From c260b0d6e1bfba9f415f23dbcc4645015bf69acd Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 23 Apr 2024 15:15:54 +0200
Subject: [PATCH] ligand scoring: refactor
- separate scrmsd and lddtpli computations in separate functions
- optionally reduce the binding site search space in the model
---
modules/mol/alg/pymod/ligand_scoring.py | 493 +++++++++++++-----------
1 file changed, 271 insertions(+), 222 deletions(-)
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index 70d8f08f0..c630598ae 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -254,6 +254,11 @@ class LigandScorer:
of None, and reason for not being assigned in the
\\*_details matrix. Defaults to False.
:type unassigned: :class:`bool`
+ :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 regions
+ around model ligands.
+ :type full_bs_search: :class:`bool`
"""
def __init__(self, model, target, model_ligands=None, target_ligands=None,
resnum_alignments=False, check_resnames=True,
@@ -263,7 +268,7 @@ class LigandScorer:
radius=4.0, lddt_pli_radius=6.0, lddt_lp_radius=10.0,
binding_sites_topn=100000, global_chain_mapping=False,
rmsd_assignment=False, n_max_naive=12, max_symmetries=1e5,
- custom_mapping=None, unassigned=False):
+ custom_mapping=None, unassigned=False, full_bs_search=True):
if isinstance(model, mol.EntityView):
self.model = mol.CreateEntityFromView(model, False)
@@ -316,6 +321,7 @@ class LigandScorer:
self.max_symmetries = max_symmetries
self.unassigned = unassigned
self.coverage_delta = coverage_delta
+ self.full_bs_search = full_bs_search
# scoring matrices
self._rmsd_matrix = None
@@ -330,15 +336,34 @@ class LigandScorer:
self._lddt_pli_details = None
# lazily precomputed variables
- self._binding_sites = {}
self.__model_mapping = None
+ # Residues that are in contact with a ligand => binding site
+ # defined as all residues with at least one atom within self.radius
+ # key: ligand.handle.hash_code, value: EntityView of whatever
+ # entity ligand belongs to
+ self._binding_sites = dict()
+
# lazily precomputed variables to speedup GetRepr chain mapping calls
+ # for localized GetRepr searches
self._chem_mapping = None
self._chem_group_alns = None
self._chain_mapping_mdl = None
self._get_repr_input = dict()
+ # the actual representations as returned by ChainMapper.GetRepr
+ # key: (target_ligand.handle.hash_code, model_ligand.handle.hash_code)
+ # value: list of repr results
+ self._repr = dict()
+
+ # cache for rmsd values
+ # rmsd is used as tie breaker in lddt-pli, we therefore need access to
+ # the rmsd for each target_ligand/model_ligand/repr combination
+ # key: (target_ligand.handle.hash_code, model_ligand.handle.hash_code,
+ # repr_id)
+ # value: rmsd
+ self._rmsd_cache = dict()
+
# Bookkeeping of unassigned ligands
self._unassigned_target_ligands = None
self._unassigned_model_ligands = None
@@ -370,6 +395,56 @@ class LigandScorer:
resnum_alignments=self.resnum_alignments)
return self._chain_mapper
+ def get_target_binding_site(self, target_ligand):
+
+ if target_ligand.handle.hash_code not in self._binding_sites:
+
+ # create view of reference binding site
+ ref_residues_hashes = set() # helper to keep track of added residues
+ ignored_residue_hashes = {target_ligand.hash_code}
+ for ligand_at in target_ligand.atoms:
+ close_atoms = self.target.FindWithin(ligand_at.GetPos(), self.radius)
+ for close_at in close_atoms:
+ # Skip any residue not in the chain mapping target
+ ref_res = close_at.GetResidue()
+ h = ref_res.handle.GetHashCode()
+ if h not in ref_residues_hashes and \
+ h not in ignored_residue_hashes:
+ if self.chain_mapper.target.ViewForHandle(ref_res).IsValid():
+ h = ref_res.handle.GetHashCode()
+ ref_residues_hashes.add(h)
+ elif ref_res.is_ligand:
+ LogWarning("Ignoring ligand %s in binding site of %s" % (
+ ref_res.qualified_name, target_ligand.qualified_name))
+ ignored_residue_hashes.add(h)
+ elif ref_res.chem_type == mol.ChemType.WATERS:
+ pass # That's ok, no need to warn
+ else:
+ LogWarning("Ignoring residue %s in binding site of %s" % (
+ ref_res.qualified_name, target_ligand.qualified_name))
+ ignored_residue_hashes.add(h)
+
+ ref_bs = self.target.CreateEmptyView()
+ if ref_residues_hashes:
+ # reason for doing that separately is to guarantee same ordering of
+ # residues as in underlying entity. (Reorder by ResNum seems only
+ # available on ChainHandles)
+ for ch in self.target.chains:
+ for r in ch.residues:
+ if r.handle.GetHashCode() in ref_residues_hashes:
+ ref_bs.AddResidue(r, mol.ViewAddFlag.INCLUDE_ALL)
+ if len(ref_bs.residues) == 0:
+ raise RuntimeError("Failed to add proximity residues to "
+ "the reference binding site entity")
+ else:
+ # Flag missing binding site
+ self._unassigned_target_ligands_reason[target_ligand] = ("binding_site",
+ "No residue in proximity of the target ligand")
+
+ self._binding_sites[target_ligand.handle.hash_code] = ref_bs
+
+ return self._binding_sites[target_ligand.handle.hash_code]
+
@property
def _model_mapping(self):
"""Get the global chain mapping for the model."""
