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::SetHybAndGeom (int)

This will be removed in future versions of Open Babel

Member OBBond::Visit

Use OBBitVec objects instead to be fully thread-safe.

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::DistanceGeometry ()

Use OBDistanceGeometry class instead

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::GetFirstAtom () const

Will be removed in favor of more standard iterator methods

Class OBProxGrid

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

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::IsNear (const double &a, const double &b, const double epsilon)

Use IsApprox() instead

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

Member OpenBabel::ThrowError (std::string &str)

Throw an error through the OpenBabel::OBMessageHandler class

Member OpenBabel::ThrowError (char *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.