#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.
| typedef std::vector<Rotamer>::const_iterator BALL::ResidueRotamerSet::const_iterator |
| typedef std::vector<Rotamer>::const_iterator BALL::ResidueRotamerSet::ConstIterator |
| typedef std::vector<Rotamer>::iterator BALL::ResidueRotamerSet::iterator |
| typedef std::vector<Rotamer>::iterator BALL::ResidueRotamerSet::Iterator |
| BALL::ResidueRotamerSet::ResidueRotamerSet | ( | ) |
Default constructor.
| BALL::ResidueRotamerSet::ResidueRotamerSet | ( | const ResidueRotamerSet & | rotamer_set | ) |
Copy constructor
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.
| ConstIterator BALL::ResidueRotamerSet::begin | ( | ) | const [inline] |
| void BALL::ResidueRotamerSet::deleteRotamer | ( | Iterator | loc | ) |
Delete the Rotamer at the given iterator location.
Delete the range of rotamers.
| ConstIterator BALL::ResidueRotamerSet::end | ( | ) | const [inline] |
| Iterator BALL::ResidueRotamerSet::end | ( | ) | [inline] |
| const String& BALL::ResidueRotamerSet::getName | ( | ) | const |
Get the name of the ResidueRotamerSet.
| Size BALL::ResidueRotamerSet::getNumberOfRotamers | ( | ) | const |
Return the number of rotamers from this residue rotamer set.
| Size BALL::ResidueRotamerSet::getNumberOfTorsions | ( | ) | const |
Return the number of valid torsions in the side chain. The number returned is between zero and four.
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.
Calculate the torsion angle of a residue. Retrieve the side-chain torsion angles from the residue's current conformation.
| 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. |
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
bool BALL::ResidueRotamerSet::has_torsion_psi_ [protected] |
true if this residue rotamer set is backbone dependent
std::vector<String> BALL::ResidueRotamerSet::movable_atoms_chi1_ [protected] |
Names of the movable atoms (names) for each of the torsions.
std::vector<String> BALL::ResidueRotamerSet::movable_atoms_chi2_ [protected] |
std::vector<String> BALL::ResidueRotamerSet::movable_atoms_chi3_ [protected] |
std::vector<String> BALL::ResidueRotamerSet::movable_atoms_chi4_ [protected] |
String BALL::ResidueRotamerSet::name_ [protected] |
Name of the residue (variant name).
Size BALL::ResidueRotamerSet::number_of_torsions_ [protected] |
Number of valid torsions in the side chain.
Original coordinates of the template residue.
Angle BALL::ResidueRotamerSet::phi_ [protected] |
The torsion phi.
Angle BALL::ResidueRotamerSet::psi_ [protected] |
The torsion psi.
std::vector<Rotamer> BALL::ResidueRotamerSet::rotamers_ [protected] |
Array containing all rotamers.
bool BALL::ResidueRotamerSet::valid_ [protected] |
Indicates whether the instance is valid.