diff --git a/coverage/coverage.xml b/coverage/coverage.xml
index e0028ac..ea483fd 100644
--- a/coverage/coverage.xml
+++ b/coverage/coverage.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" ?>
-<coverage version="7.4.3" timestamp="1710261725500" lines-valid="1556" lines-covered="1264" line-rate="0.8123" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
+<coverage version="7.4.3" timestamp="1710261854143" lines-valid="1556" lines-covered="1264" line-rate="0.8123" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
 	<!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.4.3 -->
 	<!-- Based on https://raw.githubusercontent.com/cobertura/web/master/htdocs/xml/coverage-04.dtd -->
 	<sources>
diff --git a/coverage/d_604d40b87fe2aefd_test_cat_pdb_py.html b/coverage/d_604d40b87fe2aefd_test_cat_pdb_py.html
index acfa006..54ac95d 100644
--- a/coverage/d_604d40b87fe2aefd_test_cat_pdb_py.html
+++ b/coverage/d_604d40b87fe2aefd_test_cat_pdb_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_closest_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -105,7 +105,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_closest_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_604d40b87fe2aefd_test_closest_residues_py.html b/coverage/d_604d40b87fe2aefd_test_closest_residues_py.html
index e424870..47ad045 100644
--- a/coverage/d_604d40b87fe2aefd_test_closest_residues_py.html
+++ b/coverage/d_604d40b87fe2aefd_test_closest_residues_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_extract_atoms_gro_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -105,7 +105,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_extract_atoms_gro_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_604d40b87fe2aefd_test_extract_atoms_gro_py.html b/coverage/d_604d40b87fe2aefd_test_extract_atoms_gro_py.html
index c67da3c..a687c0a 100644
--- a/coverage/d_604d40b87fe2aefd_test_extract_atoms_gro_py.html
+++ b/coverage/d_604d40b87fe2aefd_test_extract_atoms_gro_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_extract_atoms_pdb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -105,7 +105,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_extract_atoms_pdb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_604d40b87fe2aefd_test_extract_atoms_pdb_py.html b/coverage/d_604d40b87fe2aefd_test_extract_atoms_pdb_py.html
index 5698c4e..0a471a6 100644
--- a/coverage/d_604d40b87fe2aefd_test_extract_atoms_pdb_py.html
+++ b/coverage/d_604d40b87fe2aefd_test_extract_atoms_pdb_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_extract_chain_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -105,7 +105,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_extract_chain_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_604d40b87fe2aefd_test_extract_chain_py.html b/coverage/d_604d40b87fe2aefd_test_extract_chain_py.html
index ebd340b..b36c368 100644
--- a/coverage/d_604d40b87fe2aefd_test_extract_chain_py.html
+++ b/coverage/d_604d40b87fe2aefd_test_extract_chain_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_extract_heteroatom_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -105,7 +105,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_extract_heteroatom_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_604d40b87fe2aefd_test_extract_heteroatom_py.html b/coverage/d_604d40b87fe2aefd_test_extract_heteroatom_py.html
index 650fcf3..f80806c 100644
--- a/coverage/d_604d40b87fe2aefd_test_extract_heteroatom_py.html
+++ b/coverage/d_604d40b87fe2aefd_test_extract_heteroatom_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_extract_model_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -105,7 +105,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_extract_model_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_604d40b87fe2aefd_test_extract_model_py.html b/coverage/d_604d40b87fe2aefd_test_extract_model_py.html
index 2290bae..281ec02 100644
--- a/coverage/d_604d40b87fe2aefd_test_extract_model_py.html
+++ b/coverage/d_604d40b87fe2aefd_test_extract_model_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_extract_molecule_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -105,7 +105,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_extract_molecule_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_604d40b87fe2aefd_test_extract_molecule_py.html b/coverage/d_604d40b87fe2aefd_test_extract_molecule_py.html
index aabc4f7..2fad016 100644
--- a/coverage/d_604d40b87fe2aefd_test_extract_molecule_py.html
+++ b/coverage/d_604d40b87fe2aefd_test_extract_molecule_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_extract_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -105,7 +105,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_extract_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_604d40b87fe2aefd_test_extract_residues_py.html b/coverage/d_604d40b87fe2aefd_test_extract_residues_py.html
index a70fb8b..172b3d0 100644
--- a/coverage/d_604d40b87fe2aefd_test_extract_residues_py.html
+++ b/coverage/d_604d40b87fe2aefd_test_extract_residues_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_remove_ligand_gro_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -105,7 +105,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_remove_ligand_gro_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_604d40b87fe2aefd_test_remove_ligand_gro_py.html b/coverage/d_604d40b87fe2aefd_test_remove_ligand_gro_py.html
index ff6ef62..4d4bc2c 100644
--- a/coverage/d_604d40b87fe2aefd_test_remove_ligand_gro_py.html
+++ b/coverage/d_604d40b87fe2aefd_test_remove_ligand_gro_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_remove_ligand_pdb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -105,7 +105,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_remove_ligand_pdb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_604d40b87fe2aefd_test_remove_ligand_pdb_py.html b/coverage/d_604d40b87fe2aefd_test_remove_ligand_pdb_py.html
index d2efdfd..4465ae2 100644
--- a/coverage/d_604d40b87fe2aefd_test_remove_ligand_pdb_py.html
+++ b/coverage/d_604d40b87fe2aefd_test_remove_ligand_pdb_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_remove_molecules_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -105,7 +105,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_remove_molecules_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_604d40b87fe2aefd_test_remove_molecules_py.html b/coverage/d_604d40b87fe2aefd_test_remove_molecules_py.html
index 9440757..b7d0963 100644
--- a/coverage/d_604d40b87fe2aefd_test_remove_molecules_py.html
+++ b/coverage/d_604d40b87fe2aefd_test_remove_molecules_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_remove_pdb_water_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -105,7 +105,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_remove_pdb_water_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_604d40b87fe2aefd_test_remove_pdb_water_py.html b/coverage/d_604d40b87fe2aefd_test_remove_pdb_water_py.html
index 68b25c0..764f59f 100644
--- a/coverage/d_604d40b87fe2aefd_test_remove_pdb_water_py.html
+++ b/coverage/d_604d40b87fe2aefd_test_remove_pdb_water_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_renumber_structure_2vgb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -105,7 +105,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_renumber_structure_2vgb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_604d40b87fe2aefd_test_renumber_structure_2vgb_py.html b/coverage/d_604d40b87fe2aefd_test_renumber_structure_2vgb_py.html
index 7f50383..01bc26b 100644
--- a/coverage/d_604d40b87fe2aefd_test_renumber_structure_2vgb_py.html
+++ b/coverage/d_604d40b87fe2aefd_test_renumber_structure_2vgb_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_renumber_structure_gro_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -107,7 +107,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_renumber_structure_gro_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_604d40b87fe2aefd_test_renumber_structure_gro_py.html b/coverage/d_604d40b87fe2aefd_test_renumber_structure_gro_py.html
index eab442f..c4fcd1e 100644
--- a/coverage/d_604d40b87fe2aefd_test_renumber_structure_gro_py.html
+++ b/coverage/d_604d40b87fe2aefd_test_renumber_structure_gro_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_renumber_structure_pdb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -107,7 +107,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_renumber_structure_pdb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_604d40b87fe2aefd_test_renumber_structure_pdb_py.html b/coverage/d_604d40b87fe2aefd_test_renumber_structure_pdb_py.html
index b607864..21ea980 100644
--- a/coverage/d_604d40b87fe2aefd_test_renumber_structure_pdb_py.html
+++ b/coverage/d_604d40b87fe2aefd_test_renumber_structure_pdb_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_renumber_structure_smallgro_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -107,7 +107,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_renumber_structure_smallgro_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_604d40b87fe2aefd_test_renumber_structure_smallgro_py.html b/coverage/d_604d40b87fe2aefd_test_renumber_structure_smallgro_py.html
index 0582ec4..3c28a09 100644
--- a/coverage/d_604d40b87fe2aefd_test_renumber_structure_smallgro_py.html
