Load from bcif.gz; add unit test

schrodinger · May 20, 2024 · 5ba5767 · 5ba5767
1 parent 2607fff
commit 5ba5767
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Showing 5 changed files with 15 additions and 1 deletion.
diff --git a/layer3/Executive.cpp b/layer3/Executive.cpp
@@ -3693,6 +3693,7 @@ ExecutiveLoadPrepareArgs(PyMOLGlobals * G,
   case cLoadTypeSDF2Str:
   case cLoadTypeXYZStr:
   case cLoadTypeDXStr:
+  case cLoadTypeBCIFStr:
     if (!content) {
       return pymol::Error("content is nullptr");
     }
@@ -3715,6 +3716,7 @@ ExecutiveLoadPrepareArgs(PyMOLGlobals * G,
   case cLoadTypeSDF2:
   case cLoadTypeXYZ:
   case cLoadTypeDXMap:
+  case cLoadTypeBCIF:
     if (content) {
       fname_null_ok = true;
       break;

diff --git a/modules/pymol/constants.py b/modules/pymol/constants.py
@@ -84,7 +84,8 @@ def _reverse_lookup(cls, number):
               loadable.map : loadable.mapstr,
               loadable.dx : loadable.dxstr,
               loadable.xyz  : loadable.xyzstr,
-              loadable.sdf2 : loadable.sdf2str}
+              loadable.sdf2 : loadable.sdf2str,
+              loadable.bcif : loadable.bcifstr}
 
 sanitize_alpha_list_re = re.compile(r"[^a-zA-Z0-9_\'\"\.\-\[\]\,]+")
 nt_hidden_path_re = re.compile(r"\$[\/\\]")

diff --git a/modules/pymol/importing.py b/modules/pymol/importing.py
@@ -91,6 +91,9 @@ def filename_to_format(filename):
             format = 'cif'
         elif ext in ('bcif',):
             format = 'bcif'
+        elif ext in ('bcifgz',):
+            format = 'bcif'
+            zipped = 'gz'
         elif re.match(r'pdb\d+$', ext):
             format = 'pdb'
         elif re.match(r'xyz_\d+$', ext):

diff --git a/testing/data/115d.bcif.gz b/testing/data/115d.bcif.gz
diff --git a/testing/tests/api/test_importing.py b/testing/tests/api/test_importing.py
@@ -0,0 +1,8 @@
+from pymol import cmd
+from pymol import test_utils
+
+
+@test_utils.requires_version("3.0")
+def test_bcif():
+    cmd.load(test_utils.datafile("115d.bcif.gz"))
+    assert cmd.count_atoms() == 407