diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 7f35291ac4e2b14c2c5b855bfb2a05a889cfb704..82489c26e7439c3bbc71947846038bd1ab326583 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -345,7 +345,8 @@ def _ParseArgs():
help=("Compute DockQ scores and its components. Relevant interfaces "
"with at least one contact (any atom within 5A) of the reference "
"structure are available as key \"dockq_reference_interfaces\". "
- "Only interfaces between peptide chains are considered here! "
+ "Protein-protein, protein-nucleotide and nucleotide-nucleotide "
+ "interfaces are considered. "
"Key \"dockq_interfaces\" is a subset of "
"\"dockq_reference_interfaces\" that contains interfaces that "
"can be mapped to the model. They are stored as lists in format "
@@ -383,7 +384,8 @@ def _ParseArgs():
"8A in combination with only considering CB atoms for "
"protein-peptide interactions. "
"Note that the resulting DockQ is not evaluated for these "
- "slightly updated fnat and irmsd (lrmsd stays the same)."
+ "slightly updated fnat and irmsd (lrmsd stays the same). "
+ "Raises an error if reference contains nucleotide chains. "
"This flag has no influence on patch_dockq scores."))
parser.add_argument(
diff --git a/modules/doc/actions.rst b/modules/doc/actions.rst
index ac3de2abbf0cb9c831c067ea5660cc078b110aec..fb5c7b9a0ac82242bc576f076bda82850a195d6f 100644
--- a/modules/doc/actions.rst
+++ b/modules/doc/actions.rst
@@ -252,28 +252,29 @@ Details on the usage (output of ``ost compare-structures --help``):
--dockq Compute DockQ scores and its components. Relevant
interfaces with at least one contact (any atom within
5A) of the reference structure are available as key
- "dockq_reference_interfaces". Only interfaces between
- peptide chains are considered here! Key
- "dockq_interfaces" is a subset of
- "dockq_reference_interfaces" that contains interfaces
- that can be mapped to the model. They are stored as
- lists in format [ref_ch1, ref_ch2, mdl_ch1, mdl_ch2].
- The respective DockQ scores for "dockq_interfaces" are
- available as key "dockq". It's components are
- available as keys: "fnat" (fraction of reference
- contacts which are also there in model) "irmsd"
- (interface RMSD), "lrmsd" (ligand RMSD). The DockQ
- score is strictly designed to score each interface
- individually. We also provide two averaged versions to
- get one full model score: "dockq_ave", "dockq_wave".
- The first is simply the average of "dockq_scores", the
- latter is a weighted average with weights derived from
- number of contacts in the reference interfaces. These
- two scores only consider interfaces that are present
- in both, the model and the reference. "dockq_ave_full"
- and "dockq_wave_full" add zeros in the average
- computation for each interface that is only present in
- the reference but not in the model.
+ "dockq_reference_interfaces". Protein-protein,
+ protein-nucleotide and nucleotide-nucleotide
+ interfaces are considered. Key "dockq_interfaces" is a
+ subset of "dockq_reference_interfaces" that contains
+ interfaces that can be mapped to the model. They are
+ stored as lists in format [ref_ch1, ref_ch2, mdl_ch1,
+ mdl_ch2]. The respective DockQ scores for
+ "dockq_interfaces" are available as key "dockq". It's
+ components are available as keys: "fnat" (fraction of
+ reference contacts which are also there in model)
+ "irmsd" (interface RMSD), "lrmsd" (ligand RMSD). The
+ DockQ score is strictly designed to score each
+ interface individually. We also provide two averaged
+ versions to get one full model score: "dockq_ave",
+ "dockq_wave". The first is simply the average of
+ "dockq_scores", the latter is a weighted average with
+ weights derived from number of contacts in the
+ reference interfaces. These two scores only consider
+ interfaces that are present in both, the model and the
+ reference. "dockq_ave_full" and "dockq_wave_full" add
+ zeros in the average computation for each interface
+ that is only present in the reference but not in the
+ model.
--dockq-capri-peptide
Flag that changes two things in the way DockQ and its
underlying scores are computed which is proposed by
@@ -289,8 +290,9 @@ Details on the usage (output of ``ost compare-structures --help``):
only considering CB atoms for protein-peptide
interactions. Note that the resulting DockQ is not
evaluated for these slightly updated fnat and irmsd
- (lrmsd stays the same).This flag has no influence on
- patch_dockq scores.
+ (lrmsd stays the same). Raises an error if reference
+ contains nucleotide chains. This flag has no influence
+ on patch_dockq scores.
