README: propkatraj

propkatraj.py 可以用于计算蛋白质残基的 pKa 值。我们采用集合方法，通过平衡分子动力学模拟采样许多不同的构象。然后，我们将快速启发式 pKa 预测器 PROPKA 3 应用于轨迹的各个帧。通过分析 pKa 预测的统计数据，可以比从单个静态构象的 pKa 预测中获得更一致的图像。

所需软件

• PROPKA 3（作为 Python 包使用）
• MDAnalysis
• pandas

有关如何安装所有内容的说明，请参阅 INSTALL.md。

使用方法

propkatraj.PropkaTraj 类包含所有功能。使用以下方式导入：

from propkatraj import PropkaTraj

它接受一个 MDAnalysis.AtomGroup 或 MDAnalysis.Universe 实例作为参数进行初始化，并在调用 run() 方法时在轨迹的每个帧上运行 PROPKA。有关详细信息，请参阅 help(PropkaTraj)。

pkatraj = PropkaTraj(atomgroup, select='protein', skip_failure=False)

   Runs :program:`propka` on the titrateable residues of the selected AtomGroup
   on each frame in the trajectory.
   
   Parameters
   ----------
   atomgroup : :class:`MDAnalysis.Universe` or :class:`MDAnalysis.AtomGroup`
       Group of atoms containing the residues for pKa analysis. Please note
       that :class:`MDAnalysis.UpdatingAtomGroup` are not supported and will
       be automatically converted to :class:`MDAnalysis.AtomGroup`.
   select : str
       Selection string to use for selecting a subsection of atoms to use
       from the input ``atomgroup``. Note: passing non-protein residues to
       :program:`propka` may lead to incorrect results (see notes). [`protein`]
   skip_failure : bool
       If set to ``True``, skip frames where :program:`propka` fails. A list
       of failed frames is made available in
       :attr:`PropkaTraj.failed_frames_log`. If ``False`` raise a
       RuntimeError exception on those frames. [`False`]


    Notes
    -----
    Currently only the default behaviour supplemented with the `--quiet` flag
    of :program:`propka` is used.

    Temporary :program:`propka` files are written in the current working
    directory. This will leave a ``current.pka`` and ``current.propka_input``
    file. These are the temporary files for the final frame and can be removed
    safely.

    Current known issues:

    1. Due to the current behaviour of the MDAnalysis PDBWriter, non-protein
       atoms are written to PDBs using `ATOM` records instead of `HETATM`.
       This is likely to lead to undefined behaviour in :program:`propka`,
       which will likely expect `HETATM` inputs. We recommend users to only
       pass protein atoms for now. See the following issue for more details:
       https://github.com/Becksteinlab/propkatraj/issues/24


pkatraj.run()

   Perform the calculation

   Parameters
   ----------
   start : int, optional
      start frame of analysis
   stop : int, optional
      stop frame of analysis
   step : int, optional
      number of frames to skip between each analysed frame
   verbose : bool, optional
      Turn on verbosity

调用 run() 方法将创建一个 pandas.DataFrame，通过 results.pkas 访问，其中包含时间作为第一列，残基编号作为后续列。对于每个时间步，存储此残基的预测 pKa 值。处理 DataFrame 以获得如 Documentation 中所示的统计数据。例如，您可以按以下方式获取时间序列统计信息的摘要

pkatraj.results.pkas.describe()

文档

有关如何使用 propkatraj.PropkaTraj 在示例轨迹上以及如何使用 seaborn 绘制数据的说明，请参阅 Jupyter 笔记本 docs/propkatraj-example.ipynb。

引用

如果您在已发表的论文中使用 propkatraj，请引用 PROPKA 3.1 的参考文献 1 和本身合成的参考文献 2。参考文献 3 是如果您需要特定软件引用的话。

1. C. R. Søndergaard, M. H. M. Olsson, M. Rostkowski, and J. H. Jensen. Improved treatment of ligands and coupling effects in empirical calculation and rationalization of pKa values. J Chemical Theory and Computation, 7(7):2284–2295, 2011. doi: 10.1021/ct200133y.

2. C. Lee, S. Yashiro, D. L. Dotson, P. Uzdavinys, S. Iwata, M. S. P. Sansom, C. von Ballmoos, O. Beckstein, D. Drew, and A. D. Cameron. Crystal structure of the sodium-proton antiporter NhaA dimer and new mechanistic insights. J Gen Physiol, 144(6):529–544, 2014. doi: 10.1085/jgp.201411219.

3. David Dotson, Irfan Alibay, Rick Sexton, Shujie Fan, Armin Zijajo, Oliver Beckstein. (2020). Becksteinlab/propkatraj: 1.1.x. Zenodo. https://doi.org/10.5281/zenodo.3228425

联系方式

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