@@ -506,91 +581,6 @@ class LigandScorer:
new_editor.UpdateICS()
return extracted_ligands
- def _get_binding_sites(self, ligand):
- """Find representations of the binding site of *ligand* in the model.
-
- Only consider protein and nucleic acid chains that pass the criteria
- for the :class:`ost.mol.alg.chain_mapping`. This means ignoring other
- ligands, waters, short polymers as well as any incorrectly connected
- chain that may be in proximity.
-
- :param ligand: Defines the binding site to identify.
- :type ligand: :class:`~ost.mol.ResidueHandle`
- """
- if ligand.hash_code not in self._binding_sites:
-
- # create view of reference binding site
- ref_residues_hashes = set() # helper to keep track of added residues
- ignored_residue_hashes = {ligand.hash_code}
- for ligand_at in ligand.atoms:
- close_atoms = self.target.FindWithin(ligand_at.GetPos(), self.radius)
- for close_at in close_atoms:
- # Skip any residue not in the chain mapping target
- ref_res = close_at.GetResidue()
- h = ref_res.handle.GetHashCode()
- if h not in ref_residues_hashes and \
- h not in ignored_residue_hashes:
- if self.chain_mapper.target.ViewForHandle(ref_res).IsValid():
- h = ref_res.handle.GetHashCode()
- ref_residues_hashes.add(h)
- elif ref_res.is_ligand:
- LogWarning("Ignoring ligand %s in binding site of %s" % (
- ref_res.qualified_name, ligand.qualified_name))
- ignored_residue_hashes.add(h)
- elif ref_res.chem_type == mol.ChemType.WATERS:
- pass # That's ok, no need to warn
- else:
- LogWarning("Ignoring residue %s in binding site of %s" % (
- ref_res.qualified_name, ligand.qualified_name))
- ignored_residue_hashes.add(h)
-
- if ref_residues_hashes:
- # reason for doing that separately is to guarantee same ordering of
- # residues as in underlying entity. (Reorder by ResNum seems only
- # available on ChainHandles)
- ref_bs = self.target.CreateEmptyView()
- for ch in self.target.chains:
- for r in ch.residues:
- if r.handle.GetHashCode() in ref_residues_hashes:
- ref_bs.AddResidue(r, mol.ViewAddFlag.INCLUDE_ALL)
- if len(ref_bs.residues) == 0:
- raise RuntimeError("Failed to add proximity residues to "
- "the reference binding site entity")
-
- reprs = list()
- for model_ligand in self.model_ligands:
- # Find the representations
- if self.global_chain_mapping:
- reprs.extend(self.chain_mapper.GetRepr(ref_bs, self.model,
- inclusion_radius=self.lddt_lp_radius,
- chem_mapping_result = self.get_get_repr_input(model_ligand),
- global_mapping = self._model_mapping))
- else:
- reprs.extend(self.chain_mapper.GetRepr(ref_bs, self.model,
- inclusion_radius=self.lddt_lp_radius,
- topn=self.binding_sites_topn,
- chem_mapping_result = self.get_get_repr_input(model_ligand)))
-
- ################################################
- # TODO: sort by lDDT and ensure unique results #
- ################################################
-
- # Flag empty representation
- self._binding_sites[ligand.hash_code] = reprs
- if not self._binding_sites[ligand.hash_code]:
- self._unassigned_target_ligands_reason[ligand] = (
- "model_representation",
- "No representation of the reference binding site was "
- "found in the model")
-
- else: # if ref_residues_hashes
- # Flag missing binding site
- self._unassigned_target_ligands_reason[ligand] = ("binding_site",
- "No residue in proximity of the target ligand")
- self._binding_sites[ligand.hash_code] = []
-
- return self._binding_sites[ligand.hash_code]
-
@staticmethod
def _build_binding_site_entity(ligand, residues, extra_residues=[]):
""" Build an entity with all the binding site residues in chain A
@@ -646,20 +636,26 @@ class LigandScorer:
Compute the RMSD and lDDT-PLI scores for every possible target-model
ligand pair and store the result in internal matrices.
