renamed dockonsurf_input.py to dos_input.py
Added PyCharm folders to .gitignore
Reformat according to PEP 8 standard
more bugfixes after heavy testing
Corrected some bugs
Module to read dockonsurf input files
renamed the input file
add .gitignore and test directory 'test' to it
Added a folder to provide some examples at the present commit only a sample input file is provided
Start v2 from scratch
Removed the loop finished debug message once all the calculations are submitted
Enabled the possibility to do coadsorption by checking collision with neighbor lists. Removed the coadsorption box option. Included the increase in height to prevent collision as last option when rotation doesn't work
adsorption takes into account the z of the surface atom and not the highest point of the surface
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
If dockonsurf.sh is called with the only_iso flag (-i or --only-isolated), the script puts itself to run in background and gets unlinked from the terminal, allowing the script to continue even if the terminal gets destroyed
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
Once the adsorption input is typed the script puts itself to run in background and gets unlinked from the terminal, allowing the script to continue even if the terminal gets destroyed.
Changed the DockOnSurf_path location. Its location should now be in your PATH environement variable
Changed the DockOnSurf_path location. Its location should now be in your /usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/home/cmartial/dockonsurf_stable environement variable
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