The Gnome Chemistry Utils 0.12.9
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00001 // -*- C++ -*- 00002 00003 /* 00004 * GChemPaint library 00005 * molecule.h 00006 * 00007 * Copyright (C) 2001-2008 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 GCHEMPAINT_MOLECULE_H 00026 #define GCHEMPAINT_MOLECULE_H 00027 00028 #include "fragment.h" 00029 #include <list> 00030 #include <gcu/molecule.h> 00031 #include <openbabel/mol.h> 00032 00034 namespace gcp { 00035 00036 class Bond; 00037 00041 class Molecule: public gcu::Molecule 00042 { 00043 public: 00047 Molecule (gcu::TypeId Type = gcu::MoleculeType); 00054 Molecule (Atom* pAtom); 00058 virtual ~Molecule (); 00064 void AddChild (gcu::Object* object); 00070 void AddAtom (gcu::Atom* pAtom); 00076 void AddFragment (Fragment* pFragment); 00082 void AddBond (gcu::Bond* pBond); 00088 void Remove (gcu::Object* pObject); 00099 bool Merge (Molecule* pMolecule, bool RemoveDuplicates = false); 00106 bool Load (xmlNodePtr node); 00113 xmlNodePtr Save (xmlDocPtr xml) const; 00117 void Clear (); 00126 void Transform2D (gcu::Matrix2D& m, double x, double y); 00135 Object* GetAtomAt (double x, double y, double z = 0.); 00140 double GetYAlign (); 00150 bool BuildContextualMenu (GtkUIManager *UIManager, gcu::Object *object, double x, double y); 00159 bool OnSignal (gcu::SignalId Signal, gcu::Object *Child); 00164 void ExportToGhemical (); 00172 void SelectAlignmentItem (gcu::Object *child); 00176 std::string GetAlignmentId () {return (m_Alignment)? m_Alignment->GetId (): "";} 00184 void BuildOBMol (OpenBabel::OBMol &Mol); 00191 void BuildOBMol2D (OpenBabel::OBMol &Mol); 00196 void ShowInChI (); 00200 void BuildInChI (); 00205 void BuildSMILES (); 00213 void ShowWebBase (char const *uri_start, char const *uri_end); 00218 void OpenCalc (); 00225 void CheckCrossings (Bond *pBond); 00230 char const *GetInChI (); 00235 std::string GetRawFormula () const; 00239 void OnLoaded (); 00244 unsigned GetAtomsNumber () const; 00245 00246 private: 00247 std::list<Fragment*> m_Fragments; 00248 gcu::Object *m_Alignment; 00249 std::string m_InChI; 00250 bool m_Changed; 00251 bool m_IsResidue; 00252 }; 00253 00254 } // namespace gcp 00255 00256 #endif // GCHEMPAINT_MOLECULE_H