diff --git a/modules/mol/alg/pymod/ligand_scoring_lddtpli.py b/modules/mol/alg/pymod/ligand_scoring_lddtpli.py
index 96046571868d694b63698a7591d19147d85e3b8d..031ebc6a865f24ca51e9d1062e90bde5ae7d987e 100644
--- a/modules/mol/alg/pymod/ligand_scoring_lddtpli.py
+++ b/modules/mol/alg/pymod/ligand_scoring_lddtpli.py
@@ -18,9 +18,13 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer):
This means ignoring other ligands, waters, short polymers as well as any
incorrectly connected chains that may be in proximity.
- Given a target/model ligand pair, all possible mappings of model chains
- onto their chemically equivalent target chains are enumerated in order
- to compute the best possible lDDT-PLI.
+ :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
@@ -39,7 +43,25 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer):
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.
+ fulfilled and added as penalty.
+
+ Populates :attr:`LigandScorer.states` matrix with the following additional
+ error states:
+
+ * 10: No contact observed
+ * 20: Unknown error
+
+ 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`
@@ -119,8 +141,8 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer):
def _compute(self, symmetries, target_ligand, model_ligand):
-
-
+ """ Implements interface from parent
+ """
if self.add_mdl_contacts:
result = self._compute_lddt_pli_add_mdl_contacts(symmetries,
target_ligand,
@@ -133,17 +155,19 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer):
state = 0
score = result["lddt_pli"]
- if score is None:
+ if score is None or np.isnan(score):
if result["lddt_pli_n_contacts"] == 0:
# it's a space ship!
- state = 10
+ state = 10
else:
# unknwon error state
- state = 11
+ state = 20
return (score, state, result)
def _score_dir(self):
+ """ Implements interface from parent
+ """
return '+'
def _compute_lddt_pli_add_mdl_contacts(self, symmetries, target_ligand,
diff --git a/modules/mol/alg/pymod/ligand_scoring_scrmsd.py b/modules/mol/alg/pymod/ligand_scoring_scrmsd.py
index 55c64899ecc951ac47ca684ef9038f2013c3a81b..2569e8ab09d9221844738f6988598e2ab02fd7e4 100644
--- a/modules/mol/alg/pymod/ligand_scoring_scrmsd.py
+++ b/modules/mol/alg/pymod/ligand_scoring_scrmsd.py
@@ -9,26 +9,63 @@ from ost.mol.alg import ligand_scoring_base
class SCRMSDScorer(ligand_scoring_base.LigandScorer):
""" :class:`LigandScorer` implementing symmetry corrected RMSD.
- The symmetry corrected RMSD is computed based on a binding site
- superposition.
- The binding site is defined as all residues with at least one atom within
- *bs_radius* around the target ligand in the target structure.
+ :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 the best resulting SCRMSD is returned. 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.
+ 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.states` matrix with the following additional
+ error states:
+
+ * 10: binding_site - no residues were in proximity of the target ligand
+ * 11: model_representation - no representation of the reference binding site
+ was found in the model, i.e. the binding site was not modeled, or the
+ model ligand was positioned too far in combination with
+ *full_bs_search*=False
+ * 20: Unknown error
+
+ Populates :attr:`LigandScorer.aux_data` with following :class:`dict` keys:
+
+ * rmsd: The score
+ * lddt_lp: lDDT of the binding site used for superposition
+ * 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) for mapped residues
+ given transform
+ * 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`
@@ -87,7 +124,6 @@ class SCRMSDScorer(ligand_scoring_base.LigandScorer):
model_bs_radius=25, binding_sites_topn=100000,
full_bs_search=False):
-
super().__init__(model, target, model_ligands = model_ligands,
target_ligands = target_ligands,
resnum_alignments = resnum_alignments,
@@ -120,7 +156,8 @@ class SCRMSDScorer(ligand_scoring_base.LigandScorer):
self._get_repr_input = dict()
def _compute(self, symmetries, target_ligand, model_ligand):
-
+ """ Implements interface from parent
+ """
# set default to invalid scores
best_rmsd_result = {"rmsd": None,
"lddt_lp": None,
@@ -134,7 +171,9 @@ class SCRMSDScorer(ligand_scoring_base.LigandScorer):
"transform": geom.Mat4(),
"inconsistent_residues": list()}
- for r in self._get_repr(target_ligand, model_ligand):
+ representations = self._get_repr(target_ligand, model_ligand)
+
+ for r in representations:
rmsd = _SCRMSD_symmetries(symmetries, model_ligand,
target_ligand, transformation=r.transform)
@@ -151,18 +190,23 @@ class SCRMSDScorer(ligand_scoring_base.LigandScorer):
"transform": r.transform,
"inconsistent_residues": r.inconsistent_residues}
- # set default to error
- best_rmsd = np.nan
- error_state = 10
-
if best_rmsd_result["rmsd"] is not None:
- # but here we save the day
best_rmsd = best_rmsd_result["rmsd"]
error_state = 0
+ else:
+ # try to identify error states
+ best_rmsd = np.nan
+ error_state = 20 # unknown error
+ if _get_target_binding_sitce(target_ligand).GetResidueCount() == 0:
+ error_state = 10 # binding_site
+ elif len(representations) == 0:
+ error_state = 11 # model_representation
return (best_rmsd, error_state, best_rmsd_result)
def _score_dir(self):
+ """ Implements interface from parent
+ """
return '-'
def _get_repr(self, target_ligand, model_ligand):
@@ -186,13 +230,6 @@ class SCRMSDScorer(ligand_scoring_base.LigandScorer):
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]