|
| | __init__ (self, model, target, model_ligands, target_ligands, resnum_alignments=False, rename_ligand_chain=False, substructure_match=False, coverage_delta=0.2, max_symmetries=1e5, bs_radius=4.0, lddt_lp_radius=15.0, model_bs_radius=25, binding_sites_topn=100000, full_bs_search=False, min_pep_length=6, min_nuc_length=4, pep_seqid_thr=95., nuc_seqid_thr=95., mdl_map_pep_seqid_thr=0., mdl_map_nuc_seqid_thr=0., seqres=None, trg_seqres_mapping=None) |
| |
 Public Member Functions inherited from LigandScorer |
| | model (self) |
| |
| | target (self) |
| |
| | model_cleanup_log (self) |
| |
| | target_cleanup_log (self) |
| |
| | model_ligands (self) |
| |
| | target_ligands (self) |
| |
| | resnum_alignments (self) |
| |
| | min_pep_length (self) |
| |
| | min_nuc_length (self) |
| |
| | pep_seqid_thr (self) |
| |
| | nuc_seqid_thr (self) |
| |
| | mdl_map_pep_seqid_thr (self) |
| |
| | mdl_map_nuc_seqid_thr (self) |
| |
| | seqres (self) |
| |
| | trg_seqres_mapping (self) |
| |
| | substructure_match (self) |
| |
| | coverage_delta (self) |
| |
| | max_symmetries (self) |
| |
| | state_matrix (self) |
| |
| | model_ligand_states (self) |
| |
| | target_ligand_states (self) |
| |
| | score_matrix (self) |
| |
| | coverage_matrix (self) |
| |
| | aux_matrix (self) |
| |
| | assignment (self) |
| |
| | score (self) |
| |
| | aux (self) |
| |
| | unassigned_target_ligands (self) |
| |
| | unassigned_model_ligands (self) |
| |
| | get_target_ligand_state_report (self, trg_lig_idx) |
| |
| | get_model_ligand_state_report (self, mdl_lig_idx) |
| |
| | guess_target_ligand_unassigned_reason (self, trg_lig_idx) |
| |
| | guess_model_ligand_unassigned_reason (self, mdl_lig_idx) |
| |
| | unassigned_model_ligands_reasons (self) |
| |
| | unassigned_target_ligands_reasons (self) |
| |
|
| | _compute (self, symmetries, target_ligand, model_ligand) |
| |
| | _score_dir (self) |
| |
| | _get_repr (self, target_ligand, model_ligand) |
| |
| | _get_target_binding_site (self, target_ligand) |
| |
| | _get_get_repr_input (self, mdl_ligand) |
| |
| Protected Member Functions inherited from LigandScorer |
| | _get_report (self, ligand_state, pair_states) |
| |
| | _chain_mapper (self) |
| |
| | _chem_mapping (self) |
| |
| | _chem_group_alns (self) |
| |
| | _ref_mdl_alns (self) |
| |
| | _chain_mapping_mdl (self) |
| |
| | _mdl_chains_without_chem_mapping (self) |
| |
| | _compute_scores (self) |
| |
| | _copy_ligand (self, l, ent, ed, rename_ligand_chain) |
| |
| | _cleanup_polymer_ent (self, ent, clib) |
| |
:class:`LigandScorer` implementing symmetry corrected RMSD (BiSyRMSD).
:class:`SCRMSDScorer` computes a score for a specific pair of target/model
ligands.
The returned RMSD is based on a binding site superposition.
The binding site of the target structure is defined as all residues with at
least one atom within `bs_radius` around the target ligand.
It only contains protein and nucleic acid residues from chains that
pass the criteria for the
:class:`chain mapping <ost.mol.alg.chain_mapping>`. This means ignoring
other ligands, waters, short polymers as well as any incorrectly connected
chains that may be in proximity.
The respective model binding site for superposition is identified by
naively enumerating all possible mappings of model chains onto their
chemically equivalent target counterparts from the target binding site.
The `binding_sites_topn` with respect to lDDT score are evaluated and
an RMSD is computed.
You can either try to map ALL model chains onto the target binding site by
enabling `full_bs_search` or restrict the model chains for a specific
target/model ligand pair to the chains with at least one atom within
*model_bs_radius* around the model ligand. The latter can be significantly
faster in case of large complexes.
Symmetry correction is achieved by simply computing an RMSD value for
each symmetry, i.e. atom-atom assignments of the ligand as given by
:class:`LigandScorer`. The lowest RMSD value is returned.
Populates :attr:`LigandScorer.aux_data` with following :class:`dict` keys:
* rmsd: The BiSyRMSD score
* lddt_lp: lDDT of the binding pocket used for superposition (lDDT-LP)
* bs_ref_res: :class:`list` of binding site residues in target
* bs_ref_res_mapped: :class:`list` of target binding site residues that
are mapped to model
* bs_mdl_res_mapped: :class:`list` of same length with respective model
residues
* bb_rmsd: Backbone RMSD (CA, C3' for nucleotides; full backbone for
binding sites with fewer than 3 residues) for mapped binding site
residues after superposition
* target_ligand: The actual target ligand for which the score was computed
* model_ligand: The actual model ligand for which the score was computed
* chain_mapping: :class:`dict` with a chain mapping of chains involved in
binding site - key: trg chain name, value: mdl chain name
* transform: :class:`geom.Mat4` to transform model binding site onto target
binding site
* inconsistent_residues: :class:`list` of :class:`tuple` representing
residues with inconsistent residue names upon mapping (which is given by
bs_ref_res_mapped and bs_mdl_res_mapped). Tuples have two elements:
1) trg residue 2) mdl residue
:param model: Passed to parent constructor - see :class:`LigandScorer`.
:type model: :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
:param target: Passed to parent constructor - see :class:`LigandScorer`.
:type target: :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
:param model_ligands: Passed to parent constructor - see
:class:`LigandScorer`.
:type model_ligands: :class:`list`
:param target_ligands: Passed to parent constructor - see
:class:`LigandScorer`.
:type target_ligands: :class:`list`
:param resnum_alignments: Passed to parent constructor - see
:class:`LigandScorer`.
:type resnum_alignments: :class:`bool`
:param rename_ligand_chain: Passed to parent constructor - see
:class:`LigandScorer`.
:type rename_ligand_chain: :class:`bool`
:param substructure_match: Passed to parent constructor - see
:class:`LigandScorer`.
:type substructure_match: :class:`bool`
:param coverage_delta: Passed to parent constructor - see
:class:`LigandScorer`.
:type coverage_delta: :class:`float`
:param max_symmetries: Passed to parent constructor - see
:class:`LigandScorer`.
:type max_symmetries: :class:`int`
:param bs_radius: Inclusion radius for the binding site. Residues with
atoms within this distance of the ligand will be considered
for inclusion in the binding site.
:type bs_radius: :class:`float`
:param lddt_lp_radius: lDDT inclusion radius for lDDT-LP.
:type lddt_lp_radius: :class:`float`
:param model_bs_radius: inclusion radius for model binding sites.
Only used when full_bs_search=False, otherwise the
radius is effectively infinite. Only chains with
atoms within this distance of a model ligand will
be considered in the chain mapping.
:type model_bs_radius: :class:`float`
:param binding_sites_topn: maximum number of model binding site
representations to assess per target binding
site.
:type binding_sites_topn: :class:`int`
:param full_bs_search: If True, all potential binding sites in the model
are searched for each target binding site. If False,
the search space in the model is reduced to chains
around (`model_bs_radius` Å) model ligands.
This speeds up computations, but may result in
ligands not being scored if the predicted ligand
pose is too far from the actual binding site.
:type full_bs_search: :class:`bool`
:param min_pep_length: See :class:`ost.mol.alg.ligand_scoring_base.LigandScorer`.
:type min_pep_length: :class:`int`
:param min_nuc_length: See :class:`ost.mol.alg.ligand_scoring_base.LigandScorer`
:type min_nuc_length: :class:`int`
:param pep_seqid_thr: See :class:`ost.mol.alg.ligand_scoring_base.LigandScorer`
:type pep_seqid_thr: :class:`float`
:param nuc_seqid_thr: See :class:`ost.mol.alg.ligand_scoring_base.LigandScorer`
:type nuc_seqid_thr: :class:`float`
:param mdl_map_pep_seqid_thr: See :class:`ost.mol.alg.ligand_scoring_base.LigandScorer`
:type mdl_map_pep_seqid_thr: :class:`float`
:param mdl_map_nuc_seqid_thr: See :class:`ost.mol.alg.ligand_scoring_base.LigandScorer`
:type mdl_map_nuc_seqid_thr: :class:`float`
:param seqres: See :class:`ost.mol.alg.ligand_scoring_base.LigandScorer`
:type seqres: :class:`ost.seq.SequenceList`
:param trg_seqres_mapping: See :class:`ost.mol.alg.ligand_scoring_base.LigandScorer`
:type trg_seqres_mapping: :class:`dict`
Definition at line 10 of file ligand_scoring_scrmsd.py.
