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Public Member Functions | Data Fields
OligoLDDTScorer Class Reference

Inherits object.

Public Member Functions

def __init__
 
def oligo_lddt
 
def weighted_lddt
 
def lddt_ref
 
def lddt_mdl
 
def oligo_lddt_scorer
 
def mapped_lddt_scorers
 
def sc_lddt_scorers
 
def sc_lddt
 

Data Fields

 ref
 
 mdl
 
 alignments
 
 calpha_only
 
 settings
 
 penalize_extra_chains
 
 chem_mapping
 

Detailed Description

Oligo-lDDT scores.

Helper class to calculate oligomeric lDDT scores.

This class can be used independently, but commonly it will be created by
calling :func:`QSscorer.GetOligoLDDTScorer`.

.. note::

  By construction, lDDT scores are not symmetric and hence it matters which
  structure is the reference (:attr:`ref`) and which one is the model
  (:attr:`mdl`). Extra residues in the model are generally not considered.
  Extra chains in both model and reference can be considered by setting the
  :attr:`penalize_extra_chains` flag to True.

:param ref: Sets :attr:`ref`
:param mdl: Sets :attr:`mdl`
:param alignments: Sets :attr:`alignments`
:param calpha_only: Sets :attr:`calpha_only`
:param settings: Sets :attr:`settings`
:param penalize_extra_chains: Sets :attr:`penalize_extra_chains`
:param chem_mapping: Sets :attr:`chem_mapping`. Must be given if
                     *penalize_extra_chains* is True.

.. attribute:: ref
               mdl

  Full reference/model entity to be scored. The entity must contain all chains
  mapped in :attr:`alignments` and may also contain additional ones which are
  considered if :attr:`penalize_extra_chains` is True.

  :type: :class:`~ost.mol.EntityHandle`

.. attribute:: alignments

  One alignment for each mapped chain of :attr:`ref`/:attr:`mdl` as defined in
  :attr:`QSscorer.alignments`. The first sequence of each alignment belongs to
  :attr:`ref` and the second one to :attr:`mdl`. Sequences must have sequence
  naming and attached views as defined in :attr:`QSscorer.alignments`.

  :type: :class:`list` of :class:`~ost.seq.AlignmentHandle`

.. attribute:: calpha_only

  If True, restricts lDDT score to CA only.

  :type: :class:`bool`

.. attribute:: settings

  Settings to use for lDDT scoring.

  :type: :class:`~ost.mol.alg.lDDTSettings`

.. attribute:: penalize_extra_chains

  If True, extra chains in both :attr:`ref` and :attr:`mdl` will penalize the
  lDDT scores.

  :type: :class:`bool`

.. attribute:: chem_mapping

  Inter-complex mapping of chemical groups as defined in
  :attr:`QSscorer.chem_mapping`. Used to find "chem-mapped" chains in
  :attr:`ref` for unmapped chains in :attr:`mdl` when penalizing scores.
  Each unmapped model chain can add extra reference-contacts according to the
  average total contacts of each single "chem-mapped" reference chain. If
  there is no "chem-mapped" reference chain, a warning is shown and the model
  chain is ignored.


  Only relevant if :attr:`penalize_extra_chains` is True.

  :type: :class:`dict` with key = :class:`tuple` of chain names in
         :attr:`ref` and value = :class:`tuple` of chain names in
         :attr:`mdl`.

Definition at line 921 of file qsscoring.py.

Constructor & Destructor Documentation

def __init__ (   self,
  ref,
  mdl,
  alignments,
  calpha_only,
  settings,
  penalize_extra_chains = False,
  chem_mapping = None 
)

Definition at line 1003 of file qsscoring.py.

Member Function Documentation

def lddt_mdl (   self)
The model entity used for oligomeric lDDT scoring
(:attr:`oligo_lddt` / :attr:`oligo_lddt_scorer`).

Like :attr:`lddt_ref`, this is a single chain X containing all chains of
:attr:`mdl`. The residue numbers match the ones in :attr:`lddt_ref` where
aligned and have unique numbers for additional residues.

