SPyCi-PDB¶

Structural Python (Back) Calculator Interface for PDBs

Goal: User friendly Python3 based interface to generate back-calculated experimental data for singular and multiple (ensembles of) PDB structures.

Back-Calculators: The current back calculators integrated are:

PRE, NOE, J-Coupling, smFRET: Internal
Chemical shifts (CS): UCBShift
SAXS: CRYSOLv3
Hydrodynamic Radius (Rh): HullRad
Residual Dipolar Couplings (RDC): PALES

Please note for third-party software, installation instructions have been fully documented and tested for Linux Ubuntu Focal Fossa (20.04.X LTS) and Bionic Beaver (18.04.X LTS).

To make new requests and/or additions, please see docs/contributing.rst.

Developer Notes: project CI based on @joaomcteixeira’s Python-Project-Skeleton template. Developed as a standalone program with integration into the IDPConformerGenerator platform in mind.

Contents¶

Installation¶

SPyCi-PDB uses only Python-based APIs for which we expect it to run native on any system Python can run, as long as third-party back-calculator installation requirements are met.

Please note that the IDPConformerGenerator library is required for parsing PDB structure coordinates. Details for IDPConformerGenerator can be found here.

Full installation instructures are highlighted below.

Note

As highlighted in requirements.txt, listed below are all of the Python packages required. The following list will be updated if more packages are added:

numpy >= 1.22.4, < 2
numba >= 0.53.0, < 1
pybind11 >= 2.9.2, < 3
pandas >= 1.2.4, < 2
scipy >= 1.8.1, < 2
matplotlib >= 3.5.2, < 4
natsort >= 8, < 9
tox >= 3.25.0, < 4

As mentioned above, IDPConformerGenerator libraries are required.

If you already have an `idpconfgen` environment¶

It is recommended to install IDPConformerGenerator first to have the environment prepared for SPyCi-PDB. Please visit the IDPConformerGenerator repository to install IDPConformerGenerator environment first.

Activate the idpconfgen environment (conda or virtualenv) and update the environment with the dependencies seen in SPyCi-PDB:

pip install -r existing_requirements.txt --upgrade

Install SPyCi-PDB on top of IDPConformerGenerator:

python setup.py develop --no-deps

Standalone From Source¶

Clone from the official repository:

git clone https://github.com/julie-forman-kay-lab/SPyCi-PDB

Navigate to the new SPyCi-PDB folder:

cd SPyCi-PDB

Run the following commands to install spycipdb dependencies if Anaconda is used as your Python package manager:

conda env create -f requirements.yml
conda activate spycipdb

Note

If you don’t use Anaconda to manage your Python installations, you can use virtualenv and the requirements.txt file following the commands:

virtualenv spycienv --python=3.8
source spycienv/bin/activate
pip install -r requirements.txt

If you have difficulties installing spycipdb, raise an issue in the main GitHub repository, and we will help you.

Install spycipdb in development mode in order for your installation to be always up-to-date with the repository:

python setup.py develop --no-deps

Note

The above applies also if you used virtualenv instead of conda.

Remember to activate the spycipdb environment every time you open a new terminal window, from within the repository folder, choose yours:

# Installation with Anaconda
conda activate spycipdb

# Installation with virtualenv
source spycienv/bin/activate

To update to the latest version, navigate to the repository folder, activate the spycipdb python environment as described above, and run the commands:

git pull

# if you used anaconda to create the python environment, run:
conda env update -f requirements.yml

# if you used virtual env to create the python environment, run:
pip install -r requirements.txt  --upgrade

python setup.py develop --no-deps

Your installation will become up to date with the latest developments.

Please note that IDPConformerGenerator will be installed alongside SPyCi-PDB as the library is required for processing PDB files. You can find the installation of IDPConformerGenerator in src/idpconfgen/.

Updating SPyCi-PDB¶

When new back-calculators are added or when dependencies change from the GitHub, please update your environment with the latest dependencies after performing a git pull.

