Added error handling functionality to input str2lst function
Refactoring code by creating modules directory and moving dos_input.py into it.
Start v2 from scratch
In the case of launching dockOnSurf.sh with the only-refinement flag and that an analyse / relaunched_calculation directories already exists, the user is asked whether to delete or not these directories before the script puts itself to run in background; Solves #2729
Merge branch 'master' of http://forge.cbp.ens-lyon.fr/git/dockonsurf
Now modules/fe_change.sh works even if the surface file ends with blank lines; fixes #2727
Removed the possibility to remove hydrogens from the RMSD check. Changed also the RMSD check to not include atom permutations. This should speed up the RMSD check process, while distinguishing different H spatial position when important like hydrogen bond formation
Added the possibility to control the rmsd threshold in the check of different conformers
Added the possibility to remove hydrogens during the calculation of RMSD of generated structures
Sets the initial step number of the refinment calculation not to be conserved from the lower precision stage (ie. it starts always at 1); Fixes #2706
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