class jade.rosetta_jade.ScoreFiles.ScoreFile(filename)[source]
get_Dataframe(scoreterms=None, order_by='total_score', top_n=-1, reverse=True)[source]

Get data as a pandas dataframe. Definitely preferred now. :param scoreterms: list :param order_by: str :param top_n: int :param reverse: bool :rtype: pandas.DataFrame

get_decoy_count()[source]
get_decoy_names()[source]
get_ordered_decoy_list(scoreterm, decoy_names=None, top_n=-1, reverse=False)[source]

Get an ordered tuple of [[score, decoy_name], …] Will automatically order some known scoreterms (hbonds_int, dSASA_int)

Return type:list[list]
get_score(decoy, scoreterm)[source]

Get Score of a particular decoy and scoreterm :param decoy: str :param scoreterm: str :rtype: float

get_scores(scoreterm, decoy_names=None, top_n=-1, reverse=False)[source]
get_scoreterm(scoreterm)[source]
get_scoreterm_names()[source]
get_scoreterms(scoreterms='')[source]
get_stats(scoreterms='', decoy_names=None)[source]
jade.rosetta_jade.ScoreFiles.get_scorefiles(indir='/home/docs/checkouts/readthedocs.org/user_builds/bio-jade/checkouts/latest/docs')[source]

Get Score files from a directory. Walk through all directories in directory. :param indir: str :rtype: list

jade.rosetta_jade.ScoreFiles.plot_score_vs_rmsd(df, title, outpath, score='total_score', rmsd='looprms', top_p=0.95, reverse=True)[source]

Plot a typical Score VS RMSD using matplotlib, save it somewhere. Return the axes. By default, plot the top 95% :param df: pandas.DataFrame :param outpath: str :param score: str :param rmsd: str :rtype: matplotlib.Axes

jade.rosetta_jade.ScoreFiles.pymol_session_on_top_df(df, outdir, decoy_dir=None, scoreterm='total_score', top_n=10, decoy_column='decoy', native_path=None, out_prefix_override=None, ab_structure=False, superimpose=False, run_pymol=True)[source]

Make a PyMol session (or setup a scripter) on top X using a dataframe. Return the scripter for extra control.

df should have an attribute of ‘name’ or out_prefix_override should be set.

Parameters:
  • df – pandas.DataFrame
  • outdir – str
  • decoy_dir – str
  • scoreterm – str
  • top_n – int
  • decoy_column – str
  • native_path – str
  • out_prefix_override – str
  • ab_structure – boolean
  • superimpose – boolean
Return type:

PyMolScriptWriter