TEMPy.protein.scoring_functions.FastSMOC

class TEMPy.protein.scoring_functions.FastSMOC(struct, exp_map, resolution, sigma_coeff=0.225, sigma_threshold=2.5, sim_map=None, locres=None)[source]

A faster version of the sliding window SMOC score.

Unlike the original algorithm, this ones is optimized in the following ways:

  • lazily determines required voxels saving space and time.

  • The sliding-window calculation is performed in time proportional only to chain size and not window size.

This method does not offer all the bells and whistles of old SMOC function such as rigid body parameters. However, two alternative methods are provided for dealing with SMOC scores for unmodelled regions.

The function score_chain_contig, will score all contigs in a chain where each window only contains residues belonging to the contig.

The function score_chain_span mimicks the old SMOC behaviour. Windows ignore contigs boundaries (they ‘span’ them), thus residues in windows may be physically distant.

In general, the consider using the score_chain_contig method.

Parameters:

  • struct (BioPy_Structure) – Model to score

  • exp_map (EMMap) – Experimental density map

  • resolution (float) – The resolution of the experimental map

  • sigma_coeff (float, optional) – The sigma coefficient for simulating the map. Defaults to 0.225.

  • sigma_threshold (float, optional) – The sigma threshold determines the radius around the atoms to consider. Defaults to 2.5.

  • sim_map (EMMap, optional) – A simulated map to use instead of generating one.

Returns:

FastSMOC object

__init__(struct, exp_map, resolution, sigma_coeff=0.225, sigma_threshold=2.5, sim_map=None, locres=None)[source]

Methods

__init__(struct, exp_map, resolution[, ...])

score_chain_contig(chain, size)

Generate sliding window scores where windows do not span chain breaks."

score_chain_span(chain, size)

Generate sliding window scores where windows do span chain breaks.