Moved the printing of input variables from dockonsurf.py to dos_input.py
Created specific module for the reading of command-line arguments and transferred the relevant commands into it
Included requirements file to make installation easier.
Incorporated ammend from previous commit. Merge branch 'v2' of http://forge.cbp.ens-lyon.fr/git/dockonsurf into v2
Included tests to the implemented functions to check new commits don't mess things up
Refactor file dos_input.py, every option is read and checked its value with a specific function for the purpose.Included the possibility to run the file as standalone program.
Added empty init file to ease importing modules
Increase of the input errors that get caught by the program, change how the logger is setup, its message format and how it is organized internally.
Reformat files and extend documentation
Moved the input file option from 'Global' to each relative section and changed the values of options to non-default ones.
Include errors in the log, improved error handling by catching new errors.
Written the docstrings to document the code following the PEP 257 conventions
Commented out useless print statement
Reformat and cleaning the code for improved readability and adequate it to PEP 8 conventions.
Included modules subdirectory in the system path. Changed the log message to show now the timestamp. Improved code readability.
Possible errors are now printed in both the screen and the log file. More errors are now handled properly.
Implemented the read coordinates module working to read xyz and mol files and obtain rdkit and ase objects to work with
Added indentation to read variables in the log file to increase readability
Added error handling functionality to input str2lst function
Refactoring code by creating modules directory and moving dos_input.py into it.
Added first version of main dockonsurf.py script including logging, parsing arguments and reading the input.
further modified .gitignore
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
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
Revert "Changed the DockOnSurf_path location variable to be a relative path"
This reverts commit 5c78fefec772643d79cabc9f2e2bd8adbd42c33d.
Changed the DockOnSurf_path location variable to be a relative path
Added the possibility to carry out coadsorption. By adding the -b option, when the surface file already contains an adsorbed molecule, it creates a box around it to prevent the second adsorbate to overlap the first.
Added temporary vim files to .gitignore (.swp files)
Now dockonsurf takes the geometry of the optimized most stable conformer; fixes #2676
Corrected a typo in the comments
Disabled the suppression of some restart files, while preserving the deletion of heavy bak files
Now it is possible to call dockonsurf.sh script with options. These include: Usage: dockonsurf [OPTION]=PATTERN -h, --help display this help text and exit. -q=NUM, --max-qw=NUM allows a maximum of NUM jobs on 'qw' status. -a, --only-ads carry out only adsorption part. -i, --only-isolated carry out only isolated molecules part. -r, --only-refinement carry out only refinement of adsorbed structure.
The check for running jobs has changed from checking the job name to checking the job num id.
fe_change.sh now expects a surface xyz file ended with a carriage return character
Changed sleep time from 300s to 30s
Deleted DockOnSurf_path in the index as it changes from user to user, to be included in the .gitignore
Initial files