fowler-lab / sbmlcore Goto Github PK

Next steps:

1. create tests for -ve aa volume change
2. create tests for MW, hydropathy, Pi
3. consider how to implement MAPP and secondary structure

Things to consider:

1. whether we use add and radd or create a new function definition (if so, what name?) in AminoAcidProperties.py
2. I have created an overall class 'sbmlcore' in init.py - is this of any potential use?
3. Include type labelling throughout code?
4. Is there too much replication in AminoAcidProperties.py? Should we create an overall function for setting up the Pandas dataframe which could then be used for each amino acid property?

non change based amino acid properties (i.e no calculation, just properties for each aa)

To do:

1. link AminoAcidProperties module to test_aminoacidvolumechange.py
2. check test_amino_acid_volume_change_value() in test_aminoacidvolumechange.py

stride appears ancient, so bypass for now. This is a redo of dssp

https://github.com/PDB-REDO/dssp

which in turn requires

boost (I installed via macports) and

https://github.com/PDB-REDO/libcifpp

needs recent cmake as well. Will add unit test that checks if in $PATH and also on-the-fly installation in GitHub actions.