From 7ec8180c3e1338049a4848b3ad82f789f2b7949c Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 9 May 2022 17:11:08 +0200
Subject: [PATCH] lDDT: generalize calpha flag to also deal with nucleotides
(C3' as ref atom)
---
modules/mol/alg/pymod/lddt.py | 39 ++++++++++++++++++------------
modules/mol/alg/tests/test_lddt.py | 6 ++---
2 files changed, 26 insertions(+), 19 deletions(-)
diff --git a/modules/mol/alg/pymod/lddt.py b/modules/mol/alg/pymod/lddt.py
index e58784bd4..3f3c7d1eb 100644
--- a/modules/mol/alg/pymod/lddt.py
+++ b/modules/mol/alg/pymod/lddt.py
@@ -130,11 +130,12 @@ class lDDTScorer:
what the original residue numbers were.
:type seqres_mapping: :class:`dict` (key: :class:`str`, value:
:class:`ost.seq.AlignmentHandle`)
- :param calpha: Only consider atoms with name "CA". Technically this sets
- the expected atom names for each residue name to ["CA"], thus
- invalidating *compound_lib*. No check whether the target
- residues are actually amino acids!
- :type calpha: :class:`bool`
+ :param bb_only: Only consider atoms with name "CA" in case of amino acids and
+ "C3'" for Nucleotides. this invalidates *compound_lib*.
+ Raises if any residue in *target* is not
+ `r.chem_class.IsPeptideLinking()` or
+ `r.chem_class.IsNucleotideLinking()`
+ :type bb_only: :class:`bool`
:raises: :class:`RuntimeError` if *target* contains compound which is not in
*compound_lib*, :class:`RuntimeError` if *symmetry_settings*
specifies symmetric atoms that are not present in the according
@@ -154,7 +155,7 @@ class lDDTScorer:
sequence_separation=0,
symmetry_settings=None,
seqres_mapping=dict(),
- calpha=False
+ bb_only=False
):
self.target = target
@@ -171,9 +172,9 @@ class lDDTScorer:
else:
self.symmetry_settings = symmetry_settings
- # whether to only consider atoms with name "CA", invalidates
- # *compound_lib*
- self.calpha=calpha
+ # whether to only consider atoms with name "CA" (amino acids) or C3'
+ # (nucleotides), invalidates *compound_lib*
+ self.bb_only=bb_only
# names of heavy atoms of each unique compound present in *target* as
# extracted from *compound_lib*, e.g.
@@ -225,7 +226,7 @@ class lDDTScorer:
# setup members defined above
self._SetupEnv(self.compound_lib, self.symmetry_settings,
- seqres_mapping, self.calpha)
+ seqres_mapping, self.bb_only)
# distance related members are lazily computed as they're affected
# by different flavours of lDDT (e.g. lDDT including inter-chain
@@ -644,7 +645,7 @@ class lDDTScorer:
self.compound_lib,
symmetry_settings = sm,
inclusion_radius = self.inclusion_radius,
- calpha = self.calpha)
+ bb_only = self.bb_only)
penalty += dummy_scorer.n_distances
return penalty
@@ -707,7 +708,7 @@ class lDDTScorer:
def _SetupEnv(self, compound_lib, symmetry_settings, seqres_mapping,
- calpha):
+ bb_only):
"""Sets target related lDDTScorer members defined in constructor
No distance related members - see _SetupDistances
@@ -725,7 +726,7 @@ class lDDTScorer:
# sets compound info in self.compound_anames and
# self.compound_symmetric_atoms
self._SetupCompound(r, compound_lib, symmetry_settings,
- calpha)
+ bb_only)
self.res_start_indices.append(current_idx)
self.res_mapper[(ch_name, rnum)] = len(self.compound_names)
@@ -804,12 +805,18 @@ class lDDTScorer:
residue_numbers[ch_name] = rnums
return residue_numbers
- def _SetupCompound(self, r, compound_lib, symmetry_settings, calpha):
+ def _SetupCompound(self, r, compound_lib, symmetry_settings, bb_only):
"""fill self.compound_anames/self.compound_symmetric_atoms
"""
- if calpha:
+ if bb_only:
# throw away compound_lib info
- self.compound_anames[r.name] = ["CA"]
+ if r.chem_class.IsPeptideLinking():
+ self.compound_anames[r.name] = ["CA"]
+ elif r.chem_type.IsNucleotideLinking():
+ self.compound_anames[r.name] = ["C3'"]
+ else:
+ raise RuntimeError(f"Only support amino acids and nucleotides "
+ f"if bb_only is True, failed with {str(r)}")
self.compound_symmetric_atoms[r.name] = list()
else:
atom_names = list()
diff --git a/modules/mol/alg/tests/test_lddt.py b/modules/mol/alg/tests/test_lddt.py
index 6f3e3be47..a1f8bfca7 100644
--- a/modules/mol/alg/tests/test_lddt.py
+++ b/modules/mol/alg/tests/test_lddt.py
@@ -147,7 +147,7 @@ class TestlDDT(unittest.TestCase):
scorer = lDDTScorer(target, sequence_separation=42)
scorer = lDDTScorer(target, sequence_separation=0)
- def test_calpha(self):
+ def test_bb_only(self):
model = _LoadFile("7SGN_C_model.pdb")
target = _LoadFile("7SGN_C_target.pdb")
@@ -156,8 +156,8 @@ class TestlDDT(unittest.TestCase):
score_one, per_res_scores_one = scorer.lDDT(model)
score_two, per_res_scores_two = scorer.lDDT(model.Select("aname=CA"))
- # no selection, just setting calpha flag should give the same
- scorer = lDDTScorer(target, calpha=True)
+ # no selection, just setting bb_only flag should give the same
+ scorer = lDDTScorer(target, bb_only=True)
score_three, per_res_scores_three = scorer.lDDT(model)
# check
--
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