From 97a859ada4145fda33527cb9963585335d0ba32d Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 28 Feb 2023 14:52:43 +0100
Subject: [PATCH] scoring: make alignments available as attributes of Scorer
object
---
modules/mol/alg/pymod/scoring.py | 104 ++++++++++++++++++++-----------
1 file changed, 66 insertions(+), 38 deletions(-)
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index d42390eba..645a02a01 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -206,6 +206,8 @@ class Scorer:
self._mapping = None
self._model_interface_residues = None
self._target_interface_residues = None
+ self._aln = None
+ self._stereochecked_aln = None
# lazily constructed scorer objects
self._lddt_scorer = None
@@ -266,6 +268,31 @@ class Scorer:
"""
return self._target
+ @property
+ def aln(self):
+ """ Alignments of :attr:`model`/:attr:`target` chains
+
+ Alignments for each pair of chains mapped in :attr:`mapping`.
+ First sequence is target sequence, second sequence the model sequence.
+
+ :type: :class:`list` of :class:`ost.seq.AlignmentHandle`
+ """
+ if self._aln is None:
+ self._compute_aln()
+ return self._aln
+
+ @property
+ def stereochecked_aln(self):
+ """ Stereochecked equivalent of :attr:`aln`
+
+ The alignments may differ, as stereochecks potentially remove residues
+
+ :type: :class:``
+ """
+ if self._aln is None:
+ self._compute_stereochecked_aln()
+ return self._aln
+
@property
def stereochecked_model(self):
""" View of :attr:`~model` that has stereochemistry checks applied
@@ -882,35 +909,31 @@ class Scorer:
self._compute_patchdockq_scores()
return self._patch_dockq
- def _compute_lddt(self):
- # lDDT requires a flat mapping with mdl_ch as key and trg_ch as value
- flat_mapping = self.mapping.GetFlatMapping(mdl_as_key=True)
-
+ def _aln_helper(self, target, model):
# perform required alignments - cannot take the alignments from the
- # mapping results as we potentially remove stuff in the stereocheck
- # process.
+ # mapping results as we potentially remove stuff there as compared
+ # to self.model and self.target
trg_seqs = dict()
- for ch in self.stereochecked_target.chains:
+ for ch in target.chains:
cname = ch.GetName()
s = ''.join([r.one_letter_code for r in ch.residues])
s = seq.CreateSequence(ch.GetName(), s)
- s.AttachView(self.stereochecked_target.Select(f"cname={cname}"))
+ s.AttachView(target.Select(f"cname={cname}"))
trg_seqs[ch.GetName()] = s
mdl_seqs = dict()
- for ch in self.stereochecked_model.chains:
+ for ch in model.chains:
cname = ch.GetName()
s = ''.join([r.one_letter_code for r in ch.residues])
s = seq.CreateSequence(cname, s)
- s.AttachView(self.stereochecked_model.Select(f"cname={cname}"))
+ s.AttachView(model.Select(f"cname={cname}"))
mdl_seqs[ch.GetName()] = s
+ alns = list()
trg_pep_chains = [s.GetName() for s in self.chain_mapper.polypep_seqs]
trg_nuc_chains = [s.GetName() for s in self.chain_mapper.polynuc_seqs]
trg_pep_chains = set(trg_pep_chains)
trg_nuc_chains = set(trg_nuc_chains)
- lddt_alns = dict()
- lddt_chain_mapping = dict()
- for mdl_ch, trg_ch in flat_mapping.items():
+ for mdl_ch, trg_ch in self.mapping.GetFlatMapping().items():
if mdl_ch in mdl_seqs and trg_ch in trg_seqs:
if trg_ch in trg_pep_chains:
stype = mol.ChemType.AMINOACIDS
@@ -919,9 +942,32 @@ class Scorer:
else:
raise RuntimeError("Chain name inconsistency... ask "
"Gabriel")
- lddt_alns[mdl_ch] = self.chain_mapper.Align(trg_seqs[trg_ch],
- mdl_seqs[mdl_ch],
- stype)
+ alns.append(self.chain_mapper.Align(trg_seqs[trg_ch],
+ mdl_seqs[mdl_ch],
+ stype))
+ alns[-1].AttachView(0, trg_seqs[trg_ch].GetAttachedView())
+ alns[-1].AttachView(1, mdl_seqs[mdl_ch].GetAttachedView())
+ return alns
+
+ def _compute_aln(self):
+ self._aln = self._aln_helper(self.target, self.model)
+
+ def _compute_stereochecked_aln(self):
+ self._stereochecked_aln = self._aln_helper(self.stereochecked_target,
+ self.stereochecked_model)
+
+ def _compute_lddt(self):
+ # lDDT requires a flat mapping with mdl_ch as key and trg_ch as value
+ flat_mapping = self.mapping.GetFlatMapping(mdl_as_key=True)
+
+ lddt_alns = dict()
+ for aln in self.stereochecked_aln:
+ mdl_seq = aln.GetSequence(1)
+ lddt_alns[mdl_seq.name] = aln
+
+ lddt_chain_mapping = dict()
+ for mdl_ch, trg_ch in flat_mapping.items():
+ if mdl_ch in lddt_alns:
lddt_chain_mapping[mdl_ch] = trg_ch
lddt_score = self.lddt_scorer.lDDT(self.stereochecked_model,
@@ -996,30 +1042,12 @@ class Scorer:
flat_mapping = self.mapping.GetFlatMapping()
pep_seqs = set([s.GetName() for s in self.chain_mapper.polypep_seqs])
- # perform required alignments - cannot take the alignments from the
- # mapping results as we potentially remove stuff there as compared
- # to self.model and self.target
- trg_seqs = dict()
- for ch in self.target.chains:
- cname = ch.GetName()
- s = ''.join([r.one_letter_code for r in ch.residues])
- s = seq.CreateSequence(ch.GetName(), s)
- s.AttachView(self.target.Select(f"cname={cname}"))
- trg_seqs[ch.GetName()] = s
- mdl_seqs = dict()
- for ch in self.model.chains:
- cname = ch.GetName()
- s = ''.join([r.one_letter_code for r in ch.residues])
- s = seq.CreateSequence(cname, s)
- s.AttachView(self.model.Select(f"cname={cname}"))
- mdl_seqs[ch.GetName()] = s
-
dockq_alns = dict()
- for trg_ch, mdl_ch in flat_mapping.items():
+ for aln in self.aln:
+ trg_ch = aln.GetSequence(0).name
if trg_ch in pep_seqs:
- dockq_alns[(trg_ch, mdl_ch)] = \
- self.chain_mapper.Align(trg_seqs[trg_ch], mdl_seqs[mdl_ch],
- mol.ChemType.AMINOACIDS)
+ mdl_ch = aln.GetSequence(1).name
+ dockq_alns[(trg_ch, mdl_ch)] = aln
for trg_int in self.qs_scorer.qsent1.interacting_chains:
trg_ch1 = trg_int[0]
--
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