A single rotatable OBBond as part of rotamer searching. More...

#include <openbabel/rotor.h>

Public Member Functions
	OBRotor ()
	~OBRotor ()
void	RemoveSymTorsionValues (int)
Setup

void	SetBond (OBBond *bond)
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 ( )

Constructor.

~OBRotor ( ) [inline]

Destructor.

Member Function Documentation

void SetBond ( OBBond * bond ) [inline]

Set the OBBond associated with this OBRotor.

Referenced by OBRotorList::FindRotors().

void SetIdx ( int idx ) [inline]

Set the index for this rotor. Used by OBRotorList

Referenced by OBRotorList::FindRotors().

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().

void SetDihedralAtoms ( int ref[4] )

Set the dihedral atoms.

Parameters:

ref

The dihedral atom indexes. These indexes start from 1.

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().

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

Set the possible torsion values or angles.

Referenced by OBRotorList::AssignTorVals().

void SetFixedBonds ( OBBitVec & bv ) [inline]

Set the bonds that will be fixed.

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.

Referenced by OBRotorList::RemoveSymVals().

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.

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

Rotate the specified coordinates by using the specified rotation matrix.

Referenced by OBRotor::SetRotor().

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;

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.

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

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.