diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 139631e21f4afe18ea757ea66a6ebed8cbdf93bb..fc08c403c4cf898aff7a8568ddb797c9a53acdaf 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -60,6 +60,7 @@ results:
* "min_pep_length"
* "min_nuc_length"
* "lddt_add_mdl_contacts"
+ * "dockq_capri_peptide"
The pairwise sequence alignments are computed with Needleman-Wunsch using
BLOSUM62 (NUC44 for nucleotides). Many benchmarking scenarios preprocess the
@@ -363,6 +364,25 @@ def _ParseArgs():
"in the average computation for each interface that is only "
"present in the reference but not in the model."))
+ parser.add_argument(
+ "--dockq-capri-peptide",
+ dest="dockq_capri_peptide",
+ default=False,
+ action="store_true",
+ help=("Flag that changes two things in the way DockQ and its "
+ "underlying scores are computed which is proposed by the CAPRI "
+ "community when scoring peptides (PMID: 31886916). "
+ "ONE: Two residues are considered in contact if any of their "
+ "atoms is within 5A. This is relevant for fnat and fnonat "
+ "scores. CAPRI suggests to lower this threshold to 4A for "
+ "protein-peptide interactions. "
+ "TWO: irmsd is computed on interface residues. A residue is "
+ "defined as interface residue if any of its atoms is within 10A "
+ "of another chain. CAPRI suggests to lower the default of 10A to "
+ "8A in combination with only considering CB atoms for "
+ "protein-peptide interactions. "
+ "This flag has no influence on patch_dockq scores."))
+
parser.add_argument(
"--ics",
dest="ics",
@@ -757,7 +777,8 @@ def _Process(model, reference, args, model_format, reference_format):
oum = args.oum,
min_pep_length = args.min_pep_length,
min_nuc_length = args.min_nuc_length,
- lddt_add_mdl_contacts = args.lddt_add_mdl_contacts)
+ lddt_add_mdl_contacts = args.lddt_add_mdl_contacts,
+ dockq_capri_peptide = args.dockq_capri_peptide)
ir = _GetInconsistentResidues(scorer.aln)
if len(ir) > 0 and args.enforce_consistency:
@@ -937,6 +958,7 @@ def _Main():
out["min_pep_length"] = args.min_pep_length
out["min_nuc_length"] = args.min_nuc_length
out["lddt_add_mdl_contacts"] = args.lddt_add_mdl_contacts
+ out["dockq_capri_peptide"] = args.dockq_capri_peptide
out["status"] = "SUCCESS"
with open(args.output, 'w') as fh:
json.dump(out, fh, indent=4, sort_keys=False)
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index f1148dcc1bff05ede3497372b90f107cc42bdb9a..9021b1c5daba0a172af213009314b72d2700209a 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -14,6 +14,7 @@ from ost.mol.alg import dockq
from ost.mol.alg.lddt import lDDTScorer
from ost.mol.alg.qsscore import QSScorer
from ost.mol.alg.contact_score import ContactScorer
+from ost.mol.alg.contact_score import ContactEntity
from ost.mol.alg import GDT
from ost.mol.alg import Molck, MolckSettings
from ost import bindings
@@ -175,13 +176,32 @@ class Scorer:
respective atom pair is not resolved in the
target.
:type lddt_add_mdl_contacts: :class:`bool`
+ :param dockq_capri_peptide: Flag that changes two things in the way DockQ
+ and its underlying scores are computed which is
+ proposed by the CAPRI community when scoring
+ peptides (PMID: 31886916).
+ ONE: Two residues are considered in contact if
+ any of their atoms is within 5A. This is
+ relevant for fnat and fnonat scores. CAPRI
+ suggests to lower this threshold to 4A for
+ protein-peptide interactions.
+ TWO: irmsd is computed on interface residues. A
+ residue is defined as interface residue if any
+ of its atoms is within 10A of another chain.
+ CAPRI suggests to lower the default of 10A to
+ 8A in combination with only considering CB atoms
+ for protein-peptide interactions.
+ This flag has no influence on patch_dockq
+ scores.
