Use averaged bond order corrections from Pyykko and Atsumi 2009.

Slight modifications from previous versions, but likely better
overall, since they're systematically derived.
Add a threshold to single fragment scaling
Merge branch 'master' of github.com:openbabel/openbabel
Update comment
Updated abs() -> fabs()
setup.py now 2/3 compatible
Compute vibration intensities for VASP format

The vibration intensities are not explicitely present in VASP output but
can be computed from the changes of dipole moments and the normal
coordinates.

Christian Neiss (FAU Erlangen Nürnberg) wrote the Python script that
served as the basis for this patch.
Fix a performance problem with parsing PDB files that have overlapping
fragments in them.  Since the fragments overlap, ConnectTheDots adds a
ton of bonds, most of which then need to be deleted (really shouldn't add any
considering there are connect records..).  The problem is that each
call to DeleteBond triggered a re-perception since it calls EndModify.

The fix is just to wrap the whole code in Being/EndModify.
The reduces the time to parse the PDB file from minutes/hours to less than a second.
Merge pull request #106 from dkoes/upstream

Fix a performance problem with parsing PDB files that have overlapping
Merge pull request #97 from mwojcikowski/master

Parse HND1 etc atoms in DUD-E
Merge pull request #94 from leeping/master

Add a threshold to single fragment scaling
Merge pull request #84 from ghutchis/ENH-builder-covalent-bo-radii

Use averaged bond order corrections from Pyykko and Atsumi 2009.
Merge pull request #99 from patrickfuller/pip

setup.py now 2/3 compatible
remove asserts
Merge pull request #104 from Synss/vasp-intensities

Compute vibration intensities for VASP format
Changecell separated to commit branch.
Support for MDFF format added: http://code.google.com/p/mdff/
DL_POLY format plugin will read cell information now.
Fix normal mode parsing in molden format

This fixes a bug in the parsing of the normal modes in the Molden format
where the parser would keep parsing normal modes after the relevant
section actually ended.

This could make openbabel crash in some cases.
Merge pull request #111 from Synss/fix-molden

Fix normal mode parsing in molden format