It seems that the API can only output single statistics for the entire peptide chain, but I'm interested in statistics for each residue individually. I'm wondering if it might be possible to output an array/list from some of these functions instead of always averaging them as is done now.

Computed hydrophobic moment is not the same as the one computed by R. More specifically, it seems that peptides.py always outputs 0 for the hydrophobic moment when peptide length is shorter than the set window. The returned value matches the value from R when peptide length is equal to or greater than the set window length.

Example in python:

>>> import peptides`
>>> peptides.Peptide("MLK").hydrophobic_moment(window=5, angle=100)
0.0
>>> peptides.Peptide("AACQ").hydrophobic_moment(window=5, angle=100)
0.0
>>> peptides.Peptide("FGGIQ").hydrophobic_moment(window=5, angle=100)
0.31847187610377536

Example in R:

> library(Peptides)
> hmoment(seq="MLK", window=5, angle=100)
[1] 0.8099386
> hmoment(seq="AACQ", window=5, angle=100)
[1] 0.3152961
> hmoment(seq="FGGIQ", window=5, angle=100)
[1] 0.3184719

I think that it can be easily fixed by internally setting the window length to the length of the peptide if the latter is shorter. What I propose:

--- a/peptides/__init__.py
+++ b/peptides/__init__.py
@@ -657,6 +657,7 @@ class Peptide(typing.Sequence[str]):
               :doi:`10.1073/pnas.81.1.140`. :pmid:`6582470`.

         """
+        window = min(window, len(self))
         scale = tables.HYDROPHOBICITY["Eisenberg"]
         lut = [scale.get(aa, 0.0) for aa in self._CODE1]
         angles = [(angle * i) % 360 for i in range(window)]

Hi, thank you for creating peptides.py.

Some hydrophobicity tables together with certain proteins cause a runtime warning for in the function auto_correlation():

import peptides

for hydro in peptides.tables.HYDROPHOBICITY.keys():
    print(hydro)
    table = peptides.tables.HYDROPHOBICITY[hydro]
    peptides.Peptide('MANTQNISIWWWAR').auto_correlation(table)

Warning (s2 == 0):

RuntimeWarning: invalid value encountered in double_scalars
  return s1 / s2

The tables concerned are: octanolScale_pH2, interfaceScale_pH2, oiScale_pH2 Some other proteins causing the same warning: ['MSYGGSCAGFGGGFALLIVLFILLIIIGCSCWGGGGYGY', 'MFILLIIIGASCFGGGGGCGYGGYGGYAGGYGGYCC', 'MSFGGSCAGFGGGFALLIVLFILLIIIGCSCWGGGGGF']