+++ b/coverage/d_604d40b87fe2aefd_test_renumber_structure_smallgro_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_sort_gro_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -107,7 +107,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_sort_gro_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_604d40b87fe2aefd_test_sort_gro_residues_py.html b/coverage/d_604d40b87fe2aefd_test_sort_gro_residues_py.html
index e34d074..bf60421 100644
--- a/coverage/d_604d40b87fe2aefd_test_sort_gro_residues_py.html
+++ b/coverage/d_604d40b87fe2aefd_test_sort_gro_residues_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_str_check_add_hydrogens_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -105,7 +105,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_str_check_add_hydrogens_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_604d40b87fe2aefd_test_str_check_add_hydrogens_py.html b/coverage/d_604d40b87fe2aefd_test_str_check_add_hydrogens_py.html
index 45a7e72..5118180 100644
--- a/coverage/d_604d40b87fe2aefd_test_str_check_add_hydrogens_py.html
+++ b/coverage/d_604d40b87fe2aefd_test_str_check_add_hydrogens_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_structure_check_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -105,7 +105,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_structure_check_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_604d40b87fe2aefd_test_structure_check_py.html b/coverage/d_604d40b87fe2aefd_test_structure_check_py.html
index 1c9fa9e..2e7c6a1 100644
--- a/coverage/d_604d40b87fe2aefd_test_structure_check_py.html
+++ b/coverage/d_604d40b87fe2aefd_test_structure_check_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -104,7 +104,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_7351d3e0b972d178___init___py.html b/coverage/d_7351d3e0b972d178___init___py.html
index 973cc82..89348af 100644
--- a/coverage/d_7351d3e0b972d178___init___py.html
+++ b/coverage/d_7351d3e0b972d178___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_cat_pdb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -89,7 +89,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_604d40b87fe2aefd_test_cat_pdb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_8572508eb5b65ee1___init___py.html b/coverage/d_8572508eb5b65ee1___init___py.html
index 3cd2b35..f96a707 100644
--- a/coverage/d_8572508eb5b65ee1___init___py.html
+++ b/coverage/d_8572508eb5b65ee1___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_8572508eb5b65ee1_gro_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -89,7 +89,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_8572508eb5b65ee1_gro_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_8572508eb5b65ee1_gro_py.html b/coverage/d_8572508eb5b65ee1_gro_py.html
index b2b55e0..d5048f8 100644
--- a/coverage/d_8572508eb5b65ee1_gro_py.html
+++ b/coverage/d_8572508eb5b65ee1_gro_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_7351d3e0b972d178___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -435,7 +435,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_7351d3e0b972d178___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_cc8067c15db60eec___init___py.html b/coverage/d_cc8067c15db60eec___init___py.html
index 94d2247..e7e01e7 100644
--- a/coverage/d_cc8067c15db60eec___init___py.html
+++ b/coverage/d_cc8067c15db60eec___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_cat_pdb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -91,7 +91,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_cat_pdb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_cc8067c15db60eec_cat_pdb_py.html b/coverage/d_cc8067c15db60eec_cat_pdb_py.html
index 77c56f7..a91b5de 100644
--- a/coverage/d_cc8067c15db60eec_cat_pdb_py.html
+++ b/coverage/d_cc8067c15db60eec_cat_pdb_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_closest_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -237,7 +237,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_closest_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_cc8067c15db60eec_closest_residues_py.html b/coverage/d_cc8067c15db60eec_closest_residues_py.html
index 300d2b9..109348a 100644
--- a/coverage/d_cc8067c15db60eec_closest_residues_py.html
+++ b/coverage/d_cc8067c15db60eec_closest_residues_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_common_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -292,7 +292,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_common_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_cc8067c15db60eec_common_py.html b/coverage/d_cc8067c15db60eec_common_py.html
index 1cb6d17..9ba9ae2 100644
--- a/coverage/d_cc8067c15db60eec_common_py.html
+++ b/coverage/d_cc8067c15db60eec_common_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_extract_atoms_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -284,7 +284,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_extract_atoms_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_cc8067c15db60eec_extract_atoms_py.html b/coverage/d_cc8067c15db60eec_extract_atoms_py.html
index 2232a95..7e84f02 100644
--- a/coverage/d_cc8067c15db60eec_extract_atoms_py.html
+++ b/coverage/d_cc8067c15db60eec_extract_atoms_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_extract_chain_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -244,7 +244,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_extract_chain_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_cc8067c15db60eec_extract_chain_py.html b/coverage/d_cc8067c15db60eec_extract_chain_py.html
index f9ccea6..2e6f18b 100644
--- a/coverage/d_cc8067c15db60eec_extract_chain_py.html
+++ b/coverage/d_cc8067c15db60eec_extract_chain_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_extract_heteroatoms_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -258,7 +258,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_extract_heteroatoms_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_cc8067c15db60eec_extract_heteroatoms_py.html b/coverage/d_cc8067c15db60eec_extract_heteroatoms_py.html
index e806058..8063bb9 100644
--- a/coverage/d_cc8067c15db60eec_extract_heteroatoms_py.html
+++ b/coverage/d_cc8067c15db60eec_extract_heteroatoms_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_extract_model_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -262,7 +262,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_extract_model_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_cc8067c15db60eec_extract_model_py.html b/coverage/d_cc8067c15db60eec_extract_model_py.html
index 8dca308..90d7455 100644
--- a/coverage/d_cc8067c15db60eec_extract_model_py.html
+++ b/coverage/d_cc8067c15db60eec_extract_model_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_extract_molecule_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -270,7 +270,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_extract_molecule_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_cc8067c15db60eec_extract_molecule_py.html b/coverage/d_cc8067c15db60eec_extract_molecule_py.html
index 3a562fa..02855e2 100644
--- a/coverage/d_cc8067c15db60eec_extract_molecule_py.html
+++ b/coverage/d_cc8067c15db60eec_extract_molecule_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_extract_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -254,7 +254,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_extract_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_cc8067c15db60eec_extract_residues_py.html b/coverage/d_cc8067c15db60eec_extract_residues_py.html
index 073eb0b..0266cad 100644
--- a/coverage/d_cc8067c15db60eec_extract_residues_py.html
+++ b/coverage/d_cc8067c15db60eec_extract_residues_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_remove_ligand_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -253,7 +253,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_remove_ligand_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_cc8067c15db60eec_remove_ligand_py.html b/coverage/d_cc8067c15db60eec_remove_ligand_py.html
index a6f7112..51698a4 100644
--- a/coverage/d_cc8067c15db60eec_remove_ligand_py.html
+++ b/coverage/d_cc8067c15db60eec_remove_ligand_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_remove_molecules_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -230,7 +230,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_remove_molecules_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_cc8067c15db60eec_remove_molecules_py.html b/coverage/d_cc8067c15db60eec_remove_molecules_py.html
index 693b051..ef26e2a 100644
--- a/coverage/d_cc8067c15db60eec_remove_molecules_py.html
+++ b/coverage/d_cc8067c15db60eec_remove_molecules_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_remove_pdb_water_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -258,7 +258,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_remove_pdb_water_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_cc8067c15db60eec_remove_pdb_water_py.html b/coverage/d_cc8067c15db60eec_remove_pdb_water_py.html
index 05f9e16..7188a2a 100644
--- a/coverage/d_cc8067c15db60eec_remove_pdb_water_py.html
