RDKit
Open-source cheminformatics and machine learning.
atomic_data.h
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//
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// Copyright (C) 2001-2008 Greg Landrum and Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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/*! \file atomic_data.h
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\brief No user-serviceable parts inside
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This stuff is used by the PeriodicTable interface
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*/
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#include <
RDGeneral/export.h
>
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#ifndef __RD_ATOMIC_DATA_H
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#define __RD_ATOMIC_DATA_H
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#include <
RDGeneral/types.h
>
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#include <map>
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namespace
RDKit
{
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RDKIT_GRAPHMOL_EXPORT
extern
const
std::string
periodicTableAtomData
;
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RDKIT_GRAPHMOL_EXPORT
extern
const
std::string
isotopesAtomData
[];
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namespace
constants {
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RDKIT_GRAPHMOL_EXPORT
extern
const
double
electronMass
;
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}
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class
RDKIT_GRAPHMOL_EXPORT
atomicData
{
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public
:
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atomicData
(
const
std::string &dataLine);
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~atomicData
(){};
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int
AtomicNum
()
const
{
return
anum; };
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int
DefaultValence
()
const
{
return
valence.front(); };
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int
NumValence
()
const
{
return
static_cast<
int
>
(valence.size()); };
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const
INT_VECT
&
ValenceList
()
const
{
return
valence; };
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double
Mass
()
const
{
return
mass; };
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std::string
Symbol
()
const
{
return
symb; }
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double
Rcov
()
const
{
return
rCov; }
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double
Rb0
()
const
{
return
rB0; }
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double
Rvdw
()
const
{
return
rVdw; }
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int
NumOuterShellElec
()
const
{
return
nVal; }
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int
MostCommonIsotope
()
const
{
return
commonIsotope; }
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double
MostCommonIsotopeMass
()
const
{
return
commonIsotopeMass; }
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// maps isotope number -> mass
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std::map<unsigned int, std::pair<double, double>>
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d_isotopeInfoMap
;
// available isotopes
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private
:
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int
anum;
// atomic number
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std::string symb;
// atomic symbol
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double
rCov, rB0, rVdw;
// radii
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INT_VECT
valence;
// list of all valences, the first one is the default
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// valence, -1 at the end signifies that any upper valence
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// is tolerated
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double
mass;
// atomic mass
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int
nVal;
// number of outer shell electrons
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int
commonIsotope;
// most comon isotope
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double
commonIsotopeMass;
// most comon isotope
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};
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};
// namespace RDKit
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#endif
RDKit::atomicData::d_isotopeInfoMap
std::map< unsigned int, std::pair< double, double > > d_isotopeInfoMap
Definition:
atomic_data.h:62
RDKit::atomicData::NumValence
int NumValence() const
Definition:
atomic_data.h:40
RDKit::atomicData::AtomicNum
int AtomicNum() const
Definition:
atomic_data.h:36
RDKit::atomicData::DefaultValence
int DefaultValence() const
Definition:
atomic_data.h:38
RDKit::INT_VECT
std::vector< int > INT_VECT
Definition:
types.h:254
types.h
RDKit::isotopesAtomData
const RDKIT_GRAPHMOL_EXPORT std::string isotopesAtomData[]
RDKit::periodicTableAtomData
const RDKIT_GRAPHMOL_EXPORT std::string periodicTableAtomData
RDKit::atomicData::~atomicData
~atomicData()
Definition:
atomic_data.h:34
RDKit::atomicData::Symbol
std::string Symbol() const
Definition:
atomic_data.h:46
RDKit::atomicData::Mass
double Mass() const
Definition:
atomic_data.h:44
RDKIT_GRAPHMOL_EXPORT
#define RDKIT_GRAPHMOL_EXPORT
Definition:
export.h:307
RDKit::atomicData::MostCommonIsotopeMass
double MostCommonIsotopeMass() const
Definition:
atomic_data.h:58
RDKit::constants::electronMass
const RDKIT_GRAPHMOL_EXPORT double electronMass
RDKit::atomicData::MostCommonIsotope
int MostCommonIsotope() const
Definition:
atomic_data.h:56
RDKit::atomicData
Definition:
atomic_data.h:31
RDKit::atomicData::NumOuterShellElec
int NumOuterShellElec() const
Definition:
atomic_data.h:54
RDKit::atomicData::ValenceList
const INT_VECT & ValenceList() const
Definition:
atomic_data.h:42
RDKit
Std stuff.
Definition:
Atom.h:30
RDKit::atomicData::Rvdw
double Rvdw() const
Definition:
atomic_data.h:52
RDKit::atomicData::Rcov
double Rcov() const
Definition:
atomic_data.h:48
RDKit::atomicData::Rb0
double Rb0() const
Definition:
atomic_data.h:50
export.h
GraphMol
atomic_data.h
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