Merge mpmaster branch
More improvements to func group substitution code.
Improved openbabel conversion.
revert back to Yb_2 pseudo for MP as decided at today's meeting
Add a lot more doc and improve algo slightly for substitution functional groups.
Rename sub arg to func_grp for better clarity.
Minor cleanup.
More doc and cleanup.
Remove unittest for deprecated structure modifier.
 Add ntypat property to SiteCollection.
Merge remote-tracking branch 'mpmaster/master'
Cleanup.
fixed minor bug in ordering transformation
Cleanup.