Bugfix: Crash due to multiple slashes in titles in SDF files

Merge pull request #51 from molssi-seamm/dev

Fixed crash due to multiple slashes in titles.

Added writers for CIF and mmCIF.

Merge pull request #50 from molssi-seamm/dev

Added writers for CIF and mmCIF.

Initial changes to structure handling

Moving towards the standard structure handling that has developed across SEAMM.

Add support for bonds in CIF files

Now correctly handle spacegroup symmetry and bonds in CIF files.

Added ability to select ranges of structures for XYZ and SDF files

Merge pull request #47 from molssi-seamm/dev

Fixed selection of ranges

Removed debug printing left accidentally

Merge pull request #46 from molssi-seamm/dev

Removed debug printing

Support for .gz and .bz2 files, and multi-structure .xyz files

• Handle .gz and .bz2 files for .sdf and .xyz extensions.
• Handle multi-structure XYZ files with a blank line between records.

Bugfixes: improved output writing files.

• Fixed output of number of structures written to SDF files, which was off by 1.
• Cleaned up the output for the write-structure step

Corrected issue with documentation

Functionally identical to previous release; however, there was an issue creating the documentation which should be solved in this release.

Added handler for XYZ files and added properties

• Added a custom handler for XYZ files to cope with some of the variant formats. (Resolves #39)
  • Supports files with no atom count on the first line
  • Supports the variant used in the Minnesota Solubility database, which has 3 header lines.
• Add capability to store properties into the database for formats such as MOPAC and SDF that can handle properties. Also can output the properties when writing the files.
• Fixed bugs if the system name or configuration name is not a string, but rather a number.
• Moved documentation to new style (Resolves #40)