3 files changed, 149 insertions, 0 deletions
diff --git a/util/check-db-entries.py b/util/check-db-entries.py
new file mode 100644
index 0000000..7b53e19
--- /dev/null
+++ b/util/check-db-entries.py
@@ -0,0 +1,43 @@
+import unittest
+import modelcif.reader
+import modelcif.dumper
+import urllib.request
+import os
+
+
+class Tests(unittest.TestCase):
+    def _read_cif(self, url):
+        with urllib.request.urlopen(url) as fh:
+            s, = modelcif.reader.read(fh)
+        return s
+
+    def _write_cif(self, s, check=True):
+        with open('test.cif', 'w') as fh:
+            modelcif.dumper.write(fh, [s], check=check)
+        os.unlink('test.cif')
+
+    def test_modbase(self):
+        """Test ModBase structure without errors"""
+        model_id = '3c79945a94ec00cac8a03104e853ca50'
+        modbase_top = 'https://salilab.org/modbase/retrieve/modbase'
+        url = '%s/?modelID=%s&format=mmcif' % (modbase_top, model_id)
+        s = self._read_cif(url)
+        self._write_cif(s)
+
+    def test_swiss_model(self):
+        """Test SWISS-MODEL structure without errors"""
+        model_id = '680335e5cca47f7d2b00afc1'
+        url = 'https://swissmodel.expasy.org/repository/%s.cif' % model_id
+        s = self._read_cif(url)
+        self._write_cif(s)
+
+    def test_alpha_fold(self):
+        """Test AlphaFold structure without errors"""
+        model_id = 'AF-B4GKE9-F1-model_v4'
+        url = 'https://alphafold.ebi.ac.uk/files/%s.cif' % model_id
+        s = self._read_cif(url)
+        self._write_cif(s)
+
+
+if __name__ == '__main__':
+    unittest.main()
diff --git a/util/python-modelcif.spec b/util/python-modelcif.spec
new file mode 100644
index 0000000..037d238
--- /dev/null
+++ b/util/python-modelcif.spec
@@ -0,0 +1,78 @@
+Name:          python3-modelcif
+License:       MIT
+Group:         Applications/Engineering
+Version:       1.5
+Release:       1%{?dist}
+Summary:       Package for handling ModelCIF mmCIF and BinaryCIF files
+Packager:      Ben Webb <ben@salilab.org>
+URL:           https://pypi.python.org/pypi/modelcif
+Source:        modelcif-%{version}.tar.gz
+BuildRequires: python3-devel, python3-setuptools, python3-ihm >= 2.6
+Requires:      python3-ihm >= 2.6
+BuildArch:     noarch
+%if 0%{?fedora} >= 42
+BuildRequires: python3-pytest
+%endif
+
+%description
+This is a Python package to assist in handling mmCIF and BinaryCIF files
+compliant with the ModelCIF extension. It works with Python 3.6 or later.
+
+%prep
+%setup -n modelcif-%{version}
+
+%build
+%{__python3} setup.py install --root=${RPM_BUILD_ROOT} --record=INSTALLED_FILES
+
+%check
+%if 0%{?fedora} >= 42
+%pytest modelcif/test.py
+%else
+%{__python3} setup.py test
+%endif
+
+%files -f INSTALLED_FILES
+%defattr(-,root,root)
+
+%changelog
+* Wed Sep 17 2025 Ben Webb <ben@salilab.org>   1.5-1
+- Update to latest upstream.
+
+* Wed Jun 11 2025 Ben Webb <ben@salilab.org>   1.4-1
+- Update to latest upstream.
+
+* Tue Jan 14 2025 Ben Webb <ben@salilab.org>   1.3-1
+- Update to latest upstream.
+
+* Wed Oct 23 2024 Ben Webb <ben@salilab.org>   1.2-1
+- Update to latest upstream.
+
+* Fri Sep 27 2024 Ben Webb <ben@salilab.org>   1.1-1
+- Update to latest upstream.
+
+* Thu Jun 20 2024 Ben Webb <ben@salilab.org>   1.0-1
+- Update to latest upstream.
+
+* Mon Oct 02 2023 Ben Webb <ben@salilab.org>   0.9-1
+- Update to latest upstream.
+
+* Fri Aug 04 2023 Ben Webb <ben@salilab.org>   0.8-1
+- Update to latest upstream.
+
+* Mon Jul 31 2023 Ben Webb <ben@salilab.org>   0.7-1
+- Update to latest upstream.
+
+* Tue May 10 2022 Ben Webb <ben@salilab.org>   0.5-1
+- Update to latest upstream.
+
+* Thu Apr 14 2022 Ben Webb <ben@salilab.org>   0.4-1
+- Update to latest upstream.
+
+* Mon Mar 21 2022 Ben Webb <ben@salilab.org>   0.3-1
+- Update to latest upstream.
+
+* Thu Jan 27 2022 Ben Webb <ben@salilab.org>   0.2-1
+- Update to latest upstream.
+
+* Thu Jan 27 2022 Ben Webb <ben@salilab.org>   0.1-1
+- Initial package.
diff --git a/util/validate-outputs.py b/util/validate-outputs.py
new file mode 100755
index 0000000..14e1ad1
--- /dev/null
+++ b/util/validate-outputs.py
@@ -0,0 +1,28 @@
+#!/usr/bin/python3
+
+"""Check the output of each example for validity against the PDBx
+   and ModelCIF dictionaries.
+
+   This should be periodically rechecked in case the PDBx and ModelCIF
+   dictionaries are updated.
+"""
+
+import sys
+import os
+import subprocess
+import ihm.dictionary
+import urllib.request
+
+with urllib.request.urlopen(
+        'https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_ma.dic') as fh:
+    pdbx_mcif = ihm.dictionary.read(fh)
+
+for script in ('mkmodbase.py', 'ligands.py'):
+    print(script)
+    subprocess.check_call([sys.executable, '../examples/' + script])
+    with open('output.cif') as fh:
+        try:
+            pdbx_mcif.validate(fh)
+        except ihm.dictionary.ValidatorError as exc:
+            print(exc)
+os.unlink('output.cif')