Handle covalent bond leaving atoms

[wukevin]

Description

• Try to automatically remove OH groups that leave upon bond formation.
• Correctly make glycosidic bonds between O and C instead of C-C
• Update examples to use correct bond ordering information (previously was reversed due to an error).

Motivation

Chaining together sugar rings and forming bonds frequently requires removing bonds from the reference conformer. This tries to handle this logic under select cases (see updated README.md for cases). Fixes #225

Test plan

Added unit tests, checked 1AC5 example from fasta input is atomwise identical to the reference structure with the same atoms dropped out.