To update an anaconda environment:

conda env update --file requirements.yml --prune

To update a virtualenv environment:

pip install -r requirements.txt --upgrade

Then perform setup.py again for good measure:

python setup.py develop --no-deps

Installing Third-party Software¶

Some functionalities of SPyCi-PDB require third-party software. These are not mandatory to install unless you want to use such operations.

UCBShift¶

Note

Module is only required if you wish to perform Chemical Shift back-calculations. The following installation will revert Python to version 3.8.15.

You should be in the parent directory where SPyCi-PDB was cloned to with the Python environment is deactivated.

Clone the UCBShift repository from Zi Hao Liu’s fork on GitHub.:

git clone https://github.com/menoliu/CSpred

Enter the CSpred folder and make a models directory, then download and extract the latest trained models to CSpred/models directory.

Move back into the SPyCi-PDB directory and enter the thirdparty/ucbshift_reqs folder:

cd ..
cd SPyCi-PDB
cd ./thirdparty/ucbshift_reqs

Run the following commands to install UCBShift dependencies if Anaconda is used as your Python package manager:

conda env update --name spycipdb --file ucbshift_requirements.yml --prune

Run the following commands to install UCBShift dependencies if virtualenv was used to install SPyCi-PDB:

pip install -r ucbshift_requirements.txt

Go back to the SPyCi-PDB directory and reinstall spycipdb and idpconfgen if needed.:

conda activate spycipdb
cd ../..
python setup.py develop --no-deps
cd ./src/idpconfgen/
python setup.py develop --no-deps

The following is the same with virtualenv:

source spycienv/bin/activate
cd ../..
python setup.py develop --no-deps
cd ./src/idpconfgen/
python setup.py develop --no-deps

Currently, reinstallation is required as UCBShift changes the Python version. We will be working on a fix to streamline this process soon by using package handlers such as PyPi. Thank you for your patience.

ATSAS v3.1.1 - CRYSOL v3.0¶

Note

ATSAS installation is only required for the saxs module.

Please visit the ATSAS website to download v3.1.1 of ATSAS. Theoretically, SPyCi-PDB will work if you already have ATSAS v3.X installed.

Test your installation via:

crysol -h

PALES v6.0¶

Note

PALES installation is only required for the rdc module.

A package of PALES v6.0 for Linux is already included in the thirdparty/ folder. Downloaded and extracted from the Ad Bax Group.

For use with x64 bit Linux Ubuntu 20.04.X LTS and 18.04.X, you must install the i386 architecture along with required package libraries:

sudo dpkg --add-architecture i386
sudo apt update
sudo apt install libc6:i386 libncurses5:i386 libstdc++6:i386 libx11-6:i386

If the last command above fails, run the following instead:

sudo apt install multiarch-support

Usage¶

SPyCi-PDB runs entirely through command-lines. Theoretically, it is compatible with any machine that can un Python. However, it’s only been thoroughly tested on WSL 2.0 on Windows 11, Linux Ubuntu 20.04.X LTS and 18.04.X LTS.

Please follow the explanations in this page plus the documentation on the command-line themselves via:

spycipdb <MODULE> -h

Please note that SPyCi-PDB can also be used as a library as back-calculator functions are completely modular:

import spycipdb

Command-Lines¶

To execute spycipdb command-line, run spycipdb in your terminal window, after installation:

spycipdb

or:

spycipdb -h

Both will output the help menu.

Note

All subclients have the -h option to show help information.

Formatting for Input and Output Files¶

Conformers will be required in the PDB format with the .pdb file extension. For tarballs and folders, only the .pdb files in the folder/tarball will be used. Accepted tarballs include .tar, .tar.gz, and .tar.xz file extensions.

Most modules will require a sample experimental results template to base the back-calculations off of. Please note that experimental result values are not required. For the mathematical equations for the default internal calculators (pre, noe, jc, smfret) please refer to the paper.

All input files can be in the .txt file format with comma-delimitation for values. Examples can be found in the example/drksh3_exp_data/ folder. The required header formatting for the .txt file for each experimental module is highlighted below.

Output files are saved in a standard human-readable .JSON format. In most cases, the first key-value pair gives the format for each of the values in subsequent key-value pairs.

