RDKit
Open-source cheminformatics and machine learning.
RDKit::PeriodicTable Class Reference

singleton class for retrieving information about atoms More...

#include <PeriodicTable.h>

Public Member Functions

 ~PeriodicTable ()
 
double getAtomicWeight (UINT atomicNumber) const
 returns the atomic weight More...
 
double getAtomicWeight (const std::string &elementSymbol) const
 
double getAtomicWeight (const char *elementSymbol) const
 
int getAtomicNumber (const char *elementSymbol) const
 returns the atomic number More...
 
int getAtomicNumber (const std::string &elementSymbol) const
 overload More...
 
std::string getElementSymbol (UINT atomicNumber) const
 returns the atomic symbol More...
 
double getRvdw (UINT atomicNumber) const
 returns the atom's van der Waals radius More...
 
double getRvdw (const std::string &elementSymbol) const
 
double getRvdw (const char *elementSymbol) const
 
double getRcovalent (UINT atomicNumber) const
 returns the atom's covalent radius More...
 
double getRcovalent (const std::string &elementSymbol) const
 
double getRcovalent (const char *elementSymbol) const
 
double getRb0 (UINT atomicNumber) const
 returns the atom's bond radius More...
 
double getRb0 (const std::string &elementSymbol) const
 
double getRb0 (const char *elementSymbol) const
 
int getDefaultValence (UINT atomicNumber) const
 returns the atom's default valence More...
 
int getDefaultValence (const std::string &elementSymbol) const
 
int getDefaultValence (const char *elementSymbol) const
 
const INT_VECTgetValenceList (UINT atomicNumber) const
 
const INT_VECTgetValenceList (const std::string &elementSymbol) const
 
const INT_VECTgetValenceList (const char *elementSymbol) const
 
int getNouterElecs (UINT atomicNumber) const
 returns the number of outer shell electrons More...
 
int getNouterElecs (const std::string &elementSymbol) const
 
int getNouterElecs (const char *elementSymbol) const
 
int getMostCommonIsotope (UINT atomicNumber) const
 returns the number of the most common isotope More...
 
int getMostCommonIsotope (const std::string &elementSymbol) const
 
int getMostCommonIsotope (const char *elementSymbol) const
 
double getMostCommonIsotopeMass (UINT atomicNumber) const
 returns the mass of the most common isotope More...
 
double getMostCommonIsotopeMass (const std::string &elementSymbol) const
 
double getMostCommonIsotopeMass (const char *elementSymbol) const
 
double getMassForIsotope (UINT atomicNumber, UINT isotope) const
 
double getMassForIsotope (const std::string &elementSymbol, UINT isotope) const
 
double getMassForIsotope (const char *elementSymbol, UINT isotope) const
 
double getAbundanceForIsotope (UINT atomicNumber, UINT isotope) const
 
double getAbundanceForIsotope (const std::string &elementSymbol, UINT isotope) const
 
double getAbundanceForIsotope (const char *elementSymbol, UINT isotope) const
 
bool moreElectroNegative (UINT anum1, UINT anum2) const
 convenience function to determine which atom is more electronegative More...
 

Static Public Member Functions

static PeriodicTablegetTable ()
 returns a pointer to the singleton PeriodicTable More...
 

Detailed Description

singleton class for retrieving information about atoms

Use the singleton like this:

const PeriodicTable *tbl = PeriodicTable::getTable();
tbl->getAtomicWeight(6); // get atomic weight for Carbon
tbl->getAtomicWeight("C"); // get atomic weight for Carbon

Definition at line 31 of file PeriodicTable.h.

Constructor & Destructor Documentation

RDKit::PeriodicTable::~PeriodicTable ( )
inline

Definition at line 46 of file PeriodicTable.h.

Member Function Documentation

double RDKit::PeriodicTable::getAbundanceForIsotope ( UINT  atomicNumber,
UINT  isotope 
) const
inline

returns the abundance of a particular isotope; zero if that isotope is unknown.

