- Member _growbond
- (Not used)
- Member AssignBonds (OBMol &, OBBitVec &)
- second OBBitVec argument is ignored
- Member BitIsOn (int bit_offset) const
- Use BitIsSet(unsigned bit_offset) instead.
- Member CalcSignedVolume (OBMol &mol, OBAtom *, bool ReZeroZ=true)
- Use new Stereochemistry classes.
- Member construct_c_matrix (OBMol &mol, std::vector< std::vector< double > > &m)
- Member construct_g_matrix (OBMol &mol, std::vector< std::vector< double > > &m)
- Member CorrectAromaticNitrogens (OBMol &)
- Currently unused for anything significant.
- Member CorrectChirality (OBMol &mol, OBAtom *atm, atomreftype i=input, atomreftype o=output)
- Use new Stereochemistry classes.
- Member CreateAtom (void)
- Use NewAtom instead, which ensures internal connections
- Member CreateBond (void)
- Use NewBond instead, which ensures internal connections
- Member CreateResidue (void)
- Use NewResidue instead, which ensures internal connections
- Member Empty () const
- Use IsEmpty() instead.
- Member expand_kekulize (int bond_idx, std::vector< int > &atomState, std::vector< int > &bondState)
- Will no longer be a public, visible method
- Member expandcycle (OBAtom *atom, OBBitVec &avisit, const OBBitVec &potAromBonds)
- Will no longer be a public, visible method
- Member FindChiralCenters ()
- See FindStereogenicUnits
- Member Get (int row, int column) const
- use the constant operator() instead
- Member GetAtomicNum (const char *)
- Does not properly handle 'D' or 'T' hydrogen isotopes
- Member GetBO () const
- Use GetBondOrder() as this method may be removed.
- Member GetChirality (OBMol &mol, std::vector< int > &chirality)
- Use new Stereochemistry classes.
- Member GetCIdx () const
- Use GetCoordinateIdx() instead
- Member GetDelta ()
- Has no effect.
- Member GetDim (int *a)
- May be removed in future.
- Member GetEvalAtoms ()
- Member GetFirstAtom () const
- Will be removed in favor of more standard iterator methods
- Member GetFixedAtoms ()
- Member GetMax (double *a)
- Will be removed.
- Member GetMin (double *a)
- Will be removed. Use
- Member GetNextAtom ()
- Use any of the other iterator methods. This method will be removed in the future.
- Member getorden (OBAtom *atom)
- Will no longer be a public, visible method
- Member GetOriginVector (double o[3]) const
- Will be removed.
- Member GetParity4Ref (std::vector< unsigned int > pref)
- Use new Stereochemistry classes.
- Member GetResolution ()
- Bad name, see GetTorsionValues()
- Member GetRotAtoms ()
- Member GetSpacing (double &s)
- Will be removed.
- Member GetVals ()
- Will be removed.
- Member GraphPotentials (OBMol &mol, std::vector< double > &pot)
- Member has_no_leftover_electrons (std::vector< int > &atomState)
- Will no longer be a public, visible method
- Member HasChiralitySpecified ()
- Member HasChiralVolume ()
- Member HasFixedAtoms ()
- See HasFixedBonds()
- Member IdentifyEvalAtoms (OBMol &mol)
- Not declared. Use Setup() for top-level functionality
- Member IgnoreSymmetryRemoval ()
- Currently has no effect
- Member IsAntiClockwise ()
- Member IsClockwise ()
- Member IsKDouble ()
- Use IsDouble() instead
- Member IsKSingle ()
- Use IsSingle() instead
- Member IsKTriple ()
- Use IsTriple() instead
- Member IsNear (const double &a, const double &b, const double epsilon)
- Use IsApprox() instead
- Member IsNearZero (const double &a, const double epsilon)
- Member IsNegativeStereo ()
- Member IsPositiveStereo ()
- Member KBOSum () const
- Use BOSum() instead
- Member LineSearch (OBAtom *atom, vector3 &direction)
- Current code should use LineSearch(double *, double*) instead.
- Member LookupBO (const std::string &)
- Easier to use the two-argument form
- Member NewPerceiveKekuleBonds ()
- Will no longer be a public, visible method
- Class OBChiralData
- Used OBStereoFacade instead
- Member OBElement ()
- Not used. Instead, initialize element properties
- Class OBProxGrid
- May be removed in the future, since docking is not a key feature
- Class OBScoreGrid
- Will disappear in future versions. Use your own code.
- Member operator!= (const vector3 &other) const
- This method uses unreliable floating point == comparisons Use vector3::IsApprox() instead.
- Member operator== (const vector3 &) const
- This method uses unreliable floating point == comparisons Use vector3::IsApprox() instead.
- Member PathSize () const
- Use Size() instead
- 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 PlaneReflection (const vector3 &norm)
- This method will probably replaced by a safer algorithm in the future.
- Member RotAboutAxisByAngle (const vector3 &axis, const double angle)
- This method will probably replaced by a safer algorithm in the future.
- Member Set (int row, int column, double v)
- use the non-constant operator() instead
- Member SetAntiClockwiseStereo ()
- Member SetBO (int order)
- Use SetBondOrder() instead.
- Member SetClockwiseStereo ()
- Member SetDelta (double d)
- Has no effect.
- Member SetEvalAtoms (OBBitVec &bv)
- Member SetFixAtoms (OBBitVec &fix)
- See SetFixedBonds()
- Member SetFixedAtoms (OBBitVec &bv)
- See SetFixedBonds
- Member SetHybAndGeom (int)
- This will be removed in future versions of Open Babel
- Member SetKDouble ()
- Use SetBondOrder() instead
- Member SetKSingle ()
- Use SetBondOrder() instead
- Member SetKTriple ()
- Use SetBondOrder() instead
- Member SetLimits (const double origin[3], const double x[3], const double y[3], const double z[3])
- Will be removed.
- Member SetLimits (const double origin[3], const double x[3], const double y[3], const double z[3])
- Will be removed.
- Member SetNegativeStereo ()
- Member SetNumCoords (int nc)
- Member SetPositiveStereo ()
- Member SetVals (double *ptr)
- Will be removed.
- Member signed_volume (const vector3 &a, const vector3 &b, const vector3 &c, const vector3 &d)
- Use new Stereochemistry classes.
- Member start_kekulize (std::vector< OBAtom * > &cycle, std::vector< int > &electron)
- Will no longer be a public, visible method
- Member ThrowError (std::string &str)
- Throw an error through the OpenBabel::OBMessageHandler class
- Member ThrowError (char *str)
- Throw an error through the OpenBabel::OBMessageHandler class
- Member 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 UnsetStereo ()
- Member UpdateConformers (OBMol &mol)
- Use GetConformers instead.
- Member UpdateCoordinates (OBMol &mol)
- Use GetCooordinates instead.
- Member vectorAngle (const vector3 &v1, const vector3 &v2)
- This method will probably replaced by a safer algorithm in the future.
- Member VectorAngleDerivative (vector3 &a, vector3 &b, vector3 &c)
- Member VectorLengthDerivative (vector3 &a, vector3 &b)
- Member VectorOOPDerivative (vector3 &a, vector3 &b, vector3 &c, vector3 &d)
- Member VectorTorsionDerivative (vector3 &a, vector3 &b, vector3 &c, vector3 &d)
- Member Visit
- Use OBBitVec objects instead to be fully thread-safe.