Paramagnetic Resonance Entropy (PRE) module¶

Input: res1,atom1,res2,atom2
Where res1/atom1 is the residue number and atom name respectively for
the first residue and res2/atom2 is the residue number and atom name
respectively for the second residue.
Output: 'format': {'res1': [], 'atom1': [], 'res2': [], 'atom2': []}
Subsequent keys are the names of the PDB file with a value of: [dist_values].
About: The default back-calculator is a simple distance based interpretation of PRE data.
Scalar distances between pairs of atoms according to the pairs derived from the experimental template are used.

Nuclear Overhauser Effect (NOE) module¶

Input: res1,atom1,atom1_multiple_assignments,res2,atom2,atom2_multiple_assignments
Where res1/atom1 is the residue number and atom name respectively for the first residue and res2/atom2 is
the residue number and atom name respectively for the second residue.
Multiple assignments are either 0 or 1 (no/yes respectively).
Output: 'format': {'res1': [], 'atom1': [], 'atom1_multiple_assignments': [], 'res2': [], 'atom2': [], 'atom2_multiple_assignments': []}
Subsequent keys are the names of the PDB file with a value of: [dist_values].
About: The default back-calculator is a simple distance based interpretation of NOE data.
Scalar distances between pairs of atoms according to the pairs derived from the experimental template are used.

3J-HNHA coupling (JC) module¶

Input: resnum
Where resnum indicates the JC for a specific residue.
Output: 'format': [resnum]
Subsequent keys are the names of the PDB file with a value of: [jc_values].
About: The default back-calculator uses the Karplus curve, a cosine function, to back-calculate desired
J-couplings according to the residue number as provided by the experimental template file.

single-molecule Fluoresence Resonance Energy Transfer (smFRET) module¶

Input: res1,res2,scaler
Where res1/res2 is the residue number for the first and second residue respectively.
Scaler is the r0 Foster radius of the dye pair.
Output: 'format': { 'res1': [], 'res2': [], 'scale': []}
Subsequent keys are the names of the PDB file with a value of: [smfret_values].
About: The default back-calculator, abliet distance based, takes into consideration residue pairs
and a scale factor to adjust for dye size from the experimental setup to back-calculate distances between
two CA backbone atoms.

Residual Dipolar Coupling (RDC) module¶

Input: The default back-calculator for RDCs is PALES. To run PALES, however, you will need the provide an experimental file template that is the same format as for PALES. For more information, please see the Data Format section. | Output: 'format': {resnum1: [], resname1: [], atomname1: [], resnum2: [], resname2: [], atomname2: []} | Subsequent keys are the names of the PDB file with a value of: [rh_values]. | About: The default back-calculator uses the third-party program PALES, which uses the steric obstruction model to derive the RDC. It has also been chosen due to its popularity in the field for RDC back-calculations.

Note

SAXS, Rh, and CS modules do not require input files. The following is formatting for the output.

Small Angle X-ray Scattering (SAXS) module¶

Output: Each PDB name is assigned a list of index and value where index represents the X-axis and value represents the Y-axis with units I_abs(s)[cm^-1]/c[mg/ml].

About: The default back-calculator uses the third-party program CRYSOLv3, from the ATSAS suite of biological softwares. it has been chosen due to its popularity as well as its ability to evaluate the hydration shell using dummy water parameters.

Hydrodynamic Radius (Rh) module¶

Output: Each PDB name is assigned a singular hydrodynamic radius value.

About: The default back-calculator uses the third-party program HullRad. It has been chosen for its speed and usage of the convex hull model to estimate hydrodynamic properties.

Chemical Shift (CS) module¶

Output: 'format': {'res': [], 'resname': []}. Subsequent keys are the names of the PDB file with a value of: {'H': [], 'HA': [], 'C': [], 'CA': [], 'CB': [], 'N': []}.

About: The default back-calculator uses the third-party program UCBShift. It has been chosen for its two-pronged machine learning approach for both feature and sequence alignment in order to provide an accurate chemical shift prediction.

Basic Usage Examples¶

The example/ folder contains instructions to test native back-calculators on 100 test conformers of the unfolded state of the drkN SH3 domain.

To get started with using the different modules for back-calculating experimental data, we will be using the unfolded state of drkN SH3, an intensively studied intrinsically disordered protein.

The goal of these examples is to walk you through expected experimental data formatting styles, as well as how to get started with each module. The experimental files could be found in the example/drksh3_exp_data folder. A set of 100 conformers generated using IDPConformerGenerator has been provided as a tarball: example/drksh3_csss_100.tar.xz.

Note that these experimental data files are comma-delimited per CSV formatting for ease of use in pandas dataframe as well as Microsoft Excel usage.

To use the bare-bones version of spycipdb, the PRE, NOE, JC, Rh, and smFRET modules do not require third-party installation instructions.

Every module is equipped with --help sections with detailed usage examples and documentation for each functionality. For customized --output file names, the flag -o can be used with every module.

Please note for large number of PDB ensembles, it is recommended to specify the number of CPU cores you are comfortable with using to maximize speed. Having just -n will utilize all but one CPU thread.

PRE, NOE, and JC Modules¶

To perform the back-calculation using the default internal calculators, give the tarball of provided structures as the first argument as well as the path to the experimental data file to use as a template. For example, using the PRE module:

spycipdb pre ./drksh3_csss_100.tar.xz -e ./drksh3_exp_data/drksh3_PRE.txt -n

Likewise to the PRE module, the tarball of the provided structures and sample NOE experimental data file are required:

spycipdb noe ./drksh3_csss_100.tar.xz -e ./drksh3_exp_data/drksh3_NOE.txt -n

Since the J-Coupling back-calculator is also internal, the same format is as follows:

spycipdb jc ./drksh3_csss_100.tar.xz -e ./drksh3_exp_data/drksh3_JC.txt -n

CS Module - Using UCBShift¶

After ensuring UCBShift is installed, the CS module does not require experimental file samples. Furthermore, you could also adjust the pH value to be considered. The default pH value is 5.0. A sample command is as follows:

spycipdb cs ./drksh3_csss_100.tar.xz --ph 7 -n

The above command sets a custom pH of 7.0. Please also note that UCBShift is fairly RAM intensive, it’s recommended to run with less than 10 CPUs (can be changed with the flag -n 10 for example).

SAXS Module - Using CRYSOLv3¶

After ensuring the proper ATSAS/CRYSOL version is installed, the following command can be used to run the SAXS module. Please note again that an experimental template is not required:

spycipdb saxs ./drksh3_csss_100.tar.xz -n

The SAXS module is equipped with a --lm flag, as CRYSOLv3 uses an adjustable number of harmonics to perform the appropriate SAXS back-calculation. The default value is 20 (from 1-100). Increasing the number of harmonics will also increase the cost of computational time.

Rh Module - Using HullRad 8.1¶

HullRad should be working out of the box with the basic installation instructions. An experimental file template is not required:

spycipdb rh ./drksh3_csss_100.tar.xz -n

Contributing¶

There are several strategies on how to contribute to a project on GitHub. Here, I explain the one I use for all the project I am participating. You can use this same strategy to contribute to this template or to suggest contributions to your project.

Fork this repository¶

Fork this repository before contributing. It is a better practice, possibly even enforced, that only pull request from forks are accepted. In my opinion enforcing forks creates a cleaner representation of the contributions to the project.

Clone the main repository¶

Next, clone the main repository to your local machine:

git clone https://github.com/julie-forman-kay-lab/SPyCi-PDB
cd SPyCi-PDB

Add your fork as an upstream repository:

git remote add myfork git://github.com/YOUR-USERNAME/SPyCi-PDB
git fetch myfork

Install for developers¶

Create a dedicated Python environment where to develop the project.

If you are using pip follow the official instructions on Installing packages using pip and virtual environments, most likely what you want is:

python3 -m venv newenv
source newenv/bin/activate

If you are using Anaconda go for:

conda create --name newenv python=3.9
conda activate newenv

Where newenv is the name you wish to give to the environment dedicated to this project.

