The Gnome Chemistry Utils 0.13.3
gcp/molecule.h
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00001 // -*- C++ -*-
00002 
00003 /* 
00004  * GChemPaint library
00005  * molecule.h 
00006  *
00007  * Copyright (C) 2001-2011 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 
00034 namespace gcu {
00035 class UIManager;
00036 }
00037 
00038 namespace gcp {
00039 
00040 class Bond;
00041 
00045 class Molecule: public gcu::Molecule
00046 {
00047 friend class MoleculePrivate;
00048 public:
00052         Molecule (gcu::TypeId Type = gcu::MoleculeType);
00059         Molecule (Atom* pAtom);
00063         virtual ~Molecule ();
00069         void AddChild (gcu::Object* object);
00075         void AddAtom (gcu::Atom* pAtom);
00081         void AddFragment (Fragment* pFragment);
00087         void AddBond (gcu::Bond* pBond);
00093         void Remove (gcu::Object* pObject);
00104         bool Merge (Molecule* pMolecule, bool RemoveDuplicates = false);
00111         bool Load (xmlNodePtr node);
00118         xmlNodePtr Save (xmlDocPtr xml) const;
00122         void Clear ();
00131         void Transform2D (gcu::Matrix2D& m, double x, double y);
00140         Object* GetAtomAt (double x, double y, double z = 0.);
00145         double GetYAlign ();
00155         bool BuildContextualMenu (gcu::UIManager *UIManager, gcu::Object *object, double x, double y);
00164         bool OnSignal (gcu::SignalId Signal, gcu::Object *Child);
00172         void SelectAlignmentItem (gcu::Object *child);
00176         std::string GetAlignmentId () {return (m_Alignment)? m_Alignment->GetId (): "";}
00181         void OpenCalc ();
00188         void CheckCrossings (Bond *pBond);
00193         std::string GetRawFormula () const;
00197         void OnLoaded ();
00202         unsigned GetAtomsNumber () const;
00203 
00204         double GetMeanBondLength () const;
00205         void AddChiralAtom (Atom *atom) {m_ChiralAtoms.insert (atom);}
00206         bool AtomIsChiral (Atom *atom) const;
00207 
00208 private:
00209         std::list< Fragment * > m_Fragments;
00210         std::set < Atom * > m_ChiralAtoms;
00211         gcu::Object *m_Alignment;
00212         bool m_IsResidue;
00213 };
00214 
00215 }       //      namespace gcp
00216 
00217 #endif // GCHEMPAINT_MOLECULE_H