diff --git a/CMakeLists.txt b/CMakeLists.txt
index 1a90c2db8aa7c46b288535172aca89334765f8af..c4331fcb4f9f3cc4e31eeeed87d8c1133632df72 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -24,8 +24,8 @@ include(PROMOD3)
# versioning info
set(PROMOD3_VERSION_MAJOR 3)
-set(PROMOD3_VERSION_MINOR 3)
-set(PROMOD3_VERSION_PATCH 1)
+set(PROMOD3_VERSION_MINOR 4)
+set(PROMOD3_VERSION_PATCH 0)
set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR})
set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_STRING}.${PROMOD3_VERSION_PATCH})
diff --git a/container/Dockerfile b/container/Dockerfile
index bab75e94add97ed6b33f6bc0441f7bb996edd59a..e50c7956cd7f63dc590a7581eb97055e06b403fb 100644
--- a/container/Dockerfile
+++ b/container/Dockerfile
@@ -1,9 +1,9 @@
-ARG OPENSTRUCTURE_IMAGE_TAG="2.5.0-jammy"
+ARG OPENSTRUCTURE_IMAGE_TAG="2.6.0-jammy"
FROM registry.scicore.unibas.ch/schwede/openstructure:${OPENSTRUCTURE_IMAGE_TAG}
# ARGUMENTS
###########
-ARG PROMOD_VERSION="3.3.1"
+ARG PROMOD_VERSION="3.4.0"
ARG SRC_FOLDER="/usr/local/src"
diff --git a/container/Singularity b/container/Singularity
index b7cdd9c18899372ab521e848d9d39ffc3f80b3cb..21a1b71afbd39dd34c782e1df68e01d00378acf5 100644
--- a/container/Singularity
+++ b/container/Singularity
@@ -1,5 +1,5 @@
BootStrap: docker
-From: registry.scicore.unibas.ch/schwede/promod3:3.3.1-OST2.5.0-jammy
+From: registry.scicore.unibas.ch/schwede/promod3:3.4.0-OST2.6.0-jammy
%post
##############################################################################
# POST
diff --git a/doc/conf.py.in b/doc/conf.py.in
index c132f0eb3b03ddbb875e37b840497cacd498e417..d81787575eca8e01e159a5c8dc8cf5e4b3ce82e3 100644
--- a/doc/conf.py.in
+++ b/doc/conf.py.in
@@ -286,7 +286,7 @@ rst_epilog = """
.. |cmake| replace:: CMake
.. |ost_l| replace:: OpenStructure
.. |ost_s| replace:: OST
-.. |ost_version| replace:: 2.5.0
+.. |ost_version| replace:: 2.6.0
.. |python| replace:: Python
.. |sphinx| replace:: Sphinx
.. _sphinx: http://sphinx-doc.org/
diff --git a/doc/dev_setup.rst b/doc/dev_setup.rst
index 04d8450744dee2c1b26dd37b061527cc0919ee24..7506314c0141aa27825ec1a49bd2b4f9f700fb3b 100644
--- a/doc/dev_setup.rst
+++ b/doc/dev_setup.rst
@@ -251,4 +251,4 @@ modules from there, use the binaries from :file:`stage/bin`, etc..
.. |pylint| replace:: Pylint
-.. _pylint: https://www.pylint.org
+.. _pylint: https://pylint.readthedocs.io
diff --git a/doc/tests/test_doctests.py b/doc/tests/test_doctests.py
index 1fc04d24085b237adcf42e03ed0b639f78ee583f..862efe8f26adbe9c31fd496077dee59f88abc49a 100644
--- a/doc/tests/test_doctests.py
+++ b/doc/tests/test_doctests.py
@@ -153,7 +153,7 @@ class DocTests(unittest.TestCase):
"Place the description of your script right in the file and import")
self.assertEqual(out_lines[3].strip(),
"it via '__doc__' as description to the parser ('-h', '--help').")
