BuildingBlock Class Reference

#include <buildingblock.hh>

Public Member Functions
	BuildingBlock ()
	BuildingBlock (const BuildingBlock &block)
bool	Match (const ost::mol::ResidueHandle &handle, bool match_connectivity, String &info) const
void	Connect (ost::mol::ResidueHandle &handle, ost::mol::XCSEditor &ed)
std::vector< String >	GetAtoms () const
std::vector< String >	GetTypes () const
std::vector< Real >	GetCharges () const
std::vector< Real >	GetMasses () const
String	GetType (const String &name) const
Real	GetCharge (const String &name) const
Real	GetMass (const String &name) const
std::vector< InteractionPtr >	GetBonds () const
std::vector< InteractionPtr >	GetAngles () const
std::vector< InteractionPtr >	GetDihedrals () const
std::vector< InteractionPtr >	GetImpropers () const
std::vector< InteractionPtr >	GetCMaps () const
std::vector< InteractionPtr >	GetExclusions () const
std::vector< InteractionPtr >	GetConstraints () const
void	AddAtom (const String &name, const String &type, Real charge, Real mass=std::numeric_limits< Real >::quiet_NaN())
void	AddBond (InteractionPtr p, bool replace_existing=false)
void	AddAngle (InteractionPtr p, bool replace_existing=false)
void	AddDihedral (InteractionPtr p, bool replace_existing=false)
void	AddImproper (InteractionPtr p, bool replace_existing=false)
void	AddExclusion (InteractionPtr p, bool replace_existing=false)
void	AddCMap (InteractionPtr p, bool replace_existing=false)
void	AddConstraint (InteractionPtr p, bool replace_existing=false)
void	RemoveAtom (const String &name)
void	ReplaceAtom (const String &name, const String &new_name, const String &new_type, Real new_charge, Real new_mass=std::numeric_limits< Real >::quiet_NaN())
void	RemoveInteractionsToPrev ()
void	RemoveInteractionsToNext ()
template<typename DS >
void	Serialize (DS &ds)

Detailed Description

Definition at line 43 of file buildingblock.hh.

Constructor & Destructor Documentation

BuildingBlock ( )

inline

Definition at line 45 of file buildingblock.hh.

BuildingBlock

(

const BuildingBlock &

block

)

Member Function Documentation

void AddAngle	(	InteractionPtr	p,
		bool	replace_existing = false
	)

void AddAtom	(	const String &	name,
		const String &	type,
		Real	charge,
		Real	mass = std::numeric_limits< Real >::quiet_NaN()
	)

void AddBond	(	InteractionPtr	p,
		bool	replace_existing = false
	)

void AddCMap	(	InteractionPtr	p,
		bool	replace_existing = false
	)

void AddConstraint	(	InteractionPtr	p,
		bool	replace_existing = false
	)

void AddDihedral	(	InteractionPtr	p,
		bool	replace_existing = false
	)

void AddExclusion	(	InteractionPtr	p,
		bool	replace_existing = false
	)

void AddImproper	(	InteractionPtr	p,
		bool	replace_existing = false
	)

void Connect	(	ost::mol::ResidueHandle &	handle,
		ost::mol::XCSEditor &	ed
	)

std::vector<InteractionPtr> GetAngles ( ) const

inline

Definition at line 73 of file buildingblock.hh.

std::vector<String> GetAtoms ( ) const

inline

Definition at line 57 of file buildingblock.hh.

std::vector<InteractionPtr> GetBonds ( ) const

inline

Definition at line 71 of file buildingblock.hh.

Real GetCharge

(

const String &

name

)

const

std::vector<Real> GetCharges ( ) const

inline

Definition at line 61 of file buildingblock.hh.

std::vector<InteractionPtr> GetCMaps ( ) const

inline

Definition at line 79 of file buildingblock.hh.

std::vector<InteractionPtr> GetConstraints ( ) const

inline

Definition at line 83 of file buildingblock.hh.

std::vector<InteractionPtr> GetDihedrals ( ) const

inline

Definition at line 75 of file buildingblock.hh.

std::vector<InteractionPtr> GetExclusions ( ) const

inline

Definition at line 81 of file buildingblock.hh.

std::vector<InteractionPtr> GetImpropers ( ) const

inline

Definition at line 77 of file buildingblock.hh.

Real GetMass

(

const String &

name

)

const

std::vector<Real> GetMasses ( ) const

inline

Definition at line 63 of file buildingblock.hh.

String GetType

(

const String &

name

)

const

std::vector<String> GetTypes ( ) const

inline

Definition at line 59 of file buildingblock.hh.

bool Match	(	const ost::mol::ResidueHandle &	handle,
		bool	match_connectivity,
		String &	info
	)		const

void RemoveAtom

(

const String &

name

)

void RemoveInteractionsToNext

(

)

void RemoveInteractionsToPrev

(

)

void ReplaceAtom	(	const String &	name,
		const String &	new_name,
		const String &	new_type,
		Real	new_charge,
		Real	new_mass = std::numeric_limits< Real >::quiet_NaN()
	)

void Serialize ( DS &  ds )

inline

Definition at line 120 of file buildingblock.hh.

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

• stage/include/ost/mol/mm/buildingblock.hh