poweRlaw | package implements both the discrete and continuous maximum

So there's a few things going on here.

1. As you hinted at in your question, if you want to compare distributions, you need to truncate moby, so moby = moby[moby >= m_pl$getXmin()]

2. Using density() is a bit fraught. This is a kernel density smoother, that draws Normal distributions over discrete points. As the powerlaw has a very long tail, this is suspect

3. Comparing the tails of two powerlaw distributions is tricky (simulate some data and see).

Anyway, if you run

With

if line=="PhoIndex"

you're checking if the line is EQUAL to that string. You should rather verify if the checked line CONTAINS that string, by using

if "PhoIndex" in line:

to open your loop. Then, you could transform the line into a list, by separating the string elements on each space, like so:

line_array = line.split(" ")

Then, given that your numbers are always the third and second element of this list if it's the PhoIndex line, you can use

line_array.pop() ## remove the last element

line_array.pop(0)

line_array.pop(0) ## remove the first two elements

And then simply do this for every row, by using the respective string to query for the type of row (as with "PhoIndex") and the corresponding list pops according to the line structures. This works if your txt file always has a regular structure. If not then simply proceed in the same way until the splitmethod, and then just retrieve the elements of the created list you need via characteristics that differentiate them from all the rest, like containing a period character, or whatever.

All left is the definition of an empty template dictionary, as you did above "before the loop", and then assign the lists you obtained as values of their respective dictionary keys. done.