RDKit: atomic_data.h Source File

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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);
33 ~atomicData(){};
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
RDKit::constants::electronMass
const double electronMass
RDKit::atomicData::~atomicData
~atomicData()
Definition: atomic_data.h:33
types.h
RDKit::atomicData::AtomicNum
int AtomicNum() const
Definition: atomic_data.h:35
RDKit::atomicData::MostCommonIsotope
int MostCommonIsotope() const
Definition: atomic_data.h:55
RDKit::periodicTableAtomData
const std::string periodicTableAtomData
RDKit::atomicData::NumOuterShellElec
int NumOuterShellElec() const
Definition: atomic_data.h:53
RDKit::atomicData::Rb0
double Rb0() const
Definition: atomic_data.h:49
RDKit::atomicData
Definition: atomic_data.h:30
RDKit::INT_VECT
std::vector< int > INT_VECT
Definition: types.h:191
RDKit
Std stuff.
Definition: Atom.h:29
RDKit::atomicData::Rvdw
double Rvdw() const
Definition: atomic_data.h:51
RDKit::atomicData::Symbol
std::string Symbol() const
Definition: atomic_data.h:45
RDKit::atomicData::Rcov
double Rcov() const
Definition: atomic_data.h:47
RDKit::atomicData::d_isotopeInfoMap
std::map< unsigned int, std::pair< double, double > > d_isotopeInfoMap
Definition: atomic_data.h:61
RDKit::atomicData::NumValence
int NumValence() const
Definition: atomic_data.h:39
RDKit::atomicData::Mass
double Mass() const
Definition: atomic_data.h:43
RDKit::atomicData::MostCommonIsotopeMass
double MostCommonIsotopeMass() const
Definition: atomic_data.h:57
RDKit::atomicData::DefaultValence
int DefaultValence() const
Definition: atomic_data.h:37
RDKit::atomicData::ValenceList
const INT_VECT & ValenceList() const
Definition: atomic_data.h:41
RDKit::isotopesAtomData
const std::string isotopesAtomData[]