The Gnome Chemistry Utils
0.12.11
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#include <gcu/atom.h>
Public Member Functions | |
Atom () | |
Atom (int Z, double x, double y, double z=0.) | |
Atom (Atom &a) | |
Atom & | operator= (Atom &a) |
virtual | ~Atom () |
double | Distance (Atom *pAtom) |
void | zoom (double ZoomFactor) |
virtual bool | GetCoords (double *x, double *y, double *z=NULL) const |
void | SetCoords (double x, double y, double z=0) |
int | GetZ () const |
virtual void | SetZ (int Z) |
virtual void | SetCharge (char Charge) |
char | GetCharge () |
virtual const gchar * | GetSymbol () const |
virtual void | AddBond (Bond *pBond) |
virtual void | RemoveBond (Bond *pBond) |
double | x () const |
double | y () const |
double | z () const |
Vector | GetVector () const |
Bond * | GetFirstBond (std::map< Atom *, Bond * >::iterator &i) |
Bond * | GetNextBond (std::map< Atom *, Bond * >::iterator &i) |
Bond * | GetBond (Atom *pAtom) const |
int | GetBondsNumber () const |
virtual xmlNodePtr | Save (xmlDocPtr xml) const |
virtual bool | Load (xmlNodePtr node) |
virtual bool | LoadNode (xmlNodePtr node) |
virtual bool | SaveNode (xmlDocPtr xml, xmlNodePtr node) const |
virtual void | Move (double x, double y, double z=0.) |
virtual void | Transform2D (Matrix2D &m, double x, double y) |
bool | SetProperty (unsigned property, char const *value) |
std::string | GetProperty (unsigned property) const |
bool | IsInCycle (Cycle *pCycle) |
virtual bool | Match (Atom *atom, AtomMatchState &state) |
std::string | Name () |
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Object (TypeId Id=OtherType) | |
virtual | ~Object () |
TypeId | GetType () const |
void | SetId (gchar const *Id) |
gchar const * | GetId () const |
virtual void | AddChild (Object *object) |
Object * | GetMolecule () const |
Object * | GetReaction () const |
Object * | GetGroup () const |
Document * | GetDocument () const |
Object * | GetParentOfType (TypeId Id) const |
Object * | GetChild (const gchar *Id) const |
Object * | GetFirstChild (std::map< std::string, Object * >::iterator &i) |
Object * | GetNextChild (std::map< std::string, Object * >::iterator &i) |
Object * | GetDescendant (const gchar *Id) const |
Object * | GetParent () const |
void | SetParent (Object *Parent) |
bool | SaveChildren (xmlDocPtr xml, xmlNodePtr node) const |
void | SaveId (xmlNodePtr node) const |
xmlNodePtr | GetNodeByProp (xmlNodePtr node, char const *Property, char const *Id) |
xmlNodePtr | GetNextNodeByProp (xmlNodePtr node, char const *Property, char const *Id) |
xmlNodePtr | GetNodeByName (xmlNodePtr node, char const *Name) |
xmlNodePtr | GetNextNodeByName (xmlNodePtr node, char const *Name) |
bool | HasChildren () const |
unsigned | GetChildrenNumber () const |
virtual Object * | GetAtomAt (double x, double y, double z=0.) |
virtual bool | Build (std::list< Object * > &Children) throw (std::invalid_argument) |
virtual double | GetYAlign () |
virtual bool | BuildContextualMenu (GtkUIManager *UIManager, Object *object, double x, double y) |
void | EmitSignal (SignalId Signal) |
virtual bool | OnSignal (SignalId Signal, Object *Child) |
void | Lock (bool state=true) |
bool | IsLocked () |
Object * | GetFirstLink (std::set< Object * >::iterator &i) |
Object * | GetNextLink (std::set< Object * >::iterator &i) |
void | Link (Object *object) |
void | Unlink (Object *object) |
virtual void | OnUnlink (Object *object) |
void | GetPossibleAncestorTypes (std::set< TypeId > &types) const |
virtual void | OnLoaded () |
void | SetDirty (bool dirty=true) |
virtual void | Clear () |
std::string | Identity () |
virtual char const * | HasPropertiesDialog () const |
void | ShowPropertiesDialog () |
bool | GetDirty (void) const |
Protected Attributes | |
int | m_Z |
double | m_x |
double | m_y |
double | m_z |
char | m_Charge |
std::map< Atom *, Bond * > | m_Bonds |
Additional Inherited Members | |
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static TypeId | AddType (std::string TypeName, Object *(*CreateFunc)(), TypeId id=OtherType) |
static void | AddAlias (TypeId id, std::string TypeName) |
static Object * | CreateObject (const std::string &TypeName, Object *parent=NULL) |
static TypeId | GetTypeId (const std::string &Name) |
static std::string | GetTypeName (TypeId Id) |
static void | AddMenuCallback (TypeId Id, BuildMenuCb cb) |
static void | AddRule (TypeId type1, RuleId rule, TypeId type2) |
static void | AddRule (const std::string &type1, RuleId rule, const std::string &type2) |
static const std::set< TypeId > & | GetRules (TypeId type, RuleId rule) |
static const std::set< TypeId > & | GetRules (const std::string &type, RuleId rule) |
static void | SetCreationLabel (TypeId Id, std::string Label) |
static const std::string & | GetCreationLabel (TypeId Id) |
static const std::string & | GetCreationLabel (const std::string &TypeName) |
static SignalId | CreateNewSignalId () |
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virtual Dialog * | BuildPropertiesDialog () |
This class is used to represent atoms.
