Implemented function to prepare the runs and reorganized the checks for using or not energy minima as conformers
Implemented clustering for Affinity matrices
Moved adapt_format to be available in all module and catching an error on get_rmsd when its argument is not valid.
Retrieve relevant magnitudes for clustering by calling the relative functions
mmff_opt_confs function allows to carry out single point energy calculations if max_iters is set to 0.
Split the generation of conformers and computation of their rmsd in two different functions. Added new functions to obtain the conformers moment of inertia and to optimize them using MMFF force field.
Changes rms to rmsd of new files
Revert "Changed rmsd for rms"
This reverts commit 5571316d
Extended gen_confs documentation and incorporated the possibility to choose whether molecule conformers should be minimum energy conformers or not.
Changed the way RMS between two conformers gets calculated. Now the RMS is performed by not considering hydrogens bonded to carbons but it does consider hydrogens bonded to all other atoms or not bonded at all.
Disabled the removal of hydrogens when using rdkit sdl mol file reader. Now, rdkit mol object contain hydrogens explicitly.
Moved logger to a global variable
Changed rmsd for rms
Created a module for each stage of DockOnSurf and started developing the isolated one
Improved the documentation of the consequent docstrings
Included, the necessity to specify the molecule file to be adsorbed, in the input.
Changed the read_coords.py module name to formats.py which states more clearly the purpose of the module.
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 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.
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 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
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.
Now dockonsurf takes the geometry of the optimized most stable conformer; fixes #2676
Corrected a typo in the comments
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
Initial files