#include <BALL/KERNEL/atom.h>
Classes | |
class | AttributeVector |
class | BondIteratorTraits |
class | StaticAtomAttributes |
Public Types | |
Enumerations | |
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, ADD_CHAIN_RESIDUE_ID, ADD_VARIANT_EXTENSIONS_AND_CHAIN_RESIDUE_ID } |
Public Member Functions | |
Constructors | |
Atom () | |
Atom (const Atom &atom, bool deep=true) | |
Atom (Element &element, const String &name, const String &type_name=BALL_ATOM_DEFAULT_TYPE_NAME, Type atom_type=BALL_ATOM_DEFAULT_TYPE, const Vector3 &position=Vector3(BALL_ATOM_DEFAULT_POSITION), const Vector3 &velocity=Vector3(BALL_ATOM_DEFAULT_VELOCITY), const Vector3 &force=Vector3(BALL_ATOM_DEFAULT_FORCE), float charge=BALL_ATOM_DEFAULT_CHARGE, float radius=BALL_ATOM_DEFAULT_RADIUS, Index formal_charge=BALL_ATOM_DEFAULT_FORMAL_CHARGE) | |
Destructors | |
virtual | ~Atom () |
virtual void | clear () |
virtual void | destroy () |
Persistence | |
virtual void | persistentWrite (PersistenceManager &pm, const char *name=0) const throw (Exception::GeneralException) |
virtual void | persistentRead (PersistenceManager &pm) throw (Exception::GeneralException) |
Assignment methods | |
void | set (const Atom &atom, bool deep=true) |
void | get (Atom &atom, bool deep=true) const |
Atom & | operator= (const Atom &atom) |
void | swap (Atom &atom) |
bool | operator== (const Atom &atom) const |
bool | operator!= (const Atom &atom) const |
Accessors | |
void | setElement (const Element &element) |
Assign the atom's element. | |
const Element & | getElement () const |
Return the atom's element. | |
void | setCharge (float charge) |
float | getCharge () const |
void | setFormalCharge (Index formal_charge) |
Set the atom's formal charge. | |
Index | getFormalCharge () const |
Return the atom's formal charge. | |
const Molecule * | getMolecule () const |
Molecule * | getMolecule () |
Return the molecule the atom is contained in (mutable). | |
const Fragment * | getFragment () const |
Fragment * | getFragment () |
Return the fragment the atom is contained in (mutable). | |
const Residue * | getResidue () const |
Residue * | getResidue () |
Return the residue the atom is contained in (mutable). | |
const SecondaryStructure * | getSecondaryStructure () const |
SecondaryStructure * | getSecondaryStructure () |
Return the secondary structure the atom is contained in (mutable). | |
const Chain * | getChain () const |
Chain * | getChain () |
Return the chain the atom is contained in (mutable). | |
void | setName (const String &name) |
Set the atom name. | |
const String & | getName () const |
Return the atom name. | |
String | getFullName (FullNameType type=ADD_VARIANT_EXTENSIONS) const |
void | setPosition (const Vector3 &position) |
Vector3 & | getPosition () |
Return the atom coordinates (mutable). | |
const Vector3 & | getPosition () const |
Return the atom coordinates (const). | |
void | setRadius (float radius) |
float | getRadius () const |
Return the atom radius. | |
void | setType (Type atom_type) |
Assign the numerical atom type. | |
Type | getType () const |
Return the (numerical) atom type. | |
String | getTypeName () const |
Return the atom type name. | |
void | setTypeName (const String &name) |
Assign the atom type name. | |
void | setVelocity (const Vector3 &velocity) |
const Vector3 & | getVelocity () const |
void | setForce (const Vector3 &force) |
const Vector3 & | getForce () const |
Return the atom's force vector (const). | |
Vector3 & | getForce () |
Return the atom's force vector (mutable). | |
Size | countBonds () const |
Return the number of bonds. | |
Bond * | getBond (Position index) throw (Exception::IndexOverflow) |
const Bond * | getBond (Position index) const throw (Exception::IndexOverflow) |
Bond * | getBond (const Atom &atom) |
const Bond * | getBond (const Atom &atom) const |
Miscellaneous | |
Bond * | createBond (Atom &atom) throw (Exception::TooManyBonds) |
Bond * | createBond (Bond &bond, Atom &atom) throw (Exception::TooManyBonds) |
Bond * | cloneBond (Bond &bond, Atom &atom) |
bool | destroyBond (const Atom &atom) |
void | destroyBonds () |
Atom * | getPartnerAtom (Position i) throw (Exception::IndexOverflow) |
const Atom * | getPartnerAtom (Position i) const throw (Exception::IndexOverflow) |