+++ b/coverage/d_cc8067c15db60eec_remove_pdb_water_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_renumber_structure_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -214,7 +214,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_renumber_structure_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_cc8067c15db60eec_renumber_structure_py.html b/coverage/d_cc8067c15db60eec_renumber_structure_py.html
index de1b9a5..ddd13ef 100644
--- a/coverage/d_cc8067c15db60eec_renumber_structure_py.html
+++ b/coverage/d_cc8067c15db60eec_renumber_structure_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_sort_gro_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -272,7 +272,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_sort_gro_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_cc8067c15db60eec_sort_gro_residues_py.html b/coverage/d_cc8067c15db60eec_sort_gro_residues_py.html
index 20e53d3..7f16927 100644
--- a/coverage/d_cc8067c15db60eec_sort_gro_residues_py.html
+++ b/coverage/d_cc8067c15db60eec_sort_gro_residues_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_str_check_add_hydrogens_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -213,7 +213,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_str_check_add_hydrogens_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_cc8067c15db60eec_str_check_add_hydrogens_py.html b/coverage/d_cc8067c15db60eec_str_check_add_hydrogens_py.html
index d3673f4..b6b61d7 100644
--- a/coverage/d_cc8067c15db60eec_str_check_add_hydrogens_py.html
+++ b/coverage/d_cc8067c15db60eec_str_check_add_hydrogens_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_structure_check_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -254,7 +254,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_cc8067c15db60eec_structure_check_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_cc8067c15db60eec_structure_check_py.html b/coverage/d_cc8067c15db60eec_structure_check_py.html
index 188dc18..eb98318 100644
--- a/coverage/d_cc8067c15db60eec_structure_check_py.html
+++ b/coverage/d_cc8067c15db60eec_structure_check_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="index.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -255,7 +255,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="index.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/d_d361e47ffa394ddf___init___py.html b/coverage/d_d361e47ffa394ddf___init___py.html
index 4437867..462f5a1 100644
--- a/coverage/d_d361e47ffa394ddf___init___py.html
+++ b/coverage/d_d361e47ffa394ddf___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_8572508eb5b65ee1___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"/>
@@ -92,7 +92,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="d_8572508eb5b65ee1___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/index.html b/coverage/index.html
index 8600846..c0d16f5 100644
--- a/coverage/index.html
+++ b/coverage/index.html
@@ -45,7 +45,7 @@ <h1>Coverage report:
         </form>
         <p class="text">
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
 </header>
@@ -367,7 +367,7 @@ <h1>Coverage report:
     <div class="content">
         <p>
             <a class="nav" href="https://coverage.readthedocs.io/en/7.4.3">coverage.py v7.4.3</a>,
-            created at 2024-03-12 16:42 +0000
+            created at 2024-03-12 16:44 +0000
         </p>
     </div>
     <aside class="hidden">
diff --git a/coverage/status.json b/coverage/status.json
index a28293d..960e5f3 100644
--- a/coverage/status.json
+++ b/coverage/status.json
@@ -1 +1 @@
-{"note":"This file is an internal implementation detail to speed up HTML report generation. Its format can change at any time. You might be looking for the JSON report: https://coverage.rtfd.io/cmd.html#cmd-json","format":2,"version":"7.4.3","globals":"2166f304b69db4e84f973863f0926710","files":{"d_d361e47ffa394ddf___init___py":{"hash":"39f66e88c729407953908cd1a864d5f8","index":{"nums":[0,1,3,0,0,0,0,0],"html_filename":"d_d361e47ffa394ddf___init___py.html","relative_filename":"biobb_structure_utils/__init__.py"}},"d_8572508eb5b65ee1___init___py":{"hash":"3c77fc9ef7f887ac2508d4109cf92472","index":{"nums":[0,1,0,0,0,0,0,0],"html_filename":"d_8572508eb5b65ee1___init___py.html","relative_filename":"biobb_structure_utils/gro_lib/__init__.py"}},"d_8572508eb5b65ee1_gro_py":{"hash":"507959217f9a37a6b991a09fdd4a6b79","index":{"nums":[0,1,210,0,59,0,0,0],"html_filename":"d_8572508eb5b65ee1_gro_py.html","relative_filename":"biobb_structure_utils/gro_lib/gro.py"}},"d_7351d3e0b972d178___init___py":{"hash":"3c77fc9ef7f887ac2508d4109cf92472","index":{"nums":[0,1,0,0,0,0,0,0],"html_filename":"d_7351d3e0b972d178___init___py.html","relative_filename":"biobb_structure_utils/test/__init__.py"}},"d_604d40b87fe2aefd_test_cat_pdb_py":{"hash":"63c94c55621462836dff9ca1751d10c2","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_cat_pdb_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_cat_pdb.py"}},"d_604d40b87fe2aefd_test_closest_residues_py":{"hash":"1aebd5b41374d37d4b40a7c3c7a3ab64","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_closest_residues_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_closest_residues.py"}},"d_604d40b87fe2aefd_test_extract_atoms_gro_py":{"hash":"ca6303c74698ef8f96081b1e0b88ac43","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_extract_atoms_gro_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_gro.py"}},"d_604d40b87fe2aefd_test_extract_atoms_pdb_py":{"hash":"19f9ee561c08d7f2cd4b286d20fe80e0","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_extract_atoms_pdb_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_pdb.py"}},"d_604d40b87fe2aefd_test_extract_chain_py":{"hash":"9539b6b9e9fe781148de65630149ede4","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_extract_chain_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_extract_chain.py"}},"d_604d40b87fe2aefd_test_extract_heteroatom_py":{"hash":"79ff178c04de432fee5fa0d5b7c50390","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_extract_heteroatom_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_extract_heteroatom.py"}},"d_604d40b87fe2aefd_test_extract_model_py":{"hash":"0c976f0b0fd07ae3c5feb01f5c7288fe","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_extract_model_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_extract_model.py"}},"d_604d40b87fe2aefd_test_extract_molecule_py":{"hash":"dfe9cb4a8c4755784c7efcee8eb01779","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_extract_molecule_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_extract_molecule.py"}},"d_604d40b87fe2aefd_test_extract_residues_py":{"hash":"a2773ce97ee73264d721245287b4fa52","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_extract_residues_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_extract_residues.py"}},"d_604d40b87fe2aefd_test_remove_ligand_gro_py":{"hash":"c8b4b71ba3ec1de43d4e2fa500d5721d","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_remove_ligand_gro_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_gro.py"}},"d_604d40b87fe2aefd_test_remove_ligand_pdb_py":{"hash":"7f4ec67710d2ed571415c0846dac12d1","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_remove_ligand_pdb_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_pdb.py"}},"d_604d40b87fe2aefd_test_remove_molecules_py":{"hash":"aa2a9f44edd3b5e6a1280ae47701a209","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_remove_molecules_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_remove_molecules.py"}},"d_604d40b87fe2aefd_test_remove_pdb_water_py":{"hash":"4216080d72627b0575555fbc8d9eb2ad","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_remove_pdb_water_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_remove_pdb_water.py"}},"d_604d40b87fe2aefd_test_renumber_structure_2vgb_py":{"hash":"c3a77f3d80ebde0c07be62e949ce41c8","index":{"nums":[0,1,14,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_renumber_structure_2vgb_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_2vgb.py"}},"d_604d40b87fe2aefd_test_renumber_structure_gro_py":{"hash":"3b18b3928b746cbf90bb93cacea671b8","index":{"nums":[0,1,14,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_renumber_structure_gro_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_gro.py"}},"d_604d40b87fe2aefd_test_renumber_structure_pdb_py":{"hash":"b0309981b06a652705831d3693f6d391","index":{"nums":[0,1,14,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_renumber_structure_pdb_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_pdb.py"}},"d_604d40b87fe2aefd_test_renumber_structure_smallgro_py":{"hash":"f227799622cfb03c26f6d96ce4fe4108","index":{"nums":[0,1,14,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_renumber_structure_smallgro_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_smallgro.py"}},"d_604d40b87fe2aefd_test_sort_gro_residues_py":{"hash":"c31924a3cb9abc1daa2b296f7037d604","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_sort_gro_residues_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_sort_gro_residues.py"}},"d_604d40b87fe2aefd_test_str_check_add_hydrogens_py":{"hash":"b6432416151f2260b5250b1b482f411f","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_str_check_add_hydrogens_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_str_check_add_hydrogens.py"}},"d_604d40b87fe2aefd_test_structure_check_py":{"hash":"c7e3d2d1f7eeb02cba4d867f31955471","index":{"nums":[0,1,11,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