Either under pip or conda, install the package in develop mode. Install also tox.

python setup.py develop
pip install tox

This configuration, together with the use of the src folder layer, guarantees that you will always run the code after installation. Also, thanks to the develop flag, any changes in the code will be automatically reflected in the installed version.

Make a new branch¶

From the main branch create a new branch where to develop the new code.

git checkout main
git checkout -b new_branch

Note the main branch is from the main repository.

Develop the feature and keep regular pushes to your fork with comprehensible commit messages.

git status
git add (the files you want)
git commit (add a nice commit message)
git push myfork new_branch

While you are developing, you can execute tox as needed to run your unit tests or inspect lint, or other integration tests. See the last section of this page.

Update your branch¶

It is common that you need to keep your branch update to the latest version in the main branch. For that:

git checkout main  # return to the main branch
git pull  # retrieve the latest source from the main repository
git checkout new_branch  # return to your devel branch
git merge --no-ff main  # merge the new code to your branch

At this point you may need to solve merge conflicts if they exist. If you don’t know how to do this, I suggest you start by reading the official docs

You can push to your fork now if you wish:

git push myfork new_branch

And, continue doing your developments are previously discussed.

Update CHANGELOG¶

Update the changelog file under CHANGELOG.rst with an explanatory bullet list of your contribution. Add that list right after the main title and before the last version subtitle:

Changelog
=========

* here goes my new additions
* explain them shortly and well

vX.X.X (1900-01-01)
-------------------

Also add your name to the authors list at docs/AUTHORS.rst.

Pull Request¶

Once you finished, you can create a pull request to the main repository, and engage with the community.

Before submitting a Pull Request, verify your development branch passes all tests as described below . If you are developing new code you should also implement new test cases.

Uniformed Tests with tox¶

Thanks to Tox we can have a unified testing platform that runs all tests in controlled environments and that is reproducible for all developers. In other words, it is a way to welcome (force) all developers to follow the same rules.

The tox testing setup is defined in a configuration file, the tox.ini, which contains all the operations that are performed during the test phase. Therefore, to run the unified test suite, developers just need to execute tox, provided tox is installed in the Python environment in use.

pip install tox
# or
conda install tox -c conda-forge

One of the greatest advantages of using tox together with the src layout is that unit test actually perform on the installed source (our package) inside an isolated deployment environment. In order words, tests are performed in an environment simulating a post-installation state instead of a pre-deploy/development environment. Under this setup, there is no need, in general cases, to distribute unit test scripts along with the actual source, in my honest opinion - see MANIFEST.in.

Before creating a Pull Request from your branch, certify that all the tests pass correctly by running:

tox

These are exactly the same tests that will be performed online in the Github Actions.

Also, you can run individual testing environments if you wish to test only specific functionalities, for example:

tox -e lint  # code style
tox -e build  # packaging
tox -e docs  # only builds the documentation
tox -e test  # runs unit tests

How to Cite¶

If you use SPyCi-PDB, please cite:

Liu et al., (2023). SPyCi-PDB: A modular command-line interface for back-calculating experimental datatypes of protein structures.. Journal of Open Source Software, 8(85), 4861, https://doi.org/10.21105/joss.04861

Authors¶

Main Developers/Maintainers¶

Zi Hao (Nemo) Liu

Contributors¶

João M. C. Teixeira (Postdoctoral researcher, University of Padua, Italy)
Jie (Jerry) Li (PhD student, University of California Berkeley, USA)

Acknowledgements¶

Oufan Zhang
Mickaël Krzeminski
Julie D. Forman-Kay
Teresa Head-Gordon

Changelog¶

v0.3.13 (2023-07-27)¶

Correct formatting error in documentation

v0.3.12 (2023-07-27)¶

Update MANIFEST to include existing_requirements.txt

v0.3.11 (2023-07-27)¶

Update requirements for existing IDPConformerGenerator environment
Update documentations for installation for clarity

