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.

Bugfix and improved symmetry handling

• Fixed bug with symmetry operators containing blanks, e.g. 'x, y, z' rather than 'x,y,z'
• Added handling of symmetry when get properties of atoms
• Added method to lower symmetry to P1/C1

Technical release due to change in dependency

Merge pull request #69 from molssi-seamm/dev

Updating for changes in configparser.

Support for InChI improved, RMSD and PubChem added...

• Adds support for aligning structures and calculating RMSD
• Adds support for working directly with PubChem to get structures, IUPAC names, etc.
• Improves support for InChI, working around issues in both OpenBabel and RDKit.
• Added substantial new functionality for spacegroups and primitive cell handling, but still not complete.

Added support for velocities on atoms

Merge pull request #67 from molssi-seamm/dev

Support for velocities on atoms