gcp/molecule.h
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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
00040 class Molecule: public gcu::Molecule
00041 {
00042 public:
00043 Molecule (gcu::TypeId Type = gcu::MoleculeType);
00044 Molecule (Atom* pAtom);
00045 virtual ~Molecule ();
00046 void AddChild (gcu::Object* object);
00047 void AddAtom (gcu::Atom* pAtom);
00048 void AddFragment (Fragment* pFragment);
00049 void AddBond (gcu::Bond* pBond);
00050 void Add (GtkWidget* w) const;
00051 void Remove (gcu::Object* pObject);
00052 bool Merge (Molecule* pMolecule, bool RemoveDuplicates = false);
00053 bool Load (xmlNodePtr);
00054 xmlNodePtr Save (xmlDocPtr xml) const;
00055 void Clear ();
00056 void SetSelected (GtkWidget* w, int state);
00057 void Transform2D (gcu::Matrix2D& m, double x, double y);
00058 Object* GetAtomAt (double x, double y, double z = 0.);
00059 double GetYAlign ();
00060 bool BuildContextualMenu (GtkUIManager *UIManager, gcu::Object *object, double x, double y);
00061 bool OnSignal (gcu::SignalId Signal, gcu::Object *Child);
00062 void ExportToGhemical ();
00063 void SelectAlignmentItem (gcu::Object *child);
00064 std::string GetAlignmentId () {return (m_Alignment)? m_Alignment->GetId (): "";}
00065 void BuildOBMol (OpenBabel::OBMol &Mol);
00066 void BuildOBMol2D (OpenBabel::OBMol &Mol);
00067 void ShowInChI ();
00068 void BuildInChI ();
00069 void BuildSMILES ();
00070 void ShowWebBase (char const *uri_start, char const *uri_end);
00071 void OpenCalc ();
00072 void CheckCrossings (Bond *pBond);
00073 char const *GetInChI ();
00074 std::string GetRawFormula () const;
00075 void OnLoaded ();
00076 unsigned GetAtomsNumber () const;
00077
00078 private:
00079 std::list<Fragment*> m_Fragments;
00080 gcu::Object *m_Alignment;
00081 std::string m_InChI;
00082 bool m_Changed;
00083 bool m_IsResidue;
00084 };
00085
00086 }
00087
00088 #endif // GCHEMPAINT_MOLECULE_H