Added support for JSON in properties

Add JSON properties, which allows storing vectors, matrices, etc. as properties, thought they are not searchable.

Supporting in-line uncertainties for values in CIF files.

Merge pull request #59 from molssi-seamm/dev

Supporting in-line uncertainties for values in CIF files.

Enhancements to QCSchema support

• Improved naming of molecules in QCSchema, using system.name / configuration.name
• Added creating configurations from QCSchema data.

Fixed issue with valence in RDkit for cations like NH4+

This affected forcefield assignment.

Add handling of strain and improved handling of properties

Added methods for straining the unit cell, and also straining a configuration, correctly handling the coordinates for an affine transformation. In the future will add e.g. affine transformation of the centers of molecules, which is useful for molecular fluids.

Added the system for properties, in addition to the configuration. This allows system properties that are not associated with a particular configuration, which is often appropriate for experimental results. It also makes it much easier to search for systems where any configuration has a particular property.

Improved database write performance.

Switched to write-ahead mode and tweaked memory settings. This gives a large performance improvement (10x or more) for large database (~1 GB).

Added access to property metadata

Also added more standard properties to support MOPAC, DFTB+ and Psi4.

Improved handling of properties

Added ability to transfer properties between the internal SEAMM database and OpenBabel. This supports using OpenBabel to e.g. read and write SDF files that contain property data.

Bugfix: Fixed problem with groups with rotations x<->y

Fixed a problem with spacegroup with symmetry operators with terms like -x+y.

Bugfix: properties of a configuration

There was a bug getting all properties for a configuration which produced incorrect values.