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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: d6ed9ec3a6d4790c2a7793a8cd446acf
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.nojekyll b/.nojekyll
diff --git a/_images/envelope_reconstruction.png b/_images/envelope_reconstruction.png
diff --git a/_images/pigeon_feather.png b/_images/pigeon_feather.png
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diff --git a/_images/tutorials_02_peptide_level_analysis_19_0.png b/_images/tutorials_02_peptide_level_analysis_19_0.png
diff --git a/_images/tutorials_04_check_the_fitting_10_1.png b/_images/tutorials_04_check_the_fitting_10_1.png
diff --git a/_images/tutorials_04_check_the_fitting_11_1.png b/_images/tutorials_04_check_the_fitting_11_1.png
diff --git a/_images/tutorials_04_check_the_fitting_16_0.png b/_images/tutorials_04_check_the_fitting_16_0.png
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diff --git a/_sources/classes.rst.txt b/_sources/classes.rst.txt
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+pigeon_feather.data.RangeList
+-----------------------------
+
+.. currentmodule:: pigeon_feather.data
+.. autoclass:: RangeList
+
+    .. automethod:: __init__
+
+    .. rubric:: Methods
+
+    .. autosummary::
+
+     ~RangeList.to_set
+     ~RangeList.to_dataframe
+     ~RangeList.to_csv
+     ~RangeList.union
+     ~RangeList.intersection
+     ~RangeList.difference
+
+
+pigeon_feather.data.HDXMSDataCollection
+---------------------------------------
+
+.. currentmodule:: pigeon_feather.data
+.. autoclass:: HDXMSDataCollection
+
+    .. automethod:: __init__
+
+
+
+pigeon_feather.data.HDXMSData
+-----------------------------
+
+.. currentmodule:: pigeon_feather.data
+.. autoclass:: HDXMSData
+
+    .. automethod:: __init__
+
+    .. rubric:: Methods
+
+    .. autosummary::
+
+     ~HDXMSData.add_state
+     ~HDXMSData.load_protein_sequence
+     ~HDXMSData.get_state
+     ~HDXMSData.plot_res_coverage
+     ~HDXMSData.reindex_peptide_from_pdb
+     ~HDXMSData.to_dataframe
+     ~HDXMSData.to_bayesianhdx_format
+
+    .. rubric:: Attributes
+
+    .. autosummary::
+
+     ~HDXMSData.num_states
+
+
+pigeon_feather.data.ProteinState
+--------------------------------
+
+.. currentmodule:: pigeon_feather.data
+
+.. autoclass:: ProteinState
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+
+    ~ProteinState.add_peptide
+    ~ProteinState.num_peptides
+    ~ProteinState.get_peptide
+    ~ProteinState.add_new_peptides_by_subtract
+    ~ProteinState.add_all_subtract
+
+
+
+pigeon_feather.data.Peptide
+----------------------------
+
+.. currentmodule:: pigeon_feather.data
+
+.. autoclass:: Peptide
+
+
+   .. automethod:: __init__
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+    ~Peptide.add_timepoint
+    ~Peptide.get_deut
+    ~Peptide.get_deut_percent
+    ~Peptide.get_timepoint
+
+
+
+pigeon_feather.data.Timepoint
+-----------------------------
+
+.. currentmodule:: pigeon_feather.data
+
+.. autoclass:: Timepoint
+
+
+   .. automethod:: __init__
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+    ~Timepoint.load_raw_ms_csv
+
+
+
+pigeon_feather.HDXStatePeptideCompares
+---------------------------------------
+
+.. currentmodule:: pigeon_feather.data
+
+.. autoclass:: HDXStatePeptideCompares
+
+
+   .. automethod:: __init__
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+    ~HDXStatePeptideCompares.add_all_compare
+    ~HDXStatePeptideCompares.to_dataframe
+
+
+
+
+pigeon_feather.PeptideCompare
+-----------------------------
+
+.. currentmodule:: pigeon_feather.data
+
+.. autoclass:: PeptideCompare
+
+    .. automethod:: __init__
+
+    .. rubric:: Methods
+
+    .. autosummary::
+
+     ~PeptideCompare.get_deut_diff
+
+
+
+
+pigeon_feather.HDXStateResidueCompares
+--------------------------------------
+
+.. currentmodule:: pigeon_feather.data
+.. autoclass:: HDXStateResidueCompares
+
+    .. automethod:: __init__
+
+    .. rubric:: Methods
+
+    .. autosummary::
+
+     ~HDXStateResidueCompares.add_all_compare
+     ~HDXStateResidueCompares.get_residue_compare
+
+
+
+pigeon_feather.ResidueCompare
+-----------------------------
+
+.. currentmodule:: pigeon_feather.data
+.. autoclass:: ResidueCompare
+
+    .. automethod:: __init__
+
+    .. rubric:: Methods
+
+    .. autosummary::
+
+     ~ResidueCompare.find_peptides_containing_res
+     ~ResidueCompare.get_deut_diff
+
+
+
+pigeon_feather.SimulatedData
+----------------------------
+
+.. currentmodule:: pigeon_feather.data
+.. autoclass:: SimulatedData
+
+    .. automethod:: __init__
+
+    .. rubric:: Methods
+
+    .. autosummary::
+
+     ~SimulatedData.gen_seq
+     ~SimulatedData.gen_logP
+     ~SimulatedData.cal_k_init
+     ~SimulatedData.cal_k_ex
+     ~SimulatedData.calculate_incorporation
+     ~SimulatedData.gen_peptides
+     ~SimulatedData.convert_to_hdxms_data
+
+
+
+
+pigeon_feather.plot.UptakePlotsCollection
+-----------------------------------------
+
+.. currentmodule:: pigeon_feather.plot
+.. autoclass:: UptakePlotsCollection
