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Xavier Robin authoredXavier Robin authored
:mod:`mol.alg <ost.mol.alg>` -- Algorithms for Structures
Local Distance Test scores (lDDT, DRMSD)
Warning
The code that comes with Mariani et al. is considered deprecated. lDDT has been re-implemented with a focus on supporting quaternary structure and compounds beyond the 20 standard proteinogenic amino acids. The old code is still available and documented :doc:`here <lddt_deprecated>`.
Note
:class:`lddt.lDDTScorer` provides the raw Python API to compute lDDT but
stereochemistry checks as described in
Mariani et al.
must be done seperately. You may want to check out the
compare-structures
action (:ref:`ost compare structures`) to
compute lDDT with pre-processing and support for quaternary structures.
:mod:`stereochemistry <ost.mol.alg.stereochemistry>` -- Stereochemistry Checks
Warning
Stereochemistry checks described in Mariani et al. are considered deprecated. They have been re-implemented and now support nucleotides. The old code is still available and documented :doc:`here <stereochemistry_deprecated>`.
:mod:`scoring <ost.mol.alg.scoring>` -- Specialized scoring functions
:mod:`ligand_scoring <ost.mol.alg.ligand_scoring>` -- Ligand scoring functions
:mod:`chain_mapping <ost.mol.alg.chain_mapping>` -- Chain Mapping
:mod:`qsscoring <ost.mol.alg.qsscore>` -- QS score implementation
Warning
The code that comes with Bertoni et al. is considered deprecated. QS score has been re-implemented to be tightly integrated with the chain mapping algorithms. The old code is still available and documented :doc:`here <qsscoring_deprecated>`.
:mod:`DockQ <ost.mol.alg.dockq>` -- DockQ implementation
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