/usr/include/rdkit/GraphMol/PeriodicTable.h is in librdkit-dev 201106+dfsg-1build1.
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// Copyright (C) 2001-2011 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#ifndef _RD_PERIODIC_TABLE_H
#define _RD_PERIODIC_TABLE_H
#include <map>
#include <vector>
#include <RDGeneral/types.h>
#include "atomic_data.h"
namespace RDKit {
//! singleton class for retrieving information about atoms
/*!
Use the singleton like this:
\verbatim
const PeriodicTable *tbl = PeriodicTable::getTable();
tbl->getAtomicWeight(6); // get atomic weight for Carbon
tbl->getAtomicWeight("C"); // get atomic weight for Carbon
\endverbatim
*/
class PeriodicTable {
public:
//! returns a pointer to the singleton PeriodicTable
/*
\return a pointer to the singleton ParamCollection
<b>Notes:</b>
- do <b>not</b> delete the pointer returned here
- if the singleton PeriodicTable has already been instantiated and
the singleton will be returned, otherwise the singleton will
be constructed.
*/
static PeriodicTable *getTable();
~PeriodicTable() {
byanum.clear();
byname.clear();
};
//! returns the atomic weight
double getAtomicWeight( UINT atomicNumber ) const {
PRECONDITION(atomicNumber<byanum.size(),"Atomic number not found");
double mass = byanum[atomicNumber].Mass();
return mass;
}
//! \overload
double getAtomicWeight( const std::string &elementSymbol) const {
PRECONDITION(byname.count(elementSymbol),"Element not found");
int anum = byname.find(elementSymbol)->second;
double mass = byanum[anum].Mass();
return mass;
}
//! \overload
double getAtomicWeight( char * elementSymbol ) const {
return getAtomicWeight(std::string(elementSymbol));
}
//! returns the atomic number
int getAtomicNumber( char *elementSymbol ) const {
std::string symb(elementSymbol);
return getAtomicNumber(symb);
}
//! overload
int getAtomicNumber( const std::string &elementSymbol ) const {
PRECONDITION(byname.count(elementSymbol),"Element '" + elementSymbol +"' not found");
int anum = byname.find(elementSymbol)->second;
return anum;
}
//! returns the atomic symbol
std::string getElementSymbol(UINT atomicNumber) const {
PRECONDITION(atomicNumber<byanum.size(),"Atomic number not found");
return byanum[atomicNumber].Symbol();
}
//! returns the atom's van der Waals radius
double getRvdw(UINT atomicNumber) const {
PRECONDITION(atomicNumber<byanum.size(),"Atomic number not found");
return byanum[atomicNumber].Rvdw();
}
//! \overload
double getRvdw(const std::string &elementSymbol ) const {
PRECONDITION(byname.count(elementSymbol),"Element '" + elementSymbol +"' not found");
return getRvdw(byname.find(elementSymbol)->second);
}
//! \overload
double getRvdw(char *elementSymbol ) const {
return getRvdw(std::string(elementSymbol));
}
//! returns the atom's covalent radius
double getRcovalent(UINT atomicNumber) const {
PRECONDITION(atomicNumber<byanum.size(),"Atomic number not found");
return byanum[atomicNumber].Rcov();
}
//! \overload
double getRcovalent(const std::string &elementSymbol) const {
PRECONDITION(byname.count(elementSymbol),"Element '" + elementSymbol +"' not found");
return getRcovalent(byname.find(elementSymbol)->second);
}
//! \overload
double getRcovalent(char *elementSymbol ) const {
return getRcovalent(std::string(elementSymbol));
}
//! returns the atom's bond radius
double getRb0(UINT atomicNumber) const {
PRECONDITION(atomicNumber<byanum.size(),"Atomic number not found");
return byanum[atomicNumber].Rb0();
}
//! \overload
double getRb0(const std::string &elementSymbol) const {
PRECONDITION(byname.count(elementSymbol),"Element '" + elementSymbol +"' not found");
return getRb0(byname.find(elementSymbol)->second);
}
//! \overload
double getRb0(char *elementSymbol ) const {
return getRb0(std::string(elementSymbol));
}