- self.assertEqual(out_lines[5].strip(), "optional arguments:")
+ self.assertTrue(out_lines[5].strip() in ["optional arguments:", "options:"])
self.assertGreater(len(out_lines), 5)
def testCoreMsgError(self):
diff --git a/extras/data_generation/afdb_modelling/afdb_proteom_to_data_chunks.py b/extras/data_generation/afdb_modelling/afdb_proteom_to_data_chunks.py
index 895d7e44c8a83c012606e2d465ccb32e6041f88a..9107df01cb0bb8a902bb5f6bd1d505bcf5396e68 100644
--- a/extras/data_generation/afdb_modelling/afdb_proteom_to_data_chunks.py
+++ b/extras/data_generation/afdb_modelling/afdb_proteom_to_data_chunks.py
@@ -53,7 +53,7 @@ def iterate_proteom(tarball):
process=True)
yield (tar_info.name, ent, mmcif_info, seqres)
-def process_proteom(tarball, ca_only=False):
+def process_proteom(tarball, ca_only=False, omf_max_error=0.0):
""" Helper: Creates list of entries for one proteom
:param tarball: Path to proteom tarball
@@ -63,7 +63,7 @@ def process_proteom(tarball, ca_only=False):
:returns: :class: list of :class:`tuple` in format required by
:func:`FromDataChunks`
"""
- omf_opts = io.OMFOption.DEFAULT_PEPLIB | io.OMFOption.LOSSY | \
+ omf_opts = io.OMFOption.DEFAULT_PEPLIB | \
io.OMFOption.AVG_BFACTORS | io.OMFOption.ROUND_BFACTORS | \
io.OMFOption.SKIP_SS | io.OMFOption.INFER_PEP_BONDS
@@ -80,7 +80,7 @@ def process_proteom(tarball, ca_only=False):
ent = mol.CreateEntityFromView(ent, False)
ent_name = f"{uniprot_ac} {fragment} {version}"
ent.SetName(ent_name)
- omf = io.OMF.FromMMCIF(ent, entry[2], omf_opts)
+ omf = io.OMF.FromEntity(ent, max_error=omf_max_error, options=omf_opts)
omf = gzip.compress(omf.ToBytes())
entries.append([uniprot_ac, fragment, version, omf])
return entries
diff --git a/loop/tests/test_all_atom_positions.cc b/loop/tests/test_all_atom_positions.cc
index e25b4a217714c21b9e233b78f2a2b88bd5066d83..d7011d083f5143e32c0d82c60b9cb3ad548fc1ec 100644
--- a/loop/tests/test_all_atom_positions.cc
+++ b/loop/tests/test_all_atom_positions.cc
@@ -315,21 +315,21 @@ BOOST_AUTO_TEST_CASE(test_aap_torsions) {
if (!n_ter) {
tor = res_list[i].GetPhiTorsion();
if (tor.IsValid()) {
- BOOST_CHECK_EQUAL(atoms.GetPhiTorsion(i), tor.GetAngle());
+ BOOST_CHECK_CLOSE(atoms.GetPhiTorsion(i), tor.GetAngle(), 1e-5);
}
}
// psi
if (!c_ter) {
tor = res_list[i].GetPsiTorsion();
if (tor.IsValid()) {
- BOOST_CHECK_EQUAL(atoms.GetPsiTorsion(i), tor.GetAngle());
+ BOOST_CHECK_CLOSE(atoms.GetPsiTorsion(i), tor.GetAngle(), 1e-5);
}
}
// omega
if (!n_ter) {
tor = res_list[i].GetOmegaTorsion();
if (tor.IsValid()) {
- BOOST_CHECK_EQUAL(atoms.GetOmegaTorsion(i), tor.GetAngle());
+ BOOST_CHECK_CLOSE(atoms.GetOmegaTorsion(i), tor.GetAngle(), 1e-5);
}
}
}
diff --git a/loop/tests/test_mm_system_creator.cc b/loop/tests/test_mm_system_creator.cc
index 6cda3263bc2269edb62050dd4d8cce8f67573533..7a180a1fd5395a72077b61178ba1f3079fe99b24 100644
--- a/loop/tests/test_mm_system_creator.cc
+++ b/loop/tests/test_mm_system_creator.cc
@@ -240,7 +240,7 @@ void CompareFullSimulation(const AllAtomPositions& all_pos,
for (uint i = 0; i < pos_ref.size(); ++i) {
BOOST_CHECK(geom::Distance(pos[mapping[i]], pos_ref[i]) < 1e-5);
BOOST_CHECK(geom::Distance(vel[mapping[i]], vel_ref[i]) < 1e-5);
- BOOST_CHECK(geom::Distance(forces[mapping[i]], forces_ref[i]) < 1e-5);
+ BOOST_CHECK(geom::Distance(forces[mapping[i]], forces_ref[i]) < 1e-3);
}
// check mm_sim features (NOTE: DIFFs non-zero but that's expected...)