResidueTypeBase::atom_type_set_ptr(), build_positionOPs_, protocols::motifs::build_rotamers_lite(), core::conformation::Residue::clone(), core::pose::Pose::constraint_set(), core::scoring::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(), core::sequence::end, core::pose::Pose::energies(), core::scoring::get_score_function_legacy(), core::chemical::ResidueType::is_ligand(), core::chemical::ResidueTypeBase::is_protein(), protocols::motifs::make_base_pair_mutation(), minimize_, motif_library(), motif_library_, protocols::motifs::ms_tr(), core::conformation::Residue::name3(), core::chemical::name_from_aa(), core::chemical::num_canonical_aas, 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_, core::pose::Pose::size(), specific_build_position_, target_conformers_map_, target_positions(), core::scoring::Energies::total_energies(), core::conformation::Residue::type(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

Referenced by run().

init_options()

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

private

References bpdata_, bpdata_filename_, clear_bprots_, data_, data_filename_, dump_motifs_, output_, output_build_positions_only_, output_filename_, quick_and_dirty_, rots2add_, and specific_build_position_.

Referenced by LigandMotifSearch().

initialize()

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

References BuildPosition_from_Size(), core::conformation::Residue::clone(), protocols::motifs::get_LigandMotifLibrary_user(), protocols::motifs::get_targetconformers_user(), core::chemical::ResidueType::is_ligand(), protocols::motifs::MotifLibrary::library(), motif_library_, protocols::motifs::ms_tr(), position_vector_setup(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::motifs::setup_conformer_map(), core::pose::Pose::size(), and target_conformers_map_.

Referenced by run().

map2keyvector()

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

(

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

mappositions

)

References core::sequence::end.

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

minimize()

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

inline

References minimize_.

motif_library()

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

inline

References motif_library_.

Referenced by incorporate_motifs().

operator=()

LigandMotifSearch & 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_build_positions_only_, output_filename_, quick_and_dirty_, rmsd_cutoff_1_, rmsd_cutoff_2_, rot_level_, rots2add_, specific_build_position_, target_conformers_map_, target_positions_, ztest_cutoff_1_, and ztest_cutoff_2_.

output_build_positions_only()

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

inline

References output_build_positions_only_.

override_option_input()

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

References dtest_cutoff_, protocols::hybridization::r1, protocols::hybridization::r2, rmsd_cutoff_1_, rmsd_cutoff_2_, rot_level_, ztest_cutoff_1_, and ztest_cutoff_2_.

position_vector_setup()

void protocols::motifs::LigandMotifSearch::position_vector_setup

(

Pose const &

pose

)

References dna_positions_, core::sequence::end, core::chemical::ResidueTypeBase::is_DNA(), core::chemical::ResidueTypeBase::is_protein(), protein_positions_, core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by initialize().

protein_dna_motif()

bool protocols::motifs::LigandMotifSearch::protein_dna_motif

(

)

References core::conformation::ResidueFactory::create_residue(), protocols::dna::dna_full_name3(), core::chemical::FA_STANDARD, motif_library_, and protocols::motifs::ms_tr().

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

protein_DNA_motif_build_positions_JA()

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

References core::sequence::end, protocols::motifs::ms_tr(), protein_positions_, and target_positions().

Referenced by identify_motif_build_positions(), and identify_motif_BuildPositions().

protein_DNA_motif_target_positions_JA()

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

References core::sequence::end, protocols::motifs::ms_tr(), and target_positions().

Referenced by shorten_target_list().

protein_positions()

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

inline

References protein_positions_.

reset_option_input()

void protocols::motifs::LigandMotifSearch::reset_option_input

(

)

References dtest_cutoff_, protocols::hybridization::r1, protocols::hybridization::r2, rmsd_cutoff_1_, rmsd_cutoff_2_, rot_level_, ztest_cutoff_1_, and ztest_cutoff_2_.

rmsd_cutoff_1()

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

inline

References rmsd_cutoff_1_.