float | getDistance (const Atom &a) const |
Predicates | |
bool | hasBond (const Bond &bond) const |
bool | isBoundTo (const Atom &atom) const |
bool | isBound () const |
bool | isGeminal (const Atom &atom) const |
bool | isVicinal (const Atom &atom) const |
Debuggers and diagnostics | |
virtual bool | isValid () const |
virtual void | dump (std::ostream &s=std::cout, Size depth=0) const |
Internal iteration | |
bool | applyBonds (UnaryProcessor< Bond > &processor) |
Private Member Functions | |
void | clear_ () |
void | swapLastBond_ (const Atom *atom) |
Static Private Member Functions | |
static Position | nextIndex_ () |
Return the next unallocated index in the static attribute array. | |
static void | freeIndex_ (Position index) |
Free an index in the static attribute array. | |
Class friends | |
| |
typedef short | Type |
class | Bond |
External iteration | |
typedef Index | BondIteratorPosition |
typedef RandomAccessIterator < Atom, Bond, BondIteratorPosition, BondIteratorTraits > | BondIterator |
typedef ConstRandomAccessIterator < Atom, Bond, BondIteratorPosition, BondIteratorTraits > | BondConstIterator |
Constant random access iterator for bonds. | |
typedef std::reverse_iterator < BondIterator > | BondReverseIterator |
Reverse random access iterator for bonds. | |
typedef std::reverse_iterator < BondConstIterator > | BondConstReverseIterator |
Constant reverse random access iterator for bonds. | |
class | BondIteratorTraits |
BondIterator | beginBond () |
Return a bond iterator pointing to the first bond of the atom. | |
BondIterator | endBond () |
Return a past-the-end bond iterator. | |
BondConstIterator | beginBond () const |
Return a constant bond iterator pointing to the first bond. | |
BondConstIterator | endBond () const |
Return a constant past-the-end bond iterator. | |
BondReverseIterator | rbeginBond () |
Return a reverse bond iterator pointing to the last bond. | |
BondReverseIterator | rendBond () |
Return a past-the-end bond iterator for reverse traversal. | |
BondConstReverseIterator | rbeginBond () const |
Return a constant reverse bond iterator pointing to the first atom. | |
BondConstReverseIterator | rendBond () const |
Return a constant past-the-end bond iterator for reverse traversal. | |
Efficient handling of atom attributes | |
typedef std::list< Atom * > | AtomPtrList |
typedef std::list< Position > | AtomIndexList |
Position | getIndex () const |
StaticAtomAttributes * | getAttributePtr () |
const StaticAtomAttributes * | getAttributePtr () const |
static Position | compact (const AtomIndexList &indices) throw (Exception::OutOfRange) |
static AttributeVector & | getAttributes () |
static const PreciseTime & | getAttributesModificationTime () |
Attributes | |
static AttributeVector | static_attributes_ |
static AtomIndexList | free_list_ |
static PreciseTime | attributes_changed_time_ |
time of the last resize of the attributes vector | |
Position | index_ |
const Element * | element_ |
String | name_ |
String | type_name_ |
float | radius_ |
unsigned char | number_of_bonds_ |
Bond * | bond_ [MAX_NUMBER_OF_BONDS] |
Atom class. A class representing atoms. During each runtime instance of a program an atom is unique and identified by a Object::Handle . Atom equality is defined as atom identity, so there cannot be any two identical atoms. A linear ordering of atoms is defined as the linear order of the Object::Handle s.
typedef std::list<Position> BALL::Atom::AtomIndexList |
typedef std::list<Atom*> BALL::Atom::AtomPtrList |
typedef ConstRandomAccessIterator<Atom, Bond, BondIteratorPosition, BondIteratorTraits> BALL::Atom::BondConstIterator |
Constant random access iterator for bonds.
typedef std::reverse_iterator<BondConstIterator> BALL::Atom::BondConstReverseIterator |
Constant reverse random access iterator for bonds.
typedef RandomAccessIterator<Atom, Bond, BondIteratorPosition, BondIteratorTraits> BALL::Atom::BondIterator |
Random access iterator for bonds.
typedef std::reverse_iterator<BondIterator> BALL::Atom::BondReverseIterator |
Reverse random access iterator for bonds.
typedef short BALL::Atom::Type |
Atom type.
anonymous enum |
The type of name used for getFullName.
enum BALL::Atom::Property |
Predefined properties. Enumeration of all properties that are used by the BALL kernel.
