OpenStructure
Public Types | Public Member Functions | Static Public Member Functions
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:
Generated by doxygen 1.9.1