https://www.certara.com/2011/07/06/what-is-curve-stripping/?ap=&UTM_LeadSource=

Combining blocks of size 1 and 2 together should have a user configureable max value

for fitting folding kinetics

Add a figure panel where users can see how well each peptide is fitted

Mouseover peptides should tell you:
absolute uptake
normalized uptake
sequence?
max uptake?

Internally for fitting in the exponent a time constant tau is used rather then a rate k.
On the exterior rate constants are presented as this is standard in literature.

Perhaps it should be refactored to use rate constant rather time constant.

if the reset button is pressed on the rate figure, it should relimit to incorporate all currently shown data, not also data that is currently hidden

Current:

fit1:

d_list = []
for time in times:
    p = result1.get_p(time)
    p = np.nan_to_num(p)
    d = series.cov.X.dot(p)
    d_list.append(d)
d1 = np.vstack(d_list)

fit2:

d_list = []
for time in times:
    d = result2.get_d(time)
    d_list.append(d)
d2 = np.vstack(d_list)

you know what to do

 File "C:\Users\jhsmi\pp\pyhdx\pyhdx\panel\panels.py", line 180, in _renew
    self.r_max = np.log(1 - 0.98) / - self.parent.series.times[1]  # KEEP THIS

Add a checkbox to view current blocks for fit2 in the coverage window

currently set to 1/70
but of course this needs some thinking

user configure able?
whats is the influence on the rest of the fit? It should be high despite limited time resolution.

Mouseover in the coverage panel should show basic info like:

peptide number
absolute uptake
sequence?
start, end?
p value?

they are currently ordered from slow to fast but should be fast to slow

there is the possibility for mono time component or mixed models but currently only two time components are implemented.

• Implement determination of rates from these type of models
• Customizable from the GUI

The current syntax of

fr1 = kf.weighted_avg_fit()
arr = fr1.get_output(['tau1', 'tau2', 'r'])
fr2 = kf.global_fit(arr)

is cumbersome

add a button to upload fitting data

bindu's TF data at residue 410, FD norm, monomer, doesnt fit propery at residue number 410

Make is possible for users to click on peptides to exclude them from fitting

Add a function in KineticsFitting that does fitting, depending on the value of self.cluster the fitting should be done async or not.

But consider also that the GUI needs to do fitting depending on the presence of a cluster, this should go through the same function. In this case access the IOLoop is needed.

The classification panel should have several more options for coloring structures/rates:

Linear map

• number of categories
• min / max
• customize thresholds

Continuous:
select color map from
-maptlotlib
-bokeh
-custom interpolated from several colors?

See Masson 2019

• HDX time course
• Back exchange
• Number of peptides
• sequence coverage
• Average peptide length/redundancy
• replicates
• repeatability
• significant differnences

New control panel with options:

• %D graphs
• fitted peptides graphs
  • option for log/linear
• Rate graphs

button for downloading the uploaded files so that users can combine files

possibly through dask.delayed

the ylabel doenst fit inside
possible fix by a tight_layout

The relative amplitude of time components is related to the number of hydrogens exchanging with this rate constant. Therefore this value should be restricted to quantized values in the fitting.

However, currently i'm not aware of fitting algorithms which allow parameters to be restricted to integers.

this should be autogenerated to something like the state, exposure for coverage

Steps to reproduce:
load SecB apo data
select FD control
select 0 exposure
parse

change to 0.167 exposure
parse

This doenst update the series of peptides selected

Implementation:

somehow cut the prolines out of the protein so that they are completely ignored in the fitting and which then results in nan in the final result.

Maybe have a custom r_number entry with missing numbers for prolines will work

or maybe spinner or something

This should be able to be done instantaneously using interpolation to get t50 values for each peptide.

see keppel and weis 2015

move to top left

very high rates in the rate graph while fit in fit quality shows as slow

What happens is a peptides prolines only?
Or shorter than drop_first?
Trailing prolines are up to drop_first?

allow new fitting results to be parsed to rategraph correctly

keep x axis between rate and coverage figure the same

When enabled, lock aa_per_residue to have only one figure in the plot
communicate via main controller events

there seems to be one missing

Should be added in html/markdown and be consistent