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Commit 3a633773 authored by Studer Gabriel's avatar Studer Gabriel
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ligand scoring: docu / error state reporting by LigandScoring child classes

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modules/mol/alg/pymod/ligand_scoring_lddtpli.py
+ 33
− 9
View file @ 3a633773
......@@ -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,
......
modules/mol/alg/pymod/ligand_scoring_scrmsd.py
+ 64
− 27
View file @ 3a633773
......@@ -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]
......
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