gcp/molecule.h

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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

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