+ :type dockq_capri_peptide: :class:`bool`
"""
def __init__(self, model, target, resnum_alignments=False,
molck_settings = None, cad_score_exec = None,
custom_mapping=None, usalign_exec = None,
lddt_no_stereochecks=False, n_max_naive=40320,
oum=False, min_pep_length = 6, min_nuc_length = 4,
- lddt_add_mdl_contacts=False):
+ lddt_add_mdl_contacts=False,
+ dockq_capri_peptide=False):
self._target_orig = target
self._model_orig = model
@@ -270,6 +290,7 @@ class Scorer:
self.min_pep_length = min_pep_length
self.min_nuc_length = min_nuc_length
self.lddt_add_mdl_contacts = lddt_add_mdl_contacts
+ self.dockq_capri_peptide = dockq_capri_peptide
# lazily evaluated attributes
self._stereochecked_model = None
@@ -1042,18 +1063,32 @@ class Scorer:
def dockq_target_interfaces(self):
""" Interfaces in :attr:`target` that are relevant for DockQ
- In principle a subset of :attr:`~contact_target_interfaces` that only
- contains peptide sequences. Chain names are lexicographically sorted.
+ All interfaces in :attr:`~target` with non-zero contacts that are
+ relevant for DockQ. Chain names are lexicographically sorted.
:type: :class:`list` of :class:`tuple` with 2 elements each:
(trg_ch1, trg_ch2)
"""
if self._dockq_target_interfaces is None:
- self._dockq_target_interfaces = list()
+
+ # interacting chains are identified with ContactEntity
+ contact_d = 5.0
+ if self.dockq_capri_peptide:
+ contact_d = 4.0
+ cent = ContactEntity(self.target, contact_mode = "aa",
+ contact_d = contact_d)
+
+ # fetch lexicographically sorted interfaces
+ interfaces = cent.interacting_chains
+ interfaces = [(min(x[0],x[1]), max(x[0],x[1])) for x in interfaces]
+
+ # select the ones with only peptides involved
pep_seqs = set([s.GetName() for s in self.chain_mapper.polypep_seqs])
- for interface in self.contact_target_interfaces:
+ self._dockq_target_interfaces = list()
+ for interface in interfaces:
if interface[0] in pep_seqs and interface[1] in pep_seqs:
self._dockq_target_interfaces.append(interface)
+
return self._dockq_target_interfaces
@property
@@ -1882,9 +1917,17 @@ class Scorer:
mdl_ch2 = interface[3]
aln1 = dockq_alns[(trg_ch1, mdl_ch1)]
aln2 = dockq_alns[(trg_ch2, mdl_ch2)]
- res = dockq.DockQ(self.model, self.target, mdl_ch1, mdl_ch2,
- trg_ch1, trg_ch2, ch1_aln=aln1,
- ch2_aln=aln2)
+ if self.dockq_capri_peptide:
+ res = dockq.DockQ(self.model, self.target, mdl_ch1, mdl_ch2,
+ trg_ch1, trg_ch2, ch1_aln=aln1,
+ ch2_aln=aln2, contact_dist_thresh = 4.0,
+ interface_dist_thresh=8.0,
+ interface_cb = True)
+ else:
+ res = dockq.DockQ(self.model, self.target, mdl_ch1, mdl_ch2,
+ trg_ch1, trg_ch2, ch1_aln=aln1,
+ ch2_aln=aln2)
+
self._fnat.append(res["fnat"])
self._fnonnat.append(res["fnonnat"])
self._irmsd.append(res["irmsd"])
@@ -1905,8 +1948,17 @@ class Scorer:
# match for sure
trg_ch1 = interface[0]
trg_ch2 = interface[1]
- res = dockq.DockQ(self.target, self.target,
- trg_ch1, trg_ch2, trg_ch1, trg_ch2)
+
+ if self.dockq_capri_peptide:
+ res = dockq.DockQ(self.target, self.target,
+ trg_ch1, trg_ch2, trg_ch1, trg_ch2,
+ contact_dist_thresh = 4.0,
+ interface_dist_thresh=8.0,
+ interface_cb = True)
+ else:
+ res = dockq.DockQ(self.target, self.target,
+ trg_ch1, trg_ch2, trg_ch1, trg_ch2)
+
not_covered_counts.append(res["nnat"])
# there are 4 types of combined scores