Bugfix: Incorrect coordinates from PubChem

• Fixed bug where the coordinates from PubChem were accidentally the 2-D rather than 3-D coordinates.

Bugfix: current configuration not updated properly

• Existing instances of systems did not correctly update when the default configuration was changed. This is release fixes the problem.

Bugfix: creating H2 from SMILES failed

• Fixed bug where creating molecules consisting of just hydrogen failed because RDKit by default ignores all hydrogens when reorienting the molecule.

Switching default for SMILES to RDKit rather than OpenBabel

• RDKit seems more robust, and also the atom typing uses RDkit, so compatibility is important.

Added more control over RDKit and OpenBabel creating systems

• Added control to from_RDKMol and from_OBMol to allow selectively updating the atoms, coordinates, and bonds

Rotated molecule from SMILES, InChI, or InChIKey to standard orientation

• Molecules created from line notation are created in an random orientation. This enhancement rotates them to the standard orientation, which will look nice for small, symmetric molecules.

Bugfix: bonds in RDKit

• There was an indexing bug translating bonds back from RDKit to SEAMM. The famous 0/1 problem!

Added gradients to atoms

• Added gradient on atoms as a separate table alongside atoms, so they take no space unless actually used.

Handle uppercase X, Y, Z in strings for symmetry operators

• the Crystallographic Open Database CIF files seems to use upper case X, Y, Z in explicit symmetry operators. These need to be lowercased in the code.

Bugfixes in symmetry and CIF files

• Reading CIF files could fail if the symmetry operators were given
• The symmetry handling did not recognize hexagonal spacegroups without :H. Changed so if the hexagonal group name has neither :H or :R, the hexagonal setting is assumed.
• When finding the spacegroup from the symmetry operators, hard-coded to the P1 case to avoid what seems like a bug in spglib.
• Enhanced to use the full International Tables HM name for spacegroups, translating the input to that standard name.