_structure_check_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_structure_check.py"}},"d_cc8067c15db60eec___init___py":{"hash":"0904e8e2cfd96d3e285ae9ff0b048aaa","index":{"nums":[0,1,2,0,0,0,0,0],"html_filename":"d_cc8067c15db60eec___init___py.html","relative_filename":"biobb_structure_utils/utils/__init__.py"}},"d_cc8067c15db60eec_cat_pdb_py":{"hash":"f6a6dc55290ef5d3d85090ed7769c096","index":{"nums":[0,1,59,0,12,0,0,0],"html_filename":"d_cc8067c15db60eec_cat_pdb_py.html","relative_filename":"biobb_structure_utils/utils/cat_pdb.py"}},"d_cc8067c15db60eec_closest_residues_py":{"hash":"0a6437722890582913836a35450c31ac","index":{"nums":[0,1,85,0,17,0,0,0],"html_filename":"d_cc8067c15db60eec_closest_residues_py.html","relative_filename":"biobb_structure_utils/utils/closest_residues.py"}},"d_cc8067c15db60eec_common_py":{"hash":"8fb804bec8c59224f7053725e8cd6049","index":{"nums":[0,1,134,0,24,0,0,0],"html_filename":"d_cc8067c15db60eec_common_py.html","relative_filename":"biobb_structure_utils/utils/common.py"}},"d_cc8067c15db60eec_extract_atoms_py":{"hash":"6c629f0b309a9874cadd24ef85162736","index":{"nums":[0,1,68,0,14,0,0,0],"html_filename":"d_cc8067c15db60eec_extract_atoms_py.html","relative_filename":"biobb_structure_utils/utils/extract_atoms.py"}},"d_cc8067c15db60eec_extract_chain_py":{"hash":"dc9970918e284ae4d39000628f0b4428","index":{"nums":[0,1,67,0,18,0,0,0],"html_filename":"d_cc8067c15db60eec_extract_chain_py.html","relative_filename":"biobb_structure_utils/utils/extract_chain.py"}},"d_cc8067c15db60eec_extract_heteroatoms_py":{"hash":"7437cc869b81a86ee7682fcf76cabe0c","index":{"nums":[0,1,69,0,17,0,0,0],"html_filename":"d_cc8067c15db60eec_extract_heteroatoms_py.html","relative_filename":"biobb_structure_utils/utils/extract_heteroatoms.py"}},"d_cc8067c15db60eec_extract_model_py":{"hash":"5168293cc29f9083840ab7e1e6da4fb2","index":{"nums":[0,1,73,0,17,0,0,0],"html_filename":"d_cc8067c15db60eec_extract_model_py.html","relative_filename":"biobb_structure_utils/utils/extract_model.py"}},"d_cc8067c15db60eec_extract_molecule_py":{"hash":"69bbbd262629a1d9dee262e6752cfdfc","index":{"nums":[0,1,60,0,14,0,0,0],"html_filename":"d_cc8067c15db60eec_extract_molecule_py.html","relative_filename":"biobb_structure_utils/utils/extract_molecule.py"}},"d_cc8067c15db60eec_extract_residues_py":{"hash":"023dd3dcf9ab43f11057b0fab2f2b7a7","index":{"nums":[0,1,64,0,14,0,0,0],"html_filename":"d_cc8067c15db60eec_extract_residues_py.html","relative_filename":"biobb_structure_utils/utils/extract_residues.py"}},"d_cc8067c15db60eec_remove_ligand_py":{"hash":"10edbdb634fa59faf11700c223d1dbd1","index":{"nums":[0,1,55,0,11,0,0,0],"html_filename":"d_cc8067c15db60eec_remove_ligand_py.html","relative_filename":"biobb_structure_utils/utils/remove_ligand.py"}},"d_cc8067c15db60eec_remove_molecules_py":{"hash":"86d3395835bea038de4722898de757a6","index":{"nums":[0,1,67,0,14,0,0,0],"html_filename":"d_cc8067c15db60eec_remove_molecules_py.html","relative_filename":"biobb_structure_utils/utils/remove_molecules.py"}},"d_cc8067c15db60eec_remove_pdb_water_py":{"hash":"257ca9c0b3080c5fceb9baa16e38ece4","index":{"nums":[0,1,40,0,11,0,0,0],"html_filename":"d_cc8067c15db60eec_remove_pdb_water_py.html","relative_filename":"biobb_structure_utils/utils/remove_pdb_water.py"}},"d_cc8067c15db60eec_renumber_structure_py":{"hash":"4cb08f16b78fc93be9a61f5431e292dd","index":{"nums":[0,1,88,0,12,0,0,0],"html_filename":"d_cc8067c15db60eec_renumber_structure_py.html","relative_filename":"biobb_structure_utils/utils/renumber_structure.py"}},"d_cc8067c15db60eec_sort_gro_residues_py":{"hash":"80e0b9d0ebed6e7f058f76f45fd4833c","index":{"nums":[0,1,44,0,11,0,0,0],"html_filename":"d_cc8067c15db60eec_sort_gro_residues_py.html","relative_filename":"biobb_structure_utils/utils/sort_gro_residues.py"}},"d_cc8067c15db60eec_str_check_add_hydrogens_py":{"hash":"ff00656370fedb48a90b97240496bf08","index":{"nums":[0,1,64,0,14,0,0,0],"html_filename":"d_cc8067c15db60eec_str_check_add_hydrogens_py.html","relative_filename":"biobb_structure_utils/utils/str_check_add_hydrogens.py"}},"d_cc8067c15db60eec_structure_check_py":{"hash":"6ac8062443e22759165655c22d2021f6","index":{"nums":[0,1,57,0,13,0,0,0],"html_filename":"d_cc8067c15db60eec_structure_check_py.html","relative_filename":"biobb_structure_utils/utils/structure_check.py"}}}}
\ No newline at end of file
+{"note":"This file is an internal implementation detail to speed up HTML report generation. Its format can change at any time. You might be looking for the JSON report: https://coverage.rtfd.io/cmd.html#cmd-json","format":2,"version":"7.4.3","globals":"2166f304b69db4e84f973863f0926710","files":{"d_d361e47ffa394ddf___init___py":{"hash":"39f66e88c729407953908cd1a864d5f8","index":{"nums":[0,1,3,0,0,0,0,0],"html_filename":"d_d361e47ffa394ddf___init___py.html","relative_filename":"biobb_structure_utils/__init__.py"}},"d_8572508eb5b65ee1___init___py":{"hash":"3c77fc9ef7f887ac2508d4109cf92472","index":{"nums":[0,1,0,0,0,0,0,0],"html_filename":"d_8572508eb5b65ee1___init___py.html","relative_filename":"biobb_structure_utils/gro_lib/__init__.py"}},"d_8572508eb5b65ee1_gro_py":{"hash":"9c05a3d2de405e91e69bab694b8363f9","index":{"nums":[0,1,210,0,59,0,0,0],"html_filename":"d_8572508eb5b65ee1_gro_py.html","relative_filename":"biobb_structure_utils/gro_lib/gro.py"}},"d_7351d3e0b972d178___init___py":{"hash":"3c77fc9ef7f887ac2508d4109cf92472","index":{"nums":[0,1,0,0,0,0,0,0],"html_filename":"d_7351d3e0b972d178___init___py.html","relative_filename":"biobb_structure_utils/test/__init__.py"}},"d_604d40b87fe2aefd_test_cat_pdb_py":{"hash":"63c94c55621462836dff9ca1751d10c2","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_cat_pdb_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_cat_pdb.py"}},"d_604d40b87fe2aefd_test_closest_residues_py":{"hash":"1aebd5b41374d37d4b40a7c3c7a3ab64","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_closest_residues_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_closest_residues.py"}},"d_604d40b87fe2aefd_test_extract_atoms_gro_py":{"hash":"ca6303c74698ef8f96081b1e0b88ac43","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_extract_atoms_gro_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_gro.py"}},"d_604d40b87fe2aefd_test_extract_atoms_pdb_py":{"hash":"19f9ee561c08d7f2cd4b286d20fe80e0","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_extract_atoms_pdb_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_pdb.py"}},"d_604d40b87fe2aefd_test_extract_chain_py":{"hash":"9539b6b9e9fe781148de65630149ede4","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_extract_chain_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_extract_chain.py"}},"d_604d40b87fe2aefd_test_extract_heteroatom_py":{"hash":"79ff178c04de432fee5fa0d5b7c50390","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_extract_heteroatom_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_extract_heteroatom.py"}},"d_604d40b87fe2aefd_test_extract_model_py":{"hash":"0c976f0b0fd07ae3c5feb01f5c7288fe","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_extract_model_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_extract_model.py"}},"d_604d40b87fe2aefd_test_extract_molecule_py":{"hash":"dfe9cb4a8c4755784c7efcee8eb01779","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_extract_molecule_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_extract_molecule.py"}},"d_604d40b87fe2aefd_test_extract_residues_py":{"hash":"a2773ce97ee73264d721245287b4fa52","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_extract_residues_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_extract_residues.py"}},"d_604d40b87fe2aefd_test_remove_ligand_gro_py":{"hash":"c8b4b71ba3ec1de43d4e2fa500d5721d","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_remove_ligand_gro_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_gro.py"}},"d_604d40b87fe2aefd_test_remove_ligand_pdb_py":{"hash":"7f4ec67710d2ed571415c0846dac12d1","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_remove_ligand_pdb_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_pdb.py"}},"d_604d40b87fe2aefd_test_remove_molecules_py":{"hash":"aa2a9f44edd3b5e6a1280ae47701a209","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_remove_molecules_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_remove_molecules.py"}},"d_604d40b87fe2aefd_test_remove_pdb_water_py":{"hash":"4216080d72627b0575555fbc8d9eb2ad","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_remove_pdb_water_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_remove_pdb_water.py"}},"d_604d40b87fe2aefd_test_renumber_structure_2vgb_py":{"hash":"c3a77f3d80ebde0c07be62e949ce41c8","index":{"nums":[0,1,14,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_renumber_structure_2vgb_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_2vgb.py"}},"d_604d40b87fe2aefd_test_renumber_structure_gro_py":{"hash":"3b18b3928b746cbf90bb93cacea671b8","index":{"nums":[0,1,14,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_renumber_structure_gro_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_gro.py"}},"d_604d40b87fe2aefd_test_renumber_structure_pdb_py":{"hash":"b0309981b06a652705831d3693f6d391","index":{"nums":[0,1,14,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_renumber_structure_pdb_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_pdb.py"}},"d_604d40b87fe2aefd_test_renumber_structure_smallgro_py":{"hash":"f227799622cfb03c26f6d96ce4fe4108","index":{"nums":[0,1,14,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_renumber_structure_smallgro_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_smallgro.py"}},"d_604d40b87fe2aefd_test_sort_gro_residues_py":{"hash":"c31924a3cb9abc1daa2b296f7037d604","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_sort_gro_residues_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_sort_gro_residues.py"}},"d_604d40b87fe2aefd_test_str_check_add_hydrogens_py":{"hash":"b6432416151f2260b5250b1b482f411f","index":{"nums":[0,1,12,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_str_check_add_hydrogens_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_str_check_add_hydrogens.py"}},"d_604d40b87fe2aefd_test_structure_check_py":{"hash":"c7e3d2d1f7eeb02cba4d867f31955471","index":{"nums":[0,1,11,0,0,0,0,0],"html_filename":"d_604d40b87fe2aefd_test_structure_check_py.html","relative_filename":"biobb_structure_utils/test/unitests/test_utils/test_structure_check.py"}},"d_cc8067c15db60eec___init___py":{"hash":"0904e8e2cfd96d3e285ae9ff0b048aaa","index":{"nums":[0,1,2,0,0,0,0,0],"html_filename":"d_cc8067c15db60eec___init___py.html","relative_filename":"biobb_structure_utils/utils/__init__.py"}},"d_cc8067c15db60eec_cat_pdb_py":{"hash":"f6a6dc55290ef5d3d85090ed7769c096","index":{"nums":[0,1,59,0,12,0,0,0],"html_filename":"d_cc8067c15db60eec_cat_pdb_py.html","relative_filename":"biobb_structure_utils/utils/cat_pdb.py"}},"d_cc8067c15db60eec_closest_residues_py":{"hash":"0a6437722890582913836a35450c31ac","index":{"nums":[0,1,85,0,17,0,0,0],"html_filename":"d_cc8067c15db60eec_closest_residues_py.html","relative_filename":"biobb_structure_utils/utils/closest_residues.py"}},"d_cc8067c15db60eec_common_py":{"hash":"8fb804bec8c59224f7053725e8cd6049","index":{"nums":[0,1,134,0,24,0,0,0],"html_filename":"d_cc8067c15db60eec_common_py.html","relative_filename":"biobb_structure_utils/utils/common.py"}},"d_cc8067c15db60eec_extract_atoms_py":{"hash":"6c629f0b309a9874cadd24ef85162736","index":{"nums":[0,1,68,0,14,0,0,0],"html_filename":"d_cc8067c15db60eec_extract_atoms_py.html","relative_filename":"biobb_structure_utils/utils/extract_atoms.py"}},"d_cc8067c15db60eec_extract_chain_py":{"hash":"dc9970918e284ae4d39000628f0b4428","index":{"nums":[0,1,67,0,18,0,0,0],"html_filename":"d_cc8067c15db60eec_extract_chain_py.html","relative_filename":"biobb_structure_utils/utils/extract_chain.py"}},"d_cc8067c15db60eec_extract_heteroatoms_py":{"hash":"7437cc869b81a86ee7682fcf76cabe0c","index":{"nums":[0,1,69,0,17,0,0,0],"html_filename":"d_cc8067c15db60eec_extract_heteroatoms_py.html","relative_filename":"biobb_structure_utils/utils/extract_heteroatoms.py"}},"d_cc8067c15db60eec_extract_model_py":{"hash":"5168293cc29f9083840ab7e1e6da4fb2","index":{"nums":[0,1,73,0,17,0,0,0],"html_filename":"d_cc8067c15db60eec_extract_model_py.html","relative_filename":"biobb_structure_utils/utils/extract_model.py"}},"d_cc8067c15db60eec_extract_molecule_py":{"hash":"69bbbd262629a1d9dee262e6752cfdfc","index":{"nums":[0,1,60,0,14,0,0,0],"html_filename":"d_cc8067c15db60eec_extract_molecule_py.html","relative_filename":"biobb_structure_utils/utils/extract_molecule.py"}},"d_cc8067c15db60eec_extract_residues_py":{"hash":"023dd3dcf9ab43f11057b0fab2f2b7a7","index":{"nums":[0,1,64,0,14,0,0,0],"html_filename":"d_cc8067c15db60eec_extract_residues_py.html","relative_filename":"biobb_structure_utils/utils/extract_residues.py"}},"d_cc8067c15db60eec_remove_ligand_py":{"hash":"10edbdb634fa59faf11700c223d1dbd1","index":{"nums":[0,1,55,0,11,0,0,0],"html_filename":"d_cc8067c15db60eec_remove_ligand_py.html","relative_filename":"biobb_structure_utils/utils/remove_ligand.py"}},"d_cc8067c15db60eec_remove_molecules_py":{"hash":"86d3395835bea038de4722898de757a6","index":{"nums":[0,1,67,0,14,0,0,0],"html_filename":"d_cc8067c15db60eec_remove_molecules_py.html","relative_filename":"biobb_structure_utils/utils/remove_molecules.py"}},"d_cc8067c15db60eec_remove_pdb_water_py":{"hash":"257ca9c0b3080c5fceb9baa16e38ece4","index":{"nums":[0,1,40,0,11,0,0,0],"html_filename":"d_cc8067c15db60eec_remove_pdb_water_py.html","relative_filename":"biobb_structure_utils/utils/remove_pdb_water.py"}},"d_cc8067c15db60eec_renumber_structure_py":{"hash":"4cb08f16b78fc93be9a61f5431e292dd","index":{"nums":[0,1,88,0,12,0,0,0],"html_filename":"d_cc8067c15db60eec_renumber_structure_py.html","relative_filename":"biobb_structure_utils/utils/renumber_structure.py"}},"d_cc8067c15db60eec_sort_gro_residues_py":{"hash":"80e0b9d0ebed6e7f058f76f45fd4833c","index":{"nums":[0,1,44,0,11,0,0,0],"html_filename":"d_cc8067c15db60eec_sort_gro_residues_py.html","relative_filename":"biobb_structure_utils/utils/sort_gro_residues.py"}},"d_cc8067c15db60eec_str_check_add_hydrogens_py":{"hash":"ff00656370fedb48a90b97240496bf08","index":{"nums":[0,1,64,0,14,0,0,0],"html_filename":"d_cc8067c15db60eec_str_check_add_hydrogens_py.html","relative_filename":"biobb_structure_utils/utils/str_check_add_hydrogens.py"}},"d_cc8067c15db60eec_structure_check_py":{"hash":"6ac8062443e22759165655c22d2021f6","index":{"nums":[0,1,57,0,13,0,0,0],"html_filename":"d_cc8067c15db60eec_structure_check_py.html","relative_filename":"biobb_structure_utils/utils/structure_check.py"}}}}
\ No newline at end of file
diff --git a/flake8/index.html b/flake8/index.html
index 6083249..e383be9 100644
--- a/flake8/index.html
+++ b/flake8/index.html
@@ -9,7 +9,7 @@
       <div id="masthead" class="sev-4"></div>
       <div id="page">
           <h1>flake8 violations</h1>
-         <p id="versions">Generated on 2024-03-12 16:41
+         <p id="versions">Generated on 2024-03-12 16:43
             with Installed plugins: flake8-html: 0.4.3, mccabe: 0.7.0, pycodestyle: 2.11.1, pyflakes: 3.2.0
          </p>
          <ul id="index">
diff --git a/junit/junit.xml b/junit/junit.xml
index 70baf2e..73af880 100644
--- a/junit/junit.xml
+++ b/junit/junit.xml
@@ -1 +1 @@
-<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="20" time="32.701" timestamp="2024-03-12T16:41:31.530061" hostname="biobb-runners"><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_cat_pdb.TestCatPDB" name="test_launch" time="0.218" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_closest_residues.TestClosestResidues" name="test_launch" time="2.036" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_atoms_gro.TestExtractAtomsGRO" name="test_launch" time="5.452" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_atoms_pdb.TestExtractAtomsPDB" name="test_launch" time="0.073" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_chain.TestExtractChain" name="test_launch" time="0.432" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_heteroatom.TestExtractHeteroAtoms" name="test_launch" time="1.142" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_model.TestExtractModel" name="test_launch" time="3.242" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_molecule.TestExtractMolecule" name="test_launch" time="0.686" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_residues.TestExtractResidues" name="test_launch" time="0.679" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_remove_ligand_gro.TestRemoveLigandGro" name="test_launch" time="0.482" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_remove_ligand_pdb.TestRemoveLigandPDB" name="test_launch" time="2.963" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_remove_molecules.TestRemoveMolecules" name="test_launch" time="5.692" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_remove_pdb_water.TestRemovePDBWater" name="test_launch" time="0.827" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_renumber_structure_2vgb.TestRenumberStructure2VGB" name="test_launch" time="0.952" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_renumber_structure_gro.TestRenumberStructureGRO" name="test_launch" time="0.154" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_renumber_structure_pdb.TestRenumberStructurePDB" name="test_launch" time="0.035" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_renumber_structure_smallgro.TestRenumberStructureSMALLGRO" name="test_launch" time="0.034" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_sort_gro_residues.TestSortGroResidues" name="test_launch" time="4.789" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_str_check_add_hydrogens.TestStrCheckAddHydrogens" name="test_str_check_add_hydrogens" time="0.988" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_structure_check.TestStructureCheck" name="test_launch" time="1.117" /></testsuite></testsuites>
\ No newline at end of file
