Metadata-Version: 1.2
Name: HDXrate
Version: 0.2.0
Summary: Calculate HDX intrinsic exchange rates.
Home-page: https://github.com/Jhsmit/HDXrate
Author: Jochem Smit
Author-email: jhmit@gmail.com
License: GNU GPL
Description: =======
        HDXrate
        =======
        
        
        .. image:: https://img.shields.io/pypi/v/hdxrate.svg
                :target: https://pypi.python.org/pypi/hdxrate
        
        .. image:: https://img.shields.io/travis/Jhsmit/hdxrate.svg
                :target: https://travis-ci.com/Jhsmit/hdxrate
        
        .. image:: https://readthedocs.org/projects/hdxrate/badge/?version=latest
                :target: https://hdxrate.readthedocs.io/en/latest/?badge=latest
                :alt: Documentation Status
        
        
        
        
        Python package collection for HDX intrinsic exchange rate calculation. 
        The calculations are based on the following papers:
        
          Bai, Y., Milne, J. S., Mayne, L. & Englander, S. W. Primary structure effects on peptide group hydrogen exchange. `Proteins Structure, Function, and Bioinformatics <https://doi.org/10.1002/prot.340170110>`__ 17, 75–86 (1993)
        
          Connelly, G. P., Bai, Y., Jeng, M.-F. & Englander, S. W. Isotope effects in peptide group hydrogen exchange. `Proteins <http://doi.wiley.com/10.1002/prot.340170111>`__ 17, 87–92 (1993).
        
        
          Mori, S., Zijl, P. C. M. van & Shortle, D. Measurement of water–amide proton exchange rates in the denatured state of staphylococcal nuclease by a magnetization transfer technique. `Proteins Structure, Function, and Bioinformatics <https://doi.org/10.1002/(SICI)1097-0134(199707)28:3%3C325::AID-PROT3%3E3.0.CO;2-B>`__ 28, 325–332 (1997)
          
          Nguyen, D., Mayne, L., Phillips, M. C. & Walter Englander, S. Reference Parameters for Protein Hydrogen Exchange Rates. `J. Am. Soc. Mass Spectrom.  <https://pubs.acs.org/doi/abs/10.1021/jasms.8b05911>`__ 29, 1936–1939 (2018).
        
        ..
           1.Rubinson, K. A. Practical corrections for p(H,D) measurements in mixed H 2 O/D 2 O biological buffers. Anal. Methods 9, 2744–2750 (2017).
        
        
        See also the excel sheet on the Englander group website: http://hx2.med.upenn.edu/download.html
        
        
        * Free software: GNU General Public License v3
        
        
        Features
        --------
        
        Calculate intrinsic rate of amide hydrogen exchange in proteins.
        
        Installation
        ------------
        
        ::
        
           $ pip install hdxrate
        
        or
        
        ::
        
           $ conda install -c conda-forge hdxrate
        
        Usage
        -----
        
        ::
        
           >>> from hdxrate import k_int_from_sequence
           >>> k_int_from_sequence('HHHHH', 300, 7.)
           array([0.00000000e+00, 2.62430718e+03, 6.29527446e+01, 6.29527446e+01,
               9.97734191e-01])
        
        
        Credits
        -------
        
        HDXrate implementation is based on PSX intrinsic rate calculation
        https://github.com/Niels-Bohr-Institute-XNS-StructBiophys/PSX
        
         Pedersen, M. C. et al. PSX, Protein–Solvent Exchange: software for calculation of deuterium-exchange effects in small-angle neutron scattering measurements from protein coordinates. `J Appl Cryst <https://doi.org/10.1107/S1600576719012469/>`__ 52, 1427–1436 (2019).
        
        
        
        Maintenance
        ```````````
        
        * Jochem Smit <jhsmit@gmail.com> / <jochem.smit@kuleuven.be>
        
        
Keywords: HDX-MS,exchange rate
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Requires-Python: >=3.6