:getter: Computed on first use (cached)
:type: :class:`~ost.mol.EntityHandle`

Definition at line 1132 of file qsscoring.py.

def lddt_ref (   self)
The reference entity used for oligomeric lDDT scoring
(:attr:`oligo_lddt` / :attr:`oligo_lddt_scorer`).

Since the lDDT computation requires a single chain with mapped residue
numbering, all chains of :attr:`ref` are appended into a single chain X with
unique residue numbers according to the column-index in the alignment. The
alignments are in the same order as they appear in :attr:`alignments`.
Additional residues are appended at the end of the chain with unique residue
numbers. Unmapped chains are only added if :attr:`penalize_extra_chains` is
True. Only CA atoms are considered if :attr:`calpha_only` is True.

:getter: Computed on first use (cached)
:type: :class:`~ost.mol.EntityHandle`

Definition at line 1112 of file qsscoring.py.

def mapped_lddt_scorers (   self)
List of scorer objects for each chain mapped in :attr:`alignments`.

:getter: Computed on first use (cached)
:type: :class:`list` of :class:`MappedLDDTScorer`

Definition at line 1162 of file qsscoring.py.

def oligo_lddt (   self)
Oligomeric lDDT score.

The score is computed as conserved contacts divided by the total contacts
in the reference using the :attr:`oligo_lddt_scorer`, which uses the full
complex as reference/model structure. If :attr:`penalize_extra_chains` is
True, the reference/model complexes contain all chains (otherwise only the
mapped ones) and additional contacts are added to the reference's total
contacts for unmapped model chains according to the :attr:`chem_mapping`.

The main difference with :attr:`weighted_lddt` is that the lDDT scorer
"sees" the full complex here (incl. inter-chain contacts), while the
weighted single chain score looks at each chain separately.

:getter: Computed on first use (cached)
:type: :class:`float`

Definition at line 1042 of file qsscoring.py.

def oligo_lddt_scorer (   self)
lDDT Scorer object for :attr:`lddt_ref` and :attr:`lddt_mdl`.

:getter: Computed on first use (cached)
:type: :class:`~ost.mol.alg.lDDTScorer`

Definition at line 1148 of file qsscoring.py.

def sc_lddt (   self)
List of global scores extracted from :attr:`sc_lddt_scorers`.

If scoring for a mapped chain fails, an error is displayed and a score of 0
is assigned.

:getter: Computed on first use (cached)
:type: :class:`list` of :class:`float`

Definition at line 1185 of file qsscoring.py.

def sc_lddt_scorers (   self)
List of lDDT scorer objects extracted from :attr:`mapped_lddt_scorers`.

:type: :class:`list` of :class:`~ost.mol.alg.lDDTScorer`

Definition at line 1177 of file qsscoring.py.

def weighted_lddt (   self)
Weighted average of single chain lDDT scores.

The score is computed as a weighted average of single chain lDDT scores
(see :attr:`sc_lddt_scorers`) using the total contacts of each single
reference chain as weights. If :attr:`penalize_extra_chains` is True,
unmapped chains are added with a 0 score and total contacts taken from
the actual reference chains or (for unmapped model chains) using the
:attr:`chem_mapping`.

See :attr:`oligo_lddt` for a comparison of the two scores.

:getter: Computed on first use (cached)
:type: :class:`float`

Definition at line 1080 of file qsscoring.py.

Field Documentation

alignments

Definition at line 1026 of file qsscoring.py.

calpha_only

Definition at line 1027 of file qsscoring.py.

chem_mapping

Definition at line 1030 of file qsscoring.py.

mdl

Definition at line 1025 of file qsscoring.py.

penalize_extra_chains

Definition at line 1029 of file qsscoring.py.

ref

Definition at line 1024 of file qsscoring.py.

settings

Definition at line 1028 of file qsscoring.py.


The documentation for this class was generated from the following file: