BALL
1.4.1
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#include <BALL/STRUCTURE/residueRotamerSet.h>
Classes | |
struct | RotamerProbabilityGreaterThan_ |
Public Types | |
Type definitions | |
typedef std::vector< Rotamer > ::const_iterator | ConstIterator |
typedef std::vector< Rotamer > ::const_iterator | const_iterator |
typedef std::vector< Rotamer > ::iterator | Iterator |
typedef std::vector< Rotamer > ::iterator | iterator |
Public Member Functions | |
Constructors and Destructors | |
ResidueRotamerSet () | |
ResidueRotamerSet (const ResidueRotamerSet &rotamer_set) | |
ResidueRotamerSet (const Residue &residue, Size number_of_torsions) | |
virtual | ~ResidueRotamerSet () |
External Iteration | |
Iterator | begin () |
Iterator | end () |
ConstIterator | begin () const |
ConstIterator | end () const |
Assignment | |
const ResidueRotamerSet & | operator= (const ResidueRotamerSet &residue_rotamer_set) |
The assignment operator. | |
Accessors | |
const String & | getName () const |
Get the name of the ResidueRotamerSet. | |
bool | isValid () const |
Find out if the class instance is valid. | |
Size | getNumberOfRotamers () const |
Return the number of rotamers from this residue rotamer set. | |
Size | getNumberOfTorsions () const |
void | setNumberOfTorsions (Size number_of_torsions) throw (Exception::IndexOverflow) |
const Rotamer & | operator[] (Position index) const throw (Exception::IndexOverflow) |
Random access operator for single rotamers. | |
bool | hasTorsionPhi () const |
Angle | getTorsionPhi () const |
void | setTorsionPhi (const Angle &phi) |
bool | hasTorsionPsi () const |
Angle | getTorsionPsi () const |
void | setTorsionPsi (const Angle &psi) |
Rotamer Assignment | |
bool | setTemplateResidue (const Residue &residue, Size number_of_torsions) |
Set the template residue, name, base coordinates ... | |
bool | setRotamer (Residue &residue, const Rotamer &rotamer) |
Rotamer | getRotamer (const Residue &residue) const |
const Rotamer & | getRotamer (Position index) const |
void | setName (const String &name) |
Assign a new name. | |
void | addRotamer (const Rotamer &rotamer) |
Add a rotamer to the current set. | |
void | deleteRotamer (Iterator loc) |
Delete the Rotamer at the given iterator location. | |
void | deleteRotamers (Iterator begin, Iterator end) |
Delete the range of rotamers. | |
void | sort () |
Sort the rotamers descendingly according to their probability. | |
Protected Member Functions | |
void | addMovable_ (std::vector< String > &movable, const Atom &a, const HashSet< String > &assigned_atoms) |
void | setTorsionAngle_ (Residue &residue, const std::vector< String > &movable, float torsion) |
Set the torsion angles. | |
Protected Attributes | |
bool | valid_ |
Indicates whether the instance is valid. | |
String | name_ |
Name of the residue (variant name) | |
std::vector< Rotamer > | rotamers_ |
Array containing all rotamers. | |
std::vector< String > | movable_atoms_chi1_ |
Names of the movable atoms (names) for each of the torsions. | |
std::vector< String > | movable_atoms_chi2_ |
std::vector< String > | movable_atoms_chi3_ |
std::vector< String > | movable_atoms_chi4_ |
Size | number_of_torsions_ |
Number of valid torsions in the side chain. | |
StringHashMap< Vector3 > | original_coordinates_ |
Original coordinates of the template residue. | |
bool | has_torsion_phi_ |
true if this residue rotamer set is backbone dependent | |
bool | has_torsion_psi_ |
true if this residue rotamer set is backbone dependent | |
Angle | phi_ |
The torsion phi. | |
Angle | psi_ |
The torsion psi. |
This class stores all potential rotamers for a given side chain type. By linking a residue rotamer set to a specific side chain, one can iteratively try all contained rotamers for this side chain. The rotamers for a side chain are typically stored in a rotamer library .
The basic functionality is to store the rotamers and to modify residues according to this rotamers.
Definition at line 91 of file residueRotamerSet.h.
typedef std::vector<Rotamer>::const_iterator BALL::ResidueRotamerSet::const_iterator |
Definition at line 100 of file residueRotamerSet.h.
typedef std::vector<Rotamer>::const_iterator BALL::ResidueRotamerSet::ConstIterator |
Definition at line 99 of file residueRotamerSet.h.
typedef std::vector<Rotamer>::iterator BALL::ResidueRotamerSet::Iterator |
Definition at line 102 of file residueRotamerSet.h.
typedef std::vector<Rotamer>::iterator BALL::ResidueRotamerSet::iterator |
Definition at line 103 of file residueRotamerSet.h.
Default constructor.
BALL::ResidueRotamerSet::ResidueRotamerSet | ( | const ResidueRotamerSet & | rotamer_set | ) |
Copy constructor
BALL::ResidueRotamerSet::ResidueRotamerSet | ( | const Residue & | residue, |
Size | number_of_torsions | ||
) |
Detailed constructor
virtual BALL::ResidueRotamerSet::~ResidueRotamerSet | ( | ) | [virtual] |
Destructor
void BALL::ResidueRotamerSet::addMovable_ | ( | std::vector< String > & | movable, |
const Atom & | a, | ||
const HashSet< String > & | assigned_atoms | ||
) | [protected] |
Determine all movable atoms. This method walks along the bonds starting at a
and adds them to the movable
vector. Atoms whose names are contained in assigned_atoms
are ignored.
void BALL::ResidueRotamerSet::addRotamer | ( | const Rotamer & | rotamer | ) |
Add a rotamer to the current set.
Iterator BALL::ResidueRotamerSet::begin | ( | ) | [inline] |
Definition at line 136 of file residueRotamerSet.h.
ConstIterator BALL::ResidueRotamerSet::begin | ( | ) | const [inline] |
Definition at line 150 of file residueRotamerSet.h.
void BALL::ResidueRotamerSet::deleteRotamer | ( | Iterator | loc | ) |
Delete the Rotamer at the given iterator location.
void BALL::ResidueRotamerSet::deleteRotamers | ( | Iterator | begin, |
Iterator | end | ||
) |
Delete the range of rotamers.
Iterator BALL::ResidueRotamerSet::end | ( | ) | [inline] |
Definition at line 143 of file residueRotamerSet.h.
ConstIterator BALL::ResidueRotamerSet::end | ( | ) | const [inline] |
Definition at line 157 of file residueRotamerSet.h.
const String& BALL::ResidueRotamerSet::getName | ( | ) | const |
Get the name of the ResidueRotamerSet.
Return the number of rotamers from this residue rotamer set.
Return the number of valid torsions in the side chain. The number returned is between zero and four.
Rotamer BALL::ResidueRotamerSet::getRotamer | ( | const Residue & | residue | ) | const |
Calculate the torsion angle of a residue. Retrieve the side-chain torsion angles from the residue's current conformation.
const Rotamer& BALL::ResidueRotamerSet::getRotamer | ( | Position | index | ) | const |
Return a reference to a given rotamer by number. The index should be in the range [0, getNumberOfRotamers ()[, however the index is computed modulo the maximum number, so it really doesn't matter.
Angle BALL::ResidueRotamerSet::getTorsionPhi | ( | ) | const |
Angle BALL::ResidueRotamerSet::getTorsionPsi | ( | ) | const |
bool BALL::ResidueRotamerSet::hasTorsionPhi | ( | ) | const |
bool BALL::ResidueRotamerSet::hasTorsionPsi | ( | ) | const |
bool BALL::ResidueRotamerSet::isValid | ( | ) | const |
Find out if the class instance is valid.
const ResidueRotamerSet& BALL::ResidueRotamerSet::operator= | ( | const ResidueRotamerSet & | residue_rotamer_set | ) |
The assignment operator.
const Rotamer& BALL::ResidueRotamerSet::operator[] | ( | Position | index | ) | const throw (Exception::IndexOverflow) |
Random access operator for single rotamers.
void BALL::ResidueRotamerSet::setName | ( | const String & | name | ) |
Assign a new name.
void BALL::ResidueRotamerSet::setNumberOfTorsions | ( | Size | number_of_torsions | ) | throw (Exception::IndexOverflow) |
Set the number of valid torsions for this side chain.
Exception::IndexOverflow | if the number of torsions is above four. |
bool BALL::ResidueRotamerSet::setRotamer | ( | Residue & | residue, |
const Rotamer & | rotamer | ||
) |
Assign a specific rotamer. Set the side-chain torsions of residue
to the values specified by rotamer
.
bool BALL::ResidueRotamerSet::setTemplateResidue | ( | const Residue & | residue, |
Size | number_of_torsions | ||
) |
Set the template residue, name, base coordinates ...
void BALL::ResidueRotamerSet::setTorsionAngle_ | ( | Residue & | residue, |
const std::vector< String > & | movable, | ||
float | torsion | ||
) | [protected] |
Set the torsion angles.
void BALL::ResidueRotamerSet::setTorsionPhi | ( | const Angle & | phi | ) |
void BALL::ResidueRotamerSet::setTorsionPsi | ( | const Angle & | psi | ) |
void BALL::ResidueRotamerSet::sort | ( | ) |
Sort the rotamers descendingly according to their probability.
bool BALL::ResidueRotamerSet::has_torsion_phi_ [protected] |
true if this residue rotamer set is backbone dependent
Definition at line 299 of file residueRotamerSet.h.
bool BALL::ResidueRotamerSet::has_torsion_psi_ [protected] |
true if this residue rotamer set is backbone dependent
Definition at line 302 of file residueRotamerSet.h.
std::vector<String> BALL::ResidueRotamerSet::movable_atoms_chi1_ [protected] |
Names of the movable atoms (names) for each of the torsions.
Definition at line 287 of file residueRotamerSet.h.
std::vector<String> BALL::ResidueRotamerSet::movable_atoms_chi2_ [protected] |
Definition at line 288 of file residueRotamerSet.h.
std::vector<String> BALL::ResidueRotamerSet::movable_atoms_chi3_ [protected] |
Definition at line 289 of file residueRotamerSet.h.
std::vector<String> BALL::ResidueRotamerSet::movable_atoms_chi4_ [protected] |
Definition at line 290 of file residueRotamerSet.h.
String BALL::ResidueRotamerSet::name_ [protected] |
Name of the residue (variant name)
Definition at line 281 of file residueRotamerSet.h.
Size BALL::ResidueRotamerSet::number_of_torsions_ [protected] |
Number of valid torsions in the side chain.
Definition at line 293 of file residueRotamerSet.h.
Original coordinates of the template residue.
Definition at line 296 of file residueRotamerSet.h.
Angle BALL::ResidueRotamerSet::phi_ [protected] |
The torsion phi.
Definition at line 305 of file residueRotamerSet.h.
Angle BALL::ResidueRotamerSet::psi_ [protected] |
The torsion psi.
Definition at line 308 of file residueRotamerSet.h.
std::vector<Rotamer> BALL::ResidueRotamerSet::rotamers_ [protected] |
Array containing all rotamers.
Definition at line 284 of file residueRotamerSet.h.
bool BALL::ResidueRotamerSet::valid_ [protected] |
Indicates whether the instance is valid.
Definition at line 278 of file residueRotamerSet.h.