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http://sourceforge.net/tracker/index.php?func=detail&aid=1942657&group_id=160139&atid=814650 This was handled by adding error/consistency checking to Atom.calcExplicitValence() This includes another pretty big scale modification: the allowed valence list for atoms (in atomic_data.cpp) can now contain a -1 at the end. If this is the case, the atom will tolerate valences above the ones listed. This is done to allow "flexible" atoms (i.e. transition metals and the like) to accept arbitrary coordination numbers without generating errors.
62 lines
1.4 KiB
C++
Executable File
62 lines
1.4 KiB
C++
Executable File
//
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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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//
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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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#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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namespace RDKit {
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extern const std::string periodicTableAtomData;
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class 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 {
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return valence;
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};
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double Mass() const { return mass;};
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std::string Symbol() const {
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return symb;
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}
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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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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 valence, -1 at the end signifies that any upper valence 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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};
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};
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#endif
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