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< StringGetBuildingBlockNames () 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< InteractionPtrGetDihedrals (const String &type1, const String &type2, const String &type3, const String &type4) const
std::vector< InteractionPtrGetImpropers (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 AtomRenamingTypeGetAtomRenamingRules (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 205 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 189 of file forcefield.hh.

void AddBond ( InteractionPtr  p  ) 
void AddBuildingBlock ( const String name,
BuildingBlockPtr  p 
) [inline]

Definition at line 137 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 185 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 157 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
std::vector<String> GetBuildingBlockNames (  )  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 131 of file forcefield.hh.

Real GetFudgeQQ (  )  const [inline]

Definition at line 133 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 201 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 159 of file forcefield.hh.

void SetFudgeQQ ( Real  f_qq  )  [inline]

Definition at line 161 of file forcefield.hh.

void SetGenPairs ( bool  gen_pairs  )  [inline]

Definition at line 163 of file forcefield.hh.

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

Definition at line 192 of file forcefield.hh.

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

Definition at line 194 of file forcefield.hh.


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