OpenStructure: GromacsBlockModifier Class Reference

OpenStructure

#include <gromacs_block_modifiers.hh>

Inherits 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)

Public Member Functions inherited from BlockModifier
	BlockModifier ()

virtual	~BlockModifier ()

Detailed Description

Definition at line 123 of file gromacs_block_modifiers.hh.

Constructor & Destructor Documentation

◆ GromacsBlockModifier()

GromacsBlockModifier ( )

inline

Definition at line 127 of file gromacs_block_modifiers.hh.

Member Function Documentation

◆ AddAddRule()

void AddAddRule	(	int	number,
		int	method,
		const std::vector< String > &	atom_names,
		const std::vector< String > &	anchors,
		const String &	type,
		Real	charge
	)

◆ AddAngle()

void AddAngle ( InteractionPtr p )

inline

Definition at line 144 of file gromacs_block_modifiers.hh.

◆ AddBond()

void AddBond ( InteractionPtr p )

inline

Definition at line 141 of file gromacs_block_modifiers.hh.

◆ AddCMap()

void AddCMap ( InteractionPtr p )

inline

Definition at line 153 of file gromacs_block_modifiers.hh.

◆ AddDeleteAtom()

void AddDeleteAtom ( const String & atom_name )

inline

Definition at line 156 of file gromacs_block_modifiers.hh.

◆ AddDihedral()

void AddDihedral ( InteractionPtr p )

inline

Definition at line 147 of file gromacs_block_modifiers.hh.

◆ AddImproper()

void AddImproper ( InteractionPtr p )

inline

Definition at line 150 of file gromacs_block_modifiers.hh.

◆ AddReplaceRule()

void AddReplaceRule	(	const String &	name,
		const String &	new_name,
		const String &	new_type,
		Real	new_charge
	)

◆ ApplyOnBuildingBlock()

virtual void ApplyOnBuildingBlock ( BuildingBlockPtr p )

virtual

Implements BlockModifier.

◆ ApplyOnResidue()

virtual void ApplyOnResidue	(	ost::mol::ResidueHandle &	res,
		ost::mol::XCSEditor &	ed
	)

virtual

Implements BlockModifier.

◆ GetAddRuleAnchors()

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

inline

Definition at line 186 of file gromacs_block_modifiers.hh.

◆ GetAddRuleCharge()

Real GetAddRuleCharge ( uint idx ) const

inline

Definition at line 188 of file gromacs_block_modifiers.hh.

◆ GetAddRuleMethod()

int GetAddRuleMethod ( uint idx ) const

inline

Definition at line 182 of file gromacs_block_modifiers.hh.

◆ GetAddRuleNames()

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

inline

Definition at line 184 of file gromacs_block_modifiers.hh.

◆ GetAddRuleNumber()

int GetAddRuleNumber ( uint idx ) const

inline

Definition at line 181 of file gromacs_block_modifiers.hh.

◆ GetAddRuleType()

const String& GetAddRuleType ( uint idx ) const

inline

Definition at line 187 of file gromacs_block_modifiers.hh.

◆ GetAngles()

const std::vector<InteractionPtr>& GetAngles ( ) const

inline

Definition at line 160 of file gromacs_block_modifiers.hh.

◆ GetBlockModifierType()

virtual BlockModifierType GetBlockModifierType ( )

inlinevirtual

Implements BlockModifier.

Definition at line 192 of file gromacs_block_modifiers.hh.

◆ GetBonds()

const std::vector<InteractionPtr>& GetBonds ( ) const

inline

Definition at line 159 of file gromacs_block_modifiers.hh.

◆ GetCmaps()

const std::vector<InteractionPtr>& GetCmaps ( ) const

inline

Definition at line 163 of file gromacs_block_modifiers.hh.

◆ GetDeleteAtoms()

const std::vector<String>& GetDeleteAtoms ( ) const

inline

Definition at line 164 of file gromacs_block_modifiers.hh.

◆ GetDihedrals()

const std::vector<InteractionPtr>& GetDihedrals ( ) const

inline

Definition at line 161 of file gromacs_block_modifiers.hh.

◆ GetImpropers()

const std::vector<InteractionPtr>& GetImpropers ( ) const

inline

Definition at line 162 of file gromacs_block_modifiers.hh.

◆ GetNumAddRules()

uint GetNumAddRules ( ) const

inline

Definition at line 180 of file gromacs_block_modifiers.hh.

◆ GetNumReplaceRules()

uint GetNumReplaceRules ( ) const

inline

Definition at line 166 of file gromacs_block_modifiers.hh.

◆ GetReplaceRuleName()

const String& GetReplaceRuleName ( uint idx ) const

inline

Definition at line 167 of file gromacs_block_modifiers.hh.

◆ GetReplaceRuleNewCharge()

Real GetReplaceRuleNewCharge ( uint idx ) const

inline

Definition at line 176 of file gromacs_block_modifiers.hh.

◆ GetReplaceRuleNewName()

const String& GetReplaceRuleNewName ( uint idx ) const

inline

Definition at line 170 of file gromacs_block_modifiers.hh.

◆ GetReplaceRuleNewType()

const String& GetReplaceRuleNewType ( uint idx ) const

inline

Definition at line 173 of file gromacs_block_modifiers.hh.

◆ OnSave()

virtual void OnSave ( ost::io::BinaryDataSink & ds )

inlinevirtual

Implements BlockModifier.

Definition at line 190 of file gromacs_block_modifiers.hh.

◆ Serialize()

void Serialize ( DS & ds )

inline

Definition at line 195 of file gromacs_block_modifiers.hh.

The documentation for this class was generated from the following file:

build-2.9.1/stage/include/ost/mol/mm/gromacs_block_modifiers.hh