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 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)

---

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

• stage/include/ost/mol/mm/gromacs_block_modifiers.hh