OpenMD::MoleculeStamp Class Reference

Inheritance diagram for OpenMD::MoleculeStamp:

Public Member Functions
bool	addAtomStamp (AtomStamp *atom)
bool	addBondStamp (BondStamp *bond)
bool	addBendStamp (BendStamp *bend)
bool	addTorsionStamp (TorsionStamp *torsion)
bool	addInversionStamp (InversionStamp *inversion)
bool	addRigidBodyStamp (RigidBodyStamp *rigidbody)
bool	addCutoffGroupStamp (CutoffGroupStamp *cutoffgroup)
bool	addFragmentStamp (FragmentStamp *fragment)
bool	addConstraintStamp (ConstraintStamp *constraint)
void	setIdent (int id)
int	getIdent ()
void	setRegion (int r)
int	getRegion ()
std::size_t	getNAtoms ()
std::size_t	getNBonds ()
std::size_t	getNBends ()
std::size_t	getNTorsions ()
std::size_t	getNInversions ()
std::size_t	getNRigidBodies ()
std::size_t	getNCutoffGroups ()
std::size_t	getNConstraints ()
int	getNIntegrable ()
std::size_t	getNFreeAtoms ()
virtual void	validate ()
AtomStamp *	getAtomStamp (int index)
BondStamp *	getBondStamp (int index)
BendStamp *	getBendStamp (int index)
TorsionStamp *	getTorsionStamp (int index)
InversionStamp *	getInversionStamp (int index)
RigidBodyStamp *	getRigidBodyStamp (int index)
CutoffGroupStamp *	getCutoffGroupStamp (int index)
FragmentStamp *	getFragmentStamp (int index)
ConstraintStamp *	getConstraintStamp (int index)
bool	isBondInSameRigidBody (BondStamp *bond)
bool	isAtomInRigidBody (int atomIndex)
bool	isAtomInRigidBody (int atomIndex, int &whichRigidBody, int &consAtomIndex)
std::vector< std::pair< int, int > >	getJointAtoms (int rb1, int rb2)
Public Member Functions inherited from OpenMD::DataHolder
template<class T>
void	assign (const std::string &keyword, T val)

Additional Inherited Members
Protected Types inherited from OpenMD::DataHolder
using	ParamMap = std::map<std::string, ParameterBase*>
Protected Attributes inherited from OpenMD::DataHolder
ParamMap	parameters_
std::set< std::string >	deprecatedKeywords_

Detailed Description

Definition at line 65 of file MoleculeStamp.hpp.

Constructor & Destructor Documentation

MoleculeStamp()

OpenMD::MoleculeStamp::MoleculeStamp

(

)

Definition at line 69 of file MoleculeStamp.cpp.

~MoleculeStamp()

OpenMD::MoleculeStamp::~MoleculeStamp ( )

virtual

Definition at line 82 of file MoleculeStamp.cpp.

Member Function Documentation

addAtomStamp()

bool OpenMD::MoleculeStamp::addAtomStamp

(

AtomStamp *

atom

)

Definition at line 94 of file MoleculeStamp.cpp.

addBendStamp()

bool OpenMD::MoleculeStamp::addBendStamp

(

BendStamp *

bend

)

Definition at line 111 of file MoleculeStamp.cpp.

addBondStamp()

bool OpenMD::MoleculeStamp::addBondStamp

(

BondStamp *

bond

)

Definition at line 106 of file MoleculeStamp.cpp.

addConstraintStamp()

bool OpenMD::MoleculeStamp::addConstraintStamp

(

ConstraintStamp *

constraint

)

Definition at line 147 of file MoleculeStamp.cpp.

addCutoffGroupStamp()

bool OpenMD::MoleculeStamp::addCutoffGroupStamp

(

CutoffGroupStamp *

cutoffgroup

)

Definition at line 138 of file MoleculeStamp.cpp.

addFragmentStamp()

bool OpenMD::MoleculeStamp::addFragmentStamp

(

FragmentStamp *

fragment

)

Definition at line 143 of file MoleculeStamp.cpp.

addInversionStamp()

bool OpenMD::MoleculeStamp::addInversionStamp

(

InversionStamp *

inversion

)

Definition at line 121 of file MoleculeStamp.cpp.

addRigidBodyStamp()

bool OpenMD::MoleculeStamp::addRigidBodyStamp

(

RigidBodyStamp *

rigidbody

)

Definition at line 126 of file MoleculeStamp.cpp.

addTorsionStamp()

bool OpenMD::MoleculeStamp::addTorsionStamp

(

TorsionStamp *

torsion

)

Definition at line 116 of file MoleculeStamp.cpp.

getAtomStamp()

AtomStamp * OpenMD::MoleculeStamp::getAtomStamp ( int index )

inline

Definition at line 101 of file MoleculeStamp.hpp.

getBendStamp()

BendStamp * OpenMD::MoleculeStamp::getBendStamp ( int index )

inline

Definition at line 103 of file MoleculeStamp.hpp.

getBondStamp()

BondStamp * OpenMD::MoleculeStamp::getBondStamp ( int index )

inline

Definition at line 102 of file MoleculeStamp.hpp.

getConstraintStamp()

ConstraintStamp * OpenMD::MoleculeStamp::getConstraintStamp ( int index )

inline

Definition at line 117 of file MoleculeStamp.hpp.

getCutoffGroupStamp()

CutoffGroupStamp * OpenMD::MoleculeStamp::getCutoffGroupStamp ( int index )

inline

Definition at line 111 of file MoleculeStamp.hpp.

getFragmentStamp()

FragmentStamp * OpenMD::MoleculeStamp::getFragmentStamp ( int index )

inline

Definition at line 114 of file MoleculeStamp.hpp.

getIdent()

int OpenMD::MoleculeStamp::getIdent ( )

inline

Definition at line 84 of file MoleculeStamp.hpp.

getInversionStamp()

InversionStamp * OpenMD::MoleculeStamp::getInversionStamp ( int index )

inline

Definition at line 105 of file MoleculeStamp.hpp.

getJointAtoms()

std::vector< std::pair< int, int > > OpenMD::MoleculeStamp::getJointAtoms	(	int	rb1,
		int	rb2 )

Definition at line 896 of file MoleculeStamp.cpp.

getNAtoms()

std::size_t OpenMD::MoleculeStamp::getNAtoms ( )

inline

Definition at line 89 of file MoleculeStamp.hpp.

getNBends()

std::size_t OpenMD::MoleculeStamp::getNBends ( )

inline

Definition at line 91 of file MoleculeStamp.hpp.

getNBonds()

std::size_t OpenMD::MoleculeStamp::getNBonds ( )

inline

Definition at line 90 of file MoleculeStamp.hpp.

getNConstraints()

std::size_t OpenMD::MoleculeStamp::getNConstraints ( )

inline

Definition at line 96 of file MoleculeStamp.hpp.

getNCutoffGroups()

std::size_t OpenMD::MoleculeStamp::getNCutoffGroups ( )

inline

Definition at line 95 of file MoleculeStamp.hpp.

getNFreeAtoms()

std::size_t OpenMD::MoleculeStamp::getNFreeAtoms ( )

inline

Definition at line 98 of file MoleculeStamp.hpp.

getNIntegrable()

int OpenMD::MoleculeStamp::getNIntegrable ( )

inline

Definition at line 97 of file MoleculeStamp.hpp.

getNInversions()

std::size_t OpenMD::MoleculeStamp::getNInversions ( )

inline

Definition at line 93 of file MoleculeStamp.hpp.

getNRigidBodies()

std::size_t OpenMD::MoleculeStamp::getNRigidBodies ( )

inline

Definition at line 94 of file MoleculeStamp.hpp.

getNTorsions()

std::size_t OpenMD::MoleculeStamp::getNTorsions ( )

inline

Definition at line 92 of file MoleculeStamp.hpp.

getRegion()

int OpenMD::MoleculeStamp::getRegion ( )

inline

Definition at line 87 of file MoleculeStamp.hpp.

getRigidBodyStamp()

RigidBodyStamp * OpenMD::MoleculeStamp::getRigidBodyStamp ( int index )

inline

Definition at line 108 of file MoleculeStamp.hpp.

getTorsionStamp()

TorsionStamp * OpenMD::MoleculeStamp::getTorsionStamp ( int index )

inline

Definition at line 104 of file MoleculeStamp.hpp.

isAtomInRigidBody() [1/2]

bool OpenMD::MoleculeStamp::isAtomInRigidBody

(

int

atomIndex

)

Definition at line 860 of file MoleculeStamp.cpp.

isAtomInRigidBody() [2/2]

bool OpenMD::MoleculeStamp::isAtomInRigidBody	(	int	atomIndex,
		int &	whichRigidBody,
		int &	consAtomIndex )

Definition at line 871 of file MoleculeStamp.cpp.

isBondInSameRigidBody()

bool OpenMD::MoleculeStamp::isBondInSameRigidBody

(

BondStamp *

bond

)

Definition at line 841 of file MoleculeStamp.cpp.

setIdent()

void OpenMD::MoleculeStamp::setIdent ( int id )

inline

Definition at line 83 of file MoleculeStamp.hpp.

setRegion()

void OpenMD::MoleculeStamp::setRegion ( int r )

inline

Definition at line 86 of file MoleculeStamp.hpp.

validate()

void OpenMD::MoleculeStamp::validate ( )

virtual

Reimplemented from OpenMD::DataHolder.

Definition at line 152 of file MoleculeStamp.cpp.

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

• types/MoleculeStamp.hpp
• types/MoleculeStamp.cpp