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
std::vector< String >	GetBuildingBlockNames () 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

AtomRenamingType

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

Definition at line 205 of file forcefield.hh.

Constructor & Destructor Documentation

Forcefield()

Forcefield ( )

inline

Definition at line 73 of file forcefield.hh.

Member Function Documentation

AddAngle()

void AddAngle

(

InteractionPtr

p

)

AddAtomRenamingRule()

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

AddBlockModifier()

void AddBlockModifier ( const String &  modifier_name, BlockModifierPtr  p  )

inline

Definition at line 189 of file forcefield.hh.

AddBond()

void AddBond

(

InteractionPtr

p

)

AddBuildingBlock()

void AddBuildingBlock ( const String &  name, BuildingBlockPtr  p  )

inline

Definition at line 137 of file forcefield.hh.

AddCMap()

void AddCMap

(

InteractionPtr

p

)

AddConstraint()

void AddConstraint

(

InteractionPtr

p

)

AddDihedral()

void AddDihedral

(

InteractionPtr

p

)

AddHydrogenConstructor()

void AddHydrogenConstructor ( const String &  residue_name, HydrogenConstructorPtr  p  )

inline

Definition at line 185 of file forcefield.hh.

AddImplicitGenborn()

void AddImplicitGenborn

(

InteractionPtr

p

)

AddImproper()

void AddImproper

(

InteractionPtr

p

)

AddLJ()

void AddLJ

(

InteractionPtr

p

)

AddLJPair()

void AddLJPair

(

InteractionPtr

p

)

AddMass()

void AddMass ( const String &  type, Real  mass  )

inline

Definition at line 157 of file forcefield.hh.

AddResidueRenamingRule()

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
	)

AssignFFSpecificNames()

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

GetAngle()

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

GetAtomRenaming()

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

GetAtomRenamingRules()

const AtomRenamingType & GetAtomRenamingRules

(

const String &

res_name

)

const

GetAtomType()

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

GetBlockModifier()

BlockModifierPtr GetBlockModifier

(

const String &

modifier_name

)

const

GetBond()

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

GetBuildingBlock()

BuildingBlockPtr GetBuildingBlock

(

const String &

name

)

const

GetBuildingBlockNames()

std::vector< String > GetBuildingBlockNames

(

)

const

GetCMap()

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

GetConstraint()

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

GetCTerModifier()

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

GetDihedrals()

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

GetFudgeLJ()

Real GetFudgeLJ ( ) const

inline

Definition at line 131 of file forcefield.hh.

GetFudgeQQ()

Real GetFudgeQQ ( ) const

inline

Definition at line 133 of file forcefield.hh.

GetHydrogenConstructor()

HydrogenConstructorPtr GetHydrogenConstructor

(

const String &

name

)

const

GetImplicitGenborn()

InteractionPtr GetImplicitGenborn

(

const String &

type1

)

const

GetImpropers()

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

GetLJ() [1/2]

InteractionPtr GetLJ

(

const String &

type

)

const

GetLJ() [2/2]

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

GetMass()

Real GetMass

(

const String &

type

)

const

GetNTerModifier()

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

GetResidueRenamingCTer()

String GetResidueRenamingCTer

(

const String &

name

)

const

GetResidueRenamingMain()

String GetResidueRenamingMain

(

const String &

name

)

const

GetResidueRenamingNTer()

String GetResidueRenamingNTer

(

const String &

name

)

const

GetResidueRenamingTwoTer()

String GetResidueRenamingTwoTer

(

const String &

name

)

const

HasAtomRenamingRules()

bool HasAtomRenamingRules ( const String &  res_name ) const

inline

Definition at line 201 of file forcefield.hh.

Load()

static ForcefieldPtr Load ( const String &  filename )

static

Save()

void Save

(

const String &

filename

)

SetFudgeLJ()

void SetFudgeLJ ( Real  f_lj )

inline

Definition at line 159 of file forcefield.hh.

SetFudgeQQ()

void SetFudgeQQ ( Real  f_qq )

inline

Definition at line 161 of file forcefield.hh.

SetGenPairs()

void SetGenPairs ( bool  gen_pairs )

inline

Definition at line 163 of file forcefield.hh.

SetStandardCTer()

void SetStandardCTer ( const String &  res_name, const String &  ter_name  )

inline

Definition at line 192 of file forcefield.hh.

SetStandardNTer()

void SetStandardNTer ( const String &  res_name, const String &  ter_name  )

inline

Definition at line 194 of file forcefield.hh.

---

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

• build-dev/stage/include/ost/mol/mm/forcefield.hh