BALL
1.4.1
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#include <BALL/KERNEL/PDBAtom.h>
Atom class with additional attributes. This class represents atoms read from PDB files. It contains additional attributes to hold the crystallographic properties of atoms from a PDB file (e.g., temperature factor, occupancy). For details on the PDB format and the detailed meaning of those fields, please refer to the PDB documentation at http://www.rcsb.org
Properties of the PDBAtom.
PROPERTY__HETATM |
Property which indicates whether the current atom is a HETATM. |
NUMBER_OF_PROPERTIES |
The number of properties in PDBAtom. |
Reimplemented from BALL::Atom.
Possible values for the PDB remoteness indicator
Default constructor.
BALL::PDBAtom::PDBAtom | ( | const PDBAtom & | pdb_atom, |
bool | deep = true |
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) |
Copy constructor.
BALL::PDBAtom::PDBAtom | ( | const String & | name | ) |
Constructor.
BALL::PDBAtom::PDBAtom | ( | Element & | element, |
const String & | name, | ||
const String & | type_name = BALL_ATOM_DEFAULT_TYPE_NAME , |
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Atom::Type | atom_type = BALL_ATOM_DEFAULT_TYPE , |
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const Vector3 & | position = Vector3(BALL_ATOM_DEFAULT_POSITION) , |
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const Vector3 & | velocity = Vector3(BALL_ATOM_DEFAULT_VELOCITY) , |
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const Vector3 & | force = Vector3(BALL_ATOM_DEFAULT_FORCE) , |
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float | charge = BALL_ATOM_DEFAULT_CHARGE , |
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float | radius = BALL_ATOM_DEFAULT_RADIUS , |
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char | branch_designator = BALL_PDBATOM_DEFAULT_BRANCH_DESIGNATOR , |
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char | remoteness_indicator = BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR , |
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char | alternate_location_indicator = BALL_PDBATOM_DEFAULT_ALTERNATE_LOCATION_INDICATOR , |
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float | occupancy = BALL_PDBATOM_DEFAULT_OCCUPANCY , |
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float | temperature_factor = BALL_PDBATOM_DEFAULT_TEMPERATURE_FACTOR |
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) |
Detailed constructor.
virtual BALL::PDBAtom::~PDBAtom | ( | ) | [virtual] |
Destructor.
virtual void BALL::PDBAtom::clear | ( | ) | [virtual] |
Clear the contents of the atom.
Reimplemented from BALL::Atom.
void BALL::PDBAtom::clear_ | ( | ) | [private] |
Reimplemented from BALL::Atom.
virtual void BALL::PDBAtom::destroy | ( | ) | [virtual] |
Clears the contents of the atom and removes it from all composite structures.
Reimplemented from BALL::Atom.
virtual void BALL::PDBAtom::dump | ( | std::ostream & | s = std::cout , |
Size | depth = 0 |
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) | const [virtual] |
Internal state dump. Dump the current internal state of {*this} to the output ostream s with dumping depth depth .
s | output stream where to output the internal state of the instance |
depth | the dumping depth |
Reimplemented from BALL::Atom.
void BALL::PDBAtom::get | ( | PDBAtom & | pdb_atom, |
bool | deep = true |
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) | const |
Copy this instance to {pdb_atom}. The assignment is either deep or shallow (default).
pdb_atom | the PDBAtom to be assigned to |
char BALL::PDBAtom::getAlternateLocationIndicator | ( | ) | const |
Get the alternate location indicator.
char BALL::PDBAtom::getBranchDesignator | ( | ) | const |
Get the branch designator.
Get a pointer to the parent chain. The pointer is 0 if the instance does not have a parent chain.
Reimplemented from BALL::Atom.
const Chain* BALL::PDBAtom::getChain | ( | ) | const |
Get a pointer to the parent chain. The pointer is 0 if the instance does not have a parent chain.
Reimplemented from BALL::Atom.
float BALL::PDBAtom::getOccupancy | ( | ) | const |
Get the occupancy.
Get a pointer to the parent protein. The pointer is 0 if the instance does not have a parent protein.
const Protein* BALL::PDBAtom::getProtein | ( | ) | const |
Get a pointer to the parent protein. The pointer is 0 if the instance does not have a parent protein.
char BALL::PDBAtom::getRemotenessIndicator | ( | ) | const |
Get the remoteness indicator.
Get a pointer to the parent residue. The pointer is 0 if the instance does not have a parent residue.
Reimplemented from BALL::Atom.
const Residue* BALL::PDBAtom::getResidue | ( | ) | const |
Get a pointer to the parent residue. The pointer is 0 if the instance does not have a parent residue.
Reimplemented from BALL::Atom.
float BALL::PDBAtom::getTemperatureFactor | ( | ) | const |
Get the temperature factor.
Inequality operator
Assignment operator. The assignment is deep.
pdb_atom | the PDBAtom to be copied (cloned) |
Equality operator.
void BALL::PDBAtom::persistentRead | ( | PersistenceManager & | pm | ) | [virtual] |
Reads a PDBAtom object from a persistent stream.
pm | the persistence manager |
Reimplemented from BALL::Atom.
void BALL::PDBAtom::persistentWrite | ( | PersistenceManager & | pm, |
const char * | name = 0 |
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) | const [virtual] |
Writes a PDBAtom object to a persistent stream.
pm | the persistence manager |
name | the instance name |
Reimplemented from BALL::Atom.
void BALL::PDBAtom::set | ( | const PDBAtom & | pdb_atom, |
bool | deep = true |
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) |
Assignment with cloning facility. The assignment is either deep or shallow (default).
pdb_atom | the PDBAtom to be copied (cloned) |
deep | make a deep (=true ) or shallow (=false ) copy |
void BALL::PDBAtom::setAlternateLocationIndicator | ( | char | alternate_location_indicator | ) |
Set the alternate location indicator.
alternate_location_indicator | the alternate location indicator |
void BALL::PDBAtom::setBranchDesignator | ( | char | branch_designator | ) |
Set the branch designator.
branch_designator | the branch designator |
void BALL::PDBAtom::setOccupancy | ( | float | occupancy | ) |
Set the occupancy.
occupancy | the occupancy |
void BALL::PDBAtom::setRemotenessIndicator | ( | char | remoteness_indicator | ) |
Set the remoteness indicator.
remoteness_indicator | the remoteness indicator |
void BALL::PDBAtom::setTemperatureFactor | ( | float | temperature_factor | ) |
Set the temperature factor.
temperature_factor | the temperature factor |
void BALL::PDBAtom::swap | ( | PDBAtom & | pdb_atom | ) |
Swapping of PDBAtoms.
pdb_atom | the PDBAtom {*this} is being swapped with |
friend class Bond [friend] |
Reimplemented from BALL::Atom.
char BALL::PDBAtom::alternate_location_indicator_ [private] |
char BALL::PDBAtom::branch_designator_ [private] |
float BALL::PDBAtom::occupancy_ [private] |
char BALL::PDBAtom::remoteness_indicator_ [private] |
float BALL::PDBAtom::temperature_factor_ [private] |