v0.3.10 (2023-05-11)¶

Update README to include citation and JOSS button

v0.3.9 (2023-05-10)¶

Correct repository for versioning and Git actions

v0.3.8 (2023-05-10)¶

Update minor “co-ordinates” to “coordinates” in docs

v0.3.7 (2023-05-10)¶

Update changelog and minor formatting for README

v0.3.6 (2023-05-10)¶

Update paper affiliations

v0.3.5 (2023-05-02)¶

Implement minor editorial suggestions from issue #51

v0.3.4 (2023-04-26)¶

Minor corrections to documentation

v0.3.3 (2023-04-15)¶

Update acknowledgements section of manuscript

v0.3.2 (2023-04-13)¶

Update and make references uniform for manuscript

v0.3.1 (2023-04-12)¶

Correct ‘ATSAS 2.8’ formatting in references of paper
Include in RtD documentation explanations of back-calculators
Combine formatting for input/output in usage section of RtD documentation

v0.3.0 (2023-04-10)¶

Update results in the figure to include PRE and NOE as per #43
Add plotting feature to rh, jc, pre, noe modeules

v0.2.3 (2023-03-27)¶

Update example usage documentation

v0.2.2 (2023-03-07)¶

Update installation documentation
Temporarily change requirements for default IDPConformerGenerator repository link

v0.2.1 (2023-03-06)¶

Update client setup
Add warning for updating the environment when pulling

v0.2.0 (2023-01-27)¶

Adds natsort as dependency to yield ordered results
Results will be sorted as how they will appear on your OS

v0.1.16 (2023-01-18)¶

Fixes input file extension validataion for PDB files
Implements data validation for input experimental files
Clarifies documentation for these changes
Addresses issues in #35

v0.1.15 (2023-01-16)¶

Install IDPConformerGenerator while resolving the conda env
Addresses bug in issue #33

v0.1.14 (2022-11-28)¶

Automatically catch CSpred missing import issue
Addresses issue #31

v0.1.13 (2022-09-30)¶

Modify SAXS module to follow “format” in output

v0.1.12 (2022-09-29)¶

Minor edits for the paper

v0.1.11 (2022-09-28)¶

Bugfix for smFRET module with output formatting error

v0.1.10 (2022-09-20)¶

Re-test for PR

v0.1.9 (2022-09-20)¶

Add buttons on README

v0.1.8 (2022-09-19)¶

Update authors
Add ASCII art for SPyCi-PDB

v0.1.7 (2022-09-19)¶

Create unit tests for internal calculators and parsers

v0.1.6 (2022-09-14)¶

Edits to manuscript per Sept 7 comments from Dr. Julie Forman-Kay
Add figure 1 to paper

v0.1.5 (2022-09-08)¶

Edits to the manuscript per Aug 29 comments from Dr. Julie Forman-Kay
Fix documentation error for RDC module
Fix small issue of CS module output

v0.1.4 (2022-09-01)¶

Update failing tests
Upload manuscript, bibliography, and tests for JOSS (#21)

v0.1.3 (2022-09-01)¶

Update RtD link in README.rst

v0.1.2 (2022-08-31)¶

Minor fix to gitworkflows for tests

v0.1.1 (2022-08-31)¶

Modularize all calculator components
Remove Python 3.7 from requirements

v0.1.0 (2022-08-24)¶

Lint everything

v0.0.15 (2022-08-24)¶

Update README documentation
Update ReadTheDocs format and associated docs

v0.0.14 (2022-08-23)¶

Upgrade CS module for multiprocessing with UCBShift
Update installation instructions for UCBShift

v0.0.13 (2022-08-22)¶

Logic/module to link PALES v6.0 for RDC back-calculator (#14)
Documentation for installing dependencies for PALES v6.0 for Ubuntu 20.04 LTS

v0.0.12 (2022-08-12)¶

Logic/module to link HullRad for Rh back-calculator (#13)

v0.0.11 (2022-08-12)¶

Logic/module to link CRYSOL 3.0 for SAXS back-calculator (#12)
Documentation for installing CRYSOL 3.0 on top of SPyCi-PDB

v0.0.10 (2022-08-12)¶

Logic/module to link UCBShift for CS back-calculator (#10)
Documentation for installing UCBShift on top of SPyCi-PDB

v0.0.9 (2022-08-10)¶

Logic/module for smFRET back-calculator (#9)

