biu::LatticeProtein_Ipnt Class Reference
#include <LatticeProtein_Ipnt.hh>
Inheritance diagram for biu::LatticeProtein_Ipnt:
Detailed Description
A LatticeProtein implementation using a vector of 3D coordinates as internal structure representation. Move string representations are computed on demand.
Definition at line 15 of file LatticeProtein_Ipnt.hh.
Public Member Functions | |
| LatticeProtein_I * | clone () |
| LatticeProtein_I * | fromString (const std::string &stringRep) const |
| virtual DPointVec | get3Ddata () const |
| virtual double | getDRMSD (const BackboneStructure3D &other) const |
| virtual double | getEnergy () const |
| virtual const DistanceEnergyFunction * | getEnergyFunction () const |
| virtual const LatticeModel * | getLatticeModel () const |
| size_t | getLength () const |
| virtual MoveSequence | getMoveSeqAbs () const |
| virtual MoveSequence | getMoveSeqRel () const |
| virtual std::string | getMoveStrAbs () const |
| virtual std::string | getMoveStrRel () const |
| virtual IPointVec | getPoints () const |
| virtual IPointVec * | getPointsRef () |
| virtual const IPointVec *const | getPointsRef () const |
| Sequence | getSequence () const |
| virtual const Sequence * | getSequenceRef () const |
| virtual std::string | getStringRepresentation () const |
| virtual Structure | getStructure () const |
| virtual bool | isConnected () const |
| virtual bool | isSelfAvoiding () const |
| virtual bool | isSequenceShared () const |
| virtual bool | isValid () const |
| LatticeProtein_Ipnt (const LatticeProtein_Ipnt &latProt) | |
| LatticeProtein_Ipnt (const LatticeProtein &latProt) | |
| LatticeProtein_Ipnt (const LatticeModel *lattice, const DistanceEnergyFunction *energy, const Sequence *seq, const bool seqShared, const std::string &moveString, const bool isAbsoluteMove) | |
| virtual bool | operator!= (const LatticeProtein &latProt2) const |
| virtual LatticeProtein_I & | operator= (const LatticeProtein_I &latProt2) |
| virtual LatticeProtein_Ipnt & | operator= (const LatticeProtein_Ipnt &latProt2) |
| virtual bool | operator== (const LatticeProtein &latProt2) const |
| virtual void | setMoveStrAbs (const std::string &moveString) |
| virtual | ~LatticeProtein_Ipnt () |
Protected Types | |
| enum | MyBool { MyFalse, MyTrue, MyNaN } |
Protected Member Functions | |
| virtual void | updateProperties () |
Protected Attributes | |
| MyBool | connected |
| double | energy |
| DistanceEnergyFunction const * | energyFunc |
| LatticeModel const * | lattice |
| IPointVec * | points |
| MyBool | selfavoiding |
| bool | seqShared |
| Sequence const * | sequence |
Static Protected Attributes | |
| static const double | NAN_DOUBLE |
Member Enumeration Documentation
enum biu::LatticeProtein_Ipnt::MyBool [protected] |
new data type to allow indifferent state of boolean variables that allow their calculation on demand
Definition at line 25 of file LatticeProtein_Ipnt.hh.
Constructor & Destructor Documentation
| biu::LatticeProtein_Ipnt::LatticeProtein_Ipnt | ( | const LatticeModel * | lattice, | |
| const DistanceEnergyFunction * | energy, | |||
| const Sequence * | seq, | |||
| const bool | seqShared, | |||
| const std::string & | moveString, | |||
| const bool | isAbsoluteMove | |||
| ) |
Constructs a new lattice protein object based on a 3D coordinate structure representation.
- Parameters:
-
lattice the lattice model the protein structure is basing on energy the energy function including the alphabet for the sequence seq the sequence encoded using the alphabet of the energy function object seqShared false if a local copy of seq should be generated; true if seq is shared among several LatticeProtein objects using the provided seq pointer moveString a move string representation of the structure isAbsoluteMove true if moveString is an absolute move string or false if it is a relative move string
Definition at line 13 of file LatticeProtein_Ipnt.cc.
| biu::LatticeProtein_Ipnt::LatticeProtein_Ipnt | ( | const LatticeProtein & | latProt | ) |
Definition at line 39 of file LatticeProtein_Ipnt.cc.
| biu::LatticeProtein_Ipnt::LatticeProtein_Ipnt | ( | const LatticeProtein_Ipnt & | latProt | ) |
Definition at line 70 of file LatticeProtein_Ipnt.cc.
| biu::LatticeProtein_Ipnt::~LatticeProtein_Ipnt | ( | ) | [virtual] |
Destruction of the lattice protein object.
