The Gnome Chemistry Utils 0.13.3
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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) |
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 () |
Protected Attributes | |
int | m_Z |
double | m_x |
double | m_y |
double | m_z |
char | m_Charge |
std::map< Atom *, Bond * > | m_Bonds |
This class is used to represent atoms.
Definition at line 46 of file gcu/atom.h.
gcu::Atom::Atom | ( | ) |
gcu::Atom::Atom | ( | int | Z, |
double | x, | ||
double | y, | ||
double | z = 0. |
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) |
gcu::Atom::Atom | ( | Atom & | a | ) |
a | the Atom to duplicate. |
Creates a new atom identical to a without any bond.
virtual gcu::Atom::~Atom | ( | ) | [virtual] |
virtual void gcu::Atom::AddBond | ( | Bond * | pBond | ) | [virtual] |
double gcu::Atom::Distance | ( | Atom * | pAtom | ) |
int gcu::Atom::GetBondsNumber | ( | ) | const [inline] |
Definition at line 185 of file gcu/atom.h.
References m_Bonds.
char gcu::Atom::GetCharge | ( | ) | [inline] |
Definition at line 128 of file gcu/atom.h.
References m_Charge.
bool gcu::Atom::GetCoords | ( | double * | x, |
double * | y, | ||
double * | z = NULL |
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) | const [virtual] |
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.
Reimplemented from gcu::Object.
i | a C++ std::map iterator initialized by Atom::GetFirstBond. |
Use this method to iterate through the list of Bond instances of this Atom.
std::string gcu::Atom::GetProperty | ( | unsigned | property | ) | const [virtual] |
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 gcr::Atom.
virtual const gchar* gcu::Atom::GetSymbol | ( | ) | const [virtual] |
Reimplemented in gcp::FragmentResidue.
int gcu::Atom::GetZ | ( | ) | const [inline] |
bool gcu::Atom::IsInCycle | ( | Cycle * | pCycle | ) |
pCycle | a cycle in which the atom might be. |
virtual bool gcu::Atom::Load | ( | xmlNodePtr | node | ) | [virtual] |
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.
virtual bool gcu::Atom::LoadNode | ( | xmlNodePtr | node | ) | [virtual] |
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.
virtual bool gcu::Atom::Match | ( | Atom * | atom, |
AtomMatchState & | state | ||
) | [virtual] |
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.
virtual void gcu::Atom::Move | ( | double | x, |
double | y, | ||
double | z = 0. |
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) | [virtual] |
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.
Reimplemented in gcp::Atom.
std::string gcu::Atom::Name | ( | ) | [virtual] |
Reimplemented from gcu::Object.
virtual void gcu::Atom::RemoveBond | ( | Bond * | pBond | ) | [virtual] |
virtual xmlNodePtr gcu::Atom::Save | ( | xmlDocPtr | xml | ) | const [virtual] |
xml | the xmlDoc used to save the document. |
Reimplemented from gcu::Object.
Reimplemented in gcp::Atom, gcp::FragmentAtom, and gcp::FragmentResidue.
virtual bool gcu::Atom::SaveNode | ( | xmlDocPtr | xml, |
xmlNodePtr | node | ||
) | const [virtual] |
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 gcr::Atom.
virtual void gcu::Atom::SetCharge | ( | char | Charge | ) | [inline, virtual] |
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.
void gcu::Atom::SetCoords | ( | double | x, |
double | y, | ||
double | z = 0 |
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) | [inline] |
bool gcu::Atom::SetProperty | ( | unsigned | property, |
char const * | value | ||
) | [virtual] |
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.
virtual void gcu::Atom::SetZ | ( | int | Z | ) | [virtual] |
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.
virtual void gcu::Atom::Transform2D | ( | Matrix2D & | m, |
double | x, | ||
double | y | ||
) | [virtual] |
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.
double gcu::Atom::x | ( | ) | const [inline] |
Definition at line 148 of file gcu/atom.h.
References m_x.
Referenced by SetCoords().
double gcu::Atom::y | ( | ) | const [inline] |
Definition at line 152 of file gcu/atom.h.
References m_y.
Referenced by SetCoords().
double gcu::Atom::z | ( | ) | const [inline] |
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.
std::map<Atom*, Bond*> gcu::Atom::m_Bonds [protected] |
The Bond instances of the Atom. The index of the map is a pointer to the other end of the Bond.
Definition at line 294 of file gcu/atom.h.
Referenced by GetBondsNumber().
char gcu::Atom::m_Charge [protected] |
The charge of the Atom.
Definition at line 290 of file gcu/atom.h.
Referenced by gcp::Atom::GetCharge(), GetCharge(), and SetCharge().
double gcu::Atom::m_x [protected] |
The x coordinate of the Atom.
Definition at line 278 of file gcu/atom.h.
Referenced by SetCoords(), and x().
double gcu::Atom::m_y [protected] |
The x coordinate of the Atom.
Definition at line 282 of file gcu/atom.h.
Referenced by SetCoords(), and y().
double gcu::Atom::m_z [protected] |
The x coordinate of the Atom.
Definition at line 286 of file gcu/atom.h.
Referenced by SetCoords(), and z().
int gcu::Atom::m_Z [protected] |