protocols::ligand_docking::ga_ligand_dock::LigandAligner Class Reference

Aligns ligand using defined constraint information. More...

#include <LigandAligner.hh>

Public Member Functions
	LigandAligner ()
	LigandAligner (bool use_pharmacophore, utility::vector1< core::Size > const &movable_scs, bool faster)
void	apply (LigandConformer &lig)
	main apply function More...
void	set_pharmacophore_reference (core::pose::Pose const &pose)
	setup pharmacophore info from receptor More...
core::Size	estimate_nstruct_sample (core::pose::Pose const &pose, utility::vector1< core::Size > const &ligids, core::Size const ntotal)
	gets estimate of n-pharmacophore-search considering problem complexity More...
void	set_target (ConstraintInfo const &tgt_in)
void	set_sf (GridScorerOP sf_in)
void	set_trans_step (core::Size trans_step_in)
void	set_rot_step (core::Size rot_step_in)
void	set_chi_step (core::Size chi_step_in)
void	set_use_pharmacophore (bool setting)
bool	use_pharmacophore () const
void	refine_input (bool setting)
void	prealigned_input (bool setting)
bool	prealigned_input () const
void	set_sample_ring_conformers (bool const setting)
bool	sample_ring_conformers () const
void	select_points (core::pose::Pose const &pose, core::Size const ligid, core::Real skeleton_threshold_const=2.5, core::Size neighborhood_size=27)
utility::vector1< numeric::xyzVector< core::Real > >	points_to_search () const

Private Member Functions
void	set_constraints (core::pose::Pose &pose, utility::vector1< core::Size > ligids, utility::vector1< std::pair< core::Size, core::Size > > &marked_pairs, core::Real const w_prior=1.0, utility::vector1< core::Size > const &SrcPriorIDs=utility::vector1< core::Size >(), utility::vector1< core::Size > const &TgtPriorIDs=utility::vector1< core::Size >())
	set constraints to target More...
void	set_hard_constraint_on_marked (core::pose::Pose &pose, utility::vector1< core::Size > ligid, utility::vector1< std::pair< core::Size, core::Size > > const &marked_pairs) const
	set stronger constraints on specific constraint set pairs More...
void	randomize_lig (core::pose::Pose &pose, utility::vector1< core::Size > ligid, numeric::xyzVector< core::Real > const &T)
	randomize ligand about a new center 'T' More...
void	perturb_lig (core::pose::Pose &pose, utility::vector1< core::Size > ligid)
	perturb ligand More...
bool	check_voxel_distance_to_receptor (numeric::xyzVector< core::Real > voxel, core::pose::Pose const &pose, core::Size const ligid)
utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > >	erode_points (utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > selected_points, core::Size neighborhood_size=27)
std::map< core::Size, numeric::xyzVector< core::Real > >	assign_neighbors (numeric::xyzVector< core::Real > point, core::Size neighborhood_size=27)
bool	is_point_in_search_group (utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > selected_points, numeric::xyzVector< core::Real > point_to_compare)
utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > >	find_biggest_skeleton (utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > eroded_points)
bool	is_point_in_network (numeric::xyzVector< core::Real > point, utility::vector1< utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > > networks)
utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > >	find_network (numeric::xyzVector< core::Real > start_point, utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > network, utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > eroded_points)

Private Attributes
ConstraintInfo	target_
GridScorerOP	sf_
utility::vector1< core::Size >	movable_scs_
bool	refine_input_
bool	prealigned_input_
core::Real	trans_step_
core::Real	rot_step_
core::Real	chi_step_
utility::vector1< utility::vector1< core::Real > >	weighted_score_ij_
core::Size	istruct_
bool	use_pharmacophore_
bool	faster_
bool	sample_ring_conformers_ = true
	Should ring conformers be sampled? Default true. More...
utility::vector1< numeric::xyzVector< core::Real > >	points_to_search_
core::Size	gridStep_ = 1

Detailed Description

Aligns ligand using defined constraint information.