"""
- # Create the result matrices
- rmsd_full_matrix = np.empty(
+ ##############################
+ # Create the result matrices #
+ ##############################
+ self._rmsd_full_matrix = np.empty(
(len(self.target_ligands), len(self.model_ligands)), dtype=dict)
- lddt_pli_full_matrix = np.empty(
+ self._lddt_pli_full_matrix = np.empty(
(len(self.target_ligands), len(self.model_ligands)), dtype=dict)
self._assignment_isomorphisms = np.full(
(len(self.target_ligands), len(self.model_ligands)), fill_value=np.nan)
self._assignment_match_coverage = np.zeros(
(len(self.target_ligands), len(self.model_ligands)))
- for target_i, target_ligand in enumerate(self.target_ligands):
+ for target_id, target_ligand in enumerate(self.target_ligands):
LogVerbose("Analyzing target ligand %s" % target_ligand)
+ for model_id, model_ligand in enumerate(self.model_ligands):
+ LogVerbose("Compare to model ligand %s" % model_ligand)
- for model_i, model_ligand in enumerate(self.model_ligands):
+ #########################################################
+ # Compute symmetries for given target/model ligand pair #
+ #########################################################
try:
symmetries = _ComputeSymmetries(
model_ligand, target_ligand,
@@ -672,147 +668,156 @@ class LigandScorer:
# Ligands are different - skip
LogVerbose("No symmetry between %s and %s" % (
str(model_ligand), str(target_ligand)))
- self._assignment_isomorphisms[target_i, model_i] = 0.
+ self._assignment_isomorphisms[target_id, model_id] = 0.
continue
except TooManySymmetriesError:
# Ligands are too symmetrical - skip
LogVerbose("Too many symmetries between %s and %s" % (
str(model_ligand), str(target_ligand)))
- self._assignment_isomorphisms[target_i, model_i] = -1.
+ self._assignment_isomorphisms[target_id, model_id] = -1.
continue
except DisconnectedGraphError:
# Disconnected graph is handled elsewhere
continue
- # for binding_site in _get_binding_site_matches(target_ligand, model_ligand):
- for binding_site in self._get_binding_sites(target_ligand):
- LogVerbose("Found binding site with chain mapping %s" % (
- binding_site.GetFlatChainMapping()))
-
- # Build the reference binding site and scorer
- # Note: this could be refactored to avoid building the
- # binding site entity and lDDT scorer repeatedly
- ref_bs_ent = self._build_binding_site_entity(
- target_ligand, binding_site.ref_residues,
- binding_site.substructure.residues)
- ref_bs_ent_ligand = ref_bs_ent.FindResidue("_", 1) # by definition
-
- custom_compounds = {
- ref_bs_ent_ligand.name:
- mol.alg.lddt.CustomCompound.FromResidue(
- ref_bs_ent_ligand)}
- lddt_scorer = mol.alg.lddt.lDDTScorer(
- ref_bs_ent,
- custom_compounds=custom_compounds,
- inclusion_radius=self.lddt_pli_radius)
-
- substructure_match = len(symmetries[0][0]) != len(
- model_ligand.atoms)
- coverage = len(symmetries[0][0]) / len(model_ligand.atoms)
- self._assignment_match_coverage[target_i, model_i] = coverage
- self._assignment_isomorphisms[target_i, model_i] = 1.
-
- rmsd = _SCRMSD_symmetries(symmetries, model_ligand,
- target_ligand, transformation=binding_site.transform)
- LogDebug("RMSD: %.4f" % rmsd)
-
- # Save results?
- if not rmsd_full_matrix[target_i, model_i] or \
- rmsd_full_matrix[target_i, model_i]["rmsd"] > rmsd:
- rmsd_full_matrix[target_i, model_i] = {
- "rmsd": rmsd,
- "lddt_lp": binding_site.lDDT,
- "bs_ref_res": binding_site.substructure.residues,
- "bs_ref_res_mapped": binding_site.ref_residues,
- "bs_mdl_res_mapped": binding_site.mdl_residues,
- "bb_rmsd": binding_site.bb_rmsd,
- "target_ligand": target_ligand,
- "model_ligand": model_ligand,
- "chain_mapping": binding_site.GetFlatChainMapping(),
- "transform": binding_site.transform,
- "substructure_match": substructure_match,
- "coverage": coverage,
- "inconsistent_residues": binding_site.inconsistent_residues,
- }
- if self.unassigned:
- rmsd_full_matrix[target_i, model_i][
- "unassigned"] = False
- LogDebug("Saved RMSD")
-
- mdl_bs_ent = self._build_binding_site_entity(
- model_ligand, binding_site.mdl_residues, [])
- mdl_bs_ent_ligand = mdl_bs_ent.FindResidue("_", 1) # by definition
-
- # Now for each symmetry, loop and rename atoms according
- # to ref.
- mdl_editor = mdl_bs_ent.EditXCS()
- for i, (trg_sym, mdl_sym) in enumerate(symmetries):
- # Prepare Entities for RMSD
- for mdl_anum, trg_anum in zip(mdl_sym, trg_sym):
- # Rename model atoms according to symmetry
- trg_atom = ref_bs_ent_ligand.atoms[trg_anum]
- mdl_atom = mdl_bs_ent_ligand.atoms[mdl_anum]
- mdl_editor.RenameAtom(mdl_atom, trg_atom.name)
- mdl_editor.UpdateICS()
-
- global_lddt, local_lddt, lddt_tot, lddt_cons, n_res, \
- n_cont, n_cons = lddt_scorer.lDDT(
- mdl_bs_ent, chain_mapping={"A": "A", "_": "_"},
- no_intrachain=True,
- return_dist_test=True,
- check_resnames=self.check_resnames)
- if lddt_tot == 0:
- LogDebug("lDDT-PLI is undefined for %d" % i)
- self._unassigned_target_ligands_reason[
- target_ligand] = ("no_contact",
- "No lDDT-PLI contacts in the"
- " reference structure")
- else:
- LogDebug("lDDT-PLI for symmetry %d: %.4f" % (i, global_lddt))
+ substructure_match = len(symmetries[0][0]) != len(model_ligand.atoms)
+ coverage = len(symmetries[0][0]) / len(model_ligand.atoms)
+ self._assignment_match_coverage[target_id, model_id] = coverage
+ self._assignment_isomorphisms[target_id, model_id] = 1.
+
+ ################################################################
+ # Compute best rmsd/lddt-pli by naively enumerating symmetries #
+ ################################################################
+ # rmsds MUST be computed first, as lDDT uses them as tiebreaker
+ # and expects the values to be in self._rmsd_cache
+ rmsd_result = self._compute_rmsd(symmetries, target_ligand,
+ model_ligand)
+ lddt_pli_result = self._compute_lddtpli(symmetries, target_ligand,
+ model_ligand)
+
+ ###########################################
+ # Extend results by symmetry related info #
+ ###########################################
+ if rmsd_result is not None:
+ rmsd_result["substructure_match"] = substructure_match
+ rmsd_result["coverage"] = coverage
+ if self.unassigned:
+ rmsd_result["unassigned"] = False
+
+ if lddt_pli_result is not None:
+ lddt_pli_result["substructure_match"] = substructure_match
+ lddt_pli_result["coverage"] = coverage
+ if self.unassigned:
+ lddt_pli_result["unassigned"] = False
+
+ ############
+ # Finalize #
+ ############
+ self._lddt_pli_full_matrix[target_id, model_id] = lddt_pli_result
+ self._rmsd_full_matrix[target_id, model_id] = rmsd_result
+
+
+ def _compute_rmsd(self, symmetries, target_ligand, model_ligand):
+ best_rmsd_result = None
