Forcefield Class Reference

#include <forcefield.hh>

Public Types
typedef std::vector< std::pair < String, String > >	AtomRenamingType
Public Member Functions
	Forcefield ()
void	Save (const String &filename)
BuildingBlockPtr	GetBuildingBlock (const String &name) const
BlockModifierPtr	GetBlockModifier (const String &modifier_name) const
String	GetAtomType (const String &res_name, const String &atom_name) const
HydrogenConstructorPtr	GetHydrogenConstructor (const String &name) const
BlockModifierPtr	GetNTerModifier (const String &res_name, const String &ter_name="") const
BlockModifierPtr	GetCTerModifier (const String &res_name, const String &ter_name="") const
InteractionPtr	GetBond (const String &type1, const String &type2) const
InteractionPtr	GetAngle (const String &type1, const String &type2, const String &type3) const
std::vector< InteractionPtr >	GetDihedrals (const String &type1, const String &type2, const String &type3, const String &type4) const
std::vector< InteractionPtr >	GetImpropers (const String &type1, const String &type2, const String &type3, const String &type4) const
InteractionPtr	GetCMap (const String &type1, const String &type2, const String &type3, const String &type4, const String &type5) const
InteractionPtr	GetImplicitGenborn (const String &type1) const
InteractionPtr	GetLJ (const String &type1, const String &type2, bool pair=false) const
InteractionPtr	GetLJ (const String &type) const
InteractionPtr	GetConstraint (const String &type1, const String &type2)
Real	GetMass (const String &type) const
Real	GetFudgeLJ () const
Real	GetFudgeQQ () const
void	AddBuildingBlock (const String &name, BuildingBlockPtr p)
void	AddBond (InteractionPtr p)
void	AddAngle (InteractionPtr p)
void	AddDihedral (InteractionPtr p)
void	AddImproper (InteractionPtr p)
void	AddCMap (InteractionPtr p)
void	AddImplicitGenborn (InteractionPtr p)
void	AddLJ (InteractionPtr p)
void	AddLJPair (InteractionPtr p)
void	AddConstraint (InteractionPtr p)
void	AddMass (const String &type, Real mass)
void	SetFudgeLJ (Real f_lj)
void	SetFudgeQQ (Real f_qq)
void	SetGenPairs (bool gen_pairs)
void	AddResidueRenamingRule (const String &name, const String &ff_main_name, const String &ff_n_ter_name, const String &ff_c_ter_name, const String &ff_two_ter_name)
void	AddAtomRenamingRule (const String &res_name, const String &old_atom_name, const String &new_atom_name)
String	GetResidueRenamingMain (const String &name) const
String	GetResidueRenamingNTer (const String &name) const
String	GetResidueRenamingCTer (const String &name) const
String	GetResidueRenamingTwoTer (const String &name) const
String	GetAtomRenaming (const String &res_name, const String &atom_name) const
void	AddHydrogenConstructor (const String &residue_name, HydrogenConstructorPtr p)
void	AddBlockModifier (const String &modifier_name, BlockModifierPtr p)
void	SetStandardCTer (const String &res_name, const String &ter_name)
void	SetStandardNTer (const String &res_name, const String &ter_name)
void	AssignFFSpecificNames (ost::mol::EntityHandle &handle, bool reverse=false) const
bool	HasAtomRenamingRules (const String &res_name) const
const AtomRenamingType &	GetAtomRenamingRules (const String &res_name) const
Static Public Member Functions
static ForcefieldPtr	Load (const String &filename)

Detailed Description

Definition at line 70 of file forcefield.hh.

Member Typedef Documentation

typedef std::vector<std::pair<String,String> > AtomRenamingType

Definition at line 203 of file forcefield.hh.

Constructor & Destructor Documentation

Forcefield ( ) [inline]

Definition at line 73 of file forcefield.hh.

