GromacsBlockModifier Class Reference

#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 StringGetReplaceRuleName (uint idx) const
const StringGetReplaceRuleNewName (uint idx) const
const StringGetReplaceRuleNewType (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 StringGetAddRuleType (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)

Detailed Description

Definition at line 123 of file gromacs_block_modifiers.hh.


Constructor & Destructor Documentation

GromacsBlockModifier (  )  [inline]

Definition at line 127 of file gromacs_block_modifiers.hh.


Member Function Documentation

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.

const std::vector<String>& GetAddRuleAnchors ( uint  idx  )  const [inline]

Definition at line 186 of file gromacs_block_modifiers.hh.

Real GetAddRuleCharge ( uint  idx  )  const [inline]

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.

const std::vector<String>& GetAddRuleNames ( uint  idx  )  const [inline]

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.

const String& GetAddRuleType ( uint  idx  )  const [inline]

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.

const String& GetReplaceRuleName ( uint  idx  )  const [inline]

Definition at line 167 of file gromacs_block_modifiers.hh.

Real GetReplaceRuleNewCharge ( uint  idx  )  const [inline]

Definition at line 176 of file gromacs_block_modifiers.hh.

const String& GetReplaceRuleNewName ( uint  idx  )  const [inline]

Definition at line 170 of file gromacs_block_modifiers.hh.

const String& GetReplaceRuleNewType ( uint  idx  )  const [inline]

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.


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