Inherits LigandScorer.

Public Member Functions
def	__init__ (self, model, target, model_ligands=None, target_ligands=None, resnum_alignments=False, rename_ligand_chain=False, substructure_match=False, coverage_delta=0.2, max_symmetries=1e5, lddt_pli_radius=6.0, add_mdl_contacts=False, lddt_pli_thresholds=[0.5, 1.0, 2.0, 4.0], lddt_pli_binding_site_radius=None)

Public Member Functions inherited from LigandScorer
def	__init__ (self, model, target, model_ligands=None, target_ligands=None, resnum_alignments=False, rename_ligand_chain=False, substructure_match=False, coverage_delta=0.2, max_symmetries=1e5)

def	state_matrix (self)

def	model_ligand_states (self)

def	target_ligand_states (self)

def	score_matrix (self)

def	coverage_matrix (self)

def	aux_matrix (self)

def	assignment (self)

def	score (self)

def	aux (self)

def	unassigned_target_ligands (self)

def	unassigned_model_ligands (self)

def	get_target_ligand_state_report (self, trg_lig_idx)

def	get_model_ligand_state_report (self, mdl_lig_idx)

def	guess_target_ligand_unassigned_reason (self, trg_lig_idx)

def	guess_model_ligand_unassigned_reason (self, mdl_lig_idx)

def	unassigned_model_ligands_reasons (self)

def	unassigned_target_ligands_reasons (self)

Data Fields
	lddt_pli_radius

	add_mdl_contacts

	lddt_pli_thresholds

	lddt_pli_binding_site_radius

Data Fields inherited from LigandScorer
	model

	target

	target_ligands

	model_ligands

	resnum_alignments

	rename_ligand_chain

	substructure_match

	coverage_delta

	max_symmetries

	state_decoding

Detailed Description

 :class:`LigandScorer` implementing lDDT-PLI.

lDDT-PLI is an lDDT score considering contacts between ligand and
receptor. Where receptor consists of protein and nucleic acid chains that
pass the criteria for :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.

:class:`LDDTPLIScorer` computes a score for a specific pair of target/model
ligands. Given a target/model ligand pair, all possible mappings of
model chains onto their chemically equivalent target chains are enumerated.
For each of these enumerations, all possible symmetries, i.e. atom-atom
assignments of the ligand as given by :class:`LigandScorer`, are evaluated
and an lDDT-PLI score is computed. The best possible lDDT-PLI score is
returned.

By default, classic lDDT is computed. That means, contacts within
*lddt_pli_radius* are identified in the target and checked if they're
conserved in the model. Added contacts are not penalized. That means if
the ligand is nicely placed in the correct pocket, but that pocket now
suddenly interacts with MORE residues in the model, you still get a high
score. You can penalize for these added contacts with the
*add_mdl_contacts* flag. This additionally considers contacts within
*lddt_pli_radius* in the model but only if the involved atoms can
be mapped to the target. This is a requirement to 1) extract the respective
reference distance from the target 2) avoid usage of contacts for which
we have no experimental evidence. One special case are
contacts from chains that are NOT mapped to the target binding site. It is
very well possible that we have experimental evidence for this chain though
its just too far away from the target binding site.
We therefore try to map these contacts to the chain in the target with
equivalent sequence that is closest to the target binding site. If the
respective atoms can be mapped there, the contact is considered not
fulfilled and added as penalty.

Populates :attr:`LigandScorer.aux_data` with following :class:`dict` keys:

* lddt_pli: The score
* lddt_pli_n_contacts: Number of contacts considered in lDDT computation
* target_ligand: The actual target ligand for which the score was computed
* model_ligand: The actual model ligand for which the score was computed
* bs_ref_res: :class:`set` of residues with potentially non-zero
  contribution to score. That is every residue with at least one
  atom within *lddt_pli_radius* + max(*lddt_pli_thresholds*) of
  the ligand.
* bs_mdl_res: Same for model

: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 lddt_pli_radius: lDDT inclusion radius for lDDT-PLI.
:type lddt_pli_radius: :class:`float`
:param add_mdl_contacts: Whether to add mdl contacts.
:type add_mdl_contacts: :class:`bool`
:param lddt_pli_thresholds: Distance difference thresholds for lDDT.
:type lddt_pli_thresholds: :class:`list` of :class:`float`
:param lddt_pli_binding_site_radius: Pro param - dont use. Providing a value
                                     Restores behaviour from previous
                                     implementation that first extracted a
                                     binding site with strict distance
                                     threshold and computed lDDT-PLI only on
                                     those target residues whereas the
                                     current implementation includes every
                                     atom within *lddt_pli_radius*.
:type lddt_pli_binding_site_radius: :class:`float`

Definition at line 12 of file ligand_scoring_lddtpli.py.

Constructor & Destructor Documentation

◆ init()

def __init__	(	self,
		model,
		target,
		model_ligands = `None`,
		target_ligands = `None`,
		resnum_alignments = `False`,
		rename_ligand_chain = `False`,
		substructure_match = `False`,
		coverage_delta = `0.2`,
		max_symmetries = `1e5`,
		lddt_pli_radius = `6.0`,
		add_mdl_contacts = `False`,
		lddt_pli_thresholds = `[0.5, 1.0, 2.0, 4.0]`,
		lddt_pli_binding_site_radius = `None`
	)

Definition at line 102 of file ligand_scoring_lddtpli.py.

Field Documentation

◆ add_mdl_contacts

add_mdl_contacts

Definition at line 119 of file ligand_scoring_lddtpli.py.

◆ lddt_pli_binding_site_radius

lddt_pli_binding_site_radius

Definition at line 121 of file ligand_scoring_lddtpli.py.

◆ lddt_pli_radius

lddt_pli_radius

Definition at line 118 of file ligand_scoring_lddtpli.py.

◆ lddt_pli_thresholds

lddt_pli_thresholds

Definition at line 120 of file ligand_scoring_lddtpli.py.

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

build-dev-doc/stage/lib64/python3.9/site-packages/ost/mol/alg/ligand_scoring_lddtpli.py

Public Member Functions

Data Fields