Allow empty ligand, Print energy & RMSD Remarks to --local_only output, Normalize paths, and other Small fixes

[rwxayheee]

This PR attempts to address the issues listed under the Improvement wanted for input and output category for milestone /2 (https://github.com/ccsb-scripps/AutoDock-Vina/milestone/2).

[rwxayheee]

Summary

This PR includes some small fixes to address all issues listed under the Improvement wanted for input and output category for milestone /2 (https://github.com/ccsb-scripps/AutoDock-Vina/milestone/2).

For the following major changes, an update on documentation may be required:

• (Related to Running without receptor #256) Allow empty ligand (--ligand empty_file), to support covalent (tethered) docking similar to this example, which was only possible with AD-GPU:
  https://meeko.readthedocs.io/en/release-doc/tutorial3.html

• (For REMARK VINA RESULT not in PDBQT output of --local_only or --score_only type of calculations #323) The previously missing energy and RMSD remarks, are now available in the --local_only PDBQT output
  Some example output is added:
  https://github.com/ccsb-scripps/AutoDock-Vina/pull/398/files#diff-87ba257b47751739ba7a1127baf823143fd83dfca9e67b0005b771904dbaf655

• (For batch mode --dir option does not work on windows? #373) Previously, separators in paths are hard-coded. Now, paths are normalized, to have better support on Windows

Breakdown

The other small fixes are generally orthogonal (not dependent on each other).

#69

• Correction of an error message

#256

• Checks if receptor pdbqt is a regular file or invalid (potentially a directory). Allows empty receptor and empty ligand, but prints warning messages.

#265

• Restricts the usage of --autobox

#325

• Improves the error message, this is an extremely common error in user's reports due to bad geometry