fix unbound variable bug (#14)

StatPhysBio · Oct 28, 2024 · 7ca7c07 · 7ca7c07
1 parent cf57b33
commit 7ca7c07
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Showing 3 changed files with 14 additions and 1 deletion.
diff --git a/devtools/conda-build/meta.yaml b/devtools/conda-build/meta.yaml
@@ -25,7 +25,6 @@ requirements:
     - python >=3.9
     - biopython >=1.84
     - dssp
-    - git
     - h5py
     - hdf5plugin
     - numpy >=1.21.6,<1.28.0 # pinned for scipy

diff --git a/tests/struct_info/test_pyrosetta_flag.py b/tests/struct_info/test_pyrosetta_flag.py
@@ -52,6 +52,16 @@ def test_pyrosetta_flag():
     os.remove('sinfo_pyrosetta_default.hdf5')
 
 
+def test_pyrosetta_no_charge_and_sasa():
+    try:
+        import pyrosetta
+    except ModuleNotFoundError:
+        print("[warning] Cannot import pyrosetta -- skipping pyrosetta test")
+        return 
+
+    from zernikegrams.structural_info.pyrosetta_core import get_structural_info_from_protein__pyrosetta
+    get_structural_info_from_protein__pyrosetta("tests/data/pdbs/1bkx.pdb", False, False, False, False)
+
 if __name__ == '__main__':
     test_pyrosetta_flag()
 

diff --git a/zernikegrams/structural_info/pyrosetta_core.py b/zernikegrams/structural_info/pyrosetta_core.py
@@ -130,9 +130,13 @@ def get_structural_info_from_protein__pyrosetta(
             element = pose.residue_type(i).element(j).name
             if calculate_SASA:
                 sasa = atom_sasa.get(atom_id)
+            else:
+                sasa = 0
             curr_coords = coords_rows[k]
             if calculate_charge:
                 charge_pyrosetta = pose.residue_type(i).atom_charge(j)
+            else:
+                charge_pyrosetta = 0
 
             res_id = np.array([
                 aa,