Definition at line 99 of file LatticeProtein_Ipnt.cc.
Member Function Documentation
| LatticeProtein_I * biu::LatticeProtein_Ipnt::clone | ( | ) | [virtual] |
| LatticeProtein_I * biu::LatticeProtein_Ipnt::fromString | ( | const std::string & | stringRep | ) | const [virtual] |
| DPointVec biu::LatticeProtein_Ipnt::get3Ddata | ( | ) | const [virtual] |
Returns the consecutive point representation of the backbone.
Implements biu::BackboneStructure3D.
Definition at line 217 of file LatticeProtein_Ipnt.cc.
| double biu::LatticeProtein_Ipnt::getDRMSD | ( | const BackboneStructure3D & | other | ) | const [virtual] |
Returns the distance root mean square deviation (DRMSD) to an other BackboneStructure3D
Implements biu::BackboneStructure3D.
Definition at line 229 of file LatticeProtein_Ipnt.cc.
| double biu::LatticeProtein_Ipnt::getEnergy | ( | ) | const [virtual] |
Returns the contact energy of the lattice protein structure. Consecutive positions are not taken into account. Each contact is count only once.
Implements biu::BioMolecule.
Definition at line 251 of file LatticeProtein_Ipnt.cc.
| const biu::DistanceEnergyFunction * biu::LatticeProtein_I::getEnergyFunction | ( | ) | const [virtual, inherited] |
Returns the energy function this lattice protein is basing on.
Implements biu::LatticeProtein.
Definition at line 57 of file LatticeProtein_I.cc.
| const biu::LatticeModel * biu::LatticeProtein_I::getLatticeModel | ( | ) | const [virtual, inherited] |
Returns the lattice model this lattice protein is basing on.
Implements biu::LatticeProtein.
Definition at line 51 of file LatticeProtein_I.cc.
| size_t biu::LatticeProtein_I::getLength | ( | ) | const [virtual, inherited] |
Returns the length of the Biomolecule, i.e. the number of monomers.
Implements biu::BioMolecule.
Definition at line 87 of file LatticeProtein_I.cc.
| MoveSequence biu::LatticeProtein_Ipnt::getMoveSeqAbs | ( | ) | const [virtual] |
Returns the absolute move sequence of the lattice protein structure.
Implements biu::LatticeProtein.
Definition at line 346 of file LatticeProtein_Ipnt.cc.
| MoveSequence biu::LatticeProtein_Ipnt::getMoveSeqRel | ( | ) | const [virtual] |
Returns the relative move sequence of the lattice protein structure.
Implements biu::LatticeProtein.
Definition at line 354 of file LatticeProtein_Ipnt.cc.
| std::string biu::LatticeProtein_Ipnt::getMoveStrAbs | ( | ) | const [virtual] |
Returns the absolute move string representation of the lattice protein structure.
Implements biu::LatticeProtein.
Definition at line 319 of file LatticeProtein_Ipnt.cc.
| std::string biu::LatticeProtein_Ipnt::getMoveStrRel | ( | ) | const [virtual] |
Returns the relative move string representation of the lattice protein structure.
Implements biu::LatticeProtein.
Definition at line 338 of file LatticeProtein_Ipnt.cc.
| IPointVec biu::LatticeProtein_Ipnt::getPoints | ( | ) | const [virtual] |
Returns the successive 3D coordinates of the lattice protein structure.
Implements biu::LatticeProtein.
Definition at line 294 of file LatticeProtein_Ipnt.cc.
| IPointVec * biu::LatticeProtein_Ipnt::getPointsRef | ( | ) | [virtual] |
Returns a pointer to the integer-point representation of the protein for read-write access. Calling this function sets all calculated properties to an indifferent state.
Implements biu::LatticeProtein_I.
Definition at line 305 of file LatticeProtein_Ipnt.cc.
| const IPointVec *const biu::LatticeProtein_Ipnt::getPointsRef | ( | ) | const [virtual] |
Returns a pointer to the integer-point representation of the protein move sequence for read only access.
Implements biu::LatticeProtein_I.
Definition at line 300 of file LatticeProtein_Ipnt.cc.
| biu::Sequence biu::LatticeProtein_I::getSequence | ( | ) | const [virtual, inherited] |
| const Sequence * biu::LatticeProtein_I::getSequenceRef | ( | ) | const [virtual, inherited] |
Returns the pointer to the sequence.
Implements biu::LatticeProtein.
Definition at line 70 of file LatticeProtein_I.cc.
| std::string biu::LatticeProtein_Ipnt::getStringRepresentation | ( | ) | const [virtual] |
Returns a combination of absolute move string representation and sequence information of this lattice protein.
ABSOLUTEMOVESTRING(SEQUENCE)
Implements biu::BioMolecule.
Definition at line 283 of file LatticeProtein_Ipnt.cc.
| Structure biu::LatticeProtein_Ipnt::getStructure | ( | ) | const [virtual] |
Returns the relative move representation of the lattice protein structure.
Implements biu::BioMolecule.
Definition at line 273 of file LatticeProtein_Ipnt.cc.
| bool biu::LatticeProtein_Ipnt::isConnected | ( | ) | const [virtual] |
Tests whether or not consecutive structure elements are neighbored in the lattice.
Implements biu::LatticeProtein.
Definition at line 362 of file LatticeProtein_Ipnt.cc.
| bool biu::LatticeProtein_Ipnt::isSelfAvoiding | ( | ) | const [virtual] |
Tests whether or not the structure is self avoiding.
Implements biu::LatticeProtein.
Definition at line 181 of file LatticeProtein_Ipnt.cc.
| bool biu::LatticeProtein_I::isSequenceShared | ( | ) | const [virtual, inherited] |
Returns whether or not the sequence is shared among several LatticeProtein objects.
Implements biu::LatticeProtein.
Definition at line 64 of file LatticeProtein_I.cc.
| bool biu::LatticeProtein_Ipnt::isValid | ( | ) | const [virtual] |
Returns whether or not the lattice protein is connected and self avoiding.
Implements biu::BioMolecule.
Definition at line 312 of file LatticeProtein_Ipnt.cc.
| bool biu::LatticeProtein_Ipnt::operator!= | ( | const LatticeProtein & | latProt2 | ) | const [virtual] |
| LatticeProtein_I & biu::LatticeProtein_Ipnt::operator= | ( | const LatticeProtein_I & | latProt2 | ) | [virtual] |
| LatticeProtein_Ipnt & biu::LatticeProtein_Ipnt::operator= | ( | const LatticeProtein_Ipnt & | latProt2 | ) | [virtual] |
Definition at line 116 of file LatticeProtein_Ipnt.cc.
| bool biu::LatticeProtein_Ipnt::operator== | ( | const LatticeProtein & | latProt2 | ) | const [virtual] |
| void biu::LatticeProtein_Ipnt::setMoveStrAbs | ( | const std::string & | moveString | ) | [virtual] |
Sets a new absolute move string.
Implements biu::LatticeProtein_I.
Definition at line 326 of file LatticeProtein_Ipnt.cc.
| void biu::LatticeProtein_Ipnt::updateProperties | ( | ) | [protected, virtual] |
Is called if the structure or sequence of the protein has changed. Either all new properties (e.g. energy etc.) are calculated or they are triggered to be calculated on demand.
Here: Sets all calculated properties (energy, selfavoidingness and connectedness to an indifferent state.
Definition at line 388 of file LatticeProtein_Ipnt.cc.
Field Documentation
MyBool biu::LatticeProtein_Ipnt::connected [mutable, protected] |
double biu::LatticeProtein_Ipnt::energy [mutable, protected] |
the energy of this structure that is calculated lazily on demand
Definition at line 33 of file LatticeProtein_Ipnt.hh.
DistanceEnergyFunction const* biu::LatticeProtein_I::energyFunc [protected, inherited] |
LatticeModel const* biu::LatticeProtein_I::lattice [protected, inherited] |
const double biu::LatticeProtein_Ipnt::NAN_DOUBLE [static, protected] |
trigger value for double variables that they should be recalculated
Definition at line 21 of file LatticeProtein_Ipnt.hh.
IPointVec* biu::LatticeProtein_Ipnt::points [protected] |
MyBool biu::LatticeProtein_Ipnt::selfavoiding [mutable, protected] |
bool biu::LatticeProtein_I::seqShared [protected, inherited] |
whether or not the sequence is shared or has to be copied
Definition at line 27 of file LatticeProtein_I.hh.
Sequence const* biu::LatticeProtein_I::sequence [protected, inherited] |
The documentation for this class was generated from the following files:
- src/biu/LatticeProtein_Ipnt.hh
- src/biu/LatticeProtein_Ipnt.cc