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 32 of file PeriodicTable.h.

Constructor & Destructor Documentation

◆ ~PeriodicTable()

RDKit::PeriodicTable::~PeriodicTable ( )
inline

Definition at line 47 of file PeriodicTable.h.

Member Function Documentation

◆ getAbundanceForIsotope() [1/3]

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 258 of file PeriodicTable.h.

References PRECONDITION.

◆ getAbundanceForIsotope() [2/3]

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 271 of file PeriodicTable.h.

References PRECONDITION.

◆ getAbundanceForIsotope() [3/3]

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 278 of file PeriodicTable.h.

◆ getAtomicNumber() [1/2]

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

returns the atomic number

Definition at line 71 of file PeriodicTable.h.

References RDKit::StructureCheck::getAtomicNumber().

◆ getAtomicNumber() [2/2]

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

overload

Definition at line 77 of file PeriodicTable.h.

References POSTCONDITION.

◆ getAtomicWeight() [1/3]

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

returns the atomic weight

Definition at line 53 of file PeriodicTable.h.

References PRECONDITION.

◆ getAtomicWeight() [2/3]

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 59 of file PeriodicTable.h.

References PRECONDITION.

◆ getAtomicWeight() [3/3]

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 66 of file PeriodicTable.h.

◆ getDefaultValence() [1/3]

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

returns the atom's default valence

Definition at line 150 of file PeriodicTable.h.

References PRECONDITION.

◆ getDefaultValence() [2/3]

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 155 of file PeriodicTable.h.

References PRECONDITION.

◆ getDefaultValence() [3/3]

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 161 of file PeriodicTable.h.

◆ getElementSymbol()

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

returns the atomic symbol

Definition at line 96 of file PeriodicTable.h.

References PRECONDITION.

◆ getMassForIsotope() [1/3]

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 233 of file PeriodicTable.h.

References PRECONDITION.

◆ getMassForIsotope() [2/3]

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 246 of file PeriodicTable.h.

References PRECONDITION.

◆ getMassForIsotope() [3/3]

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 253 of file PeriodicTable.h.

◆ getMostCommonIsotope() [1/3]

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

returns the number of the most common isotope

Definition at line 200 of file PeriodicTable.h.

References PRECONDITION.

◆ getMostCommonIsotope() [2/3]

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 205 of file PeriodicTable.h.

References PRECONDITION.

◆ getMostCommonIsotope() [3/3]

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 211 of file PeriodicTable.h.

◆ getMostCommonIsotopeMass() [1/3]

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

returns the mass of the most common isotope

Definition at line 216 of file PeriodicTable.h.

References PRECONDITION.

◆ getMostCommonIsotopeMass() [2/3]

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 221 of file PeriodicTable.h.

References PRECONDITION.

◆ getMostCommonIsotopeMass() [3/3]

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 227 of file PeriodicTable.h.

◆ getNouterElecs() [1/3]

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

returns the number of outer shell electrons

Definition at line 184 of file PeriodicTable.h.

References PRECONDITION.

◆ getNouterElecs() [2/3]

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 189 of file PeriodicTable.h.

References PRECONDITION.

◆ getNouterElecs() [3/3]

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 195 of file PeriodicTable.h.

◆ getRb0() [1/3]

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

returns the atom's bond radius

Definition at line 134 of file PeriodicTable.h.

References PRECONDITION.

◆ getRb0() [2/3]

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 139 of file PeriodicTable.h.

References PRECONDITION.

◆ getRb0() [3/3]

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 145 of file PeriodicTable.h.

◆ getRcovalent() [1/3]

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

returns the atom's covalent radius

Definition at line 118 of file PeriodicTable.h.

References PRECONDITION.

◆ getRcovalent() [2/3]

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 123 of file PeriodicTable.h.

References PRECONDITION.

◆ getRcovalent() [3/3]

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 129 of file PeriodicTable.h.

◆ getRvdw() [1/3]

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

returns the atom's van der Waals radius

Definition at line 102 of file PeriodicTable.h.

References PRECONDITION.

◆ getRvdw() [2/3]

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 107 of file PeriodicTable.h.

References PRECONDITION.

◆ getRvdw() [3/3]

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 113 of file PeriodicTable.h.

◆ getTable()

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

returns a pointer to the singleton PeriodicTable

◆ getValenceList() [1/3]

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 168 of file PeriodicTable.h.

References PRECONDITION.

◆ getValenceList() [2/3]

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 173 of file PeriodicTable.h.

References PRECONDITION.

◆ getValenceList() [3/3]

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 179 of file PeriodicTable.h.

◆ moreElectroNegative()

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 294 of file PeriodicTable.h.

References PRECONDITION.


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