Performs ligand alignments using constraints derived from

• reference ligand pose coords or
• receptor pharmacophore info Constraint info should be properly provided in order to run this instance

Constructor & Destructor Documentation

LigandAligner() [1/2]

protocols::ligand_docking::ga_ligand_dock::LigandAligner::LigandAligner

(

)

LigandAligner() [2/2]

protocols::ligand_docking::ga_ligand_dock::LigandAligner::LigandAligner	(	bool	use_pharmacophore,
		utility::vector1< core::Size > const &	movable_scs,
		bool	faster
	)

Member Function Documentation

apply()

void protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply

(

LigandConformer &

lig

)

main apply function

References protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::align_to_current_phore_match(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::coord(), core::scoring::coordinate_constraint, core::optimization::MinimizerMap::copy_dofs_from_pose(), core::optimization::MinimizerMap::copy_dofs_to_pose(), core::scoring::ScoreFunctionFactory::create_score_function(), core::pack::interaction_graph::debug, core::pose::Pose::dump_pdb(), core::sequence::end, faster_, protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_jumpid(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::has_density_map(), istruct_, protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_ids(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::map_phores(), core::optimization::MinimizerOptions::max_iter(), movable_scs_, core::optimization::MinimizerMap::nangles(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::natoms(), perturb_lig(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::phores(), prealigned_input_, randomize_lig(), refine_input_, core::optimization::MinimizerMap::reset_jump_rb_deltas(), core::optimization::Minimizer::run(), sample_ring_conformers_, protocols::hybridization::score, protocols::ligand_docking::ga_ligand_dock::LigandConformer::score(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::select_phore_match(), set_constraints(), set_hard_constraint_on_marked(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_sample_ring_conformers(), core::optimization::MinimizerMap::setup(), sf_, protocols::loops::start, target_, protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_minipose(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_pose(), core::id::to_string(), protocols::ligand_docking::ga_ligand_dock::TR(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf_from_minipose(), and use_pharmacophore().

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures().

assign_neighbors()

std::map< core::Size, numeric::xyzVector< core::Real > > protocols::ligand_docking::ga_ligand_dock::LigandAligner::assign_neighbors ( numeric::xyzVector< core::Real >  point, core::Size  neighborhood_size = 27  )

private

References protocols::ligand_docking::ga_ligand_dock::TR().

Referenced by erode_points().

check_voxel_distance_to_receptor()

bool protocols::ligand_docking::ga_ligand_dock::LigandAligner::check_voxel_distance_to_receptor ( numeric::xyzVector< core::Real >  voxel, core::pose::Pose const &  pose, core::Size const  ligid  )

private

References core::kinematics::distance(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by select_points().

erode_points()

utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > protocols::ligand_docking::ga_ligand_dock::LigandAligner::erode_points ( utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > >  selected_points, core::Size  neighborhood_size = 27  )

private

References assign_neighbors(), core::scoring::electron_density::getDensityMap(), core::scoring::electron_density::ElectronDensity::idx2cart(), is_point_in_search_group(), core::sequence::left, core::id::to_string(), and protocols::ligand_docking::ga_ligand_dock::TR().

Referenced by select_points().

estimate_nstruct_sample()

core::Size protocols::ligand_docking::ga_ligand_dock::LigandAligner::estimate_nstruct_sample	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	ligids,
		core::Size const	ntotal
	)

gets estimate of n-pharmacophore-search considering problem complexity

References protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::map_phores(), protocols::mean_field::min(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::n_phore_match(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::phores(), target_, protocols::ligand_docking::ga_ligand_dock::TR(), and use_pharmacophore_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures().

find_biggest_skeleton()

utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > protocols::ligand_docking::ga_ligand_dock::LigandAligner::find_biggest_skeleton ( utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > >  eroded_points )

private

References find_network(), core::scoring::electron_density::getDensityMap(), core::scoring::electron_density::ElectronDensity::idx2cart(), is_point_in_network(), core::sequence::left, core::id::to_string(), and protocols::ligand_docking::ga_ligand_dock::TR().

Referenced by select_points().

find_network()

utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > protocols::ligand_docking::ga_ligand_dock::LigandAligner::find_network ( numeric::xyzVector< core::Real >  start_point, utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > >  network, utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > >  eroded_points  )

private

References core::kinematics::distance().

