protocols::ligand_docking::ga_ligand_dock::ConstraintInfo Class Reference

Constraint information about AtomProperties and/or Pharmacophores. More...

#include <LigandAligner.hh>

Public Member Functions
	ConstraintInfo ()
	ConstraintInfo (core::pose::Pose const &pose, utility::vector1< core::Size > const &ligids, bool use_pharmacophore, bool report_phore_info=false)
	ConstraintInfo (core::pose::Pose const &pose, GridScorerOP gridscore, bool const simple=false)
void	init_from_ligand (core::pose::Pose const &pose, utility::vector1< core::Size > const &ligids)
	use a (non-identical) target ligand (for reference ligand matching) More...
void	init_from_ligand_pharmacophore (core::pose::Pose const &pose, utility::vector1< core::Size > const &ligids, bool report_phore_info)
	defines pharmacophore partners in ligand (for pharmacophore matching) More...
void	init_from_receptor (core::pose::Pose const &pose, GridScorerOP gridscore, bool const simple)
core::Size	natoms () const
numeric::xyzVector< core::Real > const &	coord (core::Size i) const
AtomProperties const &	properties (core::Size i) const
core::id::AtomID const &	atomid (core::Size i) const
core::Real	limit ()
core::Real	weight ()
core::Real	polar_scale ()
bool	pharmacophores_defined () const
utility::vector1 < Pharmacophore > const &	phores () const
core::Size	n_phore_match () const
void	select_phore_match (core::Size const run_index)
	selects a phore_match and updates current_phore_match_ More...
void	align_to_current_phore_match (core::pose::Pose &pose, ConstraintInfo const &recinfo, utility::vector1< core::Size > const &ligids, utility::vector1< std::pair< core::Size, core::Size > > &marked_pairs, utility::vector1< core::Size > &SrcPriorIDs, utility::vector1< core::Size > &TgtPriorIDs)
	try aligning to the phore defined by current_phore_match_ (defined by select_phore_match) More...
void	map_phores (utility::vector1< Pharmacophore > const &receptor_phores, bool const update, core::Size const nmax=100)
	matches ligand phores (==own) to provided receptor phores and stores at phore_match_ More...

Private Member Functions
void	set_default ()
void	define_active_virtual_sites (core::pose::Pose const &pose, GridScorerOP gridscore, utility::vector1< std::pair< core::Real, core::Size > > &Vdonor_sort, utility::vector1< std::pair< core::Real, core::Size > > &Vacceptor_sort, core::Size const nneigh_cut_for_exposed_sc, core::Size const nneigh_cut_for_exposed_bb, bool const report=false)
	findes all virtual sites (for h-bonding candidates) in receptor More...
void	append_metal_vsites (core::pose::Pose const &pose, core::Size const &ires, utility::vector1< std::pair< core::Real, core::Size > > &Vacceptor_sort, bool report=false)
void	build_Dmtrx ()
void	define_all_ligand_phores (core::Size const minsize, bool report_phore_info)
	defines all ligand phores More...
bool	phore_overlaps_with_existing (Pharmacophore const &phore_i, core::Size &jphore) const
void	define_receptor_phores (utility::vector1< std::pair< core::Real, core::Size > > &Vdonor_sort, utility::vector1< std::pair< core::Real, core::Size > > &Vacceptor_sort, core::Size const nmin=10, bool report_phore_info=false)
	defines receptor phores More...
void	update_ligand_coord (core::pose::Pose const &pose)

Private Attributes
utility::vector1 < core::id::AtomID >	atmids_
utility::vector1 < numeric::xyzVector < core::Real > >	coords_
utility::vector1< AtomProperties >	properties_
core::Real	limit_
core::Real	weight_
core::Real	polar_scale_
bool	is_ligand_
core::Real	phore_dcut_
core::Size	n_match_per_ligand_motif_
core::Size	NNEIGH_CUT_FOR_EXPOSED_SC
core::Size	NNEIGH_CUT_FOR_EXPOSED_BB
core::Size	RECEPTOR_PHORE_MIN
core::Size	RECEPTOR_PHORE_MAX
utility::vector1 < utility::vector1< core::Real > >	Dmtrx_
utility::vector1< Pharmacophore >	phores_
utility::vector1< std::pair < core::Size, Pharmacophore > >	phore_match_
std::pair< core::Size, Pharmacophore >	current_phore_match_
bool	debug_

Detailed Description

Constraint information about AtomProperties and/or Pharmacophores.

