This is the readme file for the Physics-based Model of DnaK-Substrate Binding (PALADIN). Publication: https://doi.org/10.1371/journal.pcbi.1009567

Dependencies: numpy, pandas, sys, and argparse
Install these with:
  pip3 install pandas
or
  conda install pandas


The model is in paladin.py and is written with python3.

For help, execute:
  python3 paladin.py -h

There is also a test.inp input file, which can be utilized as:

   python3 paladin.py -i test.fasta [-o test.out]

If an output file is not specified, the output will only print to screen.
To quiet this output, you can supply -q/--quiet.

You should be able to make paladin.py executable and in your path, but
make sure it knows where the params.npy file is (or keep them together).


[ Input and output format and examples ]

Given an input fasta file that looks like the following (Paladin assumes forward orientation):

>example: NR peptide
NRLLLTG
>example 2
ACDEFGHI

The command:
python paladin.py -i input.fasta

returns the following output summary:

SUMMARY
                             score  reverse
label               n seq                  
example: NR peptide 0 NRLLL -3.033   -8.934
                    1 RLLLT -6.524   -8.361
                    2 LLLTG -9.841   -6.817
example 2           0 ACDEF  2.873    3.307
                    1 CDEFG  3.132    0.175
                    2 DEFGH -2.443   -2.712
                    3 EFGHI -2.995   -1.306

Where the columns refer to: 
  label - labeling string provided on the initial line in fasta format
  n     - the unique iNdex of the 5-mer for a single sequence
  seq   - sequence of the scored 5-mer (in order specified in fasta file)
  score - score of forward orientation (in kcal/mol)
  reverse - score of reverse orientation (in kcal/mol)

Reverse orientation peptides are scored by reversing the order of the input sequence.
In other words, it is the same energy terms in either orientation. See (manuscript)
for our justification of this choice.

Example: if the forward-orientation sequence is NRLTG, and the corresponding score is 
paladin(NRLTG), the reverse score is paladin(GTLRN).