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724716b2c6
* change valence model to use isolobal analogy Remove support for five-coordinate C+ and, by analogy, five-coordinate N+2 Removes support for charge states that take atoms past the end of the periodic table i.e. [Lv-4] is no longer supported * update the tests for that * remove valence state of 6 for Al * fix representation of phosphate in the mol2 parser this is a correction of what was done during #5973 * cleanup the exceptions for P, S, As, and Se * drop valence states: Si 6, P 7, As 7 * a couple of additional changes from #7397 * update java tests * fix an inconsistency: Rb now supports valence -1 * documentation * - replace operator[] with at() for bounds check - extract some code into a function to avoid duplication - use TAB as separator throughout in the periodic table data for consistency * removing the .at() usage We know that these vectors aren't empty, so there's no need for the bounds check. --------- Co-authored-by: ptosco <paolo.tosco@novartis.com>
83 lines
2.4 KiB
C++
83 lines
2.4 KiB
C++
//
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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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RDKIT_GRAPHMOL_EXPORT extern const std::vector<std::string> elementNames;
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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() = default;
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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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std::string Name() const { return name; }
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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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unsigned int Row() const { return row; }
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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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std::string name; // atomic name
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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 common isotope
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double commonIsotopeMass; // most common isotopic mass
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unsigned int row; // row in the periodic table
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};
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}; // namespace RDKit
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#endif
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