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class AtomType
{
%TypeHeaderCode
#include <BALL/KERNEL/atom.h>
using AtomType = Atom::Type;
%End
public:
%ConvertToTypeCode
if (sipIsErr == NULL)
return PyInt_Check(sipPy) || BALL_CAN_CONVERT_TO_INSTANCE(sipPy, Atom);
if (PyInt_Check(sipPy))
{
*sipCppPtr = new AtomType(PyInt_AS_LONG(sipPy));
return 1;
}
*sipCppPtr = BALL_CONVERT_TO_CPP(AtomType);
return 0;
%End
SIP_PYOBJECT __str__();
%MethodCode
sipRes = PyString_FromString(String(*sipCpp).c_str());
%End
SIP_PYOBJECT __repr__();
%MethodCode
sipRes = PyString_FromString(String(*sipCpp).c_str());
%End
};
class Atom
: Composite,
PropertyManager
{
%TypeHeaderCode
#include <BALL/KERNEL/atom.h>
using AtomType = Atom::Type;
%End
public:
enum
{
UNKNOWN_TYPE = -1,
ANY_TYPE = 0,
MAX_NUMBER_OF_BONDS = 12
};
enum Property
{
NUMBER_OF_PROPERTIES = 0
};
enum FullNameType
{
NO_VARIANT_EXTENSIONS,
ADD_VARIANT_EXTENSIONS,
ADD_RESIDUE_ID,
ADD_VARIANT_EXTENSIONS_AND_ID
};
Atom() throw();
Atom(const Atom&, bool deep = true) throw();
Atom
(Element&,
const String&, const String& type_name = "UNK" ,
int atom_type = UNKNOWN_TYPE ,
const Vector3& position = Vector3(0,0,0 ),
const Vector3& velocity = Vector3(0,0,0 ),
const Vector3& force = Vector3(0,0,0 ),
float charge = 0,
float radius = 0,
Index formal_charge = 0);
~Atom() throw();
virtual void clear() throw();
virtual void destroy() throw();
void set(const Atom&, bool deep = true) throw();
void get(Atom&, bool deep = true) const throw();
void swap(Atom&) throw();
// Predicates
bool operator == (const Atom&) const throw();
bool operator != (const Atom&) const throw();
// Accessors
void setElement(Element&) throw();
const Element& getElement() const throw();
void setCharge(float) throw();
float getCharge() const throw();
void setFormalCharge(Index) throw();
Index getFormalCharge() const throw();
Fragment* getFragment() throw();
Residue* getResidue() throw();
Chain* getChain() throw();
SecondaryStructure* getSecondaryStructure() throw();
Molecule* getMolecule() throw();
void setName(const String&) throw();
const String& getName() const throw();
String getFullName(FullNameType type = ADD_VARIANT_EXTENSIONS) const throw();
void setPosition(const Vector3&) throw();
const Vector3& getPosition() const throw();
float getDistance(const Atom& a) const;
void setRadius(float) throw();
float getRadius() const throw();
void setType(AtomType);
AtomType getType() const;
String getTypeName() const throw();
void setTypeName(const String&) throw();
void setVelocity(const Vector3&) throw();
const Vector3& getVelocity() const throw();
void setForce(const Vector3&) throw();
const Vector3& getForce() const throw();
Size countBonds() const;
Bond* getBond(Position) throw(IndexOverflow);
Bond* getBond(const Atom&) throw();
Bond* createBond(Atom&) throw(TooManyBonds);
Bond* createBond(Bond&, Atom&) throw(TooManyBonds);
Bond* cloneBond(Bond&, Atom&) throw();
bool destroyBond(const Atom&) throw();
void destroyBonds() throw();
bool hasBond(const Bond&) const throw();
bool isBoundTo(const Atom&) const throw();
bool isBound() const throw();
bool isGeminal(const Atom&) const throw();
bool isVicinal(const Atom&) const throw();
virtual bool isValid() const throw();
bool applyBonds(BondProcessor&) throw();
// convert the atom to a string representation
SIP_PYOBJECT __str__();
%MethodCode
sipRes = PyString_FromString(String(String("Atom ") + sipCpp->getName()
+ " { " + sipCpp->getElement().getSymbol() + " @ ("
+ String(sipCpp->getPosition().x) + " " + String(sipCpp->getPosition().y) + " "
+ String(sipCpp->getPosition().z) + ") }").c_str());
%End
SIP_PYOBJECT __repr__();
%MethodCode
sipRes = PyString_FromString(String(String("Atom ") + sipCpp->getName()
+ " { " + sipCpp->getElement().getSymbol() + " @ ("
+ String(sipCpp->getPosition().x) + " " + String(sipCpp->getPosition().y) + " "
+ String(sipCpp->getPosition().z) + " }").c_str());
%End
};
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