+<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="20" time="31.997" timestamp="2024-03-12T16:43:40.976354" hostname="biobb-runners"><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_cat_pdb.TestCatPDB" name="test_launch" time="0.125" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_closest_residues.TestClosestResidues" name="test_launch" time="2.039" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_atoms_gro.TestExtractAtomsGRO" name="test_launch" time="5.362" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_atoms_pdb.TestExtractAtomsPDB" name="test_launch" time="0.075" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_chain.TestExtractChain" name="test_launch" time="0.395" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_heteroatom.TestExtractHeteroAtoms" name="test_launch" time="1.111" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_model.TestExtractModel" name="test_launch" time="3.257" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_molecule.TestExtractMolecule" name="test_launch" time="0.703" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_residues.TestExtractResidues" name="test_launch" time="0.581" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_remove_ligand_gro.TestRemoveLigandGro" name="test_launch" time="0.486" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_remove_ligand_pdb.TestRemoveLigandPDB" name="test_launch" time="2.698" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_remove_molecules.TestRemoveMolecules" name="test_launch" time="5.457" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_remove_pdb_water.TestRemovePDBWater" name="test_launch" time="1.079" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_renumber_structure_2vgb.TestRenumberStructure2VGB" name="test_launch" time="0.850" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_renumber_structure_gro.TestRenumberStructureGRO" name="test_launch" time="0.157" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_renumber_structure_pdb.TestRenumberStructurePDB" name="test_launch" time="0.035" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_renumber_structure_smallgro.TestRenumberStructureSMALLGRO" name="test_launch" time="0.033" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_sort_gro_residues.TestSortGroResidues" name="test_launch" time="4.869" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_str_check_add_hydrogens.TestStrCheckAddHydrogens" name="test_str_check_add_hydrogens" time="1.018" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_structure_check.TestStructureCheck" name="test_launch" time="1.141" /></testsuite></testsuites>
\ No newline at end of file
diff --git a/junit/report.html b/junit/report.html
index cb5f161..6133308 100644
--- a/junit/report.html
+++ b/junit/report.html
@@ -7,7 +7,7 @@
   </head>
   <body>
     <h1 id="title">report.html</h1>
-    <p>Report generated on 12-Mar-2024 at 16:42:04 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
+    <p>Report generated on 12-Mar-2024 at 16:44:12 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
         v4.1.1</p>
     <div id="environment-header">
       <h2>Environment</h2>
@@ -61,7 +61,7 @@ <h2>Environment</h2>
         <h2>Summary</h2>
         <div class="additional-summary prefix">
         </div>
-        <p class="run-count">20 tests took 00:00:32.</p>
+        <p class="run-count">20 tests took 00:00:31.</p>
         <p class="filter">(Un)check the boxes to filter the results.</p>
         <div class="summary__reload">
           <div class="summary__reload__button hidden" onclick="location.reload()">
@@ -108,7 +108,7 @@ <h2>Summary</h2>
     </table>
   </body>
   <footer>
-    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.9.18&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-159-generic-x86_64-with-glibc2.31&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.1.1&#34;, &#34;pluggy&#34;: &#34;1.4.0&#34;}, &#34;Plugins&#34;: {&#34;cov&#34;: &#34;4.1.0&#34;, &#34;metadata&#34;: &#34;3.1.1&#34;, &#34;html&#34;: &#34;4.1.1&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_structure_utils/test/unitests/test_utils/test_cat_pdb.py::TestCatPDB::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_cat_pdb.py::TestCatPDB::test_launch&#34;, &#34;duration&#34;: &#34;218 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_cat_pdb.py::TestCatPDB::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;218 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:41:31,979 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.cat_pdb Version: 4.1.0\n2024-03-12 16:41:31,980 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cat_protein.pdb to /tmp/biobb/unitests_13/cat_pdb/390bd526-599a-4d32-8a4f-56fecbadbbe4\n2024-03-12 16:41:31,980 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cat_ligand.pdb to /tmp/biobb/unitests_13/cat_pdb/390bd526-599a-4d32-8a4f-56fecbadbbe4\n2024-03-12 16:41:31,982 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/cat_pdb/390bd526-599a-4d32-8a4f-56fecbadbbe4&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/cat_pdb/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_13/cat_pdb/output_structure_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_cat_pdb.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 2058\n     Atoms ALIGNED in PDB_B: 2058\n     RMS: 6.579094722437545e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/cat_pdb/cat_pdb_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.cat_pdb Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/cat_pdb/cat_pdb_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cat_protein.pdb to /tmp/biobb/unitests_13/cat_pdb/390bd526-599a-4d32-8a4f-56fecbadbbe4\nINFO     /tmp/biobb/unitests_13/cat_pdb/cat_pdb_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cat_ligand.pdb to /tmp/biobb/unitests_13/cat_pdb/390bd526-599a-4d32-8a4f-56fecbadbbe4\nINFO     /tmp/biobb/unitests_13/cat_pdb/cat_pdb_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/cat_pdb/390bd526-599a-4d32-8a4f-56fecbadbbe4&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_closest_residues.py::TestClosestResidues::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_closest_residues.py::TestClosestResidues::test_launch&#34;, &#34;duration&#34;: &#34;00:00:02&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_closest_residues.py::TestClosestResidues::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:02&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:41:32,214 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.closest_residues Version: 4.1.0\n2024-03-12 16:41:32,215 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/closest_residues/63c3d334-3dd9-4aee-b84e-adee46bd7f2f\n2024-03-12 16:41:32,618 [MainThread  ] [INFO ]  Found 548 nearby residues\n2024-03-12 16:41:33,986 [MainThread  ] [INFO ]  Writting pdb to: /tmp/biobb/unitests_13/closest_residues/63c3d334-3dd9-4aee-b84e-adee46bd7f2f/output_residues_path.pdb\n2024-03-12 16:41:33,989 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/closest_residues/63c3d334-3dd9-4aee-b84e-adee46bd7f2f&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/closest_residues/output_residues_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_13/closest_residues/output_residues_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_closest_residues.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 4251\n     Atoms ALIGNED in PDB_B: 4251\n     RMS: 1.931680690520553e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/closest_residues/closest_residues_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.closest_residues Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/closest_residues/closest_residues_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/closest_residues/63c3d334-3dd9-4aee-b84e-adee46bd7f2f\nINFO     /tmp/biobb/unitests_13/closest_residues/closest_residues_log.out:file_utils.py:390 Found 548 nearby residues\nINFO     /tmp/biobb/unitests_13/closest_residues/closest_residues_log.out:file_utils.py:390 Writting pdb to: /tmp/biobb/unitests_13/closest_residues/63c3d334-3dd9-4aee-b84e-adee46bd7f2f/output_residues_path.pdb\nINFO     /tmp/biobb/unitests_13/closest_residues/closest_residues_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/closest_residues/63c3d334-3dd9-4aee-b84e-adee46bd7f2f&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_gro.py::TestExtractAtomsGRO::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_gro.py::TestExtractAtomsGRO::test_launch&#34;, &#34;duration&#34;: &#34;00:00:05&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_gro.py::TestExtractAtomsGRO::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:05&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:41:34,253 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.extract_atoms Version: 4.1.0\n2024-03-12 16:41:34,257 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/G2S_stateA_frame92.sorted.gro to /tmp/biobb/unitests_13/extract_atoms_gro/5798e3fb-5fe4-4b98-ab1d-22378e2bcd37\n2024-03-12 16:41:34,257 [MainThread  ] [INFO ]  GRO format detected, extracting all atoms matching ^D\n2024-03-12 16:41:39,667 [MainThread  ] [INFO ]  4 atoms found writting GRO file\n2024-03-12 16:41:39,668 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_atoms_gro/5798e3fb-5fe4-4b98-ab1d-22378e2bcd37&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/extract_atoms_gro/output_structure_path.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_13/extract_atoms_gro/output_structure_path.