Flex residues JSON Nonetype error fixed

.github/workflows/python-publish.yml

@@ -35,7 +35,7 @@ jobs:
         run: |
           python3 setup.py sdist bdist_wheel
       - name: Upload artifacts for inspection
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: dist
           path: dist/*

README.md

@@ -29,6 +29,10 @@ at [Scripps Research](https://www.scripps.edu/).
 ### Documentation
 In-depth documentation can be found on [ReadTheDocs](https://ringtail.readthedocs.io).
 
+### Version 2.1.1 bug fixes
+- bugs related to ligand filtering and certain uses of the `overwrite` option in the command line have been fixed
+- enhancements to the result plotting feature
+
 ### New in version 2.0.0 and 2.1.0
 
 - changes in keywords used for the command line tool

ringtail/outputmanager.py

@@ -448,7 +448,7 @@ def plot_single_points(
 
     def save_scatterplot(self):
         """
-        Saves current figure as scatter.png
+        Saves and closes current figure as scatter.png
 
         Raises:
             OutputError

ringtail/ringtailcore.py

@@ -1498,7 +1498,9 @@ def write_flexres_pdb(
                 self.storageman.fetch_single_ligand_output_info(ligname)
             )
             flexible_residues, flexres_atomnames = self.storageman.fetch_flexres_info()
-            if flexible_residues != []:  # converts string to list
+            if flexible_residues is None:
+                flexible_residues, flexres_atomnames = [], []
+            elif flexible_residues != []:  # converts string to list
                 flexible_residues = json.loads(flexible_residues)
                 flexres_atomnames = json.loads(flexres_atomnames)
 
@@ -1532,7 +1534,7 @@ def write_flexres_pdb(
         with open(path, "w") as file:
             file.write(pdb_str)
 
-        return ligand_mol, flexmoldict 
+        return ligand_mol, flexmoldict
 
     def write_molecule_sdfs(
         self,
@@ -1665,7 +1667,9 @@ def ligands_rdkit_mol(self, bookmark_name=None, write_nonpassing=False) -> dict:
             passing_molecule_info = self.storageman.fetch_passing_ligand_output_info()
             flexible_residues, flexres_atomnames = self.storageman.fetch_flexres_info()
 
-            if flexible_residues != []:
+            if flexible_residues is None:
+                flexible_residues, flexres_atomnames = [], []
+            elif flexible_residues != []:
                 flexible_residues = json.loads(flexible_residues)
                 flexres_atomnames = json.loads(flexres_atomnames)
 
@@ -1732,9 +1736,10 @@ def plot(
         """
         Get data needed for creating Ligand Efficiency vs
         Energy scatter plot from storageManager. Call OutputManager to create plot.
+        Option to save the plot and close it immediately, or keep it open and save it manually later.
 
         Args:
-            save (bool): whether to save plot to cd
+            save (bool): whether to save plot to cd. Will save and close figure
             bookmark_name (str): bookmark from which to fetch filtered data to plot
             return_fig_handle (bool): use to return a handle to the matplotlib figure instead of saving or showing figure
 
@@ -1775,7 +1780,7 @@ def plot(
             markersize = 20
         # for smaller dataset, scale num of bins and markersize to size of dataset
         else:
-            num_of_bins = round(datalength / 10)
+            num_of_bins = max(1, round(datalength / 10))
             markersize = 60 - (datalength / 25)
 
         # plot the data
@@ -1879,7 +1884,9 @@ def onpick(event):
                 flexible_residues, flexres_atomnames = (
                     self.storageman.fetch_flexres_info()
                 )
-                if flexible_residues != []:  # converts string to list
+                if flexible_residues is None:
+                    flexible_residues, flexres_atomnames = [], []
+                elif flexible_residues != []:  # converts string to list
                     flexible_residues = json.loads(flexible_residues)
                     flexres_atomnames = json.loads(flexres_atomnames)
 

ringtail/storagemanager.py

@@ -39,7 +39,7 @@ class StorageManager:
     _db_schema_code_compatibility = {
         "1.0.0": ["1.0.0"],
         "1.1.0": ["1.1.0"],
-        "2.0.0": ["2.0.0", "2.1.0"],
+        "2.0.0": ["2.0.0", "2.1.0", "2.1.1"],
     }
 
     """Base class for a generic virtual screening database object.
@@ -1622,7 +1622,7 @@ def fetch_filters_from_bookmark(self, bookmark_name: str | None = None):
         )
 
         filters = self._run_query(sql_query).fetchone()
-        if not filters: 
+        if not filters:
             return {}
 
         return json.loads(filters[0])

setup.py

@@ -22,7 +22,7 @@ def find_files(directory):
 
 setup(
     name="ringtail",
-    version="2.1.0",
+    version="2.1.1",
     author="Forli Lab",
     author_email="forli@scripps.edu",
     url="https://github.com/forlilab/Ringtail",