Derive ΔG for single residues from HDX-MS data
MIT License
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hdxms-datasets
, allows public dataset loading from web interface (#327)proplot == 0.9.7
version requirement.Protein
object (#315).Published by Jhsmit almost 2 years ago
Fixes:
Published by Jhsmit over 2 years ago
Bugfix release and some updates to documentation:
Published by Jhsmit over 2 years ago
Release v0.4.0 is the combination of 9 beta versions, spanning a total of ~10 months of PyHDX development.
Please refer to the individual beta releases for more detail.
Major improvements of the new version 0.4.0 release are:
Base PyHDX:
.yaml
file spec$pyhdx process
CLI command (early alpha feature)PyHDX-web:
This release:
Published by Jhsmit over 2 years ago
async
handling of tasks, removed loop in main controller checking for new futures (#255)$ pyhdx process
cli command (#267)Published by Jhsmit over 2 years ago
Changes:
start
and end
fieldsMultiTransform
which takes multiple sources as input and SelectTransform
for the protein view (3d21e4d70a96cc686a085a2ed0fc21c085fa5463)Published by Jhsmit almost 3 years ago
Changes:
Published by Jhsmit almost 3 years ago
Patch release with bugfixes and packaging updates
Published by Jhsmit almost 3 years ago
This release features mostly an overhaul of the web interface (#234).
Internal changes:
Source
, Transform
, View
, Opts
Constructor
class which generates the web application from a yaml spec fileColorTransformControl
control panel.ReactiveHTML
, obviating the need for custom bokeh modelsFastGridTemplate
.New features:
Refactors:
deltaG
was refactored to dG
(ddG
for deltadeltaG
)Other changes:
csv_to_dataframe
now also accepts BytesIO
objectslocal_cluster.default_cluster
now accepts additional kwargsFull Changelog: https://github.com/Jhsmit/PyHDX/compare/v0.4.0b4...v0.4.0b5
Published by Jhsmit about 3 years ago
Major changes to plotting: (#232)
Added functions for making standard output plots in the plot.py module
Added functions for default colormaps and normalizers; defined default colormaps for standard data types (rfu, dG, ddG)
Added plotting class FitResultPlot which makes it easier to generate plots from a fit result
Updated the pdf output class (now named FitReport) which allows all standard plots to be combined into a .pdf file
SingleFitResult
and BatchFitResult
are now merged into one object.
Changes:
DataFrame
instead of numpy structured arrays for data object's internal tables (#227)uptake_corrected
to d_exp
for FD-corrected D-uptake values (#227)rfu_residues
, rfu_peptides
are now pandas Series
objects (#227)Published by Jhsmit about 3 years ago
Changes:
cluster
to scheduler_address
where applicable (#220)HDXMeasurementSet
objects to .csv/.txt file (9cca09f4f99ddc964247ccbb52f3802268e33ded)__str__
for HDXMeassurement
objects (5122d239f9f58dee003989390e0613ea96abce54)Published by Jhsmit about 3 years ago
Changes:
Fixes:
Published by Jhsmit over 3 years ago
Big changes in the new 0.4.0 version!
Major changes include an overhaul of the web interface and refactoring of major parts in the code.
Thanks for all contributions @sebaztiano @sajetan
Web interface
lumen
objects (Source
, Filter
, Transform
, View
) #188Classification
control panel can now also apply matplotlib
/colorcet
colormapsRefactoring of the PyHDX API
fit_gibbs_global(..)
, fit_gibbs_global_batch(..)
#199KineticsSeries
object was refactored to HDXMeasurement
HDXMeasurementSet
objectscores
attribute (percentage D-uptake) was refactored to rfu
(relative fractional uptake, 0-1)fileIO
functions, enable saving of kwargs to reload the file as well as saving metadata #205HDXMeasurement
objects #205versioneer
instead of pbr
(#207)k_obs
as output variable of the fit (ce4f58326e18e3e80c64f7a4bf3e19132ddc1c22)pyhdx serve
) #191exchanges
and k_int
(8301686c3cda6eed61e68215bdd3378cc6ae8f6c)Published by Jhsmit over 3 years ago
Minor release fixing a bug in requirements.txt
Published by Jhsmit over 3 years ago
Major changes:
pyhdx serve
(#191)Minor changes:
rgb_to_hex
function to work on arrays (vectorized)plot.py
)k_series
to series
in KineticsFitting
objectscov
to coverage
in KineticsSeries
objectsProtein
objectsWeb application updates:
Thanks to @sajetan for contributing (#191, #181)
Published by Jhsmit almost 4 years ago
Published by Jhsmit about 4 years ago
This release accompanies submission to bioRxiv as well as various bugfixes.
apps.py
controllers.py
and main controllers in main_controllers.py
Bugfixes:
.data
attribute (#108)Published by Jhsmit about 4 years ago
This release features an embedded Protein Viewer and implementation of Panel Themes / Templates.
Main features:
Other changes:
DataSource
object which is now used for 'publishing' datasetup_hooks()
method to couple Figures to ControllersTrue
Fixes:
Published by Jhsmit about 4 years ago
This release mostly features updates in the GUI:
publish_data
functionality which allows pushing data sources to client graphsOther changes:
RateFigureOld
and CoverageFigureOld
Fixes
Published by Jhsmit about 4 years ago
The main new feature of this beta release is the change to fitting of the whole protein in one go rather than splitting it into sections and fitting one by one.
Advantages include:
Changelog:
KineticSeries
k_int
structured array, k_int
for prolines and no coverage is now 0.TFCoverage
object to allow fitting over the whole protein, to be merged in future releases