The Gnome Chemistry Utils 0.13.3
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00001 // -*- C++ -*- 00002 00003 /* 00004 * Gnome Chemistry Utils 00005 * gcr/atom.h 00006 * 00007 * Copyright (C) 2002-2010 Jean Bréfort <jean.brefort@normalesup.org> 00008 * 00009 * This program is free software; you can redistribute it and/or 00010 * modify it under the terms of the GNU General Public License as 00011 * published by the Free Software Foundation; either version 2 of the 00012 * License, or (at your option) any later version. 00013 * 00014 * This program is distributed in the hope that it will be useful, 00015 * but WITHOUT ANY WARRANTY; without even the implied warranty of 00016 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 00017 * GNU General Public License for more details. 00018 * 00019 * You should have received a copy of the GNU General Public License 00020 * along with this program; if not, write to the Free Software 00021 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 00022 * USA 00023 */ 00024 00025 #ifndef GCR_ATOM_H 00026 #define GCR_ATOM_H 00027 00028 #include <gcu/atom.h> 00029 #include <gcu/chemistry.h> 00030 #include <gcu/macros.h> 00031 #include <libxml/parser.h> 00032 #include <libxml/parserInternals.h> 00033 #include <libxml/xmlmemory.h> 00034 #include <list> 00035 00037 namespace gcr 00038 { 00039 00040 #define PREC 1e-3 00041 00045 class Atom : public gcu::Atom 00046 { 00047 public: 00048 /* 00049 The default constructor. 00050 */ 00051 Atom (); 00052 /* 00053 The destructor of Atom. 00054 */ 00055 virtual ~Atom (); 00056 00057 public : 00058 /* 00059 @param Z: the atomic number of the new atom. 00060 @param x: the x coordinate of the new atom. 00061 @param y: the y coordinate of the new atom. 00062 @param z: the z coordinate of the new atom. 00063 00064 Creates an atom. 00065 */ 00066 Atom (int Z, double x, double y, double z); 00072 Atom (Atom& caAtom); 00073 /* 00074 @param caAtom: the Atom to copy. 00075 00076 @return an Atom identical to caAtom. 00077 */ 00078 Atom& operator= (Atom& caAtom); 00079 00088 void SetColor (float red, float green, float blue, float alpha); 00092 void SetDefaultColor (); 00096 bool HasCustomColor () {return m_bCustomColor;} 00106 void GetColor (double *red, double *green, double *blue, double *alpha); 00112 void SetSize (double r); 00116 double GetSize (); 00121 bool operator== (Atom& caAtom); 00126 void Cleave () {m_nCleave++;} 00135 double ScalProd (int h, int k, int l); 00148 void NetToCartesian (double a, double b, double c, double alpha, double beta, double gamma); 00161 double Distance (double x, double y, double z, bool bFixed); 00165 double r () {return m_Radius.value.value;} 00169 const GcuAtomicRadius& GetRadius () {return m_Radius;} 00173 void SetRadius (const GcuAtomicRadius& r); 00177 bool IsCleaved () {return m_nCleave != 0;} 00184 virtual bool SaveNode (xmlDocPtr xml, xmlNodePtr node) const; 00190 virtual bool LoadNode (xmlNodePtr node); 00191 00192 protected: 00196 float m_fBlue; 00200 float m_fRed; 00204 float m_fGreen; 00208 float m_fAlpha; 00212 bool m_bCustomColor; 00216 GcuAtomicRadius m_Radius; 00222 int m_nCleave; //0 if not cleaved 00223 00231 bool SetProperty (unsigned property, char const *value); 00232 00239 std::string GetProperty (unsigned property) const; 00240 00241 GCU_PROP (double, EffectiveRadiusRatio); 00242 }; 00243 00247 typedef std::list<Atom*> AtomList; 00248 }// namespace gcr 00249 00250 #endif // GCR_ATOM_H