not working with non-canonical amino acids

[lalalalala-ai]

Dear sir,

thx for your excellent work. i have some trouble with using modified aa. i test a few. it seems none of them the backbone is putting into the correct position. i attched two examples with yaml files i used. any advice or suggestions are greatly appreciated.

sequences:
- protein:
id: A
sequence: WKYWRKYVLKIC
modifications:
- position: 2
ccd: ALY
- position: 6
ccd: ALY

sequences:
- protein:
id: A
sequence: WTYWRTYVLKIC
modifications:
- position: 2
ccd: NMT
- position: 6
ccd: NMT

[benf549]

I think part of the reason you might be seeing this is that the default modification pipeline doesn't remove 'OXT' atoms as referenced in #94 and #93

You might be able to get a temporary fix by cloning the branch in #93 !