OBRotorList Class Reference

#include <openbabel/rotor.h>

Public Member Functions
	OBRotorList ()
	~OBRotorList ()
void	Clear ()
size_t	Size ()
bool	IsFixedBond (OBBond *)
bool	HasFixedBonds ()
void	RemoveSymVals (OBMol &)
bool	HasRingRotors ()
Setup
bool	Setup (OBMol &mol, bool sampleRings=false)
void	SetFixedBonds (OBBitVec &fix)
void	Init (std::string &fname)
void	SetQuiet ()
bool	SetRotAtoms (OBMol &)
bool	FindRotors (OBMol &mol, bool sampleRingBonds=false)
bool	SetEvalAtoms (OBMol &)
bool	AssignTorVals (OBMol &)
Iterator methods
OBRotor *	BeginRotor (OBRotorIterator &i)
OBRotor *	NextRotor (OBRotorIterator &i)
OBRotorIterator	BeginRotors ()
OBRotorIterator	EndRotors ()
Deprecated
bool	IdentifyEvalAtoms (OBMol &mol)
void	SetFixAtoms (OBBitVec &fix)
bool	HasFixedAtoms ()
void	IgnoreSymmetryRemoval ()
void	SetRotAtomsByFix (OBMol &)

Detailed Description

Given an OBMol, set up a list of possibly rotatable torsions,.

Constructor & Destructor Documentation

OBRotorList()

OBRotorList

(

)

Constructor.

~OBRotorList()

~OBRotorList

(

)

Destructor.

Member Function Documentation

Clear()

void Clear

(

void

)

Clear the internal list of rotors and reset.

Size()

size_t Size ( )

inline

Returns

the number of rotors in this list

Referenced by OBForceField::FastRotorSearch(), OBMol::NumRotors(), OBForceField::RandomRotorSearchInitialize(), OBForceField::SystematicRotorSearchInitialize(), OpenBabel::UpdateConformersFromTree(), and OBForceField::WeightedRotorSearch().

IsFixedBond()

bool IsFixedBond

(

OBBond *

bond

)

When no atoms/bonds are fixed or when bonds are fixed, this function will return true if the bond is fixed. When using the deprecated fixed atoms, this function will return true if the bond and at least one neighboring bond has fixed atoms.

HasFixedBonds()

bool HasFixedBonds ( )

inline

Returns

True if this rotor list has any fixed bonds.

RemoveSymVals()

void RemoveSymVals

(

OBMol &

mol

)

Rotates each bond to zero and 180 degrees and tests if the 2 conformers are duplicates. if so - the symmetric torsion values are removed from consideration during a search

HasRingRotors()

bool HasRingRotors ( )

inline

Returns

True if this rotor list has any ring bonds.

Since

version 2.4

Referenced by OBRotamerList::Setup().

Setup()

bool Setup	(	OBMol &	mol,
		bool	sampleRings = false
	)

Setup this rotor list for the supplied molecule. This method calls FindRotors(), SetEvalAtoms(), and AssignTorVals().

Parameters

mol	The molecule.
sampleRings	Whether to sample ring conformers - default = false

Returns

True if rotatable bonds were found.

Referenced by OBForceField::FastRotorSearch(), OBForceField::RandomRotorSearchInitialize(), OBForceField::SystematicRotorSearchInitialize(), OpenBabel::UpdateConformersFromTree(), and OBForceField::WeightedRotorSearch().

SetFixedBonds()

void SetFixedBonds ( OBBitVec &  fix )

inline

Set the bonds that will be fixed.

Init()

void Init ( std::string &  fname )

inline

Intialize the private OBRotorRules database from a specific file.

SetQuiet()

void SetQuiet ( )

inline

Turn off debugging output.

Referenced by OBForceField::FastRotorSearch(), and OpenBabel::UpdateConformersFromTree().

SetRotAtoms()

bool SetRotAtoms

(

OBMol &

mol

)

Set the atoms to rotate from the dihedral atoms for each rotor Uses OBRotor->GetDihedralAtoms() to call OBRotor->SetRotAtoms() and standarizes the dihedral angles via OBRotor->SetDihedralAtoms()

Returns

True

FindRotors()

bool FindRotors	(	OBMol &	mol,
		bool	sampleRingBonds = false
	)

Find all potentially rotatable bonds in the molecule. This method uses OBBond::IsRotor() for initial evaluation which depends on ring perception (i.e. ring bonds are considered rotatable). Fixed bonds, specified using the deprecated fixed atoms or the new fixed bonds methods are not added to the list. All rotatable bonds will be sorted by their graph theoretical distance (GTD) score (see OBMol::GetGTDVector()). This results in the the rotors going from the inside to the outside of the mol.

Parameters

mol	The molecule.
sampleRingBonds	whether to sample ring bonds from analysis (default = false)

Returns

True.

Referenced by OBMol::NumRotors().

SetEvalAtoms()

bool SetEvalAtoms

(

OBMol &

mol

)

Determines which atoms should be used to calculate the internal energy if the dihedral angle of the rotor is modified

Returns

True

AssignTorVals()

bool AssignTorVals

(

OBMol &

mol

)

Using the OBRotorRules database, set the torsion values (and delta) to be evaluated and tested. This method also sets the rotatable atoms for the rotors to the smallest possible set. For each bond there are two candidate sets, one on either side. The smallest of these is used and the torsion indexes for the rotor are inverted if needed (i.e. a-b-c-d -> d-c-b-a).

BeginRotor()

OBRotor* BeginRotor ( OBRotorIterator &  i )

inline

Initialize the i iterator and get a pointer to the first OBRotor.

Parameters

i	OBRotorIterator object.

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

NextRotor()

OBRotor* NextRotor ( OBRotorIterator &  i )

inline

Get a pointer to the next iterator.

Parameters

i	OBRotorIterator object.

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

BeginRotors()

OBRotorIterator BeginRotors ( )

inline

Get the rotor list begin iterator.

EndRotors()

OBRotorIterator EndRotors ( )

inline

Get the rotor list end iterator.

IdentifyEvalAtoms()

bool IdentifyEvalAtoms ( OBMol &  mol )

inline

Deprecated:

Not declared. Use Setup() for top-level functionality

SetFixAtoms()

void SetFixAtoms ( OBBitVec &  fix )

inline

Set the list of fixed (invariant) atoms to the supplied OBBitVec

Deprecated:

See SetFixedBonds()

Referenced by OBForceField::FastRotorSearch(), OBForceField::RandomRotorSearchInitialize(), OBForceField::SystematicRotorSearchInitialize(), OpenBabel::UpdateConformersFromTree(), and OBForceField::WeightedRotorSearch().

HasFixedAtoms()

bool HasFixedAtoms ( )

inline

Returns

whether this rotor list has any fixed (invariant) atoms

Deprecated:

See HasFixedBonds()

IgnoreSymmetryRemoval()

void IgnoreSymmetryRemoval ( )

inline

Has no effect

Deprecated:

Currently has no effect

SetRotAtomsByFix()

void SetRotAtomsByFix

(

OBMol &

mol

)

Set the atoms to rotate from the dihedral atoms for each rotor Insures the fixed atoms are respected, but otherwise functions like SetRotAtoms()

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

• rotor.h
• rotor.cpp