Reimplemented in BALL::PDBAtom.
BALL::Atom::Atom | ( | ) |
Default constructor. The state of this instance is:
Copy constructor. The copy is either deep (default) or shallow.
atom | the atom to be copied (cloned) | |
deep | make a deep (=true ) or shallow (=false ) copy of atom |
BALL::Atom::Atom | ( | Element & | element, | |
const String & | name, | |||
const String & | type_name = BALL_ATOM_DEFAULT_TYPE_NAME , |
|||
Type | atom_type = BALL_ATOM_DEFAULT_TYPE , |
|||
const Vector3 & | position = Vector3(BALL_ATOM_DEFAULT_POSITION) , |
|||
const Vector3 & | velocity = Vector3(BALL_ATOM_DEFAULT_VELOCITY) , |
|||
const Vector3 & | force = Vector3(BALL_ATOM_DEFAULT_FORCE) , |
|||
float | charge = BALL_ATOM_DEFAULT_CHARGE , |
|||
float | radius = BALL_ATOM_DEFAULT_RADIUS , |
|||
Index | formal_charge = BALL_ATOM_DEFAULT_FORMAL_CHARGE | |||
) |
Detailed state initializing constructor. The item bond table is empty (atom has no bonds).
element | element type of the constructed atom | |
name | name of the constructed atom | |
type_name | type name name of the constructed atom | |
atom_type | type of the constructed atom | |
position | position of the constructed atom | |
velocity | velocity of the constructed atom | |
force | force acting upon the constructed atom | |
charge | charge of the constructed atom | |
formal_charge | formal charge of the constructed atom | |
radius | radius of the constructed atom |
virtual BALL::Atom::~Atom | ( | ) | [virtual] |
Destructor. If the atom has bonds in common with an other atom that atom is disconnected and the associated Bond instance is destroyed. Calls Atom::destroy .
bool BALL::Atom::applyBonds | ( | UnaryProcessor< Bond > & | processor | ) |
Application of an unary processor on every contained bond.
processor | a typed unary processor for Bond instances |
true
if application has been terminated successfully, false
otherwise BondConstIterator BALL::Atom::beginBond | ( | ) | const [inline] |
Return a constant bond iterator pointing to the first bond.
BondIterator BALL::Atom::beginBond | ( | ) | [inline] |
Return a bond iterator pointing to the first bond of the atom.
virtual void BALL::Atom::clear | ( | ) | [virtual] |
Explicit default initialization. Calls Composite::clear and resets the attributes to the default values. In contrast to destroy , the atom is not removed from any composite structure, i.e. its parent fragment pointer remains unchanged.
Reimplemented from BALL::Composite.
Reimplemented in BALL::PDBAtom.
void BALL::Atom::clear_ | ( | ) | [private] |
Reimplemented in BALL::PDBAtom.
Create a copy of a bond. This is mostly for internal use and should not be required by most users.
static Position BALL::Atom::compact | ( | const AtomIndexList & | indices | ) | throw (Exception::OutOfRange) [static] |
Compact memory for a list of atoms. This method packs the static attributes of the atom in the given range into a contiguous memory segment in order to increase locality.
Size BALL::Atom::countBonds | ( | ) | const |
Return the number of bonds.
Bond* BALL::Atom::createBond | ( | Bond & | bond, | |
Atom & | atom | |||
) | throw (Exception::TooManyBonds) |
Create a new bond from an already existing instance of Bond. Initialize the bond bond to connect this instance to atom . Calls Bond::createBond . The state of the bond is initialzed to the default values.
Bond* BALL::Atom::createBond | ( | Atom & | atom | ) | throw (Exception::TooManyBonds) |
Create a new bond to an atom. Create a new instance of Bond connecting this instance to atom . Calls Bond::createBond . The state of the bond is initialized to the default values.
virtual void BALL::Atom::destroy | ( | ) | [virtual] |
Explicit destructor. Destroy this instance explicitly and reset its attributes to the default values.
Reimplemented from BALL::Composite.
Reimplemented in BALL::PDBAtom.
