Pharmacophore (aka binding-motif) definition. More...

#include <LigandAligner.hh>

Public Member Functions
	Pharmacophore ()

	Pharmacophore (utility::vector1< core::Size > atmno, utility::vector1< AtomProperties > const &p, utility::vector1< utility::vector1< core::Real > > const &Dmtrx, utility::vector1< numeric::xyzVector< core::Real > > const &coords)

core::Size	size () const

utility::vector1< core::Size >	atms () const

utility::vector1< AtomProperties >	props () const

utility::vector1 < utility::vector1< core::Real > >	dist () const

core::Real	dist (core::Size i, core::Size j) const

core::Size	atm (core::Size i) const

bool	is_polarH (core::Size i) const

bool	is_acceptor (core::Size i) const

bool	is_donor (core::Size i) const

bool	has (core::Size i) const

std::string	index () const

numeric::xyzVector< core::Real > const &	com () const

void	update_com (utility::vector1< numeric::xyzVector< core::Real > > const &coords)

std::string	show () const

bool	is_close (utility::vector1< core::Real > const &Dcol, core::Real dcut) const
	whether j is close to all own members (Dcol == Dmtrx[j]) More...

core::Real	find_type_matches (Pharmacophore const &other, bool const just_count=false) const
	find matches with proper types (e.g. acceptor - donor) More...

core::Real	match (Pharmacophore const &other, utility::vector1< core::Size > const &map_index, core::Real const unmatch_score) const
	find matches with the partner pharmacophore provided More...

void	set_map_index (utility::vector1< core::Size > map_index)

utility::vector1< core::Size > const &	map_index () const

Private Attributes
utility::vector1< core::Size >	atms_

utility::vector1< AtomProperties >	props_

utility::vector1 < utility::vector1< core::Real > >	dist_

utility::vector1< core::Size >	map_index_

numeric::xyzVector< core::Real >	com_

std::string	index_

Detailed Description

Pharmacophore (aka binding-motif) definition.

Stores collection of atom properties and their clustering info

Constructor & Destructor Documentation

protocols::ligand_docking::ga_ligand_dock::Pharmacophore::Pharmacophore ( )

References atms_, com_, dist_, index_, and props_.

protocols::ligand_docking::ga_ligand_dock::Pharmacophore::Pharmacophore	(	utility::vector1< core::Size >	atmno,
		utility::vector1< AtomProperties > const &	p,
		utility::vector1< utility::vector1< core::Real > > const &	Dmtrx,
		utility::vector1< numeric::xyzVector< core::Real > > const &	coords
	)

References atms_, com_, protocols::simple_filters::coords(), dist_, index_, props_, and core::id::to_string().

Member Function Documentation

core::Size protocols::ligand_docking::ga_ligand_dock::Pharmacophore::atm ( core::Size i ) const

inline

utility::vector1< core::Size > protocols::ligand_docking::ga_ligand_dock::Pharmacophore::atms ( ) const

inline

Referenced by protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::align_to_current_phore_match(), and protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_all_ligand_phores().

numeric::xyzVector< core::Real > const& protocols::ligand_docking::ga_ligand_dock::Pharmacophore::com ( ) const

inline

Referenced by protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::align_to_current_phore_match(), and protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::phore_overlaps_with_existing().

utility::vector1< utility::vector1< core::Real > > protocols::ligand_docking::ga_ligand_dock::Pharmacophore::dist ( ) const

inline

Referenced by match().

core::Real protocols::ligand_docking::ga_ligand_dock::Pharmacophore::dist	(	core::Size	i,
		core::Size	j
	)		const

inline

core::Real protocols::ligand_docking::ga_ligand_dock::Pharmacophore::find_type_matches	(	Pharmacophore const &	other,
		bool const	just_count = `false`
	)		const

find matches with proper types (e.g. acceptor - donor)

References is_acceptor(), is_polarH(), protocols::mean_field::min(), props(), props_, protocols::hybridization::score, and size().

Referenced by protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::map_phores(), and protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::phore_overlaps_with_existing().

bool protocols::ligand_docking::ga_ligand_dock::Pharmacophore::has ( core::Size i ) const

inline

Referenced by protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_all_ligand_phores().

std::string protocols::ligand_docking::ga_ligand_dock::Pharmacophore::index ( ) const

inline

Referenced by protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::select_phore_match().

bool protocols::ligand_docking::ga_ligand_dock::Pharmacophore::is_acceptor ( core::Size i ) const

inline

Referenced by find_type_matches(), and match().

bool protocols::ligand_docking::ga_ligand_dock::Pharmacophore::is_close	(	utility::vector1< core::Real > const &	Dcol,
		core::Real	dcut
	)		const

whether j is close to all own members (Dcol == Dmtrx[j])

References atms_.

Referenced by protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_all_ligand_phores().

bool protocols::ligand_docking::ga_ligand_dock::Pharmacophore::is_donor ( core::Size i ) const

inline

bool protocols::ligand_docking::ga_ligand_dock::Pharmacophore::is_polarH ( core::Size i ) const

inline

Referenced by find_type_matches(), and match().

utility::vector1< core::Size > const& protocols::ligand_docking::ga_ligand_dock::Pharmacophore::map_index ( ) const

inline

core::Real protocols::ligand_docking::ga_ligand_dock::Pharmacophore::match	(	Pharmacophore const &	other,
		utility::vector1< core::Size > const &	map_index,
		core::Real const	unmatch_score
	)		const

find matches with the partner pharmacophore provided

References dist(), is_acceptor(), is_polarH(), protocols::mean_field::min(), protocols::hybridization::score, and size().

utility::vector1< AtomProperties > protocols::ligand_docking::ga_ligand_dock::Pharmacophore::props ( ) const

inline

Referenced by find_type_matches().

void protocols::ligand_docking::ga_ligand_dock::Pharmacophore::set_map_index ( utility::vector1< core::Size > map_index )

inline

std::string protocols::ligand_docking::ga_ligand_dock::Pharmacophore::show ( ) const

References atms_, and props_.

Referenced by protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::map_phores(), and protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::select_phore_match().

core::Size protocols::ligand_docking::ga_ligand_dock::Pharmacophore::size ( ) const

inline

Referenced by find_type_matches(), match(), and protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::phore_overlaps_with_existing().

void protocols::ligand_docking::ga_ligand_dock::Pharmacophore::update_com ( utility::vector1< numeric::xyzVector< core::Real > > const & coords )

References atms_, com_, and protocols::simple_filters::coords().

Referenced by protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::align_to_current_phore_match().

Member Data Documentation

utility::vector1< core::Size > protocols::ligand_docking::ga_ligand_dock::Pharmacophore::atms_

private

Referenced by is_close(), Pharmacophore(), show(), and update_com().

numeric::xyzVector< core::Real > protocols::ligand_docking::ga_ligand_dock::Pharmacophore::com_

private

Referenced by Pharmacophore(), and update_com().

utility::vector1< utility::vector1< core::Real > > protocols::ligand_docking::ga_ligand_dock::Pharmacophore::dist_

private

Referenced by Pharmacophore().

std::string protocols::ligand_docking::ga_ligand_dock::Pharmacophore::index_

private

Referenced by Pharmacophore().

utility::vector1< core::Size > protocols::ligand_docking::ga_ligand_dock::Pharmacophore::map_index_

private

utility::vector1< AtomProperties > protocols::ligand_docking::ga_ligand_dock::Pharmacophore::props_

private

Referenced by find_type_matches(), Pharmacophore(), and show().

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

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation