OBConformerData Class Reference

#include <openbabel/generic.h>

Inheritance diagram for OBConformerData:

Public Member Functions
	OBConformerData ()
	OBConformerData (const OBConformerData &)
virtual OBGenericData *	Clone (OBBase *) const
	~OBConformerData ()
OBConformerData &	operator= (const OBConformerData &)
void	SetDimension (std::vector< unsigned short > vd)
void	SetEnergies (std::vector< double > ve)
void	SetForces (std::vector< std::vector< vector3 > > vf)
void	SetVelocities (std::vector< std::vector< vector3 > > vv)
void	SetDisplacements (std::vector< std::vector< vector3 > > vd)
void	SetData (std::vector< std::string > vdat)
std::vector< unsigned short >	GetDimension ()
std::vector< double >	GetEnergies ()
std::vector< std::vector< vector3 > >	GetForces ()
std::vector< std::vector< vector3 > >	GetVelocities ()
std::vector< std::vector< vector3 > >	GetDisplacements ()
std::vector< std::string >	GetData ()
void	SetAttribute (const std::string &v)
void	SetOrigin (const DataOrigin s)
virtual const std::string &	GetAttribute () const
unsigned int	GetDataType () const
virtual const std::string &	GetValue () const
virtual DataOrigin	GetOrigin () const

Protected Attributes
std::vector< unsigned short >	_vDimension
std::vector< double >	_vEnergies
std::vector< std::vector< vector3 > >	_vForces
std::vector< std::vector< vector3 > >	_vVelocity
std::vector< std::vector< vector3 > >	_vDisplace
std::vector< std::string >	_vData
std::string	_attr
unsigned int	_type
DataOrigin	_source

Detailed Description

Used to hold data on conformers or geometry optimization steps.

Supplements the support for multiple coordinate sets in OBMol, e.g., OBMol::GetConformer()

Constructor & Destructor Documentation

OBConformerData() [1/2]

OBConformerData

(

)

OBConformerData() [2/2]

OBConformerData

(

const OBConformerData &

src

)

~OBConformerData()

~OBConformerData ( )

inline

Member Function Documentation

Clone()

virtual OBGenericData* Clone ( OBBase *  ) const

inlinevirtual

Reimplemented from OBGenericData.

operator=()

OBConformerData & operator=

(

const OBConformerData &

src

)

SetDimension()

void SetDimension ( std::vector< unsigned short >  vd )

inline

SetEnergies()

void SetEnergies ( std::vector< double >  ve )

inline

Referenced by OBForceField::GetConformers(), OBForceField::GetCoordinates(), and OBMol::SetEnergies().

SetForces()

void SetForces ( std::vector< std::vector< vector3 > >  vf )

inline

Referenced by OBForceField::GetCoordinates().

SetVelocities()

void SetVelocities ( std::vector< std::vector< vector3 > >  vv )

inline

SetDisplacements()

void SetDisplacements ( std::vector< std::vector< vector3 > >  vd )

inline

SetData()

void SetData ( std::vector< std::string >  vdat )

inline

GetDimension()

std::vector<unsigned short> GetDimension ( )

inline

GetEnergies()

std::vector<double> GetEnergies ( )

inline

Referenced by OBMol::GetEnergies(), and OBMol::GetEnergy().

GetForces()

std::vector< std::vector< vector3 > > GetForces ( )

inline

GetVelocities()

std::vector< std::vector< vector3 > > GetVelocities ( )

inline

GetDisplacements()

std::vector< std::vector< vector3 > > GetDisplacements ( )

inline

GetData()

std::vector<std::string> GetData ( )

inline

SetAttribute()

void SetAttribute ( const std::string &  v )

inlineinherited

Set the attribute (key), which can be used to retrieve this data.

Referenced by OBGastChrg::AssignPartialCharges(), OpenBabel::ComparePairSecond(), OBMol::DoTransformations(), OBMol::FindLSSR(), OBMol::FindSSSR(), OBForceField::GetAtomTypes(), OBMol::GetFormula(), OBMol::GetLSSR(), OBForceField::GetPartialCharges(), OBMol::GetSSSR(), OBDescriptor::PredictAndSave(), and OBMol::SetFormula().

SetOrigin()

void SetOrigin ( const DataOrigin  s )

inlineinherited

Set the origin of this data, which can be used to filter the data.

Referenced by OBGastChrg::AssignPartialCharges(), OpenBabel::ComparePairSecond(), OBMol::DoTransformations(), OBMol::FindAngles(), OBMol::FindLSSR(), OBMol::FindSSSR(), OBMol::FindTorsions(), OBMol::GetFormula(), OBMol::GetLSSR(), OBMol::GetSSSR(), OBDescriptor::PredictAndSave(), and OBMol::SetFormula().

GetAttribute()

virtual const std::string& GetAttribute ( ) const

inlinevirtualinherited

Returns

The attribute (key), which can be used to retrieve this data

Referenced by OpenBabel::extract_thermochemistry(), and OBMoleculeFormat::MakeCombinedMolecule().

GetDataType()

unsigned int GetDataType ( ) const

inlineinherited

Returns

the data type for this object as defined in OBGenericDataType

GetValue()

virtual const std::string& GetValue ( ) const

inlinevirtualinherited

Base class returns a default value (the attribute type) but should never be called.

Reimplemented in OBPairData, and OBCommentData.

Referenced by OBDepict::AddAtomLabels(), OBDepict::DrawMolecule(), OBDescriptor::FilterCompare(), and OBDescriptor::GetValues().

GetOrigin()

virtual DataOrigin GetOrigin ( ) const

inlinevirtualinherited

Member Data Documentation

_vDimension

std::vector<unsigned short> _vDimension

protected

Dimensionalities of conformers.

Referenced by OBConformerData::operator=().

_vEnergies

std::vector<double> _vEnergies

protected

Relative energies of conformers (preferably in kJ/mol)

Referenced by OBConformerData::operator=().

_vForces

std::vector< std::vector< vector3 > > _vForces

protected

Atomic forces for each conformer.

Referenced by OBConformerData::operator=().

_vVelocity

std::vector< std::vector< vector3 > > _vVelocity

protected

Atomic velocities for each conformer (e.g., trajectories)

Referenced by OBConformerData::operator=().

_vDisplace

std::vector< std::vector< vector3 > > _vDisplace

protected

Atomic displacements for each conformer (e.g., RMS distances)

Referenced by OBConformerData::operator=().

_vData

std::vector<std::string> _vData

protected

Additional data (as strings)

Referenced by OBConformerData::operator=().

_attr

std::string _attr

protectedinherited

attribute tag (e.g., "UnitCell", "Comment" or "Author")

Referenced by OBRotamerList::Clone(), and OBNasaThermoData::OBNasaThermoData().

_type

unsigned int _type

protectedinherited

attribute type – declared for each subclass

Referenced by OBRotamerList::Clone(), and OBNasaThermoData::OBNasaThermoData().

_source

DataOrigin _source

protectedinherited

source of data for accounting

Referenced by OBConformerData::operator=(), OBSymmetryData::operator=(), OBTorsionData::operator=(), and OBAngleData::operator=().

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

• generic.h
• generic.cpp