Currently, the example pfoa.pdb works well with the ongoing pipeline, but to work with any pdb file (eg. 1BRQ.pdb) we should have an in built pdb cleaner. This is required to work with tool such a s

The options are as following :

• iGEM Kazakhstan 2022 MAWS version recommend using this utility script to clean pdbs. pdb_cleaner.py . While it provides detail controls over choosing what attributes to remove, there is little bit of ambiguity on what attributes should be saved or removed ,and we could make this either convert into separate apis for user to perform action or integrate in exsisting workflow through some otherway.

• Other convenient option is pdb4amber tool which is part of ambertools and used to clean pdb to interact with other tools, the con with this is it lacks any python bindings and need to be called from cli with arguments which would produce another output pdb file which would be prodcued further, while this would mean we have fewer custom options and relying on third-party tool to perform the action.