peppr.RamaScore#
- class peppr.RamaScore(rama_scores: list[~peppr.rotamer.ResidueRamaScore] = <factory>)[source]#
Ramachandran score for a given protein structure. This class represents calculates the likelihood of each residue’s phi/psi angles to occur in crystallized structures based on the Top8000 Ramachandran contour grids. It includes their names, IDs, observed phi, psi, omega angles, Ramachandran score percentages, and classifications. The thresholsds for classification are defined as follows: - FAVORED: pct >= _RAMA_FAVORED_THRESHOLD - ALLOWED: pct >= _RAMA_ALLOWED_THRESHOLD (or _RAMA_GENERAL_ALLOWED_THRESHOLD for “general” residues, or _RAMA_CISPRO_ALLOWED_THRESHOLD for “cispro” residues) - OUTLIER: pct < _RAMA_ALLOWED_THRESHOLD (or _RAMA_GENERAL_ALLOWED_THRESHOLD for “general” residues, or _RAMA_CISPRO_ALLOWED_THRESHOLD for “cispro” residues)
It is used to assess the quality of the protein structure based on the Ramachandran angles and to identify potential outliers in the phi/psi angles..
- Attributes:
- rama_scoreslist[ResidueRamaScore]
A list of ResidueRamaScore objects, each representing the Ramachandran score for a residue in the structure.
References
- __init__(rama_scores: list[~peppr.rotamer.ResidueRamaScore] = <factory>) None#
Methods
__init__([rama_scores])from_atoms(atom_array)Create RamaScore from a protein structure.
Attributes
rama_scores