§ Å ´iãóœ—dZddgZddlmZejd¦«Zedz  ¦«Zedz  ¦«Z[dS) aX Analysis data files =================== :mod:`MDAnalysis.analysis.data` contains data files that are used as part of analysis. These can be experimental or theoretical data. Files are stored inside the package and made accessible via variables in :mod:`MDAnalysis.analysis.data.filenames`. These variables are documented below, including references to the literature and where they are used inside :mod:`MDAnalysis.analysis`. Data files ---------- .. data:: Rama_ref Reference Ramachandran histogram for :class:`MDAnalysis.analysis.dihedrals.Ramachandran`. The data were calculated on a data set of 500 PDB structures taken from :footcite:p:`Lovell2003`. This is a numpy array in the :math:`\phi` and :math:`\psi` backbone dihedral angles. Load and plot it with :: import numpy as np import matplotlib.pyplot as plt from MDAnalysis.analysis.data.filenames import Rama_ref X, Y = np.meshgrid(np.arange(-180, 180, 4), np.arange(-180, 180, 4)) Z = np.load(Rama_ref) ax.contourf(X, Y, Z, levels=[1, 17, 15000]) The given levels will draw contours that contain 90% and 99% of the data points.The reference data are shown in :ref:`Ramachandran reference plot figure `. An example of analyzed data together with the reference data are shown in :ref:`Ramachandran plot figure ` as an example. .. _figure-rama-ref-plot: .. figure:: /images/rama_ref_plot.png :scale: 80% :alt: Ramachandran Ref Plot Reference Ramachandran plot, with contours that contain 90% ("allowed region") and 99% ("generously allowed region") of the data points from the reference data set. .. data:: Janin_ref Reference Janin histogram for :class:`MDAnalysis.analysis.dihedrals.Janin`. The data were calculated on a data set of 500 PDB structures taken from :footcite:p:`Lovell2003`. This is a numpy array in the :math:`\chi_1` and :math:`\chi_2` sidechain dihedral angles. Load and plot it with :: import numpy as np import matplotlib.pyplot as plt from MDAnalysis.analysis.data.filenames import Janin_ref X, Y = np.meshgrid(np.arange(0, 360, 6), np.arange(0, 360, 6)) Z = np.load(Janin_ref) ax.contourf(X, Y, Z, levels=[1, 6, 600]) The given levels will draw contours that contain 90% and 98% of the data. The reference data are shown in :ref:`Janin reference plot figure `. An example of analyzed data together with the reference data are shown in :ref:`Janin plot figure` as an example. .. _figure-janin-ref-plot: .. figure:: /images/janin_ref_plot.png :scale: 85 % :alt: Janin Ref Plot Janin reference plot with contours that contain 90% ("allowed region") and 98% ("generously allowed region") of the data points from the reference data set. ÚRama_refÚ Janin_refé)Ú resourceszMDAnalysis.analysis.datazrama_ref_data.npyzjanin_ref_data.npyN) Ú__doc__Ú__all__Ú importlibrÚfilesÚ _base_refÚas_posixrr©óúl/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/analysis/data/filenames.pyúrs~ðð.OðOðfØð €ð ÐÐÐÐÐà ˆIŒOÐ6Ñ 7Ô 7€ Ø Ð+Ñ +× 5Ò 5Ñ 7Ô 7€Ø Ð-Ñ -× 7Ò 7Ñ 9Ô 9€ ð€I€Ir