Open Babel: Deprecated List

# Deprecated List

Member matrix3x3::Get (int row, int column) const
  use the constant operator() instead

Member matrix3x3::PlaneReflection (const vector3 &norm)
  This method will probably replaced by a safer algorithm in the future.

Member matrix3x3::RotAboutAxisByAngle (const vector3 &axis, const double angle)
  This method will probably replaced by a safer algorithm in the future.

Member matrix3x3::Set (int row, int column, double v)
  use the non-constant operator() instead

Member OBAtom::GetCIdx () const
  Use GetCoordinateIdx() instead

Member OBAtom::GetNextAtom ()
  Use any of the other iterator methods. This method will be removed in the future.

Member OBAtom::HasChiralitySpecified ()

Member OBAtom::HasChiralVolume ()

Member OBAtom::IsAntiClockwise ()

Member OBAtom::IsClockwise ()

Member OBAtom::IsNegativeStereo ()

Member OBAtom::IsPositiveStereo ()

Member OBAtom::KBOSum () const
  Use BOSum() instead

Member OBAtom::SetAntiClockwiseStereo ()

Member OBAtom::SetClockwiseStereo ()

Member OBAtom::SetHybAndGeom (int)
  This will be removed in future versions of Open Babel

Member OBAtom::SetNegativeStereo ()

Member OBAtom::SetPositiveStereo ()

Member OBAtom::UnsetStereo ()

Member OBAtomTyper::CorrectAromaticNitrogens (OBMol &)
  Currently unused for anything significant.

Member OBBitVec::BitIsOn (int bit_offset) const
  Use BitIsSet(unsigned bit_offset) instead.

Member OBBitVec::Empty () const
  Use IsEmpty() instead.

Member OBBond::GetBO () const
  Use GetBondOrder() as this method may be removed.

Member OBBond::IsKDouble ()
  Use IsDouble() instead

Member OBBond::IsKSingle ()
  Use IsSingle() instead

Member OBBond::IsKTriple ()
  Use IsTriple() instead

Member OBBond::SetBO (int order)
  Use SetBondOrder() instead.

Member OBBond::SetKDouble ()
  Use SetBondOrder() instead

Member OBBond::SetKSingle ()
  Use SetBondOrder() instead

Member OBBond::SetKTriple ()
  Use SetBondOrder() instead

Member OBBond::Visit
  Use OBBitVec objects instead to be fully thread-safe.

Class OBChiralData
  Used OBStereoFacade instead

Member OBElement::OBElement ()
  Not used. Instead, initialize element properties

Member OBElementTable::GetAtomicNum (const char *)
  Does not properly handle 'D' or 'T' hydrogen isotopes

Member OBFloatGrid::GetDim (int *a)
  May be removed in future.

Member OBFloatGrid::GetMax (double *a)
  Will be removed.

Member OBFloatGrid::GetMin (double *a)
  Will be removed. Use

Member OBFloatGrid::GetSpacing (double &s)
  Will be removed.

Member OBFloatGrid::GetVals ()
  Will be removed.

Member OBFloatGrid::SetLimits (const double origin[3], const double x[3], const double y[3], const double z[3])
  Will be removed.

Member OBFloatGrid::SetVals (double *ptr)
  Will be removed.

Member OBForceField::LineSearch (OBAtom *atom, vector3 &direction)
  Current code should use LineSearch(double *, double*) instead.

Member OBForceField::UpdateConformers (OBMol &mol)
  Use GetConformers instead.

Member OBForceField::UpdateCoordinates (OBMol &mol)
  Use GetCooordinates instead.

Member OBForceField::VectorAngleDerivative (vector3 &a, vector3 &b, vector3 &c)

Member OBForceField::VectorLengthDerivative (vector3 &a, vector3 &b)

Member OBForceField::VectorOOPDerivative (vector3 &a, vector3 &b, vector3 &c, vector3 &d)

Member OBForceField::VectorTorsionDerivative (vector3 &a, vector3 &b, vector3 &c, vector3 &d)

Member OBGridData::GetOriginVector (double o[3]) const
  Will be removed.

Member OBGridData::SetLimits (const double origin[3], const double x[3], const double y[3], const double z[3])
  Will be removed.

