Support PDB codes in PDB-IHM

salilab · Aug 22, 2024 · 73f3af7 · 73f3af7
1 parent 55975d9
commit 73f3af7
Show file tree

Hide file tree

Showing 2 changed files with 33 additions and 5 deletions.
diff --git a/frontend/foxs/submit_page.py b/frontend/foxs/submit_page.py
@@ -115,8 +115,8 @@ def handle_pdb(pdb_code, pdb_file, job):
                 show_filename=os.path.basename(pdb_file.filename))
             return [saved_fname], saved_fname
     elif pdb_code:
-        fname = saliweb.frontend.get_pdb_chains(pdb_code, job.directory,
-                                                formats=["PDB", "MMCIF"])
+        fname = saliweb.frontend.get_pdb_chains(
+            pdb_code, job.directory, formats=["PDB", "MMCIF", "IHM"])
         return [os.path.basename(fname)], os.path.basename(fname)
     else:
         raise InputValidationError("Error in protein input: please specify "

diff --git a/test/frontend/test_submit.py b/test/frontend/test_submit.py
@@ -34,9 +34,17 @@ def make_test_pdb(tmpdir):
     fh.close()
 
 
-def make_test_mmcif(tmpdir):
-    os.mkdir(os.path.join(tmpdir, 'xy'))
-    with gzip.open(os.path.join(tmpdir, 'xy', '1xyz.cif.gz'), 'wt') as fh:
+def make_test_mmcif(tmpdir, ihm=False):
+    if ihm:
+        os.mkdir(os.path.join(tmpdir, 'zz'))
+        os.mkdir(os.path.join(tmpdir, 'zz', '1zza'))
+        os.mkdir(os.path.join(tmpdir, 'zz', '1zza', 'structures'))
+        fname = os.path.join(tmpdir, 'zz', '1zza', 'structures', '1zza.cif.gz')
+    else:
+        os.mkdir(os.path.join(tmpdir, 'xy'))
+        fname = os.path.join(tmpdir, 'xy', '1xyz.cif.gz')
+
+    with gzip.open(fname, 'wt') as fh:
         fh.write("""
 loop_
 _atom_site.group_PDB
@@ -186,6 +194,7 @@ def test_submit_pdb_code_pdb(self):
                 foxs.app.config['DIRECTORIES_INCOMING'] = incoming
                 foxs.app.config['PDB_ROOT'] = pdb_root
                 foxs.app.config['MMCIF_ROOT'] = pdb_root
+                foxs.app.config['IHM_ROOT'] = pdb_root
 
                 make_test_pdb(pdb_root)
 
@@ -203,6 +212,7 @@ def test_submit_pdb_code_mmcif(self):
                 foxs.app.config['DIRECTORIES_INCOMING'] = incoming
                 foxs.app.config['PDB_ROOT'] = pdb_root
                 foxs.app.config['MMCIF_ROOT'] = pdb_root
+                foxs.app.config['IHM_ROOT'] = pdb_root
 
                 make_test_mmcif(pdb_root)
 
@@ -213,6 +223,24 @@ def test_submit_pdb_code_mmcif(self):
                 self.assertEqual(rv.status_code, 503)
                 self.assertIn(b'Your job has been submitted', rv.data)
 
+    def test_submit_pdb_code_ihm(self):
+        """Test submit with a PDB code (PDB-IHM format)"""
+        with tempfile.TemporaryDirectory() as incoming:
+            with tempfile.TemporaryDirectory() as pdb_root:
+                foxs.app.config['DIRECTORIES_INCOMING'] = incoming
+                foxs.app.config['PDB_ROOT'] = pdb_root
+                foxs.app.config['MMCIF_ROOT'] = pdb_root
+                foxs.app.config['IHM_ROOT'] = pdb_root
+
+                make_test_mmcif(pdb_root, ihm=True)
+
+                c = foxs.app.test_client()
+                rv = c.post('/job', data={'pdb': '1zza:C',
+                                          'jobname': 'myjob'},
+                            follow_redirects=True)
+                self.assertEqual(rv.status_code, 503)
+                self.assertIn(b'Your job has been submitted', rv.data)
+
     def test_submit_zip_file(self):
         """Test submit with zip file"""
         with tempfile.TemporaryDirectory() as incoming: