#include <openbabel/rotor.h>

Public Member Functions
	OBRotor ()

	~OBRotor ()

void	RemoveSymTorsionValues (int)

Setup
void	SetBond (OBBond *bond)

void	SetRings ()

void	SetIdx (int idx)

void	SetDihedralAtoms (std::vector< int > &ref)

void	SetDihedralAtoms (int ref[4])

void	SetRotAtoms (std::vector< int > &atoms)

void	SetTorsionValues (std::vector< double > &angles)

void	SetFixedBonds (OBBitVec &bv)

Performing rotations
void	SetToAngle (double *coordinates, double setang)

void	SetRotor (double *coordinates, int next, int prev=-1)

void	Set (double *coordinates, double sine, double cosine, double translation, double invmag)

void	Precompute (double *coordinates)

void	Set (double *coordinates, int idx)

void	Precalc (std::vector< double *> &conformers)

void	Set (double *coordinates, int conformer, int idx)

Methods to retrieve information
OBBond *	GetBond ()

size_t	Size ()

int	GetIdx () const

void	GetDihedralAtoms (int ref[4])

std::vector< int > &	GetDihedralAtoms ()

const std::vector< int > &	GetRotAtoms () const

const std::vector< double > &	GetTorsionValues () const

OBBitVec &	GetFixedBonds ()

double	CalcTorsion (double *coordinates)

double	CalcBondLength (double *coordinates)

Iterator methods
std::vector< double >::iterator	BeginTorIncrement ()

std::vector< double >::iterator	EndTorIncrement ()

Deprecated
void	SetDelta (double d)

double	GetDelta ()

OBBitVec &	GetFixedAtoms ()

void	SetFixedAtoms (OBBitVec &bv)

OBBitVec &	GetEvalAtoms ()

void	SetEvalAtoms (OBBitVec &bv)

void *	GetRotAtoms ()

std::vector< double > &	GetResolution ()

void	SetNumCoords (int nc)

Detailed Description

A single rotatable OBBond as part of rotamer searching.

Constructor & Destructor Documentation

◆ OBRotor()

OBRotor ( )

Constructor.

◆ ~OBRotor()

~OBRotor ( )

inline

Destructor.

Member Function Documentation

◆ SetBond()

void SetBond ( OBBond * bond )

inline

Set the OBBond associated with this OBRotor.

Referenced by OBRotorList::FindRotors().

◆ SetRings()

void SetRings ( )

Set the rings associated with this bond (if it's a ring bond)

Since: Version 2.4

◆ SetIdx()

void SetIdx ( int idx )

inline

Set the index for this rotor. Used by OBRotorList

Referenced by OBRotorList::FindRotors().

◆ SetDihedralAtoms() [1/2]

void SetDihedralAtoms ( std::vector< int > & ref )

Set the dihedral atoms.

Parameters

ref	The dihedral atom indexes. These indexes start from 1.

Referenced by OBRotorList::AssignTorVals(), OBRotorList::SetRotAtoms(), and OBRotorList::SetRotAtomsByFix().

◆ SetDihedralAtoms() [2/2]

void SetDihedralAtoms ( int ref[4] )

Set the dihedral atoms.

Parameters

ref	The dihedral atom indexes. These indexes start from 1.

◆ SetRotAtoms()

void SetRotAtoms ( std::vector< int > & atoms )

Set the atom indexes that will be displaced when this rotor changes torsion angle. These indexes start from 0 and are multiplied by 3 for easy coordinate access.

Referenced by OBRotorList::AssignTorVals(), OBRotorList::SetRotAtoms(), and OBRotorList::SetRotAtomsByFix().

◆ SetTorsionValues()

void SetTorsionValues ( std::vector< double > & angles )

inline

Set the possible torsion values or angles.

Referenced by OBRotorList::AssignTorVals().

◆ SetFixedBonds()

void SetFixedBonds ( OBBitVec & bv )

inline

Set the bonds that will be fixed.

◆ SetToAngle()

void SetToAngle	(	double *	coordinates,
		double	setang
	)

inline

Rotate the atoms in the specified coordinates to the specified angle.

Parameters

coordinates	The coordinates to rotate.
setang	The new torsion angle in radians.

◆ SetRotor()

void SetRotor	(	double *	coordinates,
		int	next,
		int	prev = `-1`
	)

Rotate the atoms in the specified coordinates. This function does not require any precomputation and will compute all needed information when needed.

Parameters

coordinates	The coordinates for the molecules as pointer to double.
next	The index of the new rotor angle. This is an index for the GetTorsionValues() list.
prev	If specified, the torsion current torsion angle can be looked up and does not have to be calculated again.

◆ Set() [1/3]

void Set	(	double *	coordinates,
		double	sine,
		double	cosine,
		double	translation,
		double	invmag
	)

Rotate the specified coordinates by using the specified rotation matrix.

◆ Precompute()

void Precompute ( double * coordinates )

Precompute the reference angle and inverse bond length of this rotor for a single conformer. This function should be used in combination with Set(double *coordinates, int idx).

Parameters

coordinates The coordinates to use in the computation.

OBMol mol;
...
unsigned int numCoords = mol.NumAtoms() * 3;
double *coords = mol.GetCoordinates();
OBRotor rotor;
rotor.SetBond(mol.GetBond(3));
// set the possible torsion values
std::vector<double> angles;
angles.push_back(0.0);
angles.push_back(3.1415);
rotor.SetTorsionValues(angles);
// precompute inverse bond length (i.e. the bond length of bond with index 3
// using the specified coordinates) and reference angle (i.e. torsion angle
//in coords)
rotor.Precompute(coords);
// copy coordinates to coords_1
double *coords_1 = new double[numCoords];
for (unsigned int i = 0; i < numCoords; ++i)
  coords_1[i] = coords[i];
// rotate the atoms in coords_1 to angle with index 0 (i.e. 0.0 degrees)
// note: on input, the coordinates should be the same as the coordinates used
//       to precompute the inverse bond length and reference angle (in other
//       words, the inverse magnitude and reference angle in the specfied
//       coordinates should be the same as the one used for Precompute)
rotor.Set(coords_1, 0)
// copy coordinates to coords_2
double *coords_2 = new double[numCoords];
for (unsigned int i = 0; i < numCoords; ++i)
  coords_2[i] = coords[i];
// rotate the atoms in coords_2 to angle with index 1 (i.e. 180.0 degrees)
rotor.Set(coords_2, 1)
delete coords_1;
delete coords_2;

◆ Set() [2/3]

void Set	(	double *	coordinates,
		int	idx
	)

Rotate the coordinates to set the torsion angle of this rotor to the angle specified by the index idx. Make sure to call Precompute before calling this function.

Parameters

coordinates	The coordinates to rotate.
idx	The index of the torsion angle in the GetTorsionValues() list.

◆ Precalc()

void Precalc ( std::vector< double *> & conformers )

Precompute the inverse bond lengths, rotation matrices for all specified conformers and all possible torsion values. This method is used in combination with Set(double *coordinates, int conformer, int idx).

Parameters

conformers The pointers to the conformer coordinates

◆ Set() [3/3]

void Set	(	double *	coordinates,
		int	conformer,
		int	idx
	)

inline

Rotate the coordinates to set the torsion to the torsion value with the specified index. The coordinates should be the same as the conformer used for calling Precalc (i.e. conformers[conformer] == coordinates). Make sure to call Precalc before calling this method.

Parameters

coordinates	The conformer coordinates.
conformer	The conformer index in the conformer list given to Precalc().
idx	The torsion value index in the GetTorsionValues() list.

◆ GetBond()

OBBond* GetBond ( )

inline

Get the OBBond object associated with this OBRotor.

Referenced by OBRotorList::AssignTorVals(), OBRotorList::RemoveSymVals(), OBRotorList::SetEvalAtoms(), OBRotamerList::Setup(), and OBConformerSearch::Setup().

◆ Size()

size_t Size ( )

inline

Get the number of possible torsion angles for this OBRotor. This is the length of the GetTorsionValues() list.

Referenced by OBRotorList::RemoveSymVals(), and OBRotorList::Setup().

◆ GetIdx()

int GetIdx ( void ) const

inline

Get the index for this rotor (index in an OBRotorList).

Referenced by OBRotamerList::Setup().

◆ GetDihedralAtoms() [1/2]

void GetDihedralAtoms ( int ref[4] )

inline

Get the dihedral atom indexes. These indexes start from 1.

Referenced by OBRotorList::SetRotAtoms(), OBRotorList::SetRotAtomsByFix(), OBRotamerList::Setup(), and OBRotorList::Setup().

◆ GetDihedralAtoms() [2/2]

std::vector<int>& GetDihedralAtoms ( )

inline

Get the dihedral atom indexes. These indexes start from 1.

◆ GetRotAtoms() [1/2]

const std::vector<int>& GetRotAtoms ( ) const

inline

Get the atom indexes that will be displaced when this rotor changes torsion angle. These indexes start from 1.

◆ GetTorsionValues()

const std::vector<double>& GetTorsionValues ( ) const

inline

Get the possible torsion angles for this OBRotor.

◆ GetFixedBonds()

OBBitVec& GetFixedBonds ( )

inline

Get an OBBitVec objects with bits set for all bonds that are fixed. Bonds are indexed from 0.

◆ CalcTorsion()

double CalcTorsion ( double * coordinates )

Calculate the torsion for this OBRotor using the specified coordinates.

Parameters

coordinates The coordinates (e.g. OBMol::GetCoordinates()).

Returns: The torsion angle in radians.

◆ CalcBondLength()

double CalcBondLength ( double * coordinates )

Calculate the bond length for this OBRotor using the specified coordinates.

Parameters

coordinates The coordinates (e.g. OBMol::GetCoordinates()).

◆ BeginTorIncrement()

std::vector<double>::iterator BeginTorIncrement ( )

inline

◆ EndTorIncrement()

std::vector<double>::iterator EndTorIncrement ( )

inline

◆ RemoveSymTorsionValues()

void RemoveSymTorsionValues ( int fold )

Remove all torsions angles between 0 and 360/fold.

Referenced by OBRotorList::RemoveSymVals().

◆ SetDelta()

void SetDelta ( double d )

inline

Deprecated:: Has no effect.

Referenced by OBRotorList::AssignTorVals().

◆ GetDelta()

double GetDelta ( )

inline

Deprecated:: Has no effect.

◆ GetFixedAtoms()

OBBitVec& GetFixedAtoms ( )

inline

Deprecated:

◆ SetFixedAtoms()

void SetFixedAtoms ( OBBitVec & bv )

inline

Deprecated:: See SetFixedBonds

◆ GetEvalAtoms()

OBBitVec& GetEvalAtoms ( )

inline

Deprecated:

◆ SetEvalAtoms()

void SetEvalAtoms ( OBBitVec & bv )

inline

Deprecated:

Referenced by OBRotorList::SetEvalAtoms().

◆ GetRotAtoms() [2/2]

void* GetRotAtoms ( )

inline

Deprecated:

◆ GetResolution()

std::vector<double>& GetResolution ( )

inline

Deprecated:: Bad name, see GetTorsionValues()

Referenced by OBForceField::FastRotorSearch(), OBConformerSearch::GetConformers(), OBForceField::RandomRotorSearchInitialize(), OBRotamerList::Setup(), OBForceField::SystematicRotorSearchInitialize(), OpenBabel::UpdateConformersFromTree(), and OBForceField::WeightedRotorSearch().

◆ SetNumCoords()

void SetNumCoords ( int nc )

inline

Deprecated:

Referenced by OBRotorList::FindRotors().

The documentation for this class was generated from the following files:

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ OBRotor()

◆ ~OBRotor()

Member Function Documentation

◆ SetBond()

◆ SetRings()

◆ SetIdx()

◆ SetDihedralAtoms() [1/2]

◆ SetDihedralAtoms() [2/2]

◆ SetRotAtoms()

◆ SetTorsionValues()

◆ SetFixedBonds()

◆ SetToAngle()

◆ SetRotor()

◆ Set() [1/3]

◆ Precompute()

◆ Set() [2/3]

◆ Precalc()

◆ Set() [3/3]

◆ GetBond()

◆ Size()

◆ GetIdx()

◆ GetDihedralAtoms() [1/2]

◆ GetDihedralAtoms() [2/2]

◆ GetRotAtoms() [1/2]

◆ GetTorsionValues()

◆ GetFixedBonds()

◆ CalcTorsion()

◆ CalcBondLength()

◆ BeginTorIncrement()

◆ EndTorIncrement()

◆ RemoveSymTorsionValues()

◆ SetDelta()

◆ GetDelta()

◆ GetFixedAtoms()

◆ SetFixedAtoms()

◆ GetEvalAtoms()

◆ SetEvalAtoms()

◆ GetRotAtoms() [2/2]

◆ GetResolution()

◆ SetNumCoords()