Keating:FutureCode


 * DONE: Allow the parent process in specdesign to be able to run an arbitrary command (specified in the control spec file) that re-evaluates the energy of the solution. Some ideas:
 * popen is a useful function in C.
 * the specified command (most conveniently a script) must expect exactly one input string on the command line (the solution/backbone string) and output only one number is to stdout - the new energy.


 * Get to the bottom of the apparent MPI slowdown between parent and children processes - a better timing study.


 * Implement exclusion list capability (in PDB.pm probably) and allow the possibility of moving self calculations outside of CHARMM. Start by moving vdW such that arbitrary modifications can be easily applied.