New tutorial chapter
Update crystal-contacts.md
Update crystal-contacts.md
Update crystal-contacts.md
Update crystal-contacts.md
New tutorial on contact maps
Update contact-map.md
Merge pull request #1 from josemduarte/master

New tutorials on contacts and crystal interfaces
Improving descriptions of alignment algorithms
Adding bin/update_index.py script.

This script generates the footers for all files. Rerun the script after
adding new books or chapters in order to update the footer sections
on each page with links to the next and previous chapters.

The script works by recursively parsing "## Index" sections in files,
starting with README.md. The footer is marked with an HTML comment,
`<!--automatically generated footer-->`. Any text after this comment
is destroyed by the script, so all edits should be made above that
point.
Small tweeks to update_index.py

- better documentation
- no footer on the main README
- small formatting fixes
Executing bin/update_index.py for the first time.

This adds footers to every page. No text changes.
Adding addition alignment algorithms & code examples
Added database search to structure alignment chapter
Adding Command-line tools section

Also moved up the database search section & fixed some spellings.
Fixing Jmol capitalization
Update alignment.md
Update alignment.md
Update alignment.md
Update alignment.md