noncontig passthrough

[loriab]

Description

Tentative allowing noncontiguous fragment input in Molecule with validation. Partially fixes #298.

Background is that Mol can store noncontig fragments. However, the internals that the validation step uses can't store them; it can either balk or reorder the atoms so the fragments are contiguous. This PR makes the latter option accessible through the Mol constructor.

This option should be used tentatively and with results checking at first. Note that identical atom ordering is not assured with allow_noncontiguous_but_reorder=T between validate=T/F. Those wanting validation and atom order presevation may want to Molecule(..., allow_noncontiguous_but_reorder=True), and if that passes, use the results from mol = Molecule(..., validate=False).

This is not a permanent solution, and a future solution with some sort of fix_order (like fix_com; remember, "affix", not "correct") will use a different option, since reordering that is unnecessary for the schema spec is not good.

Changelog description

Status

• Code base linted
• Ready to go

[codecov]

Codecov Report

Merging #299 (0cc6ee9) into master (292350f) will increase coverage by 0.00%.
The diff coverage is 100.00%.

Additional details and impacted files

[awvwgk]

Anything blocking this from getting merged?