From ace458850561c5646b98e705b576f5abacd6a0a0 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Fri, 6 Sep 2024 11:09:53 -0700 Subject: [PATCH] Don't reference out-of-range residues Previously we were careless about whether residue numbers were actually in range, but now python-ihm checks for that. --- modules/mmcif/pyext/src/data.py | 2 +- modules/mmcif/test/test_data.py | 2 +- modules/mmcif/test/test_restraints.py | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/mmcif/pyext/src/data.py b/modules/mmcif/pyext/src/data.py index 02e08a8ae7..46d9287959 100644 --- a/modules/mmcif/pyext/src/data.py +++ b/modules/mmcif/pyext/src/data.py @@ -388,7 +388,7 @@ class _StartingModel(ihm.startmodel.StartingModel): def __init__(self, asym_unit, struc_prov): self.filename = struc_prov[0].get_filename() super().__init__( - asym_unit=asym_unit(0, 0), # will update in _add_residue() + asym_unit=asym_unit(1, 1), # will update in _add_residue() # will fill in later with _set_sources_datasets() dataset=None, asym_id=struc_prov[0].get_chain_id(), diff --git a/modules/mmcif/test/test_data.py b/modules/mmcif/test/test_data.py index 17a02b81b8..6f082f49ba 100644 --- a/modules/mmcif/test/test_data.py +++ b/modules/mmcif/test/test_data.py @@ -397,7 +397,7 @@ def test_coordinate_handler_get_structure_particles_nonseq(self): def test_coordinate_handler_add_chain(self): """Test CoordinateHandler.add_chain()""" s = ihm.System() - ent = ihm.Entity('ACGT') + ent = ihm.Entity('ACGTACGT') # Check that IMP residue numbering (11-18) maps to IHM (1-8) asym = ihm.AsymUnit(ent, auth_seq_id_map=10) m = IMP.Model() diff --git a/modules/mmcif/test/test_restraints.py b/modules/mmcif/test/test_restraints.py index 067b0d3f0d..7d3746e953 100644 --- a/modules/mmcif/test/test_restraints.py +++ b/modules/mmcif/test/test_restraints.py @@ -247,8 +247,8 @@ def test_all_restraints_cross_link(self): """Test _AllRestraints with cross-link restraint""" conv = IMP.mmcif.Writer() m = IMP.Model() - h = make_model(m, chains=[("Rpb1", "AMT", "X"), - ("Rpb2", "ACC", "Z")]) + h = make_model(m, chains=[("Rpb1", "A" * 50, "X"), + ("Rpb2", "C" * 50, "Z")]) conv.add_model([h], []) xl_csv = self.get_input_file_name('test.xlms.csv')