Explicit bond destruction. Destroy the bond connecting {*this atom} and atom explicitly. If the bond is auto-deletable the default destructor is called otherwise Bond::destroy .
delete
. This is due to erroneous explicit destruction of statically allocated bonds. atom | the atom that should be disconnected from this instance |
void BALL::Atom::destroyBonds | ( | ) |
Explicit bond table destruction. Destroy all the bonds connecting {*this atom} with another atom explicitly. If the bonds are auto-deletable the default destructors are called otherwise Bond::destroy .
delete
. This is due to erroneous explicit destruction of statically allocated bonds. atom | the atom that should be disconnected from this instance |
virtual void BALL::Atom::dump | ( | std::ostream & | s = std::cout , |
|
Size | depth = 0 | |||
) | const [virtual] |
Internal state dump. Dump the current internal state of this instance to the output ostream s with dumping depth depth . For debugging purposes only.
s | - output stream where to output the internal state | |
depth | - the dumping depth |
Reimplemented from BALL::Composite.
Reimplemented in BALL::PDBAtom.
BondConstIterator BALL::Atom::endBond | ( | ) | const [inline] |
Return a constant past-the-end bond iterator.
BondIterator BALL::Atom::endBond | ( | ) | [inline] |
Return a past-the-end bond iterator.
static void BALL::Atom::freeIndex_ | ( | Position | index | ) | [static, private] |
Free an index in the static attribute array.
const StaticAtomAttributes* BALL::Atom::getAttributePtr | ( | ) | const |
StaticAtomAttributes* BALL::Atom::getAttributePtr | ( | ) |
static AttributeVector& BALL::Atom::getAttributes | ( | ) | [static] |
Access to the static attribute array
Referenced by BALL::AmberTorsion::SingleAmberTorsion::SingleAmberTorsion().
static const PreciseTime& BALL::Atom::getAttributesModificationTime | ( | ) | [inline, static] |
Get the time, when the attributes vector was last modified. This needed for the GeometricObject 's in VIEW, because they store pointer to the position of atoms. These have to be updated, after a resize of the vector.
Return a bond by its partner atom (mutable) The reference is 0 if this instance does not have a bond with atom .
atom | the atom that is considered to have a bond with this instance |
Return a bond by its partner atom (const). The reference is 0 if this instance does not have a bond with atom .
atom | the atom that is considered to have a bond with this instance |
atom
with this instance, 0 if this instance does not have a bond with atom const Bond* BALL::Atom::getBond | ( | Position | index | ) | const throw (Exception::IndexOverflow) |
Return a bond by its index (const).
IndexOverflow | if index >= MAX_NUMBER_OF_BONDS |
Bond* BALL::Atom::getBond | ( | Position | index | ) | throw (Exception::IndexOverflow) |
Return a bond by its index (mutable). The reference is 0 if this instance does not have a bond with index index .
index | the index of the bond to be accessed to |
IndexOverflow | if index >= MAX_NUMBER_OF_BONDS |
Chain* BALL::Atom::getChain | ( | ) |
Return the chain the atom is contained in (mutable).
Reimplemented in BALL::PDBAtom.
const Chain* BALL::Atom::getChain | ( | ) | const |
Return the chain the atom is contained in (const). A NULL pointer is returned if this atom is not part of a chain.
Reimplemented in BALL::PDBAtom.
Referenced by BALL::PDB::Structure::AtomEntry::AtomEntry().
float BALL::Atom::getCharge | ( | ) | const |
Return the atom's (partial) charge. Charges should be assigned in multiples of the proton charge (elementary charge).
A convenience function for computing the distance between two atoms. This is equivalent to calling this->getPosition().getDistance(a.getPosition())
a | the atom to which to compute the distance |
const Element& BALL::Atom::getElement | ( | ) | const |
Return the atom's element.
Vector3& BALL::Atom::getForce | ( | ) |
Return the atom's force vector (mutable).
const Vector3& BALL::Atom::getForce | ( | ) | const |
Return the atom's force vector (const).
Index BALL::Atom::getFormalCharge | ( | ) | const |
Return the atom's formal charge.
Reimplemented in BALL::SmilesParser::SPAtom.
Fragment* BALL::Atom::getFragment | ( | ) |
Return the fragment the atom is contained in (mutable).
const Fragment* BALL::Atom::getFragment | ( | ) | const |
Return the fragment the atom is contained in (const). A NULL pointer is returned if this atom is not part of a fragment.
