molalg.rst

:mod:`mol.alg <ost.mol.alg>` -- Algorithms for Structures

Object containing enough information to uniquely identify an atom in a structure

Dictionary-like object containing the a list of distances that originate from the a single residue residue, to check during a run of the Local Distance Difference Test algorithm

Dictionary-like object containing all the :class:`~ost.mol.alg.ResidueRDMap` objects related to residues of a single structure

Steric Clashes

The following function detects steric clashes in atomic structures. Two atoms are clashing if their euclidian distance is smaller than a threshold value (minus a tolerance offset).

Object containing information about clashing distances between non-bonded atoms

Object containing stereo-chemical information about bonds and angles. For each item (bond or angle in a specific residue), stores the mean and standard deviation

Trajectory Analysis

This is a set of functions used for basic trajectory analysis such as extracting positions, distances, angles and RMSDs. The organization is such that most functions have their counterpart at the individual :class:`frame level <ost.mol.CoordFrame>` so that they can also be called on one frame instead of the whole trajectory.

All these functions have a "stride" argument that defaults to stride=1, which is used to skip frames in the analysis.