From 44c6ff119e50a128cf300c63cc19d24b66548307 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 28 Jul 2022 09:53:38 +0200
Subject: [PATCH] lDDT: simplify handling of views attached to sequences
---
modules/mol/alg/pymod/chain_mapping.py | 78 ++++++++++++--------------
1 file changed, 36 insertions(+), 42 deletions(-)
diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index 7f10bbb4d..839a84187 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -137,6 +137,9 @@ class ChainMapper:
def polypep_seqs(self):
"""Sequences of peptide chains in :attr:`~target`
+ Respective :class:`EntityView` from *target* for each sequence s are
+ available as ``s.GetAttachedView()``
+
:type: :class:`ost.seq.SequenceList`
"""
return self._polypep_seqs
@@ -145,6 +148,9 @@ class ChainMapper:
def polynuc_seqs(self):
"""Sequences of nucleotide chains in :attr:`~target`
+ Respective :class:`EntityView` from *target* for each sequence s are
+ available as ``s.GetAttachedView()``
+
:type: :class:`ost.seq.SequenceList`
"""
return self._polynuc_seqs
@@ -168,7 +174,8 @@ class ChainMapper:
def chem_group_alignments(self):
"""MSA for each group in :attr:`~chem_groups`
- Sequences in MSAs exhibit same order as in :attr:`~chem_groups`
+ Sequences in MSAs exhibit same order as in :attr:`~chem_groups` and
+ have the respective :class:`EntityView` from *target* attached.
:getter: Computed on first use (cached)
:type: :class:`ost.seq.AlignmentList`
@@ -188,6 +195,9 @@ class ChainMapper:
def chem_group_ref_seqs(self):
"""Reference (longest) sequence for each group in :attr:`~chem_groups`
+ Respective :class:`EntityView` from *target* for each sequence s are
+ available as ``s.GetAttachedView()``
+
:getter: Computed on first use (cached)
:type: :class:`ost.seq.SequenceList`
"""
@@ -196,8 +206,7 @@ class ChainMapper:
for a in self.chem_group_alignments:
s = seq.CreateSequence(a.GetSequence(0).GetName(),
a.GetSequence(0).GetGaplessString())
- if a.GetSequence(0).HasAttachedView():
- s.AttachView(a.GetSequence(0).GetAttachedView())
+ s.AttachView(a.GetSequence(0).GetAttachedView())
self._chem_group_ref_seqs.AddSequence(s)
return self._chem_group_ref_seqs
@@ -642,38 +651,8 @@ def _ProcessStructure(ent):
"""
view = _StructureSelection(ent)
polypep_seqs, polynuc_seqs = _GetAtomSeqs(view)
-
- for s in polypep_seqs:
- _AttachSeq(view, s)
-
- for s in polynuc_seqs:
- _AttachSeq(view, s)
-
return (view, polypep_seqs, polynuc_seqs)
-def _AttachSeq(view, s):
- """ Helper for _ProcessStructure
-
- Attaches view of chain with name s.GetName() to s and does sanity checks on
- residue numbers in that view
- """
- chain_view = view.Select(f"cname={s.GetName()}")
-
- # check if no insertion codes are present in residue numbers
- ins_codes = [r.GetNumber().GetInsCode() for r in chain_view.residues]
- if len(set(ins_codes)) != 1 or ins_codes[0] != '\0':
- raise RuntimeError("Residue numbers in input structures must not "
- "contain insertion codes")
-
- # check if residue numbers are strictly increasing
- nums = [r.GetNumber().GetNum() for r in chain_view.residues]
- if not all(i < j for i, j in zip(nums, nums[1:])):
- raise RuntimeError("Residue numbers in input structures must be "
- "strictly increasing for each chain")
-
- # attach
- s.AttachView(chain_view)
-
def _StructureSelection(ent):
""" Helper for _ProcessStructure
@@ -694,16 +673,18 @@ def _StructureSelection(ent):
def _GetAtomSeqs(ent):
""" Helper for _ProcessStructure
- Extracts and returns atomseqs for polypeptide/nucleotide chains in ent
+ Extracts and returns atomseqs for polypeptide/nucleotide chains with
+ attached :class:`ost.mol.EntityView`
:param ent: Entity for which you want to extract atomseqs
:type ent: :class:`ost.mol.EntityView`/:class:`ost.mol.EntityHandle`
:returns: Two lists, first containing atomseqs for all polypeptide chains,
the second is the same for polynucleotides
- :raises: :class:`RuntimeError` if ent contains any residue which doesn't
- evaluate True for `r.IsPeptideLinking() or r.IsNucleotideLinking()`
- or when these two types are not strictly separated in different
- chains.
+ :raises: :class:`RuntimeError` if ent contains any residue which evaluates
+ False for `r.IsPeptideLinking() or r.IsNucleotideLinking()`,
+ these two types are not strictly separated in different chains,
+ residue numbers in a chain are not strictly increasing or contain
+ insertion codes.
"""
polypep_seqs = seq.CreateSequenceList()
polynuc_seqs = seq.CreateSequenceList()
@@ -722,11 +703,25 @@ def _GetAtomSeqs(ent):
raise RuntimeError("All residues must either be peptide_linking "
"or nucleotide_linking")
+ # check if no insertion codes are present in residue numbers
+ ins_codes = [r.GetNumber().GetInsCode() for r in ch.residues]
+ if len(set(ins_codes)) != 1 or ins_codes[0] != '\0':
+ raise RuntimeError("Residue numbers in input structures must not "
+ "contain insertion codes")
+
+ # check if residue numbers are strictly increasing
+ nums = [r.GetNumber().GetNum() for r in ch.residues]
+ if not all(i < j for i, j in zip(nums, nums[1:])):
+ raise RuntimeError("Residue numbers in input structures must be "
+ "strictly increasing for each chain")
+
s = ''.join([r.one_letter_code for r in ch.residues])
+ s = seq.CreateSequence(ch.GetName(), s)
+ s.AttachView(ent.Select(f"cname={ch.GetName()}"))
if n_pep == n_res:
- polypep_seqs.AddSequence(seq.CreateSequence(ch.GetName(), s))
+ polypep_seqs.AddSequence(s)
elif n_nuc == n_res:
- polynuc_seqs.AddSequence(seq.CreateSequence(ch.GetName(), s))
+ polynuc_seqs.AddSequence(s)
else:
raise RuntimeError("This shouldnt happen")
@@ -950,8 +945,7 @@ def _GroupSequences(seqs, seqid_thr, gap_thr, aligner, chem_type):
for aln_s_idx in range(aln_list[aln_idx].GetCount()):
s_name = aln_list[aln_idx].GetSequence(aln_s_idx).GetName()
s = seq_dict[s_name]
- if s.HasAttachedView():
- aln_list[aln_idx].AttachView(aln_s_idx, s.GetAttachedView())
+ aln_list[aln_idx].AttachView(aln_s_idx, s.GetAttachedView())
return aln_list
--
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