String BALL::Atom::getFullName | ( | FullNameType | type = ADD_VARIANT_EXTENSIONS |
) | const |
Assemble a fully specified atom name. This method returns at fully specified atom name as used for charge and type assignments. The name consists of the name of the residue the atom is contained in, a colon, and the atom name. Blanks are removed from both names. For example, for the alpha carbon atom of isoleucine getFullName
will return the name ILE:CA
. For N terminal residues, -N
is appended to the residue name, for C terminal residues -C
. If the residue is a CYS involved in a disulphide bridge, an additional -S
or S
(for terminal residue) is appended. For single amino acids (C and N terminal) -M
is added.
type | if type is set to Atom::NO_VARIANT_EXTENSIONS , the variant extension (-XX ) is omitted |
Position BALL::Atom::getIndex | ( | ) | const |
Return the index in the static attribute array
Referenced by BALL::AmberTorsion::SingleAmberTorsion::SingleAmberTorsion().
Molecule* BALL::Atom::getMolecule | ( | ) |
Return the molecule the atom is contained in (mutable).
const Molecule* BALL::Atom::getMolecule | ( | ) | const |
Return the molecule the atom is contained in (const). A NULL pointer is returned if this atom is not part of a molecule.
const String& BALL::Atom::getName | ( | ) | const |
Return the atom name.
const Atom* BALL::Atom::getPartnerAtom | ( | Position | i | ) | const throw (Exception::IndexOverflow) |
Returns the Atom bound at the i-th bond. This is a convenience function for: getBond(i)->getBoundAtom(*this)
i | The index of the partner atom |
Atom* BALL::Atom::getPartnerAtom | ( | Position | i | ) | throw (Exception::IndexOverflow) |
Returns the Atom bound at the i-th bond. This is a convenience function for: getBond(i)->getBoundAtom(*this)
i | The index of the partner atom |
Exception::IndexOverflow | is thrown if i >= countBonds(). This exception originates from getBond(i) |
const Vector3& BALL::Atom::getPosition | ( | ) | const |
Return the atom coordinates (const).
Vector3& BALL::Atom::getPosition | ( | ) |
Return the atom coordinates (mutable).
Referenced by BALL::GeometricCenterProcessor::operator()(), and BALL::BoundingBoxProcessor::operator()().
float BALL::Atom::getRadius | ( | ) | const |
Return the atom radius.
Residue* BALL::Atom::getResidue | ( | ) |
Return the residue the atom is contained in (mutable).
Reimplemented in BALL::PDBAtom.
const Residue* BALL::Atom::getResidue | ( | ) | const |
Return the residue the atom is contained in (const). A NULL pointer is returned if this atom is not part of a residue.
Reimplemented in BALL::PDBAtom.
Referenced by BALL::PDB::Structure::AtomEntry::AtomEntry().
SecondaryStructure* BALL::Atom::getSecondaryStructure | ( | ) |
Return the secondary structure the atom is contained in (mutable).
const SecondaryStructure* BALL::Atom::getSecondaryStructure | ( | ) | const |
Return the secondary structure the atom is contained in (const). A NULL pointer is returned if this atom is not part of a secondary structure.
Referenced by BALL::PDB::Structure::AtomEntry::AtomEntry().
Type BALL::Atom::getType | ( | ) | const |
Return the (numerical) atom type.
String BALL::Atom::getTypeName | ( | ) | const |
Return the atom type name.
const Vector3& BALL::Atom::getVelocity | ( | ) | const |
Return the atom velocity. BALL uses units of for the velocity.
Determine whether the atom takes part in a certain bond.
bond | the bond in question |
true
if the bond bond connects this instance with another atom, false
otherwise bool BALL::Atom::isBound | ( | ) | const |
Determine whether the atom has any bond.
true
if an atom is bound to this instance, false
otherwise Determine whether there exists a bond to another atom. Calls Atom::getBond . Hydrogen bonds (type = Bond::TYPE__HYDROGEN) are ignored.
atom | the atom in question |
true
if bond connects atom with {*this atom}, false
otherwise True if the two atoms are geminal. Two atoms are geminal if they do not share a common bond but both have a bond to a third atom. For example the two hydrogen atoms in water are geminal. Hydrogen bonds (type = Bond::TYPE__HYDROGEN) are ignored.
atom | the second atom |
atom
is geminal to this instance virtual bool BALL::Atom::isValid | ( | ) | const [virtual] |
Internal state and consistency self-validation.
true
if the internal state of this instance is correct (self-validated) and consistent, false
otherwise Reimplemented from BALL::Composite.
