OBRotorList Class Reference

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

#include <rotor.h>

List of all members.

Public Member Functions

 OBRotorList ()
 ~OBRotorList ()
void Clear ()
int Size ()
void Init (std::string &fname)
void SetQuiet ()
void SetFixAtoms (OBBitVec &fix)
bool IsFixedBond (OBBond *)
bool HasFixedAtoms ()
void SetRotAtomsByFix (OBMol &)
bool SetRotAtoms (OBMol &)
bool Setup (OBMol &)
bool FindRotors (OBMol &)
bool SetEvalAtoms (OBMol &)
bool AssignTorVals (OBMol &)
void IgnoreSymmetryRemoval ()
void RemoveSymVals (OBMol &)
bool IdentifyEvalAtoms (OBMol &mol)
Iterator methods
OBRotor * BeginRotor (OBRotorIterator &i)
OBRotor * NextRotor (OBRotorIterator &i)
OBRotorIterator BeginRotors ()
OBRotorIterator EndRotors ()

Detailed Description

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

Constructor & Destructor Documentation

OBRotorList (  ) 

~OBRotorList (  ) 

Member Function Documentation

void Clear ( void   ) 

Clear the internal list of rotors and reset.

Referenced by OBRotorList::Setup().

int Size (  )  [inline]

Returns:
the number of rotors in this list

Referenced by OBForceField::RandomRotorSearchInitialize(), OBRotorList::Setup(), OBForceField::SystematicRotorSearchInitialize(), and OBForceField::WeightedRotorSearch().

void Init ( std::string &  fname  )  [inline]

Intialize the private OBRotorRules database from a specific file.

void SetQuiet (  )  [inline]

Turn off debugging output.

void SetFixAtoms ( OBBitVec &  fix  )  [inline]

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

bool IsFixedBond ( OBBond *  bond  ) 

Return whether this bond is fixed and thus not rotatable.

Returns:
true if the bond and at least one neighboring bond has fixed atoms

Referenced by OBRotorList::FindRotors(), and OBRotorList::SetEvalAtoms().

bool HasFixedAtoms (  )  [inline]

Returns:
whether this rotor list has any fixed (invariant) atoms

Referenced by OBRotorList::FindRotors(), and OBRotorList::SetEvalAtoms().

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().

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

bool Setup ( OBMol &  mol  ) 

Setup this rotor list for the supplied molecule Calls FindRotors(), SetEvalAtoms(), and AssignTorVals()

Returns:
True if rotatable bonds were found

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

bool FindRotors ( OBMol &  mol  ) 

Find all potentially rotatable bonds in the molecule Uses OBBond::IsRotor() for initial evaluation

Returns:
True

Referenced by OBRotorList::Setup().

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

Referenced by OBRotorList::Setup().

bool AssignTorVals ( OBMol &  mol  ) 

Using the OBRotorRules database, set the torsion values (and delta) to be evaluated and tested

Referenced by OBRotorList::Setup().

void IgnoreSymmetryRemoval (  )  [inline]

Has no effect

Deprecated:
Currently has no effect

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

OBRotor* BeginRotor ( OBRotorIterator &  i  )  [inline]

Referenced by OBForceField::RandomRotorSearchInitialize(), OBRotorList::RemoveSymVals(), OBRotorList::SetEvalAtoms(), OBRotorList::SetRotAtoms(), OBRotorList::SetRotAtomsByFix(), OBRotorList::Setup(), OBRotamerList::Setup(), OBForceField::SystematicRotorSearchInitialize(), and OBForceField::WeightedRotorSearch().

OBRotor* NextRotor ( OBRotorIterator &  i  )  [inline]

Referenced by OBForceField::RandomRotorSearchInitialize(), OBRotorList::RemoveSymVals(), OBRotorList::SetEvalAtoms(), OBRotorList::SetRotAtoms(), OBRotorList::SetRotAtomsByFix(), OBRotorList::Setup(), OBRotamerList::Setup(), OBForceField::SystematicRotorSearchInitialize(), and OBForceField::WeightedRotorSearch().

OBRotorIterator BeginRotors (  )  [inline]

OBRotorIterator EndRotors (  )  [inline]

bool IdentifyEvalAtoms ( OBMol &  mol  )  [inline]

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

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