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)

Fixed bug reading cif and mmcif files

• There was a bug that caused a crash when reading cif and mmcif files, and potentially some other formats. It has been fixed throughout.
• The standard error for properties were missing a commma in the property name. The comma is standard elsewhere in SEAMM so add it here: ', stderr'

Handling OpenBabel error messages for MOPAC .mop files

Hiding messages about errors Kekulizing structures, which doesn't seem to be a serious issue, and printing any other messages as warnings.

Updated for the new, open source MOPAC

Merge pull request #35 from molssi-seamm/dev

Updated for new open source mop and properties

Improved handling of SDF files

Added reading & writing properties, better handling of multiple structures, and ability to directly use gzipped files.