Referenced by find_biggest_skeleton().

is_point_in_network()

bool protocols::ligand_docking::ga_ligand_dock::LigandAligner::is_point_in_network ( numeric::xyzVector< core::Real >  point, utility::vector1< utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > >  networks  )

private

Referenced by find_biggest_skeleton().

is_point_in_search_group()

bool protocols::ligand_docking::ga_ligand_dock::LigandAligner::is_point_in_search_group ( utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > >  selected_points, numeric::xyzVector< core::Real >  point_to_compare  )

private

Referenced by erode_points().

perturb_lig()

void protocols::ligand_docking::ga_ligand_dock::LigandAligner::perturb_lig ( core::pose::Pose &  pose, utility::vector1< core::Size >  ligid  )

private

perturb ligand

References core::chemical::ResidueType::bond_type(), core::pose::Pose::chi(), core::chemical::ResidueType::chi_atoms(), chi_step_, core::chemical::DoubleBond, core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nchi(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue_type(), core::scoring::rg, rot_step_, core::pose::Pose::set_chi(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_xyz(), trans_step_, and core::pose::Pose::xyz().

Referenced by apply().

points_to_search()

utility::vector1< numeric::xyzVector< core::Real > > protocols::ligand_docking::ga_ligand_dock::LigandAligner::points_to_search ( ) const

inline

References points_to_search_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures().

prealigned_input() [1/2]

bool protocols::ligand_docking::ga_ligand_dock::LigandAligner::prealigned_input ( ) const

inline

References prealigned_input_.

prealigned_input() [2/2]

void protocols::ligand_docking::ga_ligand_dock::LigandAligner::prealigned_input ( bool  setting )

inline

References prealigned_input_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures().

randomize_lig()

void protocols::ligand_docking::ga_ligand_dock::LigandAligner::randomize_lig ( core::pose::Pose &  pose, utility::vector1< core::Size >  ligid, numeric::xyzVector< core::Real > const &  T  )

private

randomize ligand about a new center 'T'

References core::chemical::ResidueType::bond_type(), core::chemical::ResidueType::chi_atoms(), core::chemical::DoubleBond, core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nchi(), core::scoring::motif::random_rotation(), core::pose::Pose::residue_type(), core::scoring::rg, core::pose::Pose::set_chi(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_xyz(), trans_step_, and core::pose::Pose::xyz().

Referenced by apply().

refine_input()

void protocols::ligand_docking::ga_ligand_dock::LigandAligner::refine_input ( bool  setting )

inline

References refine_input_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::setup_ligand_aligner().

sample_ring_conformers()

bool protocols::ligand_docking::ga_ligand_dock::LigandAligner::sample_ring_conformers ( ) const

inline

References sample_ring_conformers_.

select_points()

void protocols::ligand_docking::ga_ligand_dock::LigandAligner::select_points	(	core::pose::Pose const &	pose,
		core::Size const	ligid,
		core::Real	skeleton_threshold_const = 2.5,
		core::Size	neighborhood_size = 27
	)

References check_voxel_distance_to_receptor(), erode_points(), find_biggest_skeleton(), core::scoring::electron_density::ElectronDensity::get_data(), core::scoring::electron_density::ElectronDensity::get_voxel_volume(), core::scoring::electron_density::getDensityMap(), gridStep_, core::scoring::electron_density::ElectronDensity::idx2cart(), core::sequence::left, core::conformation::Residue::nheavyatoms(), points_to_search_, core::pose::Pose::residue(), core::id::to_string(), protocols::ligand_docking::ga_ligand_dock::TR(), and core::conformation::Residue::xyz().

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::setup_ligand_aligner().

set_chi_step()

void protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_chi_step ( core::Size  chi_step_in )

inline

References chi_step_.

set_constraints()

void protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_constraints ( core::pose::Pose &  pose, utility::vector1< core::Size >  ligids, utility::vector1< std::pair< core::Size, core::Size > > &  marked_pairs, core::Real const  w_prior = 1.0, utility::vector1< core::Size > const &  SrcPriorIDs = utility::vector1< core::Size >(), utility::vector1< core::Size > const &  TgtPriorIDs = utility::vector1< core::Size >()  )

private

set constraints to target

References protocols::ligand_docking::ga_ligand_dock::AtomProperties::ambiguity(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::atomid(), core::pose::Pose::constraint_set(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::coord(), core::pose::Pose::fold_tree(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::limit(), protocols::ligand_docking::ga_ligand_dock::AtomProperties::match(), protocols::mean_field::max(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::natoms(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::polar_scale(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::properties(), core::kinematics::FoldTree::root(), target_, use_pharmacophore(), and protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::weight().

