Clean up conformer_generator module

[xiaoruiDong]

The major focus on this PR is really to reduce the usage of Copy functions to save time.

First commit

• mol.Copy().GetConformer is avoided.
• mol.Copy is avoided if the upstream function makes a copy already.
• Try to use a single molecule with multiple conformed whenever possible
  • re-write dict_to_mol and mol_to_dict such that only a single molecule object will be created

Second commit Fix self.min_iters and self.max_iters called before creation

Third commit Replace mol.Copy; mol.RemoveAllConformers() to mol.Copy(quickCopy=True)

Fourth commit Refactorize the embedded module to avoid repeated blocks and make implementation of new embedders easier (maybe?)

Fifth commit Renumber the optimized mol according to atom map numbers