True if the two atoms are vicinal. Two atoms are vicinal if they are separated by three bonds (1-4 position). Hydrogen bonds (type = Bond::TYPE__HYDROGEN) are ignored.
atom | the second atom |
atom
is vicinal to this instance static Position BALL::Atom::nextIndex_ | ( | ) | [static, private] |
Return the next unallocated index in the static attribute array.
Predicates Equality operator. Two atoms are equal if they have the same handle.
virtual void BALL::Atom::persistentRead | ( | PersistenceManager & | pm | ) | throw (Exception::GeneralException) [virtual] |
Read an Atom from a persistent stream.
pm | the persistence manager |
Reimplemented from BALL::Composite.
Reimplemented in BALL::PDBAtom.
virtual void BALL::Atom::persistentWrite | ( | PersistenceManager & | pm, | |
const char * | name = 0 | |||
) | const throw (Exception::GeneralException) [virtual] |
Write an Atom to a persistent stream.
pm | the persistence manager |
Reimplemented from BALL::Composite.
Reimplemented in BALL::PDBAtom.
BondConstReverseIterator BALL::Atom::rbeginBond | ( | ) | const [inline] |
Return a constant reverse bond iterator pointing to the first atom.
BondReverseIterator BALL::Atom::rbeginBond | ( | ) | [inline] |
Return a reverse bond iterator pointing to the last bond.
BondConstReverseIterator BALL::Atom::rendBond | ( | ) | const [inline] |
Return a constant past-the-end bond iterator for reverse traversal.
BondReverseIterator BALL::Atom::rendBond | ( | ) | [inline] |
Return a past-the-end bond iterator for reverse traversal.
Deep/shallow assignment. The assignment is either deep or shallow (default is deep). In the case of a deep assignment, all composites contained in atom
are copied as well.
atom | the atom to be copied | |
deep | make a deep (=true) or shallow (=false) copy of atom |
void BALL::Atom::setCharge | ( | float | charge | ) |
Set the atom's (partial) charge. Charges should be assigned in multiples of the proton charge (elementary charge).
void BALL::Atom::setElement | ( | const Element & | element | ) |
Assign the atom's element.
void BALL::Atom::setForce | ( | const Vector3 & | force | ) |
Assign the atom's force vevtor. BALL uses units of Newton (1 N = 1 J/m) as the unit of force.
void BALL::Atom::setFormalCharge | ( | Index | formal_charge | ) |
Set the atom's formal charge.
Reimplemented in BALL::SmilesParser::SPAtom.
void BALL::Atom::setName | ( | const String & | name | ) |
Set the atom name.
void BALL::Atom::setPosition | ( | const Vector3 & | position | ) |
Assign the atom coordinates. BALL uses units of Angstrom for atom coordinates.
void BALL::Atom::setRadius | ( | float | radius | ) |
Set the atom radius. BALL uses units of Angstrom for the atom radii.
void BALL::Atom::setType | ( | Type | atom_type | ) |
Assign the numerical atom type.
void BALL::Atom::setTypeName | ( | const String & | name | ) |
Assign the atom type name.
void BALL::Atom::setVelocity | ( | const Vector3 & | velocity | ) |
Set the atom velocity BALL uses units of for the velocity.
void BALL::Atom::swap | ( | Atom & | atom | ) |
Swap the contents of two atoms. The static attributes are swapped by exchanging the indices of the two atoms!
atom | the atom being swapped with this instance |
void BALL::Atom::swapLastBond_ | ( | const Atom * | atom | ) | [private] |
friend class Bond [friend] |
Reimplemented in BALL::PDBAtom.
friend class BondIteratorTraits [friend] |
PreciseTime BALL::Atom::attributes_changed_time_ [static, protected] |
time of the last resize of the attributes vector
Bond* BALL::Atom::bond_[MAX_NUMBER_OF_BONDS] [protected] |
const Element* BALL::Atom::element_ [protected] |
AtomIndexList BALL::Atom::free_list_ [static, protected] |
Position BALL::Atom::index_ [protected] |
String BALL::Atom::name_ [protected] |
unsigned char BALL::Atom::number_of_bonds_ [protected] |
float BALL::Atom::radius_ [protected] |
AttributeVector BALL::Atom::static_attributes_ [static, protected] |
String BALL::Atom::type_name_ [protected] |