AliasData Class Reference

Indicate atoms as aliases for larger functional groups. More...

#include <openbabel/alias.h>

Inheritance diagram for AliasData:

List of all members.

Classes
struct	AliasItem
Public Member Functions
	AliasData ()
virtual OBGenericData *	Clone (OBBase *) const
void	SetAlias (const std::string &alias)
void	SetAlias (const char *alias)
std::string	GetAlias (bool rightAligned=false) const
std::string	GetColor () const
void	SetColor (std::string color)
bool	IsExpanded () const
bool	Expand (OBMol &mol, const unsigned int atomindex)
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
Static Public Member Functions
static void	RevertToAliasForm (OBMol &mol)
Protected Attributes
std::string	_alias
std::string	_right_form
std::vector< unsigned long >	_expandedatoms
std::string	_color
std::string	_attr
unsigned int	_type
DataOrigin	_source

---

Detailed Description

Indicate atoms as aliases for larger functional groups.

Since:

version 2.2

An object of this class can be attached to an OBAtom if it is considered to be a placeholder for an alias, such as Ph, COOH, etc.

If the alias has not been interpreted chemically (expanded), the element type of the placeholder atom should be set to Xx so that the molecule is not interpreted incorrectly by formats which do not consider this class.

If the alias has been interpreted chemically (which formats, etc. should normally do immediately), the alias may remain as extra information or as a hint for an alternative representation, for example to a chemical drawing program. The _expandedatoms vector would then contains the ids of the atoms to which the alias is an alternative.

---

Constructor & Destructor Documentation

AliasData

(

)

[inline]

---

Member Function Documentation

virtual OBGenericData* Clone

(

OBBase *

)

const [inline, virtual]

Reimplemented from OBGenericData.

void SetAlias

(

const std::string &

alias )

[inline]

Add an alias.

void SetAlias

(

const char *

alias )

[inline]

std::string GetAlias

(

bool

rightAligned = false )

const

/return value of alias or its version intended to be connected at its right hand end.

Referenced by OBDepict::DrawMolecule().

std::string GetColor

(

)

const [inline]

Return the color which has been assigned to this alias.

Referenced by OBDepict::DrawMolecule().

void SetColor

(

std::string

color )

[inline]

Assign a color to this alias.

bool IsExpanded

(

)

const [inline]

Referenced by OBDepict::DrawMolecule(), and AliasData::RevertToAliasForm().

void RevertToAliasForm

(

OBMol &

mol )

[static]

Converts all the expanded aliases in a molecule to the alias form. Note that this deletes atoms and bonds. Use only as a preparation for display.

bool Expand	(	OBMol &	mol,
		const unsigned int	atomindex
	)

Interprets the alias text and adds atoms as appropriate to mol.

void SetAttribute

(

const std::string &

v )

[inline, inherited]

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

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

void SetOrigin

(

const DataOrigin

s )

[inline, inherited]

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

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

virtual const std::string& GetAttribute

(

)

const [inline, virtual, inherited]

Returns:

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

Referenced by OBMoleculeFormat::MakeCombinedMolecule().

unsigned int GetDataType

(

)

const [inline, inherited]

Returns:

the data type for this object as defined in OBGenericDataType

virtual const std::string& GetValue

(

)

const [inline, virtual, inherited]

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

Reimplemented in OBCommentData, and OBPairData.

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

virtual DataOrigin GetOrigin

(

)

const [inline, virtual, inherited]

---

Member Data Documentation

std::string _alias [protected]

std::string _right_form [protected]

std::vector<unsigned long> _expandedatoms [protected]

std::string _color [protected]

std::string _attr [protected, inherited]

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

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

unsigned int _type [protected, inherited]

attribute type -- declared for each subclass

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

DataOrigin _source [protected, inherited]

source of data for accounting

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

---

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

• alias.h
• alias.cpp