v0.0.8 (2022-08-10)¶

Logic/module for NOE back-calculator (#8)
Refractor get_pdb_paths

v0.0.7 (2022-08-10)¶

Examples folder and some usage documentation (#7)

v0.0.6 (2022-08-10)¶

Logic/module for JC back-calculator (#6)

v0.0.5 (2022-08-09)¶

Logic/module for PRE back-calculator (#5)

v0.0.4 (2022-08-08)¶

Documentation for installing IDPConformerGenerator as a library (#4)

v0.0.3 (2022-08-08)¶

Core CLI backbone and base libs required (#2)
Basic documentation for installation and updates

v0.0.2 (2022-08-08)¶

Fix reference to python-project-skeleton (#3)

v0.0.1 (2022-07-28)¶

Housekeeping items (#1)
Building based on python-project-skeleton
Renaming and changing base structure

SPyCi-PDB¶

Contents¶

Installation¶

If you already have an idpconfgen environment¶

Standalone From Source¶

Updating SPyCi-PDB¶

Installing Third-party Software¶

UCBShift¶

ATSAS v3.1.1 - CRYSOL v3.0¶

PALES v6.0¶

Usage¶

Command-Lines¶

Formatting for Input and Output Files¶

Paramagnetic Resonance Entropy (PRE) module¶

Nuclear Overhauser Effect (NOE) module¶

3J-HNHA coupling (JC) module¶

single-molecule Fluoresence Resonance Energy Transfer (smFRET) module¶

Residual Dipolar Coupling (RDC) module¶

Small Angle X-ray Scattering (SAXS) module¶

Hydrodynamic Radius (Rh) module¶

Chemical Shift (CS) module¶

Basic Usage Examples¶

PRE, NOE, and JC Modules¶

CS Module - Using UCBShift¶

SAXS Module - Using CRYSOLv3¶

Rh Module - Using HullRad 8.1¶

Contributing¶

Fork this repository¶

Clone the main repository¶

Install for developers¶

Make a new branch¶

Update your branch¶

Update CHANGELOG¶

Pull Request¶

Uniformed Tests with tox¶

How to Cite¶

Authors¶

Main Developers/Maintainers¶

Contributors¶

Acknowledgements¶

Changelog¶

v0.3.13 (2023-07-27)¶

v0.3.12 (2023-07-27)¶

v0.3.11 (2023-07-27)¶

v0.3.10 (2023-05-11)¶

v0.3.9 (2023-05-10)¶

v0.3.8 (2023-05-10)¶

v0.3.7 (2023-05-10)¶

v0.3.6 (2023-05-10)¶

v0.3.5 (2023-05-02)¶

v0.3.4 (2023-04-26)¶

v0.3.3 (2023-04-15)¶

v0.3.2 (2023-04-13)¶

v0.3.1 (2023-04-12)¶

v0.3.0 (2023-04-10)¶

v0.2.3 (2023-03-27)¶

v0.2.2 (2023-03-07)¶

v0.2.1 (2023-03-06)¶

v0.2.0 (2023-01-27)¶

v0.1.16 (2023-01-18)¶

v0.1.15 (2023-01-16)¶

v0.1.14 (2022-11-28)¶

v0.1.13 (2022-09-30)¶

v0.1.12 (2022-09-29)¶

v0.1.11 (2022-09-28)¶

v0.1.10 (2022-09-20)¶

v0.1.9 (2022-09-20)¶

v0.1.8 (2022-09-19)¶

v0.1.7 (2022-09-19)¶

v0.1.6 (2022-09-14)¶

v0.1.5 (2022-09-08)¶

v0.1.4 (2022-09-01)¶

v0.1.3 (2022-09-01)¶

v0.1.2 (2022-08-31)¶

v0.1.1 (2022-08-31)¶

v0.1.0 (2022-08-24)¶

v0.0.15 (2022-08-24)¶

v0.0.14 (2022-08-23)¶

v0.0.13 (2022-08-22)¶

v0.0.12 (2022-08-12)¶

If you already have an `idpconfgen` environment¶