Definition at line 257 of file PeriodicTable.h.

References PRECONDITION.

Referenced by getAbundanceForIsotope().

double RDKit::PeriodicTable::getAbundanceForIsotope ( const std::string &  elementSymbol,
UINT  isotope 
) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 270 of file PeriodicTable.h.

References getAbundanceForIsotope(), and PRECONDITION.

double RDKit::PeriodicTable::getAbundanceForIsotope ( const char *  elementSymbol,
UINT  isotope 
) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 277 of file PeriodicTable.h.

References getAbundanceForIsotope().

int RDKit::PeriodicTable::getAtomicNumber ( const char *  elementSymbol) const
inline

returns the atomic number

Definition at line 70 of file PeriodicTable.h.

int RDKit::PeriodicTable::getAtomicNumber ( const std::string &  elementSymbol) const
inline

overload

Definition at line 76 of file PeriodicTable.h.

References POSTCONDITION.

double RDKit::PeriodicTable::getAtomicWeight ( UINT  atomicNumber) const
inline

returns the atomic weight

Definition at line 52 of file PeriodicTable.h.

References PRECONDITION.

Referenced by getAtomicWeight().

double RDKit::PeriodicTable::getAtomicWeight ( const std::string &  elementSymbol) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 58 of file PeriodicTable.h.

References PRECONDITION.

double RDKit::PeriodicTable::getAtomicWeight ( const char *  elementSymbol) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 65 of file PeriodicTable.h.

References getAtomicWeight().

int RDKit::PeriodicTable::getDefaultValence ( UINT  atomicNumber) const
inline

returns the atom's default valence

Definition at line 149 of file PeriodicTable.h.

References PRECONDITION.

Referenced by getDefaultValence().

int RDKit::PeriodicTable::getDefaultValence ( const std::string &  elementSymbol) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 154 of file PeriodicTable.h.

References getDefaultValence(), and PRECONDITION.

int RDKit::PeriodicTable::getDefaultValence ( const char *  elementSymbol) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 160 of file PeriodicTable.h.

References getDefaultValence().

std::string RDKit::PeriodicTable::getElementSymbol ( UINT  atomicNumber) const
inline

returns the atomic symbol

Definition at line 95 of file PeriodicTable.h.

References PRECONDITION.

double RDKit::PeriodicTable::getMassForIsotope ( UINT  atomicNumber,
UINT  isotope 
) const
inline

returns the mass of a particular isotope; zero if that isotope is unknown.

Definition at line 232 of file PeriodicTable.h.

References PRECONDITION.

Referenced by getMassForIsotope().

double RDKit::PeriodicTable::getMassForIsotope ( const std::string &  elementSymbol,
UINT  isotope 
) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 245 of file PeriodicTable.h.

References getMassForIsotope(), and PRECONDITION.

double RDKit::PeriodicTable::getMassForIsotope ( const char *  elementSymbol,
UINT  isotope 
) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 252 of file PeriodicTable.h.

References getMassForIsotope().

int RDKit::PeriodicTable::getMostCommonIsotope ( UINT  atomicNumber) const
inline

returns the number of the most common isotope

Definition at line 199 of file PeriodicTable.h.

References PRECONDITION.

Referenced by getMostCommonIsotope().

int RDKit::PeriodicTable::getMostCommonIsotope ( const std::string &  elementSymbol) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 204 of file PeriodicTable.h.

References getMostCommonIsotope(), and PRECONDITION.

int RDKit::PeriodicTable::getMostCommonIsotope ( const char *  elementSymbol) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 210 of file PeriodicTable.h.

References getMostCommonIsotope().

double RDKit::PeriodicTable::getMostCommonIsotopeMass ( UINT  atomicNumber) const
inline

returns the mass of the most common isotope

Definition at line 215 of file PeriodicTable.h.

References PRECONDITION.

Referenced by getMostCommonIsotopeMass().

double RDKit::PeriodicTable::getMostCommonIsotopeMass ( const std::string &  elementSymbol) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 220 of file PeriodicTable.h.

