Remove warning and fix plotting 3 points

ViennaRNA · Nov 28, 2021 · 10ca32a · 10ca32a
1 parent ba376fd
commit 10ca32a
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Showing 3 changed files with 12 additions and 10 deletions.
diff --git a/forgi/graph/bulge_graph.py b/forgi/graph/bulge_graph.py
@@ -894,9 +894,9 @@ def get_node_dimensions(self, node, with_missing=False):
         :return: A pair containing its dimensions
         """
         if node[0] == 's':
-            if with_missing:
-                warnings.warn(
-                    "get_node_dimensions: 'with_missing'-flag is currently ignored for stems!")
+            # if with_missing:
+            #     warnings.warn(
+            #         "get_node_dimensions: 'with_missing'-flag is currently ignored for stems!")
             return (self.stem_length(node), self.stem_length(node))
         else:
             bd = self.get_bulge_dimensions(node, with_missing)

diff --git a/forgi/threedee/visual/pymol.py b/forgi/threedee/visual/pymol.py
@@ -359,12 +359,14 @@ def add_cg(self, cg, labels, color_modifier=1.0, plot_core_bulge_graph=True):
 
         if self.display_3_points:
             for i in range(1, cg.seq_length + 1):
-                for pos in cg.iter_three_points(i):
-                    if cg.get_node_from_residue_num(i)[0] == "s":
-                        c = "cyan"
-                    else:
-                        c = "magenta"
-                    rna_plotter.add_sphere(pos, c, 0.4)
+                elem =  cg.get_node_from_residue_num(i)
+                if not self.only_elements or elem in self.only_elements:
+                    for pos in cg.iter_three_points(i):
+                        if cg.get_node_from_residue_num(i)[0] == "s":
+                            c = "cyan"
+                        else:
+                            c = "magenta"
+                        rna_plotter.add_sphere(pos, c, 0.4)
 
         if self.add_longrange:
             for key1 in cg.longrange.keys():

diff --git a/setup.py b/setup.py
@@ -79,7 +79,7 @@ def build_extension(self, ext):
       "zip_safe":False,
       "cmdclass":{'build_py': build_py, 'build_ext':construct_build_ext(build_ext)},
       "name":'forgi',
-      "version":'2.1.0',
+      "version":'2.1.1',
       "description":'RNA Graph Library',
       "author":'Bernhard Thiel, Peter Kerpedjiev',
       "author_email":'[email protected]',