Referenced by apply().

set_hard_constraint_on_marked()

void protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_hard_constraint_on_marked ( core::pose::Pose &  pose, utility::vector1< core::Size >  ligid, utility::vector1< std::pair< core::Size, core::Size > > const &  marked_pairs  ) const

private

set stronger constraints on specific constraint set pairs

References protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::atomid(), core::pose::Pose::constraint_set(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::coord(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::root(), target_, and use_pharmacophore().

Referenced by apply().

set_pharmacophore_reference()

void protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_pharmacophore_reference

(

core::pose::Pose const &

pose

)

setup pharmacophore info from receptor

References faster_, sf_, and target_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::setup_ligand_aligner().

set_rot_step()

void protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_rot_step ( core::Size  rot_step_in )

inline

References rot_step_.

set_sample_ring_conformers()

void protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_sample_ring_conformers ( bool const  setting )

inline

References sample_ring_conformers_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::setup_ligand_aligner().

set_sf()

void protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_sf ( GridScorerOP  sf_in )

inline

References sf_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::setup_ligand_aligner().

set_target()

void protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_target ( ConstraintInfo const &  tgt_in )

inline

References target_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures().

set_trans_step()

void protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_trans_step ( core::Size  trans_step_in )

inline

References trans_step_.

set_use_pharmacophore()

void protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_use_pharmacophore ( bool  setting )

inline

References use_pharmacophore_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures().

use_pharmacophore()

bool protocols::ligand_docking::ga_ligand_dock::LigandAligner::use_pharmacophore ( ) const

inline

References use_pharmacophore_.

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

Member Data Documentation

chi_step_

core::Real protocols::ligand_docking::ga_ligand_dock::LigandAligner::chi_step_

private

Referenced by perturb_lig(), and set_chi_step().

faster_

bool protocols::ligand_docking::ga_ligand_dock::LigandAligner::faster_

private

Referenced by apply(), and set_pharmacophore_reference().

gridStep_

core::Size protocols::ligand_docking::ga_ligand_dock::LigandAligner::gridStep_ = 1

private

Referenced by select_points().

istruct_

core::Size protocols::ligand_docking::ga_ligand_dock::LigandAligner::istruct_

private

Referenced by apply().

movable_scs_

utility::vector1< core::Size > protocols::ligand_docking::ga_ligand_dock::LigandAligner::movable_scs_

private

Referenced by apply().

points_to_search_

utility::vector1< numeric::xyzVector< core::Real > > protocols::ligand_docking::ga_ligand_dock::LigandAligner::points_to_search_

private

Referenced by points_to_search(), and select_points().

prealigned_input_

bool protocols::ligand_docking::ga_ligand_dock::LigandAligner::prealigned_input_

private

Referenced by apply(), and prealigned_input().

refine_input_

bool protocols::ligand_docking::ga_ligand_dock::LigandAligner::refine_input_

private

Referenced by apply(), and refine_input().

rot_step_

core::Real protocols::ligand_docking::ga_ligand_dock::LigandAligner::rot_step_

private

Referenced by perturb_lig(), and set_rot_step().

sample_ring_conformers_

bool protocols::ligand_docking::ga_ligand_dock::LigandAligner::sample_ring_conformers_ = true

private

Should ring conformers be sampled? Default true.

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

Referenced by apply(), sample_ring_conformers(), and set_sample_ring_conformers().

sf_

GridScorerOP protocols::ligand_docking::ga_ligand_dock::LigandAligner::sf_

private

Referenced by apply(), set_pharmacophore_reference(), and set_sf().

target_

ConstraintInfo protocols::ligand_docking::ga_ligand_dock::LigandAligner::target_

private

Referenced by apply(), estimate_nstruct_sample(), set_constraints(), set_hard_constraint_on_marked(), set_pharmacophore_reference(), and set_target().

trans_step_

core::Real protocols::ligand_docking::ga_ligand_dock::LigandAligner::trans_step_

private

Referenced by perturb_lig(), randomize_lig(), and set_trans_step().

use_pharmacophore_

bool protocols::ligand_docking::ga_ligand_dock::LigandAligner::use_pharmacophore_

private

Referenced by estimate_nstruct_sample(), set_use_pharmacophore(), and use_pharmacophore().

weighted_score_ij_

utility::vector1< utility::vector1< core::Real > > protocols::ligand_docking::ga_ligand_dock::LigandAligner::weighted_score_ij_

private

---

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