atomic_data.h
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//
// Copyright (C) 2001-2008 Greg Landrum and 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.
//
/*! \file atomic_data.h
\brief No user-serviceable parts inside
This stuff is used by the PeriodicTable interface
*/
#ifndef __RD_ATOMIC_DATA_H
#define __RD_ATOMIC_DATA_H
#include <RDGeneral/types.h>
#include <map>
namespace RDKit {
extern const std::string periodicTableAtomData;
extern const std::string isotopesAtomData[];
namespace constants {
extern const double electronMass;
}
class atomicData {
public:
atomicData(const std::string &dataLine);
~atomicData(){};
int AtomicNum() const { return anum; };
int DefaultValence() const { return valence.front(); };
int NumValence() const { return static_cast<int>(valence.size()); };
const INT_VECT &ValenceList() const { return valence; };
double Mass() const { return mass; };
std::string Symbol() const { return symb; }
double Rcov() const { return rCov; }
double Rb0() const { return rB0; }
double Rvdw() const { return rVdw; }
int NumOuterShellElec() const { return nVal; }
int MostCommonIsotope() const { return commonIsotope; }
double MostCommonIsotopeMass() const { return commonIsotopeMass; }
// maps isotope number -> mass
std::map<unsigned int, std::pair<double, double> >
d_isotopeInfoMap; // available isotopes
private:
int anum; // atomic number
std::string symb; // atomic symbol
double rCov, rB0, rVdw; // radii
INT_VECT valence; // list of all valences, the first one is the default
// valence, -1 at the end signifies that any upper valence
// is tolerated
double mass; // atomic mass
int nVal; // number of outer shell electrons
int commonIsotope; // most comon isotope
double commonIsotopeMass; // most comon isotope
};
};
#endif
RDKit::constants::electronMass
const double electronMass
RDKit::atomicData::~atomicData
~atomicData()
Definition: atomic_data.h:33
types.h
RDKit::atomicData::Mass
double Mass() const
Definition: atomic_data.h:43
RDKit::atomicData::MostCommonIsotope
int MostCommonIsotope() const
Definition: atomic_data.h:55
RDKit::periodicTableAtomData
const std::string periodicTableAtomData
RDKit::atomicData::Rvdw
double Rvdw() const
Definition: atomic_data.h:51
RDKit::atomicData::DefaultValence
int DefaultValence() const
Definition: atomic_data.h:37
RDKit::atomicData
Definition: atomic_data.h:30
RDKit::atomicData::NumOuterShellElec
int NumOuterShellElec() const
Definition: atomic_data.h:53
RDKit::atomicData::Rb0
double Rb0() const
Definition: atomic_data.h:49
RDKit::atomicData::Symbol
std::string Symbol() const
Definition: atomic_data.h:45
RDKit::INT_VECT
std::vector< int > INT_VECT
Definition: types.h:146
RDKit::atomicData::ValenceList
const INT_VECT & ValenceList() const
Definition: atomic_data.h:41
RDKit
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:28
RDKit::atomicData::AtomicNum
int AtomicNum() const
Definition: atomic_data.h:35
RDKit::atomicData::MostCommonIsotopeMass
double MostCommonIsotopeMass() const
Definition: atomic_data.h:57
RDKit::atomicData::NumValence
int NumValence() const
Definition: atomic_data.h:39
RDKit::atomicData::d_isotopeInfoMap
std::map< unsigned int, std::pair< double, double > > d_isotopeInfoMap
Definition: atomic_data.h:61
RDKit::atomicData::Rcov
double Rcov() const
Definition: atomic_data.h:47
RDKit::isotopesAtomData
const std::string isotopesAtomData[]