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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::conformation::Residue const &ligand, 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)
 

Private Member Functions

void set_constraints (core::pose::Pose &pose, core::Size ligid, 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, core::Size const 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, core::Size ligid, numeric::xyzVector< core::Real > const &T)
 randomize ligand about a new center 'T' More...
 
void perturb_lig (core::pose::Pose &pose, core::Size ligid)
 perturb ligand More...
 

Private Attributes

ConstraintInfo target_
 
GridScorerOP sf_
 
utility::vector1< core::Sizemovable_scs_
 
bool refine_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_
 

Detailed Description

Aligns ligand using defined constraint information.

Performs ligand alignments using constraints derived from

Constructor & Destructor Documentation

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

Member Function Documentation

void protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply ( LigandConformer lig)

main apply function

References 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_, istruct_, protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_id(), 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(), randomize_lig(), refine_input_, core::optimization::MinimizerMap::reset_jump_rb_deltas(), core::optimization::Minimizer::run(), protocols::hybridization::score, protocols::ligand_docking::ga_ligand_dock::LigandConformer::score(), set_constraints(), set_hard_constraint_on_marked(), 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().

core::Size protocols::ligand_docking::ga_ligand_dock::LigandAligner::estimate_nstruct_sample ( core::conformation::Residue const &  ligand,
core::Size const  ntotal 
)
void protocols::ligand_docking::ga_ligand_dock::LigandAligner::perturb_lig ( core::pose::Pose pose,
core::Size  ligid 
)
private
void protocols::ligand_docking::ga_ligand_dock::LigandAligner::randomize_lig ( core::pose::Pose pose,
core::Size  ligid,
numeric::xyzVector< core::Real > const &  T 
)
private
void protocols::ligand_docking::ga_ligand_dock::LigandAligner::refine_input ( bool  setting)
inline
void protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_chi_step ( core::Size  chi_step_in)
inline

References chi_step_.

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

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

References rot_step_.

void protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_sf ( GridScorerOP  sf_in)
inline
void protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_target ( ConstraintInfo const &  tgt_in)
inline
void protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_trans_step ( core::Size  trans_step_in)
inline

References trans_step_.

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

References use_pharmacophore_.

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

Member Data Documentation

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

Referenced by perturb_lig(), and set_chi_step().

bool protocols::ligand_docking::ga_ligand_dock::LigandAligner::faster_
private
core::Size protocols::ligand_docking::ga_ligand_dock::LigandAligner::istruct_
private

Referenced by apply().

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

Referenced by apply().

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

Referenced by apply(), and refine_input().

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

Referenced by perturb_lig(), and set_rot_step().

GridScorerOP protocols::ligand_docking::ga_ligand_dock::LigandAligner::sf_
private
ConstraintInfo protocols::ligand_docking::ga_ligand_dock::LigandAligner::target_
private
core::Real protocols::ligand_docking::ga_ligand_dock::LigandAligner::trans_step_
private
bool protocols::ligand_docking::ga_ligand_dock::LigandAligner::use_pharmacophore_
private
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: