OpenStructure
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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 | |
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.
def __init__ | ( | self, | |
ref, | |||
mdl, | |||
alignments, | |||
calpha_only, | |||
settings, | |||
penalize_extra_chains = False , |
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chem_mapping = None |
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) |
Definition at line 1003 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 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.
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.