Member OBMol::CreateAtom (void)
  Use NewAtom instead, which ensures internal connections

Member OBMol::CreateBond (void)
  Use NewBond instead, which ensures internal connections

Member OBMol::CreateResidue (void)
  Use NewResidue instead, which ensures internal connections

Member OBMol::expand_kekulize (int bond_idx, std::vector< int > &atomState, std::vector< int > &bondState)
  Will no longer be a public, visible method

Member OBMol::expandcycle (OBAtom *atom, OBBitVec &avisit, const OBBitVec &potAromBonds)
  Will no longer be a public, visible method

Member OBMol::FindChiralCenters ()
  See FindStereogenicUnits

Member OBMol::GetFirstAtom () const
  Will be removed in favor of more standard iterator methods

Member OBMol::getorden (OBAtom *atom)
  Will no longer be a public, visible method

Member OBMol::has_no_leftover_electrons (std::vector< int > &atomState)
  Will no longer be a public, visible method

Member OBMol::NewPerceiveKekuleBonds ()
  Will no longer be a public, visible method

Member OBMol::start_kekulize (std::vector< OBAtom * > &cycle, std::vector< int > &electron)
  Will no longer be a public, visible method

Class OBProxGrid
  May be removed in the future, since docking is not a key feature

Member OBResidueData::AssignBonds (OBMol &, OBBitVec &)
  second OBBitVec argument is ignored

Member OBResidueData::LookupBO (const std::string &)
  Easier to use the two-argument form

Member OBRing::PathSize () const
  Use Size() instead

Member OBRotor::GetDelta ()
  Has no effect.

Member OBRotor::GetEvalAtoms ()

Member OBRotor::GetFixedAtoms ()

Member OBRotor::GetResolution ()
  Bad name, see GetTorsionValues()

Member OBRotor::GetRotAtoms ()

Member OBRotor::SetDelta (double d)
  Has no effect.

Member OBRotor::SetEvalAtoms (OBBitVec &bv)

Member OBRotor::SetFixedAtoms (OBBitVec &bv)
  See SetFixedBonds

Member OBRotor::SetNumCoords (int nc)

Member OBRotorList::HasFixedAtoms ()
  See HasFixedBonds()

Member OBRotorList::IdentifyEvalAtoms (OBMol &mol)
  Not declared. Use Setup() for top-level functionality

Member OBRotorList::IgnoreSymmetryRemoval ()
  Currently has no effect

Member OBRotorList::SetFixAtoms (OBBitVec &fix)
  See SetFixedBonds()

Class OBScoreGrid
  Will disappear in future versions. Use your own code.

Member OBSmartsPattern::_growbond
  (Not used)

Member OBTypeTable::Translate (char *to, const char *from)
  Because there is no guarantee on the length of an atom type you should consider using std::string instead

Member OpenBabel::CalcSignedVolume (OBMol &mol, OBAtom *, bool ReZeroZ=true)
  Use new Stereochemistry classes.

Member OpenBabel::construct_c_matrix (OBMol &mol, std::vector< std::vector< double > > &m)

Member OpenBabel::construct_g_matrix (OBMol &mol, std::vector< std::vector< double > > &m)

Member OpenBabel::CorrectChirality (OBMol &mol, OBAtom *atm, atomreftype i=input, atomreftype o=output)
  Use new Stereochemistry classes.

Member OpenBabel::GetChirality (OBMol &mol, std::vector< int > &chirality)
  Use new Stereochemistry classes.

Member OpenBabel::GetParity4Ref (std::vector< unsigned int > pref)
  Use new Stereochemistry classes.

Member OpenBabel::GraphPotentials (OBMol &mol, std::vector< double > &pot)

Member OpenBabel::IsNear (const double &a, const double &b, const double epsilon)
  Use IsApprox() instead

Member OpenBabel::IsNearZero (const double &a, const double epsilon)

Member OpenBabel::signed_volume (const vector3 &a, const vector3 &b, const vector3 &c, const vector3 &d)
  Use new Stereochemistry classes.

Member OpenBabel::ThrowError (char *str)
  Throw an error through the OpenBabel::OBMessageHandler class

Member OpenBabel::ThrowError (std::string &str)
  Throw an error through the OpenBabel::OBMessageHandler class

Member OpenBabel::vectorAngle (const vector3 &v1, const vector3 &v2)
  This method will probably replaced by a safer algorithm in the future.

Class patty
  This code is currently not used by the Open Babel library. Instead, OBAtomTyper and OBAromaticTyper are used. Unless there is interest in retaining this independent class, it will be removed in the future.

Member vector3::operator!= (const vector3 &other) const
  This method uses unreliable floating point == comparisons Use vector3::IsApprox() instead.

Member vector3::operator== (const vector3 &) const
  This method uses unreliable floating point == comparisons Use vector3::IsApprox() instead.

All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines