Merging updates for CLI interface and tutorials.

The updated CLI code helps display progress bars in CLI executions of network analysis. New toolkit functions help users determine nodegroups for non-canonical amino acid residues or other residues such as sugars, lipids, and small molecules.
melomcr · Aug 25, 2022 · d301b1f · d301b1f
2 parents d3c053b + 2dce6b0
commit d301b1f
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Showing 5 changed files with 189 additions and 217 deletions.
diff --git a/dynetan/datastorage.py b/dynetan/datastorage.py
@@ -91,7 +91,8 @@ def saveToFile(self, fileNameRoot):
 
             f_numNodes = f.create_dataset("numNodes", dtype='i', data= self.numNodes)
 
-            f_nodeDists = f.create_dataset("nodeDists", 
+            if self.nodeDists is not None:
+                f_nodeDists = f.create_dataset("nodeDists",
                                             shape= self.nodeDists.shape, 
                                             dtype= self.nodeDists.dtype,
                                             data= self.nodeDists)
@@ -110,12 +111,14 @@ def saveToFile(self, fileNameRoot):
 
             f_maxDirectDist = f.create_dataset("maxDirectDist", dtype='f8', data= self.maxDirectDist ) 
 
-            f_interNodePairs = f.create_dataset("interNodePairs", 
+
+            if self.interNodePairs is not None:
+                f_interNodePairs = f.create_dataset("interNodePairs",
                                             shape= self.interNodePairs.shape, 
                                             dtype= self.interNodePairs.dtype,
                                             data= self.interNodePairs)
-
-            f_contactNodesInter = f.create_dataset("contactNodesInter", 
+            if self.contactNodesInter is not None:
+                f_contactNodesInter = f.create_dataset("contactNodesInter",
                                             shape= self.contactNodesInter.shape, 
                                             dtype= self.contactNodesInter.dtype,
                                             data= self.contactNodesInter)