Frame - The Rigid Part

In contrast to the rotamers, the frame is a rigid object. It either represents the protein backbone or sidechains kept rigid during the sidechain modelling process. Regions, that should not be occupied by any sidechain atoms can also be blocked by adding particles to the frame. The frame is built using single frame residues, all of them associated to a residues index. If a rotamer associated to the same residue index enters the frame energy calculation, all interaction with particles belonging to the frame residue with the same residue index are neglected.

The Frame Objects

class promod3.sidechain.FrameResidue(particles, residue_index)
Parameters:

  • particles (list of Particle) – particles building frame residue

  • residue_index (int) – Interaction energies between the constructed frame residue and any rotamer associated to the same residue index are neglected

__len__()
Returns:

Number of particles in FrameResidue

__getitem__(index)
Parameters:

index (int) – Particle index

Returns:

Particle at position index

Raises:

RuntimeError if index is invalid

class promod3.sidechain.Frame(frame_residues)

The Frame object is used as a container for rigid particles, that can be passed to rotamer groups for calculating frame energies.

Parameters:

frame_residues (list of FrameResidue) – residues building the frame.

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