Referenced by incorporate_motifs().

rmsd_cutoff_2()

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

inline

References rmsd_cutoff_2_.

Referenced by incorporate_motifs().

rot_level()

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

inline

References rot_level_.

run() [1/3]

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

References build_positionOPs_, clear_bprots_, get_sphere_aa(), incorporate_motifs(), initialize(), protocols::motifs::LIGAND, protocols::motifs::load_build_position_data(), motif_library_, protocols::motifs::ms_tr(), output_, and output_filename_.

run() [2/3]

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_, incorporate_motifs(), initialize(), core::conformation::Residue::is_protein(), protocols::motifs::LIGAND, protocols::motifs::load_build_position_data(), motif_library_, protocols::motifs::ms_tr(), core::pack::task::PackerTask::nonconst_residue_task(), output_, output_build_positions_only_, output_filename_, core::pose::Pose::residue(), rot(), core::pose::Pose::size(), core::chemical::SPECIAL_ROT, and target_positions().

run() [3/3]

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

References incorporate_motifs(), and initialize().

set_motif_library()

void protocols::motifs::LigandMotifSearch::set_motif_library

(

MotifLibrary &

motiflibrary

)

References motif_library_.

shorten_target_list()

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

References protein_DNA_motif_target_positions_JA().

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

specific_build_position()

core::Size const& protocols::motifs::LigandMotifSearch::specific_build_position ( ) const

inline

References specific_build_position_.

target_conformers_map()

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

inline

References target_conformers_map_.

target_positions()

std::map< core::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(), protein_DNA_motif_build_positions_JA(), protein_DNA_motif_target_positions_JA(), and run().

ztest_cutoff_1()

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

inline

References ztest_cutoff_1_.

ztest_cutoff_2()

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

inline

References ztest_cutoff_2_.

Member Data Documentation

bpdata_

bool protocols::motifs::LigandMotifSearch::bpdata_

private

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

bpdata_filename_

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

private

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

build_positionOPs_

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().

clear_bprots_

bool protocols::motifs::LigandMotifSearch::clear_bprots_

private

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

data_

bool protocols::motifs::LigandMotifSearch::data_

private

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

data_filename_

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

private

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

dna_positions_

Sizes protocols::motifs::LigandMotifSearch::dna_positions_

private

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

dtest_cutoff_

Real protocols::motifs::LigandMotifSearch::dtest_cutoff_

private

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

dump_motifs_

bool protocols::motifs::LigandMotifSearch::dump_motifs_

private

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

minimize_

bool protocols::motifs::LigandMotifSearch::minimize_

private

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

motif_library_

MotifCOPs protocols::motifs::LigandMotifSearch::motif_library_

private

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

output_

bool protocols::motifs::LigandMotifSearch::output_

private

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

output_build_positions_only_

bool protocols::motifs::LigandMotifSearch::output_build_positions_only_

private

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

output_filename_

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

private

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

protein_positions_

Sizes protocols::motifs::LigandMotifSearch::protein_positions_

private

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

quick_and_dirty_

bool protocols::motifs::LigandMotifSearch::quick_and_dirty_

private

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

rmsd_cutoff_1_

Real protocols::motifs::LigandMotifSearch::rmsd_cutoff_1_

private

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

rmsd_cutoff_2_

Real protocols::motifs::LigandMotifSearch::rmsd_cutoff_2_

private

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

rot_level_

core::Size protocols::motifs::LigandMotifSearch::rot_level_

private

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

rots2add_

core::Size protocols::motifs::LigandMotifSearch::rots2add_

private

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

specific_build_position_

core::Size protocols::motifs::LigandMotifSearch::specific_build_position_

private

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

target_conformers_map_

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

private

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

target_positions_

std::map< core::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().

ztest_cutoff_1_

Real protocols::motifs::LigandMotifSearch::ztest_cutoff_1_

private

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

ztest_cutoff_2_

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