Open Babel: OBElementTable Class Reference

Public Member Functions | Protected Attributes

# 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

## 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)

## 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().

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.

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.

const char* _dataptr`[protected, inherited]`

Default data table if file is unreadable.

std::string _filename`[protected, inherited]`

File to search for.

std::string _dir`[protected, inherited]`

Data directory for file if _envvar fails.

std::string _subdir`[protected, inherited]`

Subdirectory (if using environment variable)

std::string _envvar`[protected, inherited]`

Environment variable to check first.

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

- data.h
- data.cpp

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