Downgrade remark type number invalid error

[y1zhou]

Fixes #123 and adds a test PDB file containing such REMARK records.

[y1zhou]

@douweschulte It seems the ReadOptions hasn't made its way into the core parser yet? The open_with_options function only passes ReadOptions.level into the open_pdb / open_mmcif function and ignores all other fields.

pdbtbx/src/read/general.rs

Lines 34 to 50 in 7af6cc8

	pub(in crate::read) fn open_with_options(
	filename: impl AsRef<str>,
	options: &ReadOptions,
	) -> ReadResult {
	if check_extension(&filename, "pdb") {
	open_pdb(filename, options.level)
	} else if check_extension(&filename, "cif") {
	open_mmcif(filename, options.level)
	} else {
	Err(vec![PDBError::new(
	ErrorLevel::BreakingError,
	"Incorrect extension",
	"Could not determine the type of the given file, make it .pdb or .cif",
	Context::show(filename.as_ref()),
	)])
	}
	}

To implement the only_atomic_data read option we'd need corresponding open_pdb_with_options and open_mmcif_with_options as well, right? I assume you don't want to modify the original signatures directly for backward compatibility.

[douweschulte]

Yes something like that has to be added. On not changing the API, you can change the 'core' methods (meaning the one that actually does the parsing), but make sure to keep this one private and keep the current open functions as calls to the core functions with the default ReadOptions for example.

[OWissett]

I have created another issue for finishing my implementation of the ReadOptions. #125

Sorry for leaving it half done, I got stuck with some other PhD work.

[y1zhou]

Cool I'll try to add in the functions that parse ReadOptions.

Sorry for leaving it half done, I got stuck with some other PhD work.

No worries we are all aware how stressful that can be :)

[douweschulte]

Perfect!! I am fine with merging right away and doing the only_load_atomic together with #125 in another PR or doing that work right here whatever works best for you.

[y1zhou]

Perfect!! I am fine with merging right away and doing the only_load_atomic together with #125 in another PR or doing that work right here whatever works best for you.

Yes taking that in another PR seems more reasonable. Will send as more work is done!