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/********************************************************************** |
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|
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This basic Periodic Table class was originally taken from the data.h |
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file in OpenBabel. The code has been modified to match the OOPSE coding style. |
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We have retained the OpenBabel copyright and GPL license on this class: |
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|
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Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
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Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
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|
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This file is part of the Open Babel project. |
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For more information, see <http://openbabel.sourceforge.net/> |
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|
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This program is free software; you can redistribute it and/or modify |
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it under the terms of the GNU General Public License as published by |
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the Free Software Foundation version 2 of the License. |
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|
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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***********************************************************************/ |
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|
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/** |
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* @file ElementsTable.hpp |
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* @author gezelter |
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* @date 12/21/2007 |
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* @time 11:30am |
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* @version 1.0 |
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*/ |
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|
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#ifndef UTILS_ELEMENTSTABLE_HPP |
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#define UTILS_ELEMENTSTABLE_HPP |
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|
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#include "config.h" |
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#include <vector> |
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#include "primitives/Element.hpp" |
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|
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namespace oopse { |
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|
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/** |
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* @class ElementsTable.hpp "util/ElementsTable.hpp" |
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* @brief Periodic Table of the Elements |
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* Using element data is a place holder when we lack information about |
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* a specific atom type. In particular, the Langevin algorithms must |
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* assume specific atomic radii to predict drag and random forces on those |
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* atoms. For force fields which do not specify Lennard-Jones radii, |
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* the element's van der Waals radius is used instead. |
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* The ElementsTable class (etab) is declared as external in |
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* ElementsTable.cpp. Source files that include the header file |
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* ElementsTable.hpp automatically have an extern definition to etab. |
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* The following code sample demonstrates the use of the ElementsTable class: |
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* @code |
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* cout << "The symbol for element 6 is " << etab.GetSymbol(6) << endl; |
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* cout << "The atomic number for Sulfur is " << etab.GetAtomicNum(16) << endl; |
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* cout << "The van der Waal radius for Nitrogen is " << etab.GetVdwRad(7); |
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* @endcode |
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* Stored information in the OBElementTable includes elemental: |
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* - symbols |
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* - covalent radii |
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* - van der Waal radii |
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* - expected maximum bonding valence |
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* - molar mass (by IUPAC recommended atomic masses) |
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* - electronegativity |
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* - ionization potential |
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* - electron affinity |
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* - RGB colors for visualization programs |
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* - names (by IUPAC recommendation) |
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*/ |
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class ElementsTable { |
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public: |
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/** Constructor */ |
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ElementsTable(); |
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/** Destructor */ |
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~ElementsTable(); |
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|
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/** |
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* Read in the data file. |
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*/ |
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void Init(); |
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/** |
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* Set the directory before calling Init() |
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*/ |
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void SetReadDirectory(char *dir) { dir_ = dir; } |
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/** |
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* Set the environment variable to use before calling Init() |
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*/ |
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void SetEnvironmentVariable(char *var) { envvar_ = var; } |
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/** |
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* Specified by particular table classes (parses an individual data line) |
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* @param line the data line to parse |
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*/ |
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void ParseLine(const char *line); |
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/** |
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* @return the number of elements in the periodic table |
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*/ |
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unsigned int GetNumberOfElements(); |
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unsigned int GetSize() { return GetNumberOfElements(); } |
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/** |
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* @return the atomic number matching the element symbol passed |
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* or 0 if not defined. For 'D' or 'T' hydrogen isotopes, will return |
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* a value in the second argument |
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* @param str the element symbol |
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* @param iso the isotope index for Deuterium or Tritium |
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*/ |
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int GetAtomicNum(const char *str); |
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int GetAtomicNum(const char *str, int &iso); |
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/** |
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* @return the element symbol matching the atomic number passed |
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* @param atomicnum the atomic number of the element |
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*/ |
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const char *GetSymbol(int atomicnum); |
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/** |
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* @return the van der Waals radius for this atomic number |
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* @param atomicnum the atomic number of the element |
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*/ |
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RealType GetVdwRad(int atomicnum); |
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/** |
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* @return the covalent radius for this atomic number |
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* @param atomicnum the atomic number of the element |
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*/ |
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RealType GetCovalentRad(int atomicnum); |
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/** |
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* @return the average atomic mass for this element. |
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* @param atomicnum the atomic number of the element |
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*/ |
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RealType GetMass(int atomicnum); |
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/** |
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* @return a "corrected" bonding radius based on the hybridization. |
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* Scales the covalent radius by 0.95 for sp2 and 0.90 for sp hybrids |
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* @param atomicnum the atomic number of the element |
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* @param hyb the hybridization of the element |
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*/ |
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RealType CorrectedBondRad(int atomicnum, int hyb = 3); |
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/** |
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* @return a "corrected" vdW radius based on the hybridization. |
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* Scales the van der Waals radius by 0.95 for sp2 and 0.90 for sp hybrids |
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* @param atomicnum the atomic number of the element |
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* @param hyb the hybridization of the element |
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*/ |
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RealType CorrectedVdwRad(int atomicnum, int hyb = 3); |
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/** |
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* @return the maximum expected number of bonds to this element |
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* @param atomicnum the atomic number of the element |
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*/ |
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int GetMaxBonds(int atomicnum); |
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/** |
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* @return the Pauling electronegativity for this element |
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* @param atomicnum the atomic number of the element |
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*/ |
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RealType GetElectroNeg(int atomicnum); |
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/** |
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* @return the ionization potential (in eV) for this element |
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* @param atomicnum the atomic number of the element |
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*/ |
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RealType GetIonization(int atomicnum); |
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/** |
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* @return the electron affinity (in eV) for this element |
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* @param atomicnum the atomic number of the element |
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*/ |
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RealType GetElectronAffinity(int atomicnum); |
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/** |
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* @return a vector with red, green, blue color values for this element |
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* @param atomicnum the atomic number of the element |
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*/ |
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std::vector<RealType> GetRGB(int atomicnum); |
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|
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/** |
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* @return the name of this element |
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* @param atomicnum the atomic number of the element |
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*/ |
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std::string GetName(int atomicnum); |
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|
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protected: |
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bool init_; //!< whether the data been read already |
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std::string filename_; //!< file to search for |
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std::string dir_; //!< data directory for file if _envvar fails |
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std::string subdir_; //!< subdirectory (if using environment variable) |
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std::string envvar_; //!< environment variable to check first |
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std::vector<Element*> elements_; |
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const char *dataptr_; //!< default data table if file is unreadable |
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|
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}; |
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extern ElementsTable etab; |
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} |
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|
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#endif |
