#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) |
Definition at line 70 of file forcefield.hh.
typedef std::vector<std::pair<String,String> > AtomRenamingType |
Definition at line 205 of file forcefield.hh.
Forcefield | ( | ) | [inline] |
Definition at line 73 of file forcefield.hh.
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 | ) |
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 |
const AtomRenamingType& GetAtomRenamingRules | ( | const String & | res_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 |
BlockModifierPtr GetNTerModifier | ( | const String & | res_name, | |
const String & | ter_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.
Definition at line 192 of file forcefield.hh.
Definition at line 194 of file forcefield.hh.