TEMPy.protein.scoring_functions
+++++++++++++++++++++++++++++++

TEMPy has a range of functions to assess the similarity between a range of
data types.

TEMPy's scoring functions have diverse applicability and can be used to
assess the similarity between two cryo EM maps, between a model (e.g. from a
pdb file) and a cryo EM map or between two models. All map to map scores
can also be used to score models in maps, after a simulated map has been
calculated using the
:class:`StructureBlurrer <TEMPy.protein.structure_blurrer.StructureBlurrer>`
class.

Additionally, TEMPy has local scoring functions (e.g. SMOC), that score
only a portion of the input data at a time, for example producing a unique
score for each residue in a protein, in addition to global scoring functions
that average across the whole input map or model.

Global Scores
======

TEMPy scoring functions to assess the overall agreements between two data types
include:

.. currentmodule:: TEMPy.protein.
.. automodule:: TEMPy.protein
.. autosummary::
  :toctree: generated
  :nosignatures:

  scoring_functions.CCC
  scoring_functions.laplace_CCC
  scoring_functions.LSF
  scoring_functions.get_partial_DLSF
  scoring_functions.MI_new
  scoring_functions.calculate_overlap_scores
  scoring_functions.envelope_score_map
  scoring_functions.normal_vector_score
  scoring_functions.envelope_score
  scoring_functions.map_model_fsc_resolution
  scoring_functions.map_model_fsc
  scoring_functions.map_resolution_FSC
  scoring_functions.calculate_alcps
  scoring_functions.get_log10_alcps
  scoring_functions.get_sm_score

Segment Scores
===============

There are also scoring functions to assess the fit of models at the
level of segments. These segments are generally multiple

  .. currentmodule:: TEMPy.protein.
  .. automodule:: TEMPy.protein
  .. autosummary::
    :toctree: generated
    :nosignatures:

    scoring_functions.SCCC
    scoring_functions.SCCC_MI
    scoring_functions.SCCC_LAP
    scoring_functions.FastSCCC


Residue Scores
===============

Finally, there are also scoring functions for assessing model fit at
the level of single residues. These scores include:

.. autosummary::
  :toctree: generated
  :nosignatures:

  scoring_functions.FastSMOC
  scoring_functions.ScoringFunctions.SMOC
  scoring_functions.LoQFit
  scoring_functions.LocalMI