Add an emitChanged method to QtGui::Molecule.

This allows users of the reference methods to indicate that the
molecule has changed.

Change-Id: Ie764155bd82752ef50e0fc4d5f76370c3d9d9f8f
Use a temporary OBProcess for querying read formats.

This is necessary for later changes, which call other query
methods in QtPlugin::OpenBabel that would clash if they shared
the same process.

Also make the handleReadFormatUpdate argument const& and make a
trivial organizational change in OBProcess::readFile.

Change-Id: I439116eefddf7b3683f7410567a9739a7accf02c
Expose obabel --minimize in the OpenBabel extension.

Pop up a configuration gui, start the minimization, show
step and energy info in a progress bar, and load the molecule
when finished.

Change-Id: Iaffdd581425e8e356caf33546c4f3e20a4ecf29c
Add gaussian input generator script.

Change-Id: I068ea83954de364d8a0a3cbcfe79136746b70c71
Add numberOfCores to the input generator settings.

This allows input generator scripts to adapt themselves for
parallel calculations.

Change-Id: I62d810fc4a8e3d339a4a4e50c9f50820ebfa6a90
Add type metadata to input generator user options.

Extends the dynamic input generator GUI to handle strings,
integers, and booleans.

Updated the existing input generators.

Added a "Title" parameter special case.

Updated and organized the InputGenerator documentation.

Change-Id: If732e0c68d961f5aa71bb8b7c49955d59fbb49cd
Check that scripts are executable before trying to run them.

Should help catch a common mistake.

Change-Id: I4e0d1391ff76fce90a8d04614c1a924c8d7bbb76
Remove dead code in class definition.

Missed this when I move the function earlier...

Change-Id: Iecbd1844db25ef96fbf99c93b2ec7d910e1d8863
Fix bug when building dynamic input generator GUI.

If only theory or basis were specified, the option would appear
twice in the GUI.

Change-Id: I6ccdc1571d2fb03787e7bf628f6e7ad628802d64
Add support for literal '1' or '0' in coord. spec.

These are widely used for optimization flags, needed for MOPAC.

Change-Id: I892f3197c51f60cd354f57887d4db010f03e5f6d
Add MOPAC input generator.

Change-Id: I759e0a325da283ef30cd1a93aa6d67d91f2b39e5
Add '_' to coordinate specification character set.

Allows a single space to be inserted. Handy for aligning
coordinate blocks with surrounding text.

Change-Id: I8060384efda3f1b8a3978c4e008893efd012ba9c
Port the Q-Chem input generator from 1.x.

Change-Id: Iee33db3d5eef457cdb50d9e8a65c2dda072f35b9
Port the GAMESS-UK input generator from 1.x.

Change-Id: I356b61bafa2e6162286c8c14ea2843cca26e8d15
Fix bug passing molecule to input generator scripts.

* Missed error case
* Insert cjson directly into the JSON option structure, rather
  than a cjson string

Change-Id: Ia546d985b91eba4f3044740bc1eb307a38cef546
Port the MOLPRO input generator from 1.x.

Change-Id: I1f6ae27c2907255f63813664fc17c9a7e7d8691f
Add more keywords to inputgenerator.

$$atomCount$$ Molecule::atomCount()
$$bondCount$$ Molecule::bondCount()

Change-Id: I09b422b50d8ea32b6a7bb475253ea933f05f8e4b
Use monospaced font in the input generator dialog.

Change-Id: I33b0245f9813191bca561d2f79d9bf54890b509f
Port the TeraChem input generator from 1.x.

Change-Id: I2e37add1ba67303de6949f47980020801da6a467
Merge remote-tracking branch 'origin/master' into 116-OpenBabelForceFields

Conflicts:
	avogadro/qtplugins/openbabel/obprocess.cpp

Change-Id: I14b9fbf0cf416f5acf24ecb84c1845e3015610e8