protocols::pockets::SmallMol Class Reference

#include <GenPharmacophore.hh>

Public Member Functions
	SmallMol ()
	SmallMol (const SmallMol &other)
	SmallMol (SmallMol &&)=default
SmallMol &	operator= (SmallMol &&)=default
SmallMol &	operator= (SmallMol const &rhs)
	~SmallMol ()
void	add_atom (std::string line)
void	update_center ()
void	set_name (std::string name)
std::string	get_name ()
int	numberOfAtoms () const
std::vector< std::vector< core::Real > > const &	get_coordinates ()
void	printCoordinates () const
void	printContent () const
std::string	getContent () const
core::Real	get_rmsd ()
core::Real	get_center (int c)
core::Real	cal_distance (SmallMol *other)
core::Real	cal_min_dist (SmallMol *other)
bool	operator< (const SmallMol &other) const
SmallMol *	findRoot ()
bool	connected (SmallMol *m)
void	connect (SmallMol *m)
int	get_size ()
void	set_size (int t)
SmallMol *	get_parent ()
void	set_parent (SmallMol *p)
SmallMol *	get_root ()
bool	get_visited ()
void	set_visited (bool v)

Static Public Member Functions
static core::Real	calRMSD (SmallMol &mol1, SmallMol &mol2)

Private Member Functions
std::vector< std::string >	tokenize_connected (std::vector< std::string > &fields)

Private Attributes
std::string	molName
std::string	pdbContent
std::vector< std::vector< core::Real > >	coordinates
core::Real	rmsd
std::vector< core::Real >	cen
int	s
SmallMol *	parent
bool	visited

Constructor & Destructor Documentation

SmallMol() [1/3]

protocols::pockets::SmallMol::SmallMol ( )

inline

SmallMol() [2/3]

protocols::pockets::SmallMol::SmallMol

(

const SmallMol &

other

)

SmallMol() [3/3]

protocols::pockets::SmallMol::SmallMol ( SmallMol &&  )

default

~SmallMol()

protocols::pockets::SmallMol::~SmallMol ( )

default

Member Function Documentation

add_atom()

void protocols::pockets::SmallMol::add_atom

(

std::string

line

)

Referenced by protocols::pockets::GenPharmacophore::cluster_KeyFeatures().

cal_distance()

core::Real protocols::pockets::SmallMol::cal_distance

(

SmallMol *

other

)

References get_center().

cal_min_dist()

core::Real protocols::pockets::SmallMol::cal_min_dist

(

SmallMol *

other

)

References protocols::pockets::calDist(), and get_coordinates().

Referenced by protocols::pockets::UnionEdge::UnionEdge().

calRMSD()

core::Real protocols::pockets::SmallMol::calRMSD ( SmallMol &  mol1, SmallMol &  mol2  )

static

References protocols::pockets::calDist(), coordinates, and rmsd.

connect()

void protocols::pockets::SmallMol::connect

(

SmallMol *

m

)

References findRoot(), get_size(), set_parent(), and set_size().

connected()

bool protocols::pockets::SmallMol::connected

(

SmallMol *

m

)

References findRoot().

findRoot()

SmallMol * protocols::pockets::SmallMol::findRoot

(

)

References protocols::hybridization::u.

Referenced by connect(), connected(), and get_root().

get_center()

core::Real protocols::pockets::SmallMol::get_center

(

int

c

)

Referenced by cal_distance().

get_coordinates()

std::vector< std::vector<core::Real> > const& protocols::pockets::SmallMol::get_coordinates ( )

inline

References coordinates.

Referenced by cal_min_dist().

get_name()

std::string protocols::pockets::SmallMol::get_name ( )

inline

References molName.

get_parent()

SmallMol* protocols::pockets::SmallMol::get_parent ( )

inline

References parent.

get_rmsd()

core::Real protocols::pockets::SmallMol::get_rmsd ( )

inline

References rmsd.

get_root()

SmallMol* protocols::pockets::SmallMol::get_root ( )

inline

References findRoot().

Referenced by protocols::pockets::GenPharmacophore::cluster_KeyFeatures().

get_size()

int protocols::pockets::SmallMol::get_size ( )

inline

References s.

Referenced by connect().

get_visited()

bool protocols::pockets::SmallMol::get_visited ( )

inline

References visited.

getContent()

string protocols::pockets::SmallMol::getContent

(

)

const

numberOfAtoms()

int protocols::pockets::SmallMol::numberOfAtoms ( ) const

inline

References coordinates.

operator<()

bool protocols::pockets::SmallMol::operator< ( const SmallMol &  other ) const

inline

References rmsd.

operator=() [1/2]

SmallMol& protocols::pockets::SmallMol::operator= ( SmallMol &&  )

default

operator=() [2/2]

SmallMol& protocols::pockets::SmallMol::operator= ( SmallMol const &  rhs )

inline

References core::id::swap().

printContent()

void protocols::pockets::SmallMol::printContent

(

)

const

printCoordinates()

void protocols::pockets::SmallMol::printCoordinates

(

)

const

set_name()

void protocols::pockets::SmallMol::set_name ( std::string  name )

inline

References molName.

Referenced by protocols::pockets::GenPharmacophore::cluster_KeyFeatures().

set_parent()

void protocols::pockets::SmallMol::set_parent ( SmallMol *  p )

inline

References parent.

Referenced by connect().

set_size()

void protocols::pockets::SmallMol::set_size ( int  t )

inline

References s, and protocols::hybridization::t.

Referenced by connect().

set_visited()

void protocols::pockets::SmallMol::set_visited ( bool  v )

inline

References visited.

tokenize_connected()

std::vector<std::string> protocols::pockets::SmallMol::tokenize_connected ( std::vector< std::string > &  fields )

private

update_center()

void protocols::pockets::SmallMol::update_center

(

)

Member Data Documentation

cen

std::vector<core::Real> protocols::pockets::SmallMol::cen

private

coordinates

std::vector< std::vector<core::Real> > protocols::pockets::SmallMol::coordinates

private

Referenced by calRMSD(), get_coordinates(), and numberOfAtoms().

molName

std::string protocols::pockets::SmallMol::molName

private

Referenced by get_name(), and set_name().

parent

SmallMol* protocols::pockets::SmallMol::parent

private

Referenced by get_parent(), and set_parent().

pdbContent

std::string protocols::pockets::SmallMol::pdbContent

private

rmsd

core::Real protocols::pockets::SmallMol::rmsd

private

Referenced by calRMSD(), get_rmsd(), and operator<().

s

int protocols::pockets::SmallMol::s

private

Referenced by get_size(), and set_size().

visited

bool protocols::pockets::SmallMol::visited

private

Referenced by get_visited(), and set_visited().

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

• src/protocols/pockets/GenPharmacophore.hh
• src/protocols/pockets/GenPharmacophore.cc