From 77efa561590181329ede13d847a7c000492c2e6c Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 21 Feb 2023 15:50:20 +0100
Subject: [PATCH] scoring: Adapt Scorer to reduced restrictions on rnums in
chain mapping
---
modules/mol/alg/pymod/scoring.py | 44 +++++++++++++--------
modules/mol/alg/tests/test_chain_mapping.py | 6 ++-
2 files changed, 32 insertions(+), 18 deletions(-)
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index 70f2dd5b2..d42390eba 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -144,27 +144,39 @@ class Scorer:
for ch in self._model.chains:
if ch.GetName().strip() == "":
raise RuntimeError("Model chains must have valid chain names")
-
- # catch models with residue numbers that are not strictly increasing
- # (requirement of ChainMapper)
- for ch in self._model.chains:
- 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 each model chain must "
- "be strictly increasing")
-
+
# catch targets which have empty chain names
for ch in self._target.chains:
if ch.GetName().strip() == "":
raise RuntimeError("Target chains must have valid chain names")
- # catch targets with residue numbers that are not strictly increasing
- # (requirement of ChainMapper)
- for ch in self._target.chains:
- 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 each target chain must "
- "be strictly increasing")
+ if resnum_alignments:
+ # In case of resnum_alignments, we have some requirements on
+ # residue numbers in the chain mapping: 1) no ins codes 2) strictly
+ # increasing residue numbers.
+ for ch in self._model.chains:
+ 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 each model chain "
+ "must not contain insertion codes if "
+ "resnum_alignments are enabled")
+ 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 each model chain "
+ "must be strictly increasing if "
+ "resnum_alignments are enabled")
+
+ for ch in self._target.chains:
+ 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 each target chain "
+ "must not contain insertion codes if "
+ "resnum_alignments are enabled")
+ 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 each target chain "
+ "must be strictly increasing if "
+ "resnum_alignments are enabled")
if molck_settings is None:
molck_settings = MolckSettings(rm_unk_atoms=True,
diff --git a/modules/mol/alg/tests/test_chain_mapping.py b/modules/mol/alg/tests/test_chain_mapping.py
index 106f849a3..d012f1e65 100644
--- a/modules/mol/alg/tests/test_chain_mapping.py
+++ b/modules/mol/alg/tests/test_chain_mapping.py
@@ -118,18 +118,20 @@ class TestChainMapper(unittest.TestCase):
self.assertTrue(_CompareViews(mapper.chem_group_alignments[2].GetSequence(0).GetAttachedView(), nuc_view_two))
# ensure that error is triggered if there are insertion codes
+ # and resnum_alignments are enabled
tmp_ent = ent.Copy()
ed = tmp_ent.EditXCS()
r = tmp_ent.residues[0]
ed.SetResidueNumber(r, mol.ResNum(r.GetNumber().GetNum(), 'A'))
- self.assertRaises(Exception, ChainMapper, tmp_ent)
+ self.assertRaises(Exception, ChainMapper, tmp_ent, resnum_alignments=True)
# ensure that error is triggered if resnums are not strictly increasing
+ # and resnum_alignments are enabled
tmp_ent = ent.Copy()
ed = tmp_ent.EditXCS()
r = tmp_ent.residues[0]
ed.SetResidueNumber(r, mol.ResNum(r.GetNumber().GetNum() + 42))
- self.assertRaises(Exception, ChainMapper, tmp_ent)
+ self.assertRaises(Exception, ChainMapper, tmp_ent, resnum_alignments=True)
# chain B has a missing Valine... set pep_gap_thr to 0.0 should give an
# additional chem group
--
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