RDKit
Open-source cheminformatics and machine learning.
atomic_data.h
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1 //
2 // Copyright (C) 2001-2008 Greg Landrum and Rational Discovery LLC
3 //
4 // @@ All Rights Reserved @@
5 // This file is part of the RDKit.
6 // The contents are covered by the terms of the BSD license
7 // which is included in the file license.txt, found at the root
8 // of the RDKit source tree.
9 //
10 
11 /*! \file atomic_data.h
12 
13  \brief No user-serviceable parts inside
14 
15  This stuff is used by the PeriodicTable interface
16 
17 */
18 #ifndef __RD_ATOMIC_DATA_H
19 #define __RD_ATOMIC_DATA_H
20 
21 #include <RDGeneral/types.h>
22 #include <map>
23 
24 namespace RDKit {
25 extern const std::string periodicTableAtomData;
26 extern const std::string isotopesAtomData[];
27 namespace constants {
28 extern const double electronMass;
29 }
30 class atomicData {
31  public:
32  atomicData(const std::string &dataLine);
34 
35  int AtomicNum() const { return anum; };
36 
37  int DefaultValence() const { return valence.front(); };
38 
39  int NumValence() const { return static_cast<int>(valence.size()); };
40 
41  const INT_VECT &ValenceList() const { return valence; };
42 
43  double Mass() const { return mass; };
44 
45  std::string Symbol() const { return symb; }
46 
47  double Rcov() const { return rCov; }
48 
49  double Rb0() const { return rB0; }
50 
51  double Rvdw() const { return rVdw; }
52 
53  int NumOuterShellElec() const { return nVal; }
54 
55  int MostCommonIsotope() const { return commonIsotope; }
56 
57  double MostCommonIsotopeMass() const { return commonIsotopeMass; }
58 
59  // maps isotope number -> mass
60  std::map<unsigned int, std::pair<double, double> >
61  d_isotopeInfoMap; // available isotopes
62  private:
63  int anum; // atomic number
64  std::string symb; // atomic symbol
65  double rCov, rB0, rVdw; // radii
66  INT_VECT valence; // list of all valences, the first one is the default
67  // valence, -1 at the end signifies that any upper valence
68  // is tolerated
69  double mass; // atomic mass
70  int nVal; // number of outer shell electrons
71  int commonIsotope; // most comon isotope
72  double commonIsotopeMass; // most comon isotope
73 };
74 };
75 #endif
const double electronMass
int AtomicNum() const
Definition: atomic_data.h:35
int MostCommonIsotope() const
Definition: atomic_data.h:55
const std::string periodicTableAtomData
int NumOuterShellElec() const
Definition: atomic_data.h:53
double Rb0() const
Definition: atomic_data.h:49
std::vector< int > INT_VECT
Definition: types.h:191
Std stuff.
Definition: Atom.h:29
double Rvdw() const
Definition: atomic_data.h:51
std::string Symbol() const
Definition: atomic_data.h:45
double Rcov() const
Definition: atomic_data.h:47
std::map< unsigned int, std::pair< double, double > > d_isotopeInfoMap
Definition: atomic_data.h:61
int NumValence() const
Definition: atomic_data.h:39
double Mass() const
Definition: atomic_data.h:43
double MostCommonIsotopeMass() const
Definition: atomic_data.h:57
int DefaultValence() const
Definition: atomic_data.h:37
const INT_VECT & ValenceList() const
Definition: atomic_data.h:41
const std::string isotopesAtomData[]