Abstract the modofication of CHARM scripts by users of the program #12
Description
It is very likely that we are not going to stop using CHARMM or Reduce to do some of the intermediate steps that Entropy Maxima does not do in the short term. It would just be time consuming to develop scripts that are solutions to problems CHARMM and Reduce already solve well. As part of the process of working with the advance capabilities of Entropy Maxima, users are require to modify CHARMM scripts on the fly to generated output files that Entropy Maxima uses as input. This would be avoided, and made the user experience better, if CHARMM scripts are generated on the fly by Entropy Maxima, and perhaps even run them for the user. This would avoid some complex, error prone manual manipulation by the user. The script em/in_development/charmm_setup.py is an attempt to do that. The docker image has CHARMM installed in it. To run charmm, just ddo 'charmm < input_file.inp > output_file.out'