Added array inputs and rdmol input for separate ligand analysis

[jaclark5]

• Added ability to pass arrays in lieu of xyz files.
• Separated ligand charge analysis to allow ligand inputs
• Updated ligand charge analysis to avoid while loops and provide errors/warnings

[Strandgaard96]

Thanks for working on this!

I did a few tests to ensure that current functionality is not broken with these changes.
I encounter a few error messages and its probably a good idea to check and ensure that running the python command below from the main branch is also working with these new changes (which is not the case currently).

python --xyz_file ACUZEG.xyz --charge 0 

The ACUZEG.xyz file is given here:

33

Co 0.0 0.0 -0.0
Cl -0.450769 2.211585 -6.3e-05
N -1.341014 -0.365514 -1.419166
H -0.992943 0.00531 -2.315921
H -1.298494 -1.399314 -1.498501
C -2.743512 0.097156 -1.270956
H -3.32621 -0.226969 -2.159089
H -2.718259 1.204907 -1.258636
C -3.388695 -0.43548 2e-06
H -3.386932 -1.548944 1.9e-05
H -4.455695 -0.135439 -7e-06
C -2.743532 0.097202 1.27095
H -2.718328 1.204954 1.258601
H -3.326222 -0.226923 2.159087
N -1.34101 -0.36539 1.419198
H -1.298434 -1.399174 1.498697
H -0.99295 0.005609 2.315884
Cl 0.450768 -2.211585 6e-05
N 1.341014 0.36552 1.419166
H 0.992941 -0.005292 2.315924
H 1.298496 1.39932 1.498488
C 2.74351 -0.097155 1.270959
H 3.326208 0.226971 2.159092
H 2.718255 -1.204905 1.258641
C 3.388696 0.435478 1e-06
H 3.386934 1.548943 -1.8e-05
H 4.455696 0.135436 1e-05
C 2.743533 -0.097205 -1.270947
H 2.718329 -1.204957 -1.258597
H 3.326224 0.226919 -2.159084
N 1.34101 0.365386 -1.419199
H 1.298435 1.399169 -1.498706
H 0.992953 -0.005622 -2.315882

[jaclark5]

Do you mean: python xyz2mol_tmc.py --xyz_file ACUZEG.xyz --charge 0, in order for that to work don't I need to add stuff/xyz2mol_tm/xyz2mol_tm/huckel_to_smiles/xyz2mol_tmc.py to my python path, or operate from the package directory with a full path to the XYZ file? I think it would be more pythonic to add entry points so that one can run this for any directory.