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OpenStructure
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Inherits object.
Public Member Functions | |
| def | __init__ (self, ref, mdl, alignments, calpha_only, settings, penalize_extra_chains=False, chem_mapping=None) |
| def | oligo_lddt (self) |
| def | weighted_lddt (self) |
| def | lddt_ref (self) |
| def | lddt_mdl (self) |
| def | oligo_lddt_scorer (self) |
| def | mapped_lddt_scorers (self) |
| def | sc_lddt_scorers (self) |
| def | sc_lddt (self) |
Data Fields | |
| ref | |
| mdl | |
| alignments | |
| calpha_only | |
| settings | |
| penalize_extra_chains | |
| chem_mapping | |
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 956 of file qsscoring.py.
| def __init__ | ( | self, | |
| ref, | |||
| mdl, | |||
| alignments, | |||
| calpha_only, | |||
| settings, | |||
penalize_extra_chains = False, |
|||
chem_mapping = None |
|||
| ) |
Definition at line 1037 of file qsscoring.py.
| 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 1167 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 1147 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 1197 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 1077 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 1183 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 1220 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 1212 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 1115 of file qsscoring.py.
| alignments |
Definition at line 1061 of file qsscoring.py.
| calpha_only |
Definition at line 1062 of file qsscoring.py.
| chem_mapping |
Definition at line 1065 of file qsscoring.py.
| mdl |
Definition at line 1060 of file qsscoring.py.
| penalize_extra_chains |
Definition at line 1064 of file qsscoring.py.
| ref |
Definition at line 1059 of file qsscoring.py.
| settings |
Definition at line 1063 of file qsscoring.py.
1.9.1