#207 Add support for {X} in custom-enzyme rules

[Kaipo]

From https://groups.google.com/forum/?fromgroups#!topic/crux-users/spbgiLKCu1A

For custom-enzyme, Crux doesn't handle {X}, only [X]. This should be fixed in parse_custom_enzyme in parameter.cpp.

I think any {X} in a custom-enzyme rule would mean never cleave anywhere.

[William S Noble]

Kaipo,
Once you get this fixed, please also add a sentence to the tide-search documentation (and search-for-xlinks) saying something like, "To prevent any cleavages from occurring (i.e., if you want to provide a pre-digested set of peptides, you can use the digestion rule {X}|{X}."
Bill

[William S Noble]

Kaipo says: "Thanks for pointing out this bug - the case of "{X}" is not currently handled in the Crux code (only "[X]").

If you want to prevent the sequences from being digested, you can try setting custom-enzyme to a value like "[Z]|[Z]" - by this rule, there won't be any cleavage locations since there are no Zs in the sequences."