# 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);
    00089         void Add (GtkWidget* w) const;
    00095         void Remove (gcu::Object* pObject);
    00106         bool Merge (Molecule* pMolecule, bool RemoveDuplicates = false);
    00113         bool Load (xmlNodePtr node);
    00120         xmlNodePtr Save (xmlDocPtr xml) const;
    00124         void Clear ();
    00133         void Transform2D (gcu::Matrix2D& m, double x, double y);
    00142         Object* GetAtomAt (double x, double y, double z = 0.);
    00147         double GetYAlign ();
    00157         bool BuildContextualMenu (GtkUIManager *UIManager, gcu::Object *object, double x, double y);
    00166         bool OnSignal (gcu::SignalId Signal, gcu::Object *Child);
    00171         void ExportToGhemical ();
    00179         void SelectAlignmentItem (gcu::Object *child);
    00183         std::string GetAlignmentId () {return (m_Alignment)? m_Alignment->GetId (): "";}
    00191         void BuildOBMol (OpenBabel::OBMol &Mol);
    00198         void BuildOBMol2D (OpenBabel::OBMol &Mol);
    00203         void ShowInChI ();
    00207         void BuildInChI ();
    00212         void BuildSMILES ();
    00220         void ShowWebBase (char const *uri_start, char const *uri_end);
    00225         void OpenCalc ();
    00232         void CheckCrossings (Bond *pBond);
    00237         char const *GetInChI ();
    00242         std::string GetRawFormula () const;
    00246         void OnLoaded ();
    00251         unsigned GetAtomsNumber () const;
    00252
    00253 private:
    00254         std::list<Fragment*> m_Fragments;
    00255         gcu::Object *m_Alignment;
    00256         std::string m_InChI;
    00257         bool m_Changed;
    00258         bool m_IsResidue;
    00259 };
    00260
    00261 }       //      namespace gcp
    00262
    00263 #endif // GCHEMPAINT_MOLECULE_H