Member Function Documentation

void AddAngle ( InteractionPtr p )

void AddAtomRenamingRule	(	const String &	res_name,
		const String &	old_atom_name,
		const String &	new_atom_name
	)

void AddBlockModifier	(	const String &	modifier_name,
		BlockModifierPtr	p
	)			`[inline]`

Definition at line 187 of file forcefield.hh.

void AddBond ( InteractionPtr p )

void AddBuildingBlock	(	const String &	name,
		BuildingBlockPtr	p
	)			`[inline]`

Definition at line 135 of file forcefield.hh.

void AddCMap ( InteractionPtr p )

void AddConstraint ( InteractionPtr p )

void AddDihedral ( InteractionPtr p )

void AddHydrogenConstructor	(	const String &	residue_name,
		HydrogenConstructorPtr	p
	)			`[inline]`

Definition at line 183 of file forcefield.hh.

void AddImplicitGenborn ( InteractionPtr p )

void AddImproper ( InteractionPtr p )

void AddLJ ( InteractionPtr p )

void AddLJPair ( InteractionPtr p )

void AddMass	(	const String &	type,
		Real	mass
	)			`[inline]`

Definition at line 155 of file forcefield.hh.

void AddResidueRenamingRule	(	const String &	name,
		const String &	ff_main_name,
		const String &	ff_n_ter_name,
		const String &	ff_c_ter_name,
		const String &	ff_two_ter_name
	)

void AssignFFSpecificNames	(	ost::mol::EntityHandle &	handle,
		bool	reverse = `false`
	)			const

InteractionPtr GetAngle	(	const String &	type1,
		const String &	type2,
		const String &	type3
	)			const

String GetAtomRenaming	(	const String &	res_name,
		const String &	atom_name
	)			const

const AtomRenamingType& GetAtomRenamingRules ( const String & res_name ) const

String GetAtomType	(	const String &	res_name,
		const String &	atom_name
	)			const

BlockModifierPtr GetBlockModifier ( const String & modifier_name ) const

InteractionPtr GetBond	(	const String &	type1,
		const String &	type2
	)			const

BuildingBlockPtr GetBuildingBlock ( const String & name ) const

InteractionPtr GetCMap	(	const String &	type1,
		const String &	type2,
		const String &	type3,
		const String &	type4,
		const String &	type5
	)			const

InteractionPtr GetConstraint	(	const String &	type1,
		const String &	type2
	)

BlockModifierPtr GetCTerModifier	(	const String &	res_name,
		const String &	ter_name = `""`
	)			const

std::vector<InteractionPtr> GetDihedrals	(	const String &	type1,
		const String &	type2,
		const String &	type3,
		const String &	type4
	)			const

Real GetFudgeLJ ( ) const [inline]

Definition at line 129 of file forcefield.hh.

Real GetFudgeQQ ( ) const [inline]

Definition at line 131 of file forcefield.hh.

HydrogenConstructorPtr GetHydrogenConstructor ( const String & name ) const

InteractionPtr GetImplicitGenborn ( const String & type1 ) const

std::vector<InteractionPtr> GetImpropers	(	const String &	type1,
		const String &	type2,
		const String &	type3,
		const String &	type4
	)			const

InteractionPtr GetLJ ( const String & type ) const

InteractionPtr GetLJ	(	const String &	type1,
		const String &	type2,
		bool	pair = `false`
	)			const

Real GetMass ( const String & type ) const

BlockModifierPtr GetNTerModifier	(	const String &	res_name,
		const String &	ter_name = `""`
	)			const

String GetResidueRenamingCTer ( const String & name ) const

String GetResidueRenamingMain ( const String & name ) const

String GetResidueRenamingNTer ( const String & name ) const

String GetResidueRenamingTwoTer ( const String & name ) const

bool HasAtomRenamingRules ( const String & res_name ) const [inline]

Definition at line 199 of file forcefield.hh.

static ForcefieldPtr Load ( const String & filename ) [static]

void Save ( const String & filename )

void SetFudgeLJ ( Real f_lj ) [inline]

Definition at line 157 of file forcefield.hh.

void SetFudgeQQ ( Real f_qq ) [inline]

Definition at line 159 of file forcefield.hh.

void SetGenPairs ( bool gen_pairs ) [inline]

Definition at line 161 of file forcefield.hh.

void SetStandardCTer	(	const String &	res_name,
		const String &	ter_name
	)			`[inline]`

Definition at line 190 of file forcefield.hh.

void SetStandardNTer	(	const String &	res_name,
		const String &	ter_name
	)			`[inline]`

Definition at line 192 of file forcefield.hh.

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

stage/include/ost/mol/mm/forcefield.hh

Forcefield Class Reference

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation