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protocols::ligand_docking::ga_ligand_dock::Pharmacophore Class Reference

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::Sizeatms () const
 
utility::vector1< AtomPropertiesprops () 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::Sizeatms_
 
utility::vector1< AtomPropertiesprops_
 
utility::vector1
< utility::vector1< core::Real > > 
dist_
 
utility::vector1< core::Sizemap_index_
 
numeric::xyzVector< core::Realcom_
 
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 
)

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
numeric::xyzVector< core::Real > const& protocols::ligand_docking::ga_ligand_dock::Pharmacophore::com ( ) const
inline
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
bool protocols::ligand_docking::ga_ligand_dock::Pharmacophore::has ( core::Size  i) const
inline
std::string protocols::ligand_docking::ga_ligand_dock::Pharmacophore::index ( ) const
inline
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
core::Size protocols::ligand_docking::ga_ligand_dock::Pharmacophore::size ( ) const
inline
void protocols::ligand_docking::ga_ligand_dock::Pharmacophore::update_com ( utility::vector1< numeric::xyzVector< core::Real > > const &  coords)

Member Data Documentation

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

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