+ for r_i, r in enumerate(self.get_repr(target_ligand, model_ligand)):
+ rmsd = _SCRMSD_symmetries(symmetries, model_ligand,
+ target_ligand, transformation=r.transform)
+
+ cache_key = (target_ligand.handle.hash_code,
+ model_ligand.handle.hash_code, r_i)
+ self._rmsd_cache[cache_key] = rmsd
+
+ if best_rmsd_result is None or rmsd < best_rmsd_result["rmsd"]:
+ best_rmsd_result = {"rmsd": rmsd,
+ "lddt_lp": r.lDDT,
+ "bs_ref_res": r.substructure.residues,
+ "bs_ref_res_mapped": r.ref_residues,
+ "bs_mdl_res_mapped": r.mdl_residues,
+ "bb_rmsd": r.bb_rmsd,
+ "target_ligand": target_ligand,
+ "model_ligand": model_ligand,
+ "chain_mapping": r.GetFlatChainMapping(),
+ "transform": r.transform,
+ "inconsistent_residues": r.inconsistent_residues}
+
+ return best_rmsd_result
+
+
+ def _compute_lddtpli(self, symmetries, target_ligand, model_ligand):
+ ref_bs = self.get_target_binding_site(target_ligand)
+ best_lddt_result = None
+ for r_i, r in enumerate(self.get_repr(target_ligand, model_ligand)):
+ ref_bs_ent = self._build_binding_site_entity(
+ target_ligand, r.ref_residues,
+ r.substructure.residues)
+ ref_bs_ent_ligand = ref_bs_ent.FindResidue("_", 1) # by definition
+
+ custom_compounds = {
+ ref_bs_ent_ligand.name:
+ mol.alg.lddt.CustomCompound.FromResidue(
+ ref_bs_ent_ligand)}
+ lddt_scorer = mol.alg.lddt.lDDTScorer(
+ ref_bs_ent,
+ custom_compounds=custom_compounds,
+ inclusion_radius=self.lddt_pli_radius)
+
+ lddt_tot = 4 * sum([len(x) for x in lddt_scorer.ref_indices_ic])
+ if lddt_tot == 0:
+ # it's a space ship in the reference!
+ self._unassigned_target_ligands_reason[
+ target_ligand] = ("no_contact",
+ "No lDDT-PLI contacts in the"
+ " reference structure")
+ #continue
+ mdl_bs_ent = self._build_binding_site_entity(
+ model_ligand, r.mdl_residues, [])
+ mdl_bs_ent_ligand = mdl_bs_ent.FindResidue("_", 1) # by definition
+ # Now for each symmetry, loop and rename atoms according
+ # to ref.
+ mdl_editor = mdl_bs_ent.EditXCS()
+ for i, (trg_sym, mdl_sym) in enumerate(symmetries):
+ for mdl_anum, trg_anum in zip(mdl_sym, trg_sym):
+ # Rename model atoms according to symmetry
+ trg_atom = ref_bs_ent_ligand.atoms[trg_anum]
+ mdl_atom = mdl_bs_ent_ligand.atoms[mdl_anum]
+ mdl_editor.RenameAtom(mdl_atom, trg_atom.name)
+ mdl_editor.UpdateICS()
+
+ global_lddt, local_lddt = lddt_scorer.lDDT(
+ mdl_bs_ent, chain_mapping={"A": "A", "_": "_"},
+ no_intrachain=True,
+ check_resnames=self.check_resnames)
+
+ its_awesome = (best_lddt_result is None) or \
+ (global_lddt > best_lddt_result["lddt_pli"])
+
+ # additionally consider rmsd as tiebreaker
+ if (not its_awesome) and (global_lddt == best_lddt_result["lddt_pli"]):
+ rmsd_cache_key = (target_ligand.handle.hash_code,
+ model_ligand.handle.hash_code, r_i)
+ rmsd = self._rmsd_cache[rmsd_cache_key]
+ if rmsd < best_lddt_result["rmsd"]:
+ its_awesome = True
+
+ if its_awesome:
+ rmsd_cache_key = (target_ligand.handle.hash_code,
+ model_ligand.handle.hash_code, r_i)
+ best_lddt_result = {"lddt_pli": global_lddt,
+ "lddt_lp": r.lDDT,
+ "lddt_pli_n_contacts": lddt_tot,
+ "rmsd": self._rmsd_cache[rmsd_cache_key],
+ "bs_ref_res": r.substructure.residues,
+ "bs_ref_res_mapped": r.ref_residues,
+ "bs_mdl_res_mapped": r.mdl_residues,
+ "bb_rmsd": r.bb_rmsd,
+ "target_ligand": target_ligand,
+ "model_ligand": model_ligand,
+ "chain_mapping": r.GetFlatChainMapping(),
+ "transform": r.transform,
+ "inconsistent_residues": r.inconsistent_residues}
+
+ return best_lddt_result
- # Save results?
