OBElementTable Class Reference

Periodic Table of the Elements. More...

#include <openbabel/data.h>

Inheritance diagram for OBElementTable:

List of all members.

Public Member Functions
	OBElementTable (void)
	~OBElementTable ()
void	ParseLine (const char *)
unsigned int	GetNumberOfElements ()
size_t	GetSize ()
int	GetAtomicNum (const char *)
int	GetAtomicNum (const char *, int &iso)
int	GetAtomicNum (std::string name, int &iso)
const char *	GetSymbol (int)
double	GetVdwRad (int)
double	GetCovalentRad (int)
double	GetMass (int)
double	CorrectedBondRad (int, int=3)
double	CorrectedVdwRad (int, int=3)
int	GetMaxBonds (int)
double	GetElectroNeg (int)
double	GetAllredRochowElectroNeg (int)
double	GetIonization (int)
double	GetElectronAffinity (int)
std::vector< double >	GetRGB (int)
std::string	GetName (int)
void	Init ()
void	SetReadDirectory (char *dir)
void	SetEnvironmentVariable (char *var)
Protected Attributes
bool	_init
const char *	_dataptr
std::string	_filename
std::string	_dir
std::string	_subdir
std::string	_envvar

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Detailed Description

Periodic Table of the Elements.

Translating element data is a common task given that many file formats give either element symbol or atomic number information, but not both. The OBElementTable class facilitates conversion between textual and numeric element information. An instance of the OBElementTable class (etab) is declared as external in data.cpp. Source files that include the header file mol.h automatically have an extern definition to etab. The following code sample demonstrates the use of the OBElementTable class:

      cout << "The symbol for element 6 is " << etab.GetSymbol(6) << endl;
      cout << "The atomic number for Sulfur is " << etab.GetAtomicNum(16) << endl;
      cout << "The van der Waal radius for Nitrogen is " << etab.GetVdwRad(7);

Stored information in the OBElementTable includes elemental:

• symbols
• covalent radii
• van der Waal radii
• expected maximum bonding valence
• molar mass (by IUPAC recommended atomic masses)
• electronegativity (Pauling and Allred-Rochow)
• ionization potential
• electron affinity
• RGB colors for visualization programs
• names (by IUPAC recommendation)

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Constructor & Destructor Documentation

OBElementTable

(

void

)

~OBElementTable

(

)

---

Member Function Documentation

void ParseLine

(

const char *

)

[virtual]

Specified by particular table classes (parses an individual data line).

Reimplemented from OBGlobalDataBase.

unsigned int GetNumberOfElements

(

)

Returns:

the number of elements in the periodic table

size_t GetSize

(

)

[inline, virtual]

Returns:

the number of elements in the periodic table

Reimplemented from OBGlobalDataBase.

int GetAtomicNum

(

const char *

sym

)

Deprecated:

Does not properly handle 'D' or 'T' hydrogen isotopes

Referenced by AliasData::Expand(), and OBElementTable::GetAtomicNum().

int GetAtomicNum	(	const char *	identifier,
		int &	iso
	)

Returns:

the atomic number matching the element symbol or IUPAC name passed or 0 if not defined. For 'D' or 'T' hydrogen isotopes, will return a value in the second argument

int GetAtomicNum	(	std::string	name,
		int &	iso
	)

Overloads GetAtomicNum(const char *, int &iso).

const char * GetSymbol

(

int

atomicnum

)

Returns:

the element symbol matching the atomic number passed

Referenced by OBDepict::DrawMolecule(), and OBMol::GetSpacedFormula().

double GetVdwRad

(

int

atomicnum

)

Returns:

the van der Waals radius for this atomic number

double GetCovalentRad

(

int

atomicnum

)

Returns:

the covalent radius for this atomic number

Referenced by OBMol::ConnectTheDots().

double GetMass

(

int

atomicnum

)

Returns:

the average atomic mass for this element. For exact isotope masses, use OpenBabel::OBIsotopeTable

Referenced by OBAtom::GetAtomicMass(), and OBMol::GetMolWt().

double CorrectedBondRad	(	int	atomicnum,
		int	hyb = 3
	)

Returns:

a "corrected" bonding radius based on the hybridization. Scales the covalent radius by 0.95 for sp2 and 0.90 for sp hybrids

Referenced by OBMol::AddHydrogens(), OpenBabel::GetCorrectedBondVector(), OBBond::GetEquibLength(), OBAtom::HtoMethyl(), OBMol::PerceiveBondOrders(), and OBAtom::SetHybAndGeom().

double CorrectedVdwRad	(	int	atomicnum,
		int	hyb = 3
	)

Returns:

a "corrected" vdW radius based on the hybridization. Scales the van der Waals radius by 0.95 for sp2 and 0.90 for sp hybrids

int GetMaxBonds

(

int

atomicnum

)

Returns:

the maximum expected number of bonds to this element

Referenced by OBMol::ConnectTheDots(), and OBMol::PerceiveBondOrders().

double GetElectroNeg

(

int

atomicnum

)

Returns:

the Pauling electronegativity for this element

Referenced by OBMol::PerceiveBondOrders().

double GetAllredRochowElectroNeg

(

int

atomicnum

)

Returns:

the Allred-Rochow electronegativity for this element

double GetIonization

(

int

atomicnum

)

Returns:

the ionization potential (in eV) for this element

double GetElectronAffinity

(

int

atomicnum

)

Returns:

the electron affinity (in eV) for this element

vector< double > GetRGB

(

int

atomicnum

)

Returns:

a vector with red, green, blue color values for this element

Referenced by OBDepict::DrawMolecule().

string GetName

(

int

atomicnum

)

Returns:

the name of this element

void Init

(

)

[inherited]

Read in the data file, falling back as needed.

Referenced by OBAromaticTyper::AssignAromaticFlags(), OBResidueData::AssignBonds(), OBBondTyper::AssignFunctionalGroupBonds(), OBAtomTyper::AssignHyb(), OBAtomTyper::AssignImplicitValence(), OBPhModel::AssignSeedPartialCharge(), OBRingTyper::AssignTypes(), OBAtomTyper::AssignTypes(), OBAtomTyper::CorrectAromaticNitrogens(), OBElementTable::CorrectedBondRad(), OBElementTable::CorrectedVdwRad(), OBPhModel::CorrectForPH(), OBElementTable::GetAllredRochowElectroNeg(), OBElementTable::GetAtomicNum(), OBElementTable::GetCovalentRad(), OBElementTable::GetElectronAffinity(), OBElementTable::GetElectroNeg(), OBIsotopeTable::GetExactMass(), OBTypeTable::GetFromType(), OBElementTable::GetIonization(), OBElementTable::GetMass(), OBElementTable::GetMaxBonds(), OBElementTable::GetName(), OBElementTable::GetNumberOfElements(), OBElementTable::GetRGB(), OBRotorRules::GetRotorIncrements(), OBElementTable::GetSymbol(), OBTypeTable::GetToType(), OBElementTable::GetVdwRad(), OBTypeTable::SetFromType(), OBResidueData::SetResName(), OBTypeTable::SetToType(), and OBTypeTable::Translate().

void SetReadDirectory

(

char *

dir

)

[inline, inherited]

Set the directory before calling Init().

void SetEnvironmentVariable

(

char *

var

)

[inline, inherited]

Set the environment variable to use before calling Init().

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Member Data Documentation

bool _init [protected, inherited]

Whether the data been read already.

Referenced by OBAromaticTyper::AssignAromaticFlags(), OBResidueData::AssignBonds(), OBBondTyper::AssignFunctionalGroupBonds(), OBAtomTyper::AssignHyb(), OBAtomTyper::AssignImplicitValence(), OBPhModel::AssignSeedPartialCharge(), OBRingTyper::AssignTypes(), OBAtomTyper::AssignTypes(), OBAtomTyper::CorrectAromaticNitrogens(), OBElementTable::CorrectedBondRad(), OBElementTable::CorrectedVdwRad(), OBPhModel::CorrectForPH(), OBElementTable::GetAllredRochowElectroNeg(), OBElementTable::GetAtomicNum(), OBElementTable::GetCovalentRad(), OBElementTable::GetElectronAffinity(), OBElementTable::GetElectroNeg(), OBIsotopeTable::GetExactMass(), OBTypeTable::GetFromType(), OBElementTable::GetIonization(), OBElementTable::GetMass(), OBElementTable::GetMaxBonds(), OBElementTable::GetName(), OBElementTable::GetNumberOfElements(), OBElementTable::GetRGB(), OBRotorRules::GetRotorIncrements(), OBElementTable::GetSymbol(), OBTypeTable::GetToType(), OBElementTable::GetVdwRad(), OBGlobalDataBase::Init(), OBAromaticTyper::OBAromaticTyper(), OBAtomTyper::OBAtomTyper(), OBBondTyper::OBBondTyper(), OBElementTable::OBElementTable(), OBIsotopeTable::OBIsotopeTable(), OBPhModel::OBPhModel(), OBResidueData::OBResidueData(), OBRingTyper::OBRingTyper(), OBRotorRules::OBRotorRules(), OBTypeTable::OBTypeTable(), OBTypeTable::SetFromType(), OBResidueData::SetResName(), OBTypeTable::SetToType(), and OBTypeTable::Translate().

const char* _dataptr [protected, inherited]

Default data table if file is unreadable.

Referenced by OBGlobalDataBase::Init(), OBAromaticTyper::OBAromaticTyper(), OBAtomTyper::OBAtomTyper(), OBBondTyper::OBBondTyper(), OBElementTable::OBElementTable(), OBIsotopeTable::OBIsotopeTable(), OBPhModel::OBPhModel(), OBResidueData::OBResidueData(), OBRotorRules::OBRotorRules(), and OBTypeTable::OBTypeTable().

std::string _filename [protected, inherited]

File to search for.

Referenced by OBGlobalDataBase::Init(), OBAromaticTyper::OBAromaticTyper(), OBAtomTyper::OBAtomTyper(), OBBondTyper::OBBondTyper(), OBElementTable::OBElementTable(), OBIsotopeTable::OBIsotopeTable(), OBPhModel::OBPhModel(), OBResidueData::OBResidueData(), OBRingTyper::OBRingTyper(), OBRotorRules::OBRotorRules(), and OBTypeTable::OBTypeTable().

std::string _dir [protected, inherited]

Data directory for file if _envvar fails.

Referenced by OBAromaticTyper::OBAromaticTyper(), OBAtomTyper::OBAtomTyper(), OBBondTyper::OBBondTyper(), OBElementTable::OBElementTable(), OBIsotopeTable::OBIsotopeTable(), OBPhModel::OBPhModel(), OBResidueData::OBResidueData(), OBRingTyper::OBRingTyper(), OBRotorRules::OBRotorRules(), and OBTypeTable::OBTypeTable().

std::string _subdir [protected, inherited]

Subdirectory (if using environment variable).

Referenced by OBAromaticTyper::OBAromaticTyper(), OBAtomTyper::OBAtomTyper(), OBBondTyper::OBBondTyper(), OBElementTable::OBElementTable(), OBIsotopeTable::OBIsotopeTable(), OBPhModel::OBPhModel(), OBResidueData::OBResidueData(), OBRingTyper::OBRingTyper(), OBRotorRules::OBRotorRules(), and OBTypeTable::OBTypeTable().

std::string _envvar [protected, inherited]

Environment variable to check first.

Referenced by OBGlobalDataBase::Init(), OBAromaticTyper::OBAromaticTyper(), OBAtomTyper::OBAtomTyper(), OBBondTyper::OBBondTyper(), OBElementTable::OBElementTable(), OBIsotopeTable::OBIsotopeTable(), OBPhModel::OBPhModel(), OBResidueData::OBResidueData(), OBRingTyper::OBRingTyper(), OBRotorRules::OBRotorRules(), and OBTypeTable::OBTypeTable().

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

• data.h
• data.cpp