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Raise an error if no configurations are generated at the Screening stage. Corrected fallback value of collision_threshold option in input file.
Corrected bug when pre_opt was set to false, the default value of force_field parameter, in pre_opt_confs function, was 'MMFF' (in capitals) while inside the function it was compared to 'mmff' (in lower).
Added random seed to EmbedMultipleConfs to enable reproducibility
Removed unnecesary statements
Corrected typos and letter case errors.
Changed min_confs option name to pre_opt which accept a turn_false_answer, uff and mmff.
Included extra arguments for the proper working of special atoms.
Added logging entries at the beginning and end of each section.
Added punctuation marks at the end of every log messages.
Function get_surf_norm_vect returns a numpy.ndarray instead of a list. Function get_pts_per_angle checks that the number of points per angle to be positive. Added TODO on get_moments_of_inertia
Corrected the extraction of MOI from a list of mol objects. For the plotting of graphs in clustering.py renamed boolean var debug to plot and added a check-backup on the plot file. Removed useless chunk on isolated.py.
Moved get_rmsd from isolated.py to clustering.py and changed its functionality, now it expects a list of mol objects instead of a single mol object with multiple conformers in it.
Add hydrogen atoms before the conformer generation.
Added hidden files to .gitignore and Changed Information displayed on the log for the MMFF Opt.
Added fallback value for project_name in dos_input.py. Included log messages for submitted jobs on calculation.py, added TODO tasks and changed documentation on all three files.
Moved confs_to_mol_list function from isolated.py to formats.py module and generalised the calculations functions to be able to work with no matter which kind of calculation
Created calculation.py module and moved prep_run from isolated.py to it
Included printing the number of conformers generated and reformat documentation in isolated.py
Removed redundant UFF optimization, corrected type on conformer index in the writing of XYZ file and added debugging functionality for clustering.
Changed import statements and added shebang to increase portability
Extended documentation of run_isolated and prep_run
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
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.
Created a module for each stage of DockOnSurf and started developing the isolated one