Definition at line 46 of file gcu/atom.h.
gcu::Atom::Atom | ( | ) |
The default constructor. Creates an atom with atomic number set to 0.
Reimplemented in gcp::Atom.
gcu::Atom::Atom | ( | int | Z, |
double | x, | ||
double | y, | ||
double | z = 0. |
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Z | the atomic number of the new atom. |
x | the x coordinate of the new atom. |
y | the y coordinate of the new atom. |
z | the z coordinate of the new atom. |
Creates an atom.
Reimplemented in gcp::Atom.
gcu::Atom::Atom | ( | Atom & | a | ) |
a | the Atom to duplicate. |
Creates a new atom identical to a without any bond.
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double gcu::Atom::Distance | ( | Atom * | pAtom | ) |
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Definition at line 183 of file gcu/atom.h.
References m_Bonds.
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Definition at line 128 of file gcu/atom.h.
References m_Charge.
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x | a pointer to the double value which will receive the x coordinate of the Atom. |
y | a pointer to the double value which will receive the y coordinate of the Atom. |
z | a pointer to the double value which will receive the z coordinate of the Atom or NULL for 2D representations. |
Retrieves the coordinates of this Atom.
i | a C++ std::map iterator initialized by Atom::GetFirstBond. |
Use this method to iterate through the list of Bond instances of this Atom.
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property | the identity of the property as defined in objprops.h. |
Used by the gcu::Loader mechanism to retrieve properties of atoms.
Reimplemented from gcu::Object.
Reimplemented in gcu::CrystalAtom.
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Reimplemented in gcp::FragmentResidue.
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bool gcu::Atom::IsInCycle | ( | Cycle * | pCycle | ) |
pCycle | a cycle in which the atom might be. |
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node | a pointer to the xmlNode containing the serialized Atom. |
Loads an atom from an xmlNode.
Reimplemented from gcu::Object.
Reimplemented in gcp::Atom, gcp::FragmentAtom, and gcp::FragmentResidue.
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node | a pointer to the xmlNode containing the serialized Atom. |
This virtual method is called at the end of the Atom::Load method. The default behavior is to do nothing. It might be overrided for derived class when it is not convenient to override the Atom::Load method.
Reimplemented in gcp::Atom, and gcu::CrystalAtom.
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atom | the atom to which the this instance is to be compared. |
state | the AtomMatchState representing the current comparison state. |
Try to match atoms from two molecules which are compared. This function calls itself recursively until all atoms from the two molecules have been matched or until an difference is found. Overriden methods should call this base function and return its result.
Reimplemented in gcp::Atom, and gcp::FragmentAtom.
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x | the x component of the transation vector. |
y | the y component of the transation vector. |
z | the z component of the transation vector. |
Used to move an Atom.
Reimplemented from gcu::Object.
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Reimplemented from gcu::Object.
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xml | the xmlDoc used to save the document. |
Reimplemented from gcu::Object.
Reimplemented in gcp::Atom, gcp::FragmentAtom, and gcp::FragmentResidue.
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xml | the xmlDoc used to save the document. |
node | a pointer to the xmlNode to which this Atom is serialized. |
This virtual method is called at the end of the Atom::Save method. The default behavior is to do nothing. It might be overrided for derived class when it is not convenient to override the Atom::Save method.
Reimplemented in gcu::CrystalAtom.
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Charge | the new formal charge of the Atom. |
Changes the formal charge of this Atom.
Definition at line 124 of file gcu/atom.h.
References m_Charge.
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property | the identity of the property as defined in objprops.h. |
value | the value of the property as a string. |
Used by the gcu::Loader mechanism to load properties of atoms.
Reimplemented from gcu::Object.
Reimplemented in gcu::CrystalAtom.
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Z | the new atomic number of the Atom. |
This method might be overrided by derived class since changing the atomic number generally changes most properties. The default behavior is just to change the atomic number and nothing else.
Reimplemented in gcp::Atom, and gcp::FragmentAtom.
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m | the 2D Matrix of the transformation. |
x | the x component of the center of the transformation. |
y | the y component of the center of the transformation. |
Used to move and/or transform an atom.
Reimplemented from gcu::Object.
Reimplemented in gcp::Atom.
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Definition at line 148 of file gcu/atom.h.
References m_x.
Referenced by SetCoords().
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Definition at line 152 of file gcu/atom.h.
References m_y.
Referenced by SetCoords().
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Definition at line 156 of file gcu/atom.h.
References m_z.
Referenced by SetCoords().
void gcu::Atom::zoom | ( | double | ZoomFactor | ) |
ZoomFactor | the zoom factor. |
Multiplies all three coordinates of this Atom by ZoomFactor.
The Bond instances of the Atom. The index of the map is a pointer to the other end of the Bond.
Definition at line 292 of file gcu/atom.h.
Referenced by GetBondsNumber().
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The charge of the Atom.
Definition at line 288 of file gcu/atom.h.
Referenced by GetCharge(), gcp::Atom::GetCharge(), and SetCharge().
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The x coordinate of the Atom.
Definition at line 276 of file gcu/atom.h.
Referenced by SetCoords(), and x().
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The x coordinate of the Atom.
Definition at line 280 of file gcu/atom.h.
Referenced by SetCoords(), and y().
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The x coordinate of the Atom.
Definition at line 284 of file gcu/atom.h.
Referenced by SetCoords(), and z().