Enhancement to 'For' loops

• For integer loops, ensure that the loop variable is an integer and make the directory name be value of the loop variable to make it easier to find the iteration of interest.

Bugfix: Error selecting systems by name

• There was a bug selecting system by name in the For Systems in Database branch.

Improved handling for For Systems in Database

Added ability to get all configurations for each system, as well as using matching or regexps for the names of configurations to select.

Further improving naming of loop subdirectories

• For loops now use the value of loop index as the subdirectory
• Improved handling of lists for ForEach loops so blank-delimited lists work properly. Quotes can be used for values with embedded blanks, much like the Linux commandline.

Improved naming of loop subdirectories

• The subdirectories now start at 1, not 0, to make counting more normal
• When looping over systems, now have the option to name the directories after the system or configuration name, not the iteration number.

Bugfix: Crash in "For" loops

• For loops could crash writing to write final_structure.mmcif before the directory had been made.

Improved consistency of printing loop information

Merge pull request #22 from molssi-seamm/dev

Improved consistency of printing loop information

Better support for rerunning/restarting jobs

• Remove 'iteration.out' if it already exists.

Starting to add loops over structures in the database

• Reorganized the documentation and changed to the standard MolSSI theme

Improved error handling

Wrote the traceback for any errors caught to item_nnn/stderr.out to aid debugging.