+
+    .. automethod:: __init__
+
+    .. rubric:: Methods
+
+    .. autosummary::
+
+     ~UptakePlotsCollection.add_plot
+     ~UptakePlotsCollection.add_plot_all
+     ~UptakePlotsCollection.save_plots
+
+
+pigeon_feather.plot.UptakePlot
+------------------------------
+
+.. currentmodule:: pigeon_feather.plot
+.. autoclass:: UptakePlot
+
+    .. automethod:: __init__
+
+    .. rubric:: Methods
+
+    .. autosummary::
+
+     ~UptakePlot.make_uptakeplot
+     ~UptakePlot.get_average_peptide
+     ~UptakePlot.make_title
+     ~UptakePlot.make_color_dict
+
+
+
+
diff --git a/_sources/documentation.rst.txt b/_sources/documentation.rst.txt
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+Documentation
+=============
+
+.. toctree::
+   :maxdepth: 1
+
+   hdx
+   pigeon
+   feather
+
diff --git a/_sources/feather.rst.txt b/_sources/feather.rst.txt
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+
+FEATHER
+=======
+
+**FEATHER** (Free Energy Assignment Through Hydrogen Exchange Rates) is a 
+is a Bayesian method that combines peptide subtraction, isotopic mass 
+envelope reconstruction, and Monte Carlo (MC) sampling to assign PFs for each individual residue.
+
+
+.. figure:: ../image/envelope_reconstruction.png
+   :alt: FEATHER
+   :width: 800px
+   :figclass: align-center
+
+classes
+-------
+
+.. toctree::
+   :maxdepth: 1
+
+   classes
diff --git a/_sources/hdx.rst.txt b/_sources/hdx.rst.txt
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+HDX/MS
+======
+
+Hydrogen exchange with mass spectrometry (HX/MS) measures
+the rate of exchange of labile hydrogen atoms with deuterium 
+in a protein's backbone amide groups to report on structural 
+changes in protein ensembles but at the peptide level, not individual amino acids.
+With the advent of integrated robotics for automated sample preparation
+and accurate protein structure prediction methods
+for improved data interpretation, HX/MS is an increasingly 
+powerful method for probing solution-state protein ensembles. 
+However, the technique is not used to its full potential due to 
+its peptide resolution.
+
+To address this problem, we developed **PIGEON-FEATHER** (Peptide ID Generation 
+for Exchange Of Nuclei-Free Energy Assignment Through Hydrogen Exchange Rates): 
+an HX/MS analysis method to calculate the absolute free energy of opening (∆Gop) 
+for almost all the amino acids in a protein ensemble. 
diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt
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+
+===========================================
+Welcome to  PIGEON-FEATHER's documentation!
+===========================================
+
+.. figure:: ../image/pigeon_feather.png
+   :alt: PIGEON-FEATHER
+   :width: 800px
+   :figclass: align-center
+
+**PIGEON-FEATHER** (*Peptide ID Generation for Exchange Of Nuclei-Free 
+Energy Assignment Through Hydrogen Exchange Rates*): a method 
+for calculating free energies of opening (∆Gop) at single- or 
+near-single-amino acid resolution for protein ensembles of all 
+sizes from hydrogen exchange/mass spectrometry (HX/MS) data. 
+
+
+
+
+.. toctree::
+   :maxdepth: 2
+
+   installation
+   documentation
+   tutorial
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/_sources/installation.rst.txt b/_sources/installation.rst.txt
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+Installation
+============
+
+Conda
+-----
+
+.. code-block:: bash
+
+    # install mamba
+    wget "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
+    bash Mambaforge-$(uname)-$(uname -m).sh 
+
+    # create a conda environment and install the required packages
+    conda create --name pigeon_feather python=3.11
+    conda activate pigeon_feather
+
+    conda install jupyterlab mdanalysis numba
+    conda install pymol-open-source
+
+    pip install pyopenms hdxrate
+
+    # clone the PIGEON-FEATHER repo
+    git clone https://github.com/glasgowlab/PIGEON-FEATHER.git
+
+    # clone the bayesian hdx iso repo
+    git clone https://github.com/lucl13/bayesian_hdx.git
+
+    cd PIGEON-FEATHER
+    pip install .
+
+    cd ../bayesian_hdx
+    pip install .
+
+
+
+Docker
+------
+
+.. code-block:: bash
+
+    docker build -f docker/Dockerfile -t pigeon_feather:0.9 .
+    docker run -it -v $(pwd):/work -p 8889:8889 --rm pigeon_feather:0.9 jupyter-lab --port 8889
+
+To open the Jupyter notebook, please click the link displayed in the terminal. 
+For users operating on Apple Silicon machines, it may be necessary to append 
+`--platform amd64` when building the image, as `pyopenms` is not supported on 
+the linux/arm64 architecture. It is advisable to avoid running the Docker container 
+on Apple Silicon machines due to the significant performance degradation 
+caused by the emulation of the x86_64 architecture.
+
+Note: ``bayesian_hdx`` at the above link is a fork of the `original repo <https://github.com/salilab/bayesian_hdx>`_ , 
+which has been modified for compatibility with the PIGEON-FEATHER workflow and support for isotopic envelope fitting.