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/dummy_atoms.gro\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.extract_atoms Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/G2S_stateA_frame92.sorted.gro to /tmp/biobb/unitests_13/extract_atoms_gro/5798e3fb-5fe4-4b98-ab1d-22378e2bcd37\nINFO     /tmp/biobb/unitests_13/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:390 GRO format detected, extracting all atoms matching ^D\nINFO     /tmp/biobb/unitests_13/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:390 4 atoms found writting GRO file\nINFO     /tmp/biobb/unitests_13/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_atoms_gro/5798e3fb-5fe4-4b98-ab1d-22378e2bcd37&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_pdb.py::TestExtractAtomsPDB::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_pdb.py::TestExtractAtomsPDB::test_launch&#34;, &#34;duration&#34;: &#34;73 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_pdb.py::TestExtractAtomsPDB::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;73 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:41:39,705 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.extract_atoms Version: 4.1.0\n2024-03-12 16:41:39,706 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/extract_atoms/274d547f-389f-4f04-b149-8f90e1cf183c\n2024-03-12 16:41:39,707 [MainThread  ] [INFO ]  PDB format detected, extracting all atoms matching OE2\n2024-03-12 16:41:39,735 [MainThread  ] [INFO ]  141 atoms found writting PDB file\n2024-03-12 16:41:39,735 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_atoms/274d547f-389f-4f04-b149-8f90e1cf183c&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/extract_atoms/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_13/extract_atoms/output_structure_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/OE2_atoms.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 141\n     Atoms ALIGNED in PDB_B: 141\n     RMS: 1.3133613935773403e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/extract_atoms/extract_atoms_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.extract_atoms Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/extract_atoms/extract_atoms_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/extract_atoms/274d547f-389f-4f04-b149-8f90e1cf183c\nINFO     /tmp/biobb/unitests_13/extract_atoms/extract_atoms_log.out:file_utils.py:390 PDB format detected, extracting all atoms matching OE2\nINFO     /tmp/biobb/unitests_13/extract_atoms/extract_atoms_log.out:file_utils.py:390 141 atoms found writting PDB file\nINFO     /tmp/biobb/unitests_13/extract_atoms/extract_atoms_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_atoms/274d547f-389f-4f04-b149-8f90e1cf183c&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_chain.py::TestExtractChain::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_chain.py::TestExtractChain::test_launch&#34;, &#34;duration&#34;: &#34;432 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_chain.py::TestExtractChain::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;432 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:41:39,781 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.extract_chain Version: 4.1.0\n2024-03-12 16:41:39,782 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_chain.pdb to /tmp/biobb/unitests_13/extract_chain/2ed77cd9-5989-4fb9-929f-0f37618a2f16\n2024-03-12 16:41:39,782 [MainThread  ] [INFO ]  Selected Chains: B,C\n2024-03-12 16:41:39,782 [MainThread  ] [INFO ]  Warning: Use permissive=True is a risky option use it under your own responsability\n2024-03-12 16:41:39,795 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_chain/2ed77cd9-5989-4fb9-929f-0f37618a2f16&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/extract_chain/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_13/extract_chain/output_structure_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_extract_chain.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 7893\n     Atoms ALIGNED in PDB_B: 7893\n     RMS: 1.6129351886983116e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/extract_chain/extract_chain_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.extract_chain Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/extract_chain/extract_chain_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_chain.pdb to /tmp/biobb/unitests_13/extract_chain/2ed77cd9-5989-4fb9-929f-0f37618a2f16\nINFO     /tmp/biobb/unitests_13/extract_chain/extract_chain_log.out:file_utils.py:390 Selected Chains: B,C\nINFO     /tmp/biobb/unitests_13/extract_chain/extract_chain_log.out:file_utils.py:390 Warning: Use permissive=True is a risky option use it under your own responsability\nINFO     /tmp/biobb/unitests_13/extract_chain/extract_chain_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_chain/2ed77cd9-5989-4fb9-929f-0f37618a2f16&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_heteroatom.py::TestExtractHeteroAtoms::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_heteroatom.py::TestExtractHeteroAtoms::test_launch&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_heteroatom.py::TestExtractHeteroAtoms::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:41:40,214 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.extract_heteroatoms Version: 4.1.0\n2024-03-12 16:41:40,217 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_heteroatom.pdb to /tmp/biobb/unitests_13/extract_heteroatoms/90d90d2b-8f7b-4e32-bd98-b2414c2bf3a5\n2024-03-12 16:41:41,321 [MainThread  ] [INFO ]  Writting pdb to: /tmp/biobb/unitests_13/extract_heteroatoms/90d90d2b-8f7b-4e32-bd98-b2414c2bf3a5/output_heteroatom_path.pdb\n2024-03-12 16:41:41,322 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_heteroatoms/90d90d2b-8f7b-4e32-bd98-b2414c2bf3a5&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/extract_heteroatoms/output_heteroatom_path.pdb\nComparing: \n        File_A: /tmp/biobb/unitests_13/extract_heteroatoms/output_heteroatom_path.pdb\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_extract_heteroatom.pdb\n        File_A hash: b&amp;#x27;\\x1e\\x83\\x13\\xbd\\xed\\xd0\\xcb0J\\xed\\x0eCp\\xe8\\xe2\\x91\\xf0w~x\\xd5\\x95\\xfc^9\\x83J\\x00\\x0f!^\\x04&amp;#x27;\n        File_B hash: b&amp;#x27;\\x1e\\x83\\x13\\xbd\\xed\\xd0\\xcb0J\\xed\\x0eCp\\xe8\\xe2\\x91\\xf0w~x\\xd5\\x95\\xfc^9\\x83J\\x00\\x0f!^\\x04&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/extract_heteroatoms/extract_heteroatoms_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.extract_heteroatoms Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/extract_heteroatoms/extract_heteroatoms_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_heteroatom.pdb to /tmp/biobb/unitests_13/extract_heteroatoms/90d90d2b-8f7b-4e32-bd98-b2414c2bf3a5\nINFO     /tmp/biobb/unitests_13/extract_heteroatoms/extract_heteroatoms_log.out:file_utils.py:390 Writting pdb to: /tmp/biobb/unitests_13/extract_heteroatoms/90d90d2b-8f7b-4e32-bd98-b2414c2bf3a5/output_heteroatom_path.pdb\nINFO     /tmp/biobb/unitests_13/extract_heteroatoms/extract_heteroatoms_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_heteroatoms/90d90d2b-8f7b-4e32-bd98-b2414c2bf3a5&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_model.py::TestExtractModel::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_model.py::TestExtractModel::test_launch&#34;, &#34;duration&#34;: &#34;00:00:03&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_model.py::TestExtractModel::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:03&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:41:41,357 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.extract_model Version: 4.1.0\n2024-03-12 16:41:41,359 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_model.pdb to /tmp/biobb/unitests_13/extract_model/241161f0-bb04-4e9b-b343-40a27c531821\n2024-03-12 16:41:41,359 [MainThread  ] [INFO ]  Creating 51471411-e1c1-4871-866f-b9b8ad420818 temporary folder\n2024-03-12 16:41:41,359 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_13/extract_model/241161f0-bb04-4e9b-b343-40a27c531821/extract_model.pdb -o 51471411-e1c1-4871-866f-b9b8ad420818/model1.pdb --force_save models --select 1\n\n2024-03-12 16:41:42,905 [MainThread  ] [INFO ]  Exit code 0\n\n2024-03-12 16:41:42,905 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_13/extract_model/241161f0-bb04-4e9b-b343-40a27c531821/extract_model.pdb loaded\n PDB id: 1NMR \n Title: solution structure of c-terminal domain from trypanosoma cruzi poly(a)-binding protein\n Experimental method: solution nmr\n Keywords: all helical domain, peptide binding protein\n Resolution (A): N.A.\n\n Num. models: 20 (type: Ensembl/NMR,    6.831 A)\n Num. chains: 20 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein|A/15: Protein|A/16: Protein|A/17: Protein|A/18: Protein|A/19: Protein)\n Num. residues:  1700\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 1700 (total 13080 H atoms)\n Num. HETATM residues:  0\n Num. ligands or modified residues:  0\n Num. water mol.:  0\n Num. atoms:  25800\nRunning models. Options: --select 1\nDetected 20 Model(s)\nModels  superimpose, RMSd:    6.831 A, guessed as Ensembl/NMR \nSelecting model num. 1\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  85\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 85 (total 654 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1290\nStructure saved on 51471411-e1c1-4871-866f-b9b8ad420818/model1.pdb\n\n2024-03-12 16:41:42,905 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_13/extract_model/241161f0-bb04-4e9b-b343-40a27c531821/extract_model.pdb -o 51471411-e1c1-4871-866f-b9b8ad420818/model4.pdb --force_save models --select 4\n\n2024-03-12 16:41:44,461 [MainThread  ] [INFO ]  Exit code 0\n\n2024-03-12 16:41:44,461 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_13/extract_model/241161f0-bb04-4e9b-b343-40a27c531821/extract_model.pdb loaded\n PDB id: 1NMR \n Title: solution structure of c-terminal domain from trypanosoma cruzi poly(a)-binding protein\n Experimental method: solution nmr\n Keywords: all helical domain, peptide binding protein\n Resolution (A): N.A.