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molalg.rst 52.66 KiB

: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`)

:mod:`qsscoring <ost.mol.alg.qsscoring>` -- Quaternary Structure (QS) scores

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