//! returns the atom's default valence
int getDefaultValence(UINT atomicNumber) const {
PRECONDITION(atomicNumber<byanum.size(),"Atomic number not found");
return byanum[atomicNumber].DefaultValence();
}
//! \overload
int getDefaultValence(const std::string &elementSymbol) const {
PRECONDITION(byname.count(elementSymbol),"Element '" + elementSymbol +"' not found");
return getDefaultValence(byname.find(elementSymbol)->second);
}
//! \overload
int getDefaultValence(char *elementSymbol ) const {
return getDefaultValence(std::string(elementSymbol));
}
//! 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
const INT_VECT &getValenceList( UINT atomicNumber ) const {
PRECONDITION(atomicNumber<byanum.size(),"Atomic number not found");
return byanum[atomicNumber].ValenceList();
}
//! \overload
const INT_VECT &getValenceList( const std::string &elementSymbol) const {
PRECONDITION(byname.count(elementSymbol),"Element '" + elementSymbol +"' not found");
return getValenceList(byname.find(elementSymbol)->second);
}
//! \overload
const INT_VECT &getValenceList(char *elementSymbol ) const {
return getValenceList(std::string(elementSymbol));
}
//! returns the number of outer shell electrons
int getNouterElecs( UINT atomicNumber ) const {
PRECONDITION(atomicNumber<byanum.size(),"Atomic number not found");
return byanum[atomicNumber].NumOuterShellElec();
}
//! \overload
int getNouterElecs( const std::string &elementSymbol) const {
PRECONDITION(byname.count(elementSymbol),"Element '" + elementSymbol +"' not found");
return getNouterElecs(byname.find(elementSymbol)->second);
}
//! \overload
int getNouterElecs(char *elementSymbol ) const {
return getNouterElecs(std::string(elementSymbol));
}
//! returns the number of the most common isotope
int getMostCommonIsotope( UINT atomicNumber ) const {
PRECONDITION(atomicNumber<byanum.size(),"Atomic number not found");
return byanum[atomicNumber].MostCommonIsotope();
}
//! \overload
int getMostCommonIsotope( const std::string &elementSymbol) const {
PRECONDITION(byname.count(elementSymbol),"Element '" + elementSymbol +"' not found");
return getMostCommonIsotope(byname.find(elementSymbol)->second);
}
//! \overload
int getMostCommonIsotope(char *elementSymbol ) const {
return getMostCommonIsotope(std::string(elementSymbol));
}
//! returns the mass of the most common isotope
double getMostCommonIsotopeMass( UINT atomicNumber ) const {
PRECONDITION(atomicNumber<byanum.size(),"Atomic number not found");
return byanum[atomicNumber].MostCommonIsotopeMass();
}
//! \overload
double getMostCommonIsotopeMass( const std::string &elementSymbol) const {
PRECONDITION(byname.count(elementSymbol),"Element '" + elementSymbol +"' not found");
return getMostCommonIsotopeMass(byname.find(elementSymbol)->second);
}
//! \overload
double getMostCommonIsotopeMass(char *elementSymbol ) const {
return getMostCommonIsotopeMass(std::string(elementSymbol));
}
//! convenience function to determine which atom is more electronegative
/*!
check if atom with atomic number \c anum1 is more
electronegative than the one with \c 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
*/
bool moreElectroNegative(UINT anum1, UINT anum2) const {
PRECONDITION(anum1<byanum.size(),"Atomic number not found");
PRECONDITION(anum2<byanum.size(),"Atomic number not found");
// FIX: the atomic_data needs to have real electronegativity values
UINT ne1 = getNouterElecs(anum1);
UINT ne2 = getNouterElecs(anum2);
if (ne1 > ne2) {
return true;
}
if (ne1 == ne2) {
if (anum1 < anum2) {
return true;
}
}
return false;
}
private:
PeriodicTable();
PeriodicTable &operator =( const PeriodicTable & );
static class PeriodicTable *ds_instance;
std::vector<atomicData> byanum;
STR_UINT_MAP byname;
};
};
#endif
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