#include <gromacs_block_modifiers.hh>
Inherits ost::mol::mm::BlockModifier.
Public Member Functions | |
GromacsBlockModifier () | |
virtual void | ApplyOnBuildingBlock (BuildingBlockPtr p) |
virtual void | ApplyOnResidue (ost::mol::ResidueHandle &res, ost::mol::XCSEditor &ed) |
void | AddReplaceRule (const String &name, const String &new_name, const String &new_type, Real new_charge) |
void | AddAddRule (int number, int method, const std::vector< String > &atom_names, const std::vector< String > &anchors, const String &type, Real charge) |
void | AddBond (InteractionPtr p) |
void | AddAngle (InteractionPtr p) |
void | AddDihedral (InteractionPtr p) |
void | AddImproper (InteractionPtr p) |
void | AddCMap (InteractionPtr p) |
void | AddDeleteAtom (const String &atom_name) |
const std::vector < InteractionPtr > & | GetBonds () const |
const std::vector < InteractionPtr > & | GetAngles () const |
const std::vector < InteractionPtr > & | GetDihedrals () const |
const std::vector < InteractionPtr > & | GetImpropers () const |
const std::vector < InteractionPtr > & | GetCmaps () const |
const std::vector< String > & | GetDeleteAtoms () const |
uint | GetNumReplaceRules () const |
const String & | GetReplaceRuleName (uint idx) const |
const String & | GetReplaceRuleNewName (uint idx) const |
const String & | GetReplaceRuleNewType (uint idx) const |
Real | GetReplaceRuleNewCharge (uint idx) const |
uint | GetNumAddRules () const |
int | GetAddRuleNumber (uint idx) const |
int | GetAddRuleMethod (uint idx) const |
const std::vector< String > & | GetAddRuleNames (uint idx) const |
const std::vector< String > & | GetAddRuleAnchors (uint idx) const |
const String & | GetAddRuleType (uint idx) const |
Real | GetAddRuleCharge (uint idx) const |
virtual void | OnSave (ost::io::BinaryDataSink &ds) |
virtual BlockModifierType | GetBlockModifierType () |
template<typename DS > | |
void | Serialize (DS &ds) |
Definition at line 123 of file gromacs_block_modifiers.hh.
GromacsBlockModifier | ( | ) | [inline] |
Definition at line 127 of file gromacs_block_modifiers.hh.
void AddAddRule | ( | int | number, | |
int | method, | |||
const std::vector< String > & | atom_names, | |||
const std::vector< String > & | anchors, | |||
const String & | type, | |||
Real | charge | |||
) |
void AddAngle | ( | InteractionPtr | p | ) | [inline] |
Definition at line 144 of file gromacs_block_modifiers.hh.
void AddBond | ( | InteractionPtr | p | ) | [inline] |
Definition at line 141 of file gromacs_block_modifiers.hh.
void AddCMap | ( | InteractionPtr | p | ) | [inline] |
Definition at line 153 of file gromacs_block_modifiers.hh.
void AddDeleteAtom | ( | const String & | atom_name | ) | [inline] |
Definition at line 156 of file gromacs_block_modifiers.hh.
void AddDihedral | ( | InteractionPtr | p | ) | [inline] |
Definition at line 147 of file gromacs_block_modifiers.hh.
void AddImproper | ( | InteractionPtr | p | ) | [inline] |
Definition at line 150 of file gromacs_block_modifiers.hh.
void AddReplaceRule | ( | const String & | name, | |
const String & | new_name, | |||
const String & | new_type, | |||
Real | new_charge | |||
) |
virtual void ApplyOnBuildingBlock | ( | BuildingBlockPtr | p | ) | [virtual] |
Implements BlockModifier.
virtual void ApplyOnResidue | ( | ost::mol::ResidueHandle & | res, | |
ost::mol::XCSEditor & | ed | |||
) | [virtual] |
Implements BlockModifier.
Definition at line 186 of file gromacs_block_modifiers.hh.
Definition at line 188 of file gromacs_block_modifiers.hh.
int GetAddRuleMethod | ( | uint | idx | ) | const [inline] |
Definition at line 182 of file gromacs_block_modifiers.hh.
Definition at line 184 of file gromacs_block_modifiers.hh.
int GetAddRuleNumber | ( | uint | idx | ) | const [inline] |
Definition at line 181 of file gromacs_block_modifiers.hh.
Definition at line 187 of file gromacs_block_modifiers.hh.
const std::vector<InteractionPtr>& GetAngles | ( | ) | const [inline] |
Definition at line 160 of file gromacs_block_modifiers.hh.
virtual BlockModifierType GetBlockModifierType | ( | ) | [inline, virtual] |
Implements BlockModifier.
Definition at line 192 of file gromacs_block_modifiers.hh.
const std::vector<InteractionPtr>& GetBonds | ( | ) | const [inline] |
Definition at line 159 of file gromacs_block_modifiers.hh.
const std::vector<InteractionPtr>& GetCmaps | ( | ) | const [inline] |
Definition at line 163 of file gromacs_block_modifiers.hh.
const std::vector<String>& GetDeleteAtoms | ( | ) | const [inline] |
Definition at line 164 of file gromacs_block_modifiers.hh.
const std::vector<InteractionPtr>& GetDihedrals | ( | ) | const [inline] |
Definition at line 161 of file gromacs_block_modifiers.hh.
const std::vector<InteractionPtr>& GetImpropers | ( | ) | const [inline] |
Definition at line 162 of file gromacs_block_modifiers.hh.
uint GetNumAddRules | ( | ) | const [inline] |
Definition at line 180 of file gromacs_block_modifiers.hh.
uint GetNumReplaceRules | ( | ) | const [inline] |
Definition at line 166 of file gromacs_block_modifiers.hh.
Definition at line 167 of file gromacs_block_modifiers.hh.
Definition at line 176 of file gromacs_block_modifiers.hh.
Definition at line 170 of file gromacs_block_modifiers.hh.
Definition at line 173 of file gromacs_block_modifiers.hh.
virtual void OnSave | ( | ost::io::BinaryDataSink & | ds | ) | [inline, virtual] |
Implements BlockModifier.
Definition at line 190 of file gromacs_block_modifiers.hh.
void Serialize | ( | DS & | ds | ) | [inline] |
Definition at line 195 of file gromacs_block_modifiers.hh.