molalg.rst

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

Local Distance Test scores (lDDT, DRMSD)

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

Dictionary-like object containing the list of interatomic distances that originate from a single residue to be checked during a run of the Local Distance Difference Test algorithm (key = pair of :class:`UniqueAtomIdentifier`, value = pair of floats)

Dictionary-like object containing all the :class:`~ost.mol.alg.ResidueRDMap` objects related to residues of a single structure (key = :class:`~ost.mol.ResNum`, value = :class:`ResidueRDMap`)

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).

This object is returned by the :func:`FilterClashes` function, and contains information about the clashes detected by the function.

This object contains all the information relative to a single clash detected by the :func:`FilterClashes` function

This object is returned by the :func:`CheckStereoChemistry` function, and contains information about bond lengths and planar angle widths in the structure that diverge from the parameters tabulated by Engh and Huber in the International Tables of Crystallography. Only elements that diverge from the tabulated value by a minimumnumber of standard deviations (defined when the CheckStereoChemistry function is called) are reported.

This object contains all the information relative to a single detected violation of stereo-chemical parameters in a bond length

This object contains all the information relative to a single detected violation of stereo-chemical parameters in a planar angle width

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

Superposing structures

Algorithms on Structures

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.

:mod:`helix_kinks <ost.mol.alg.helix_kinks>` -- Algorithms to calculate Helix Kinks

:mod:`trajectory_analysis <ost.mol.alg.trajectory_analysis>` -- DRMSD, pairwise distances and more

:mod:`structure_analysis <ost.mol.alg.structure_analysis>` -- Functions to analyze structures