Implemented the possibility to chose the surface H acceptors
Implemented Chemcat Angles
A maximum number of jobs can be set to, not only the pending ones, but now also the running ones.
Changed min_confs option name to pre_opt which accept a turn_false_answer, uff and mmff.
Implemented the possibility to dissociatie H atoms
Added punctuation marks at the end of every log messages.
Allow 'surf_norm_vect' to accept the shortcut values '-x' '-y' '-z' equivalent to [-1, 0, 0] [0, -1, 0] [0, 0, -1] respectively. Changed When min_coll_height is not False collision is checked only by checking the height of the atoms.
Changed collision_bottom option name to min_coll_height
Updated tests for reading norm_vect
Check for options 'code', 'subm_script' is consistent with dry runs and running locally.
Changed input option from collision_bottom_z to collision_bottom
Added surf_file and molec_neigh_ctrs options to the input reading. Added hematite surface file to tests.
Included surf_file, molec_neigh_ctrs and surf_norm_vect as input parameters
str2list accepts float numbers if it is called with the func=float argument.
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.
Added cp2k.inp and cp2k.sub
Deleted test_confs_to_mol_list as now it is in test_formats.py.
Added tests for 'confs_to_mol_list' and 'rdkit_mol_to_ase_atoms' functions. Reformated the import of modules in the test.
Added tests for the reading of subm_script and project_name options. Changed tests/isolated.inp to tests/cp2k.inp as its content is irrelevant for testing. Reformated the import of modules in the test.
Check if the input file of the code used for calculations is readable by the relevant library. Removed project_name from the mandatory options in Global.
Removed non used options from input and added new option on tests
Added the submission of jobs to the SGE batch queuing system
mmff_opt_confs function allows to carry out single point energy calculations if max_iters is set to 0.
Implemented tests for the new functions
Revert "Changed rmsd for rms"
This reverts commit 5571316d
Added molec_file to wrong.inp
Extended gen_confs documentation and incorporated the possibility to choose whether molecule conformers should be minimum energy conformers or not.
Added tests for functions in isolated.py
Changed rmsd for rms
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.
Included tests to the implemented functions to check new commits don't mess things up