protocols::ligand_docking::ga_ligand_dock::MCSAligner Class Reference

#include <MCSAligner.hh>

Public Member Functions
	MCSAligner (core::pose::Pose const &reference_pose, core::Size reference_ligres_idx, MCSAlignerOptions &options)
void	set_options (MCSAlignerOptions const &options)
	set MCSAligner options More...
void	apply (LigandConformer &lig)
	main apply function More...
void	align_pose (core::pose::Pose const &template_pose, core::pose::Pose &ligand_pose, std::map< core::Size, core::Size > const &pair_indices_map, core::Size const &template_idx, core::Size const &ligand_idx)
void	set_torsion_and_align (core::pose::Pose const &template_pose, core::pose::Pose &ligand_pose, std::map< core::Size, core::Size > const &pair_indices_map, core::Size const &template_idx, core::Size const &ligand_idx)
utility::vector1< bool > const &	torsion_in_align () 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...

Private Attributes
core::pose::Pose const &	reference_pose_
core::Size	reference_ligres_idx_
MCSAlignerOptions	options_
bool	perturb_rb_
bool	perturb_torsion_
utility::vector1< bool >	torsion_in_align_

Constructor & Destructor Documentation

MCSAligner()

protocols::ligand_docking::ga_ligand_dock::MCSAligner::MCSAligner	(	core::pose::Pose const &	reference_pose,
		core::Size	reference_ligres_idx,
		MCSAlignerOptions &	options
	)

References set_options().

Member Function Documentation

align_pose()

void protocols::ligand_docking::ga_ligand_dock::MCSAligner::align_pose	(	core::pose::Pose const &	template_pose,
		core::pose::Pose &	ligand_pose,
		std::map< core::Size, core::Size > const &	pair_indices_map,
		core::Size const &	template_idx,
		core::Size const &	ligand_idx
	)

References core::pose::Pose::dump_pdb(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::set_xyz(), protocols::ligand_docking::ga_ligand_dock::TR(), and core::conformation::Residue::xyz().

Referenced by set_torsion_and_align().

apply()

void protocols::ligand_docking::ga_ligand_dock::MCSAligner::apply

(

LigandConformer &

lig

)

main apply function

References core::chemical::MutableResidueType::atom_index(), core::chemical::MutableResidueType::atom_name(), core::chemical::AtomRefMapping< FromRef, ToRef >::begin(), core::chemical::AtomRefMapping< FromRef, ToRef >::end(), core::chemical::rdkit::find_mapping(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_ref_pose(), core::chemical::rdkit::RestypeToRDMol::index_to_vd(), protocols::sewing::data_storage::ligand, protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_ids(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_residue(), core::chemical::rdkit::RestypeToRDMol::Mol(), options_, protocols::ligand_docking::ga_ligand_dock::perturb_ligand_rb(), protocols::ligand_docking::ga_ligand_dock::perturb_ligand_torsions(), protocols::ligand_docking::ga_ligand_dock::MCSAlignerOptions::perturb_rb, protocols::ligand_docking::ga_ligand_dock::MCSAlignerOptions::perturb_rb_rotation, protocols::ligand_docking::ga_ligand_dock::MCSAlignerOptions::perturb_rb_translation, protocols::ligand_docking::ga_ligand_dock::MCSAlignerOptions::perturb_torsion, protocols::ligand_docking::ga_ligand_dock::MCSAlignerOptions::perturb_torsion_rotation, reference_ligres_idx_, reference_pose_, core::pose::Pose::residue(), protocols::ligand_docking::ga_ligand_dock::MCSAlignerOptions::restype_to_rdmol_options, set_torsion_and_align(), core::chemical::AtomRefMapping< FromRef, ToRef >::show(), core::pose::Pose::size(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_pose(), torsion_in_align_, protocols::ligand_docking::ga_ligand_dock::TR(), core::conformation::Residue::type(), and protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf().

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

set_constraints()

void protocols::ligand_docking::ga_ligand_dock::MCSAligner::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

set_options()

void protocols::ligand_docking::ga_ligand_dock::MCSAligner::set_options ( MCSAlignerOptions const &  options )

inline

set MCSAligner options

References options_.

Referenced by MCSAligner().

set_torsion_and_align()

void protocols::ligand_docking::ga_ligand_dock::MCSAligner::set_torsion_and_align	(	core::pose::Pose const &	template_pose,
		core::pose::Pose &	ligand_pose,
		std::map< core::Size, core::Size > const &	pair_indices_map,
		core::Size const &	template_idx,
		core::Size const &	ligand_idx
	)

References align_pose(), core::conformation::Residue::chi(), core::conformation::Residue::chi_atoms(), core::pose::Pose::dump_pdb(), core::conformation::Residue::nchi(), core::pose::Pose::residue(), core::pose::Pose::set_chi(), torsion_in_align_, protocols::ligand_docking::ga_ligand_dock::TR(), and core::conformation::Residue::xyz().

Referenced by apply().

torsion_in_align()

utility::vector1<bool> const& protocols::ligand_docking::ga_ligand_dock::MCSAligner::torsion_in_align ( ) const

inline

References torsion_in_align_.

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

Member Data Documentation

options_

MCSAlignerOptions protocols::ligand_docking::ga_ligand_dock::MCSAligner::options_

private

Referenced by apply(), and set_options().

perturb_rb_

bool protocols::ligand_docking::ga_ligand_dock::MCSAligner::perturb_rb_

private

perturb_torsion_

bool protocols::ligand_docking::ga_ligand_dock::MCSAligner::perturb_torsion_

private

reference_ligres_idx_

core::Size protocols::ligand_docking::ga_ligand_dock::MCSAligner::reference_ligres_idx_

private

Referenced by apply().

reference_pose_

core::pose::Pose const& protocols::ligand_docking::ga_ligand_dock::MCSAligner::reference_pose_

private

Referenced by apply().

torsion_in_align_

utility::vector1<bool> protocols::ligand_docking::ga_ligand_dock::MCSAligner::torsion_in_align_

private

Referenced by apply(), set_torsion_and_align(), and torsion_in_align().

---

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

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