References getMostCommonIsotopeMass(), and PRECONDITION.

double RDKit::PeriodicTable::getMostCommonIsotopeMass ( const char *  elementSymbol) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 226 of file PeriodicTable.h.

References getMostCommonIsotopeMass().

int RDKit::PeriodicTable::getNouterElecs ( UINT  atomicNumber) const
inline

returns the number of outer shell electrons

Definition at line 183 of file PeriodicTable.h.

References PRECONDITION.

Referenced by getNouterElecs(), and moreElectroNegative().

int RDKit::PeriodicTable::getNouterElecs ( const std::string &  elementSymbol) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 188 of file PeriodicTable.h.

References getNouterElecs(), and PRECONDITION.

int RDKit::PeriodicTable::getNouterElecs ( const char *  elementSymbol) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 194 of file PeriodicTable.h.

References getNouterElecs().

double RDKit::PeriodicTable::getRb0 ( UINT  atomicNumber) const
inline

returns the atom's bond radius

Definition at line 133 of file PeriodicTable.h.

References PRECONDITION.

Referenced by getRb0().

double RDKit::PeriodicTable::getRb0 ( const std::string &  elementSymbol) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 138 of file PeriodicTable.h.

References getRb0(), and PRECONDITION.

double RDKit::PeriodicTable::getRb0 ( const char *  elementSymbol) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 144 of file PeriodicTable.h.

References getRb0().

double RDKit::PeriodicTable::getRcovalent ( UINT  atomicNumber) const
inline

returns the atom's covalent radius

Definition at line 117 of file PeriodicTable.h.

References PRECONDITION.

Referenced by getRcovalent().

double RDKit::PeriodicTable::getRcovalent ( const std::string &  elementSymbol) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 122 of file PeriodicTable.h.

References getRcovalent(), and PRECONDITION.

double RDKit::PeriodicTable::getRcovalent ( const char *  elementSymbol) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 128 of file PeriodicTable.h.

References getRcovalent().

double RDKit::PeriodicTable::getRvdw ( UINT  atomicNumber) const
inline

returns the atom's van der Waals radius

Definition at line 101 of file PeriodicTable.h.

References PRECONDITION.

Referenced by getRvdw().

double RDKit::PeriodicTable::getRvdw ( const std::string &  elementSymbol) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 106 of file PeriodicTable.h.

References getRvdw(), and PRECONDITION.

double RDKit::PeriodicTable::getRvdw ( const char *  elementSymbol) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 112 of file PeriodicTable.h.

References getRvdw().

static PeriodicTable* RDKit::PeriodicTable::getTable ( )
static

returns a pointer to the singleton PeriodicTable

const INT_VECT& RDKit::PeriodicTable::getValenceList ( UINT  atomicNumber) const
inline

returns a vector of all stable valences. For atoms where we really don't have any idea what a reasonable maximum valence is (like transition metals), the vector ends with -1

Definition at line 167 of file PeriodicTable.h.

References PRECONDITION.

Referenced by getValenceList().

const INT_VECT& RDKit::PeriodicTable::getValenceList ( const std::string &  elementSymbol) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 172 of file PeriodicTable.h.

References getValenceList(), and PRECONDITION.

const INT_VECT& RDKit::PeriodicTable::getValenceList ( const char *  elementSymbol) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 178 of file PeriodicTable.h.

References getValenceList().

bool RDKit::PeriodicTable::moreElectroNegative ( UINT  anum1,
UINT  anum2 
) const
inline

convenience function to determine which atom is more electronegative

check if atom with atomic number anum1 is more electronegative than the one with anum2 this is rather lame but here is how we do it

  • the atom with the higher number of outer shell electrons is considered more electronegative
  • if the # of outer shell elecs are the same the atom with the lower atomic weight is more electronegative

Definition at line 293 of file PeriodicTable.h.

References getNouterElecs(), and PRECONDITION.


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