From 10ca32a1e36b9150c05428b0d7f00d6aebb08985 Mon Sep 17 00:00:00 2001
From: "Bernhard C. Thiel" <thiel@tbi.univie.ac.at>
Date: Sun, 28 Nov 2021 20:43:13 +0100
Subject: [PATCH] Remove warning and fix plotting 3 points

---
 forgi/graph/bulge_graph.py     |  6 +++---
 forgi/threedee/visual/pymol.py | 14 ++++++++------
 setup.py                       |  2 +-
 3 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/forgi/graph/bulge_graph.py b/forgi/graph/bulge_graph.py
index d1f0c9d..43368e6 100755
--- 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
index a10b6a2..2d6e072 100644
--- 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
index 2b8b562..9051f8c 100644
--- 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":'thiel@tbi.univie.ac.at',