- if not lddt_pli_full_matrix[target_i, model_i]:
- # First iteration
- save_lddt = True
- else:
- last_best_lddt = lddt_pli_full_matrix[
- target_i, model_i]["lddt_pli"]
- last_best_rmsd = lddt_pli_full_matrix[
- target_i, model_i]["rmsd"]
- if global_lddt > last_best_lddt:
- # Better lDDT-PLI
- save_lddt = True
- elif global_lddt == last_best_lddt and \
- rmsd < last_best_rmsd:
- # Same lDDT-PLI, better RMSD
- save_lddt = True
- else:
- save_lddt = False
- if save_lddt:
- lddt_pli_full_matrix[target_i, model_i] = {
- "lddt_pli": global_lddt,
- "rmsd": rmsd,
- "lddt_lp": binding_site.lDDT,
- "lddt_pli_n_contacts": lddt_tot,
- "bs_ref_res": binding_site.substructure.residues,
- "bs_ref_res_mapped": binding_site.ref_residues,
- "bs_mdl_res_mapped": binding_site.mdl_residues,
- "bb_rmsd": binding_site.bb_rmsd,
- "target_ligand": target_ligand,
- "model_ligand": model_ligand,
- "chain_mapping": binding_site.GetFlatChainMapping(),
- "transform": binding_site.transform,
- "substructure_match": substructure_match,
- "coverage": coverage,
- "inconsistent_residues": binding_site.inconsistent_residues,
- }
- if self.unassigned:
- lddt_pli_full_matrix[target_i, model_i][
- "unassigned"] = False
- LogDebug("Saved lDDT-PLI")
-
- self._rmsd_full_matrix = rmsd_full_matrix
- self._lddt_pli_full_matrix = lddt_pli_full_matrix
@staticmethod
def _find_ligand_assignment(mat1, mat2=None, coverage=None, coverage_delta=None):
@@ -1781,6 +1786,50 @@ class LigandScorer:
self._get_repr_input[mdl_ligand.hash_code][0])
+ def get_repr(self, target_ligand, model_ligand):
+
+ key = None
+ if self.full_bs_search:
+ # all possible binding sites, independent from actual model ligand
+ key = (target_ligand.handle.hash_code, 0)
+ else:
+ key = (target_ligand.handle.hash_code, model_ligand.handle.hash_code)
+
+ if key not in self._repr:
+ reprs = list()
+ ref_bs = self.get_target_binding_site(target_ligand)
+ if self.full_bs_search:
+ if self.global_chain_mapping:
+ reprs = self.chain_mapper.GetRepr(
+ ref_bs, self.model, inclusion_radius=self.lddt_lp_radius,
+ global_mapping = self._model_mapping)
+ else:
+ reprs = self.chain_mapper.GetRepr(
+ ref_bs, self.model, inclusion_radius=self.lddt_lp_radius,
+ topn=self.binding_sites_topn)
+ else:
+ if self.global_chain_mapping:
+ reprs = self.chain_mapper.GetRepr(ref_bs, self.model,
+ inclusion_radius=self.lddt_lp_radius,
+ chem_mapping_result = self.get_get_repr_input(model_ligand),
+ global_mapping = self._model_mapping)
+ else:
+ reprs = self.chain_mapper.GetRepr(ref_bs, self.model,
+ inclusion_radius=self.lddt_lp_radius,
+ topn=self.binding_sites_topn,
+ chem_mapping_result = self.get_get_repr_input(model_ligand))
+ self._repr[key] = reprs
+ if len(reprs) == 0:
+ # whatever is in there already has precedence
+ if target_ligand not in self._unassigned_target_ligands_reason:
+ self._unassigned_target_ligands_reason[target_ligand] = (
+ "model_representation",
+ "No representation of the reference binding site was "
+ "found in the model")
+
+ return self._repr[key]
+
+
def _ResidueToGraph(residue, by_atom_index=False):
"""Return a NetworkX graph representation of the residue.
--
GitLab