2-D torsion surface driver script "crank"

[leeping]

Added script to scan the torsional surface of general molecules. Example added for propanol.

--== Ramachandran Plot of Optimization Status for propanol.0-1-6-10-11 ==--
--==  Blue: Optimized, Green: Found Lower, Red: Next  ==--
   -165  -120   -75   -30    15    60   105   150
 180 ----／--／                              ＼--＼--
 165 --／--／                                  ＼--＼
 150 ><--／                                      ＼--
 135 --／                                          ＼
 120 \/                                              
 105                                                 
  90 /\                                              
  75 --＼                                          ／
  60 ><--＼                                      ／--
  45 --＼--＼                                  ／--／
  30 ----＼--＼                              ／--／--
  15 ------＼--＼                          ／--／----
   0 --------＼--＼                      ／--／------
 -15 ----------＼--＼                  ／--／--------
 -30 ------------＼--＼              ／--／----------
 -45 --------------＼--＼          ／--／------------
 -60 ----------------＼--＼      ／--／--------------
 -75 ------------------><--＞  ＜--><----------------
 -90 ----------------／--／      ＼--＼--------------
-105 --------------／--／          ＼--＼------------
-120 ------------／--／              ＼--＼----------
-135 ----------／--／                  ＼--＼--------
-150 --------／--／                      ＼--＼------
-165 ------／--／                          ＼--＼----

Still need to do these things in order to make it a usable tool:

• The quantum chemistry code should be psi4 instead of Q-Chem. I was using Q-Chem because the geometry optimization is more reliable. Q-Chem is also an option but it costs money.
  • I was using psi4 to refine the surfaces at a higher level of theory (MP2/aug-cc-pVDZ) after they were generated by Q-Chem at a lower level (MP2/6-31G*).
• The scanner doesn't work with force fields right now because atom typing is required and it calls TINKER. We should either implement this properly or take it out.
• (Optional) Eliminate dependency on my support modules, nifty.py and molecule.py (included).
• Automatic detection of which dihedral angles to scan.
  • Which bonds are important?
  • Which are the "handle" atoms?