includes constrained xyzs & important properties we do not use a residue type (which already has this info) because in "pharmicophore mode" we generate virtual sites from the protein side. we want targets generated in both ways to run through the same machinery therefore, we instead we have two initialization routines:

• from the ligand side (from restype)
• from the receptor side (building programmatically)

Constructor & Destructor Documentation

protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::ConstraintInfo ( )

inline

protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::ConstraintInfo ( core::pose::Pose const &  pose, utility::vector1< core::Size > const &  ligids, bool  use_pharmacophore, bool  report_phore_info = false  )

inline

protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::ConstraintInfo ( core::pose::Pose const &  pose, GridScorerOP  gridscore, bool const  simple = false  )

inline

Member Function Documentation

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::align_to_current_phore_match	(	core::pose::Pose &	pose,
		ConstraintInfo const &	recinfo,
		utility::vector1< core::Size > const &	ligids,
		utility::vector1< std::pair< core::Size, core::Size > > &	marked_pairs,
		utility::vector1< core::Size > &	SrcPriorIDs,
		utility::vector1< core::Size > &	TgtPriorIDs
	)

try aligning to the phore defined by current_phore_match_ (defined by select_phore_match)

References protocols::ligand_docking::ga_ligand_dock::Pharmacophore::atms(), protocols::ligand_docking::ga_ligand_dock::Pharmacophore::com(), coords_, current_phore_match_, is_ligand_, core::conformation::Residue::natoms(), phores_, core::pose::Pose::residue(), core::scoring::rg, core::pose::Pose::set_xyz(), protocols::ligand_docking::ga_ligand_dock::Pharmacophore::update_com(), update_ligand_coord(), and core::pose::Pose::xyz().

Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply().

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites ( core::pose::Pose const &  pose, core::Size const &  ires, utility::vector1< std::pair< core::Real, core::Size > > &  Vacceptor_sort, bool  report = false  )

private

References core::conformation::Residue::aa(), core::chemical::aa_asp, core::chemical::aa_cys, core::chemical::aa_glu, core::chemical::aa_his, atmids_, core::conformation::Residue::atom_name(), coords_, core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::get_metal_binding_atoms(), core::conformation::Residue::is_protein(), core::conformation::Residue::name(), core::conformation::Residue::nbr_atom_xyz(), properties_, core::pose::Pose::residue(), core::pose::Pose::size(), core::id::to_string(), protocols::ligand_docking::ga_ligand_dock::TR(), and core::conformation::Residue::xyz().

Referenced by define_active_virtual_sites().

core::id::AtomID const& protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::atomid ( core::Size  i ) const

inline

Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_constraints(), and protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_hard_constraint_on_marked().

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::build_Dmtrx ( )

private

References coords_, Dmtrx_, protocols::mean_field::max(), and properties_.

Referenced by define_all_ligand_phores(), and define_receptor_phores().

numeric::xyzVector< core::Real > const& protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::coord ( core::Size  i ) const

inline

Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_constraints(), and protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_hard_constraint_on_marked().

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites ( core::pose::Pose const &  pose, GridScorerOP  gridscore, utility::vector1< std::pair< core::Real, core::Size > > &  Vdonor_sort, utility::vector1< std::pair< core::Real, core::Size > > &  Vacceptor_sort, core::Size const  nneigh_cut_for_exposed_sc, core::Size const  nneigh_cut_for_exposed_bb, bool const  report = false  )

private

findes all virtual sites (for h-bonding candidates) in receptor

References append_metal_vsites(), atmids_, core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::chemical::AtomType::atom_type_name(), coords_, protocols::ligand_docking::ga_ligand_dock::count_neighbors(), core::conformation::Residue::data_ptr(), core::scoring::hbonds::fill_hbond_set(), core::chemical::element::H, core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_donor(), core::conformation::Residue::is_metal(), core::conformation::Residue::is_protein(), core::conformation::Residue::last_backbone_atom(), core::conformation::residue_datacache::LK_BALL_INFO, core::scoring::lkball::LKB_ResidueInfo::n_attached_waters(), core::conformation::Residue::natoms(), properties_, core::pose::Pose::residue(), core::scoring::hbonds::HBondSet::residue_hbonds(), core::pose::Pose::size(), core::id::to_string(), core::pose::Pose::total_residue(), protocols::ligand_docking::ga_ligand_dock::TR(), core::scoring::lkball::LKB_ResidueInfo::water_offset_for_atom(), core::scoring::lkball::LKB_ResidueInfo::waters(), and core::conformation::Residue::xyz().

Referenced by init_from_receptor().

