Todo List

File bondtyper.cpp

Needs to add aromatic ring bond order assignment. Eventually need to migrate OBMol::PerceiveBondOrders(), OBMol::ConnectTheDots(), and possibly some of the Kekulize routines

Member Clone (OBBase *) const

Needs to be updated to rebase atom pointers (or use indexes)

Member GetA ()

Remove nonconst overloads in OBUnitCell on next version bump

Member IdentifyPointGroup ()

Compatibility function; remove at next ABI break, update default arg in overload.

Remove this on next ABI break

Member IsAromatic ()

This method uses implicit bonding -- bond info is not stored in OBRing

Member IsChiral ()

Member IsMember (OBBond *b)

This method uses implicit bonding -- bond info is not stored in OBRing

Class OBSymmetryData

Add support for translation between symbol notations. Add symmetry perception routines.

Member OBUNITCELL_CALL_CONST_OVERLOAD (_type, _name)

Remove nonconst overloads in OBUnitCell on next version bump.

Member operator*= (const matrix3x3 &)

Currently unimplemented

Member PlaneReflection (const vector3 &norm)

Replace this method with a more fool-proof version.

Member RotAboutAxisByAngle (const vector3 &axis, const double angle)

Replace this method with a more fool-proof version.

Member SetRotorToAngle (double *c, OBAtom **ref, double ang, vector< int > atoms)

This code is identical to OBMol::SetTorsion() and should be combined

Member TetrahedralFrom2D (OBMol *mol, const OBStereoUnitSet &stereoUnits, bool addToMol=true)

document bond property interpretation!

Member UpdatePairsSimple ()

set the criteria as squared values

Member vectorAngle (const vector3 &v1, const vector3 &v2)

Replace this method with a more fool-proof version.

Member WrapFractionalCoordinate (vector3 frac)

Make OBUnitCell::WrapFractionalCoordinate static in the next ABI break