OBElementTable Class Reference

Periodic Table of the Elements. More...

#include <openbabel/data.h>

Inheritance diagram for OBElementTable:

Inheritance graph
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List of all members.

Public Member Functions

 OBElementTable (void)
 ~OBElementTable ()
void ParseLine (const char *)
unsigned int GetNumberOfElements ()
unsigned int GetSize ()
int GetAtomicNum (const char *)
int GetAtomicNum (const char *, 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

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:

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

unsigned int 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().

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

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

const char * GetSymbol ( int  atomicnum  ) 

Returns:
the element symbol matching the atomic number passed

Referenced by OpenBabel::CalculateSymmetry(), 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(), OBBond::GetEquibLength(), OBAtom::HtoMethyl(), 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

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().

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().

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