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_all_ligand_phores ( core::Size const  minsize, bool  report_phore_info  )

private

defines all ligand phores

References protocols::ligand_docking::ga_ligand_dock::Pharmacophore::atms(), build_Dmtrx(), coords_, Dmtrx_, protocols::ligand_docking::ga_ligand_dock::Pharmacophore::has(), protocols::ligand_docking::ga_ligand_dock::Pharmacophore::is_close(), is_ligand_, phore_dcut_, phore_overlaps_with_existing(), phores_, properties_, and protocols::ligand_docking::ga_ligand_dock::TR().

Referenced by init_from_ligand_pharmacophore().

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_receptor_phores ( utility::vector1< std::pair< core::Real, core::Size > > &  Vdonor_sort, utility::vector1< std::pair< core::Real, core::Size > > &  Vacceptor_sort, core::Size const  nmin = 10, bool  report_phore_info = false  )

private

defines receptor phores

References core::pose::motif::a(), protocols::match::upstream::b, build_Dmtrx(), coords_, debug_, Dmtrx_, is_ligand_, protocols::mean_field::max(), phore_dcut_, phore_overlaps_with_existing(), phores_, properties_, protocols::hybridization::score, protocols::ligand_docking::ga_ligand_dock::TR(), and protocols::kinmatch::xyz().

Referenced by init_from_receptor().

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	ligids
	)

use a (non-identical) target ligand (for reference ligand matching)

References atmids_, core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), coords_, core::chemical::AtomType::element(), core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_donor(), core::chemical::AtomType::is_hydrogen(), is_ligand_, core::chemical::AtomType::is_polar_hydrogen(), core::conformation::Residue::natoms(), core::conformation::Residue::nheavyatoms(), properties_, core::pose::Pose::residue(), set_default(), core::pose::Pose::total_residue(), protocols::ligand_docking::ga_ligand_dock::TR(), and core::conformation::Residue::xyz().

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	ligids,
		bool	report_phore_info
	)

defines pharmacophore partners in ligand (for pharmacophore matching)

References atmids_, core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::conformation::Residue::atomic_charge(), coords_, define_all_ligand_phores(), core::chemical::AtomType::element(), core::conformation::Residue::heavyatom_has_polar_hydrogens(), core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_donor(), is_ligand_, core::chemical::AtomType::is_polar_hydrogen(), core::conformation::Residue::natoms(), core::conformation::Residue::nheavyatoms(), properties_, core::pose::Pose::residue(), set_default(), and core::conformation::Residue::xyz().

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_receptor	(	core::pose::Pose const &	pose,
		GridScorerOP	gridscore,
		bool const	simple
	)

build up binding locations from a receptor gridscorer is used to define the bounding box

References debug_, define_active_virtual_sites(), define_receptor_phores(), is_ligand_, NNEIGH_CUT_FOR_EXPOSED_BB, NNEIGH_CUT_FOR_EXPOSED_SC, phore_dcut_, phores_, RECEPTOR_PHORE_MAX, RECEPTOR_PHORE_MIN, set_default(), and protocols::ligand_docking::ga_ligand_dock::TR().

core::Real protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::limit ( )

inline

Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_constraints().

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::map_phores	(	utility::vector1< Pharmacophore > const &	receptor_phores,
		bool const	update,
		core::Size const	nmax = 100
	)

matches ligand phores (==own) to provided receptor phores and stores at phore_match_

References core::pose::motif::a(), protocols::match::upstream::b, debug_, protocols::ligand_docking::ga_ligand_dock::Pharmacophore::find_type_matches(), is_ligand_, n_match_per_ligand_motif_, phore_match_, phores_, protocols::hybridization::score, protocols::ligand_docking::ga_ligand_dock::Pharmacophore::show(), and protocols::ligand_docking::ga_ligand_dock::TR().

Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), and protocols::ligand_docking::ga_ligand_dock::LigandAligner::estimate_nstruct_sample().

core::Size protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::n_phore_match ( ) const

inline

Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::estimate_nstruct_sample().

core::Size protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::natoms ( ) const

inline

Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), and protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_constraints().

bool protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::pharmacophores_defined ( ) const

inline

bool protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::phore_overlaps_with_existing ( Pharmacophore const &  phore_i, core::Size &  jphore  ) const

private

References protocols::ligand_docking::ga_ligand_dock::Pharmacophore::com(), protocols::ligand_docking::ga_ligand_dock::Pharmacophore::find_type_matches(), protocols::mean_field::min(), phores_, and protocols::ligand_docking::ga_ligand_dock::Pharmacophore::size().

