command line is always looking for .mol, independent of options and crashes if not found

[punkpony]

Hi!

I think there is a bug in LigGenPar 2.3 command line

I have installed it as advised, liked BOSS, etc.. when I do a test with smiles I get such output:

❯❯❯ LigParGen -s 'c1ccc(cc1)O' -r PHN -c 0 -o 0
error: unknown option '-i'
Traceback (most recent call last):
  File "/usr/local/bin/LigParGen", line 11, in <module>
    load_entry_point('LigParGen==2.3', 'console_scripts', 'LigParGen')()
  File "/usr/local/lib/python3.8/site-packages/LigParGen-2.3-py3.8.egg/LigParGen/Converter.py", line 99, in main
  File "/usr/local/lib/python3.8/site-packages/LigParGen-2.3-py3.8.egg/LigParGen/Converter.py", line 164, in convert
  File "/usr/local/lib/python3.8/site-packages/LigParGen-2.3-py3.8.egg/LigParGen/CreatZmat.py", line 51, in GenMolRep
  File "/usr/local/lib/python3.8/site-packages/LigParGen-2.3-py3.8.egg/LigParGen/CreatZmat.py", line 29, in AsitIsZmat
FileNotFoundError: [Errno 2] No such file or directory: 'PHN.mol'

There shouldn't be either'-i' error or the .mol one.

if I instead go and provide .pdb file i still have the .mol problem

❯❯❯ LigParGen -p AOTaa.pdb  -r AOT -c -1 -o 0                                                ✘ 1 
Traceback (most recent call last):
  File "/usr/local/bin/LigParGen", line 11, in <module>
    load_entry_point('LigParGen==2.3', 'console_scripts', 'LigParGen')()
  File "/usr/local/lib/python3.8/site-packages/LigParGen-2.3-py3.8.egg/LigParGen/Converter.py", line 99, in main
  File "/usr/local/lib/python3.8/site-packages/LigParGen-2.3-py3.8.egg/LigParGen/Converter.py", line 174, in convert
  File "/usr/local/lib/python3.8/site-packages/LigParGen-2.3-py3.8.egg/LigParGen/CreatZmat.py", line 51, in GenMolRep
  File "/usr/local/lib/python3.8/site-packages/LigParGen-2.3-py3.8.egg/LigParGen/CreatZmat.py", line 29, in AsitIsZmat
FileNotFoundError: [Errno 2] No such file or directory: 'AOTaa.mol'