Added Vina_use_appropriate_ligand3d

[sts-isobe]

Add preprocess functions used to make appropriate 3d coordinates of ligands to preprocessing.py. Add some utility functions to utils.py, Add data used by functions added to preprocess.py to data directory. Add Vina_use_appropriate_ligand3d.py to reward directory.

[sishida21]

@sts-isobe, Please add the description about additional requirements and how to install them in reward/README.md, following the Additional packages for prepared reward files section. It seems necessary to at least install openbabel binary package when using get_appropriate_ligand3d function.

[sts-isobe]

@sishida21 Added requirements for get_appropriate_ligand3d function and how to install them in reward/README.md. Requirements are below.

• vina (Python package)
• meeko (Python package)
• openbabel (binary)

[sishida21]

Memo: update path to data in preprocessing.py update readme