- 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.
1.7.5.1.
