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
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 }
00255
00256 #endif // GCHEMPAINT_MOLECULE_H