Referenced by define_all_ligand_phores(), and define_receptor_phores().

utility::vector1< Pharmacophore > const& protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::phores ( ) const

inline

Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), and protocols::ligand_docking::ga_ligand_dock::LigandAligner::estimate_nstruct_sample().

core::Real protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::polar_scale ( )

inline

Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_constraints().

AtomProperties const& protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::properties ( core::Size  i ) const

inline

Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_constraints().

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::select_phore_match

(

core::Size const

run_index

)

selects a phore_match and updates current_phore_match_

References current_phore_match_, protocols::ligand_docking::ga_ligand_dock::Pharmacophore::index(), phore_match_, phores_, protocols::ligand_docking::ga_ligand_dock::Pharmacophore::show(), and protocols::ligand_docking::ga_ligand_dock::TR().

Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply().

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::set_default ( )

private

References debug_, limit_, n_match_per_ligand_motif_, NNEIGH_CUT_FOR_EXPOSED_BB, NNEIGH_CUT_FOR_EXPOSED_SC, phore_dcut_, polar_scale_, RECEPTOR_PHORE_MAX, RECEPTOR_PHORE_MIN, protocols::ligand_docking::ga_ligand_dock::TR(), and weight_.

Referenced by init_from_ligand(), init_from_ligand_pharmacophore(), and init_from_receptor().

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::update_ligand_coord ( core::pose::Pose const &  pose )

private

References atmids_, coords_, and core::pose::Pose::xyz().

Referenced by align_to_current_phore_match().

core::Real protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::weight ( )

inline

Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_constraints().

Member Data Documentation

utility::vector1< core::id::AtomID > protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::atmids_

private

Referenced by append_metal_vsites(), define_active_virtual_sites(), init_from_ligand(), init_from_ligand_pharmacophore(), and update_ligand_coord().

utility::vector1< numeric::xyzVector< core::Real > > protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::coords_

private

Referenced by align_to_current_phore_match(), append_metal_vsites(), build_Dmtrx(), define_active_virtual_sites(), define_all_ligand_phores(), define_receptor_phores(), init_from_ligand(), init_from_ligand_pharmacophore(), and update_ligand_coord().

std::pair< core::Size, Pharmacophore > protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::current_phore_match_

private

Referenced by align_to_current_phore_match(), and select_phore_match().

bool protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::debug_

private

Referenced by define_receptor_phores(), init_from_receptor(), map_phores(), and set_default().

utility::vector1< utility::vector1< core::Real > > protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::Dmtrx_

private

Referenced by build_Dmtrx(), define_all_ligand_phores(), and define_receptor_phores().

bool protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::is_ligand_

private

Referenced by align_to_current_phore_match(), define_all_ligand_phores(), define_receptor_phores(), init_from_ligand(), init_from_ligand_pharmacophore(), init_from_receptor(), and map_phores().

core::Real protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::limit_

private

Referenced by set_default().

core::Size protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::n_match_per_ligand_motif_

private

Referenced by map_phores(), and set_default().

core::Size protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::NNEIGH_CUT_FOR_EXPOSED_BB

private

Referenced by init_from_receptor(), and set_default().

core::Size protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::NNEIGH_CUT_FOR_EXPOSED_SC

private

Referenced by init_from_receptor(), and set_default().

core::Real protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::phore_dcut_

private

Referenced by define_all_ligand_phores(), define_receptor_phores(), init_from_receptor(), and set_default().

utility::vector1< std::pair< core::Size, Pharmacophore > > protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::phore_match_

private

Referenced by map_phores(), and select_phore_match().

utility::vector1< Pharmacophore > protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::phores_

private

Referenced by align_to_current_phore_match(), define_all_ligand_phores(), define_receptor_phores(), init_from_receptor(), map_phores(), phore_overlaps_with_existing(), and select_phore_match().

core::Real protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::polar_scale_

private

Referenced by set_default().

utility::vector1< AtomProperties > protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::properties_

private

Referenced by append_metal_vsites(), build_Dmtrx(), define_active_virtual_sites(), define_all_ligand_phores(), define_receptor_phores(), init_from_ligand(), and init_from_ligand_pharmacophore().

core::Size protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::RECEPTOR_PHORE_MAX

private

Referenced by init_from_receptor(), and set_default().

core::Size protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::RECEPTOR_PHORE_MIN

private

Referenced by init_from_receptor(), and set_default().

core::Real protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::weight_

private

Referenced by set_default().

---

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

• src/protocols/ligand_docking/GALigandDock/LigandAligner.hh
• src/protocols/ligand_docking/GALigandDock/LigandAligner.cc