mol.alg – Algorithms for Structures¶
- ost.mol.alg.LocalDistTest(model, reference, tolerance, radius)¶
This function calculates the agreement of local contacts between the model and the reference structure. The overlap is a number between zero and one, where one indicates complete agreement, zero indicates no agreement at all. This score is similar to the GDT, but does not require any superposition of the model and the reference.
The distance of atom pairs in the reference structure that are closer than a certain distance (radius) to each other is compared to the distance found in the model. If the difference between these two distances is smaller than a threshold value (tolerance), the model and the reference agree. Missing atoms in the model are treated disagreement and thus lower the score.
For residue with symmetric sidechains (GLU, ASP, ARG, VAL, PHE, TYR), the naming of the atoms is ambigous. For these residues, the overlap of both possible solutions to the fixed atoms, that is, everything that is not ambigous is calculated. The solution that gives higher overlap is then used to calculate the actual overlap score.
- ost.mol.alg.SuperposeFrames(frames, sel, from=0, to=-1, ref=-1)¶
This function superposes the frames of the given coord group and returns them as a new coord group.
Parameters: - frames – The source coord group.
- from – index of the first frame
- to – index of the last frame plus one. If set to -1, the value is set to the number of frames in the coord group
- sel – An entity view containing the selection of atoms to be used for superposition. If set to an invalid view, all atoms in the coord group are used.
- ref – The index of the reference frame to use for superposition. If set to -1, the each frame is superposed to the previous frame.
Returns: A newly created coord group containing the superposed frames.
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. The threshold values are calculated from high-resolution X-ray structures for each possible element pair. The value is chosen such that 99.99% of observed distances between 0 and 5 Angstroem are above the threshold.
- ost.mol.alg.FilterClashes(ent, tolerance=0.0)¶
This function filters out residues with clashing atoms. If the clashing atom is a backbone atom, the complete residue is removed, if the atom is part of the sidechain, only the sidechain atoms are removed.
Hydrogen and deuterium atoms are ignored.
Parameters: - ent (EntityView or EntityHandle) – The input entity
- tolerance – The tolerance in (Angstroem) is substracted from the thresholds calculated from high resolution X-ray structures to make the function less pedantic. Negative values are also allowed and make the function more stringent.
Returns: The filtered EntityView