--ics Computes interface contact similarity (ICS) related
scores. A contact between two residues of different
chains is defined as having at least one heavy atom
diff --git a/modules/mol/alg/pymod/dockq.py b/modules/mol/alg/pymod/dockq.py
index 7be3ca5d2a235bc58f5f15a7172a32f3a1da1e88..b448e8b1e29262a097e8ba4f7556f2a6705bd1ad 100644
--- a/modules/mol/alg/pymod/dockq.py
+++ b/modules/mol/alg/pymod/dockq.py
@@ -158,7 +158,9 @@ def _RMSDScores(mdl, ref, mdl_ch1, mdl_ch2, ref_ch1, ref_ch2, dist_thresh=10.0,
cb_mode=False):
# backbone atoms used for superposition
- sup_atoms = ['CA','C','N','O']
+ sup_atoms = ["CA","C","N","O",
+ "P", "OP1", "OP2", "O2'", "O3'", "O4'", "O5'", "C1'", "C2'",
+ "C3'", "C4'", "C5'"]
# make mapped residues accessible by the dockq_idx property
mapped_mdl = mdl.Select(f"cname={mol.QueryQuoteName(mdl_ch1)},{mol.QueryQuoteName(mdl_ch2)} and grdockq_mapped=1")
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index 13cc7615eab7157f6be7c3d7b938e77ea641f704..37304aa94cae1a4daacefd499d1fc0bd5da897ba 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -1104,7 +1104,9 @@ class Scorer:
""" Interfaces in :attr:`target` that are relevant for DockQ
All interfaces in :attr:`~target` with non-zero contacts that are
- relevant for DockQ. Chain names are lexicographically sorted.
+ relevant for DockQ. Includes protein-protein, protein-nucleotide and
+ nucleotide-nucleotide interfaces. Chain names for each interface are
+ lexicographically sorted.
:type: :class:`list` of :class:`tuple` with 2 elements each:
(trg_ch1, trg_ch2)
@@ -1122,19 +1124,13 @@ class Scorer:
interfaces = cent.interacting_chains
interfaces = [(min(x[0],x[1]), max(x[0],x[1])) for x in interfaces]
- nuc_seqs = set([s.GetName() for s in self.chain_mapper.polynuc_seqs])
- interface_chains = {c for i in interfaces for c in i}
- nuc_interface_chains = interface_chains.intersection(nuc_seqs)
- if nuc_interface_chains:
- msg = "OST doesn't support nucleic acid chains for DockQ: "
- msg += ", ".join(nuc_interface_chains)
- raise NotImplementedError(msg)
-
- # select the ones with only peptides involved
pep_seqs = set([s.GetName() for s in self.chain_mapper.polypep_seqs])
+ nuc_seqs = set([s.GetName() for s in self.chain_mapper.polynuc_seqs])
+
+ seqs = pep_seqs.union(nuc_seqs)
self._dockq_target_interfaces = list()
for interface in interfaces:
- if interface[0] in pep_seqs and interface[1] in pep_seqs:
+ if interface[0] in seqs and interface[1] in seqs:
self._dockq_target_interfaces.append(interface)
return self._dockq_target_interfaces
@@ -1217,9 +1213,11 @@ class Scorer:
def irmsd(self):
""" irmsd scores for interfaces in :attr:`~dockq_interfaces`
- irmsd: RMSD of interface (RMSD computed on N, CA, C, O atoms) which
+ irmsd: RMSD of interface (RMSD computed on backbone atoms) which
consists of each residue that has at least one heavy atom within 10A of
- other chain.
+ other chain. Backbone atoms for proteins: "CA","C","N","O", for
+ nucleotides: "P", "OP1", "OP2", "O2'", "O3'", "O4'", "O5'", "C1'",
+ "C2'", "C3'", "C4'", "C5'".
:class:`list` of :class:`float`
"""
@@ -1231,11 +1229,10 @@ class Scorer:
def lrmsd(self):
""" lrmsd scores for interfaces in :attr:`~dockq_interfaces`
- lrmsd: The interfaces are superposed based on the receptor (rigid
- min RMSD superposition) and RMSD for the ligand is reported.
- Superposition and RMSD are based on N, CA, C and O positions,
- receptor is the chain contributing to the interface with more
- residues in total.
+ lrmsd: The two chains involved in the interface are superposed based on
+ the receptor (rigid min RMSD superposition) and the ligand RMSD is
+ reported. Receptor is the chain with more residues. Superposition and
+ RMSD is computed on same backbone atoms as :attr:`irmsd`.
:class:`list` of :class:`float`
"""
@@ -2050,6 +2047,12 @@ class Scorer:
def _compute_dockq_scores(self):
LogScript("Computing DockQ")
+
+ if self.dockq_capri_peptide and len(self.chain_mapper.polynuc_seqs) > 0:
+ raise RuntimeError("Cannot compute DockQ for reference structures "
+ "with nucleotide chains if dockq_capri_peptide "
+ "is enabled.")
+
# lists with values in contact_target_interfaces
self._dockq_scores = list()
self._fnat = list()