\n\n Num. models: 20 (type: Ensembl/NMR,    6.831 A)\n Num. chains: 20 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein|A/15: Protein|A/16: Protein|A/17: Protein|A/18: Protein|A/19: Protein)\n Num. residues:  1700\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 1700 (total 13080 H atoms)\n Num. HETATM residues:  0\n Num. ligands or modified residues:  0\n Num. water mol.:  0\n Num. atoms:  25800\nRunning models. Options: --select 4\nDetected 20 Model(s)\nModels  superimpose, RMSd:    6.831 A, guessed as Ensembl/NMR \nSelecting model num. 4\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  85\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 85 (total 654 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1290\nStructure saved on 51471411-e1c1-4871-866f-b9b8ad420818/model4.pdb\n\n2024-03-12 16:41:44,464 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_model/241161f0-bb04-4e9b-b343-40a27c531821&amp;#x27;, &amp;#x27;51471411-e1c1-4871-866f-b9b8ad420818&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/extract_model/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_13/extract_model/output_structure_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_extract_model.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 636\n     Atoms ALIGNED in PDB_B: 636\n     RMS: 5.262008214811879e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/extract_model/extract_model_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.extract_model Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/extract_model/extract_model_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_model.pdb to /tmp/biobb/unitests_13/extract_model/241161f0-bb04-4e9b-b343-40a27c531821\nINFO     /tmp/biobb/unitests_13/extract_model/extract_model_log.out:file_utils.py:390 Creating 51471411-e1c1-4871-866f-b9b8ad420818 temporary folder\nINFO     /tmp/biobb/unitests_13/extract_model/extract_model_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_13/extract_model/241161f0-bb04-4e9b-b343-40a27c531821/extract_model.pdb -o 51471411-e1c1-4871-866f-b9b8ad420818/model1.pdb --force_save models --select 1\n\nINFO     /tmp/biobb/unitests_13/extract_model/extract_model_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_13/extract_model/extract_model_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_13/extract_model/241161f0-bb04-4e9b-b343-40a27c531821/extract_model.pdb loaded\n PDB id: 1NMR \n Title: solution structure of c-terminal domain from trypanosoma cruzi poly(a)-binding protein\n Experimental method: solution nmr\n Keywords: all helical domain, peptide binding protein\n Resolution (A): N.A.\n\n Num. models: 20 (type: Ensembl/NMR,    6.831 A)\n Num. chains: 20 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein|A/15: Protein|A/16: Protein|A/17: Protein|A/18: Protein|A/19: Protein)\n Num. residues:  1700\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 1700 (total 13080 H atoms)\n Num. HETATM residues:  0\n Num. ligands or modified residues:  0\n Num. water mol.:  0\n Num. atoms:  25800\nRunning models. Options: --select 1\nDetected 20 Model(s)\nModels  superimpose, RMSd:    6.831 A, guessed as Ensembl/NMR \nSelecting model num. 1\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  85\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 85 (total 654 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1290\nStructure saved on 51471411-e1c1-4871-866f-b9b8ad420818/model1.pdb\n\nINFO     /tmp/biobb/unitests_13/extract_model/extract_model_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_13/extract_model/241161f0-bb04-4e9b-b343-40a27c531821/extract_model.pdb -o 51471411-e1c1-4871-866f-b9b8ad420818/model4.pdb --force_save models --select 4\n\nINFO     /tmp/biobb/unitests_13/extract_model/extract_model_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_13/extract_model/extract_model_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_13/extract_model/241161f0-bb04-4e9b-b343-40a27c531821/extract_model.pdb loaded\n PDB id: 1NMR \n Title: solution structure of c-terminal domain from trypanosoma cruzi poly(a)-binding protein\n Experimental method: solution nmr\n Keywords: all helical domain, peptide binding protein\n Resolution (A): N.A.\n\n Num. models: 20 (type: Ensembl/NMR,    6.831 A)\n Num. chains: 20 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein|A/15: Protein|A/16: Protein|A/17: Protein|A/18: Protein|A/19: Protein)\n Num. residues:  1700\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 1700 (total 13080 H atoms)\n Num. HETATM residues:  0\n Num. ligands or modified residues:  0\n Num. water mol.:  0\n Num. atoms:  25800\nRunning models. Options: --select 4\nDetected 20 Model(s)\nModels  superimpose, RMSd:    6.831 A, guessed as Ensembl/NMR \nSelecting model num. 4\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  85\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 85 (total 654 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1290\nStructure saved on 51471411-e1c1-4871-866f-b9b8ad420818/model4.pdb\n\nINFO     /tmp/biobb/unitests_13/extract_model/extract_model_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_model/241161f0-bb04-4e9b-b343-40a27c531821&amp;#x27;, &amp;#x27;51471411-e1c1-4871-866f-b9b8ad420818&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_molecule.py::TestExtractMolecule::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_molecule.py::TestExtractMolecule::test_launch&#34;, &#34;duration&#34;: &#34;686 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_molecule.py::TestExtractMolecule::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;686 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:41:44,602 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.extract_molecule Version: 4.1.0\n2024-03-12 16:41:44,603 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb to /tmp/biobb/unitests_13/extract_molecule/5e013476-8fd5-4229-9883-127be60e8f4a\n2024-03-12 16:41:44,603 [MainThread  ] [INFO ]  Creating 7d1a565a-3b0f-410e-b073-15015683be21 temporary folder\n2024-03-12 16:41:44,603 [MainThread  ] [INFO ]  check_structure -i /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb -o /tmp/biobb/unitests_13/extract_molecule/output_molecule_path.pdb --force_save --non_interactive command_list --list 7d1a565a-3b0f-410e-b073-15015683be21/extract_prot.lst\n\n2024-03-12 16:41:45,156 [MainThread  ] [INFO ]  Exit code 0\n\n2024-03-12 16:41:45,156 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb loaded\n PDB id: 1G54 \n Title: carbonic anhydrase ii complexed with 4-(aminosulfonyl)-n-[(2,3,4,5,6- pentafluorophenyl)methyl]-benzamide\n Experimental method: x-ray diffraction\n Keywords: carbonic anhydrase ii, 4-(aminosulfonyl)-n-[(2, 3, 4, 5, 6- pentafluorophenyl)methyl]-benzamide, lyase\n Resolution (A): 1.86\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  332\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  74\n Num. ligands or modified residues:  3\n Num. water mol.:  71\n Num. atoms:  2156\nMetal/Ion residues found\n ZN A262\n HG A263\nSmall mol ligands found\nFFB A555\n\nStep 1: ligands --remove All\n\nRunning ligands. Options: --remove All\nDetected 3 Ligands\n  ZN A262\n  HG A263\n FFB A555\nLigands removed All (3)\n\nStep 2: water --remove Yes\n\nRunning water. Options: --remove Yes\nDetected 71 Water molecules\nRemoved 71 Water molecules\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  258\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  2058\nStructure saved on /tmp/biobb/unitests_13/extract_molecule/output_molecule_path.pdb\n\n2024-03-12 16:41:45,157 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_molecule/5e013476-8fd5-4229-9883-127be60e8f4a&amp;#x27;, &amp;#x27;7d1a565a-3b0f-410e-b073-15015683be21&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/extract_molecule/output_molecule_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_13/extract_molecule/output_molecule_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_extract_molecule.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 2058\n     Atoms ALIGNED in PDB_B: 2058\n     RMS: 6.579094722437545e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/extract_molecule/extract_molecule_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.extract_molecule Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/extract_molecule/extract_molecule_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb to /tmp/biobb/unitests_13/extract_molecule/5e013476-8fd5-4229-9883-127be60e8f4a\nINFO     /tmp/biobb/unitests_13/extract_molecule/extract_molecule_log.out:file_utils.py:390 Creating 7d1a565a-3b0f-410e-b073-15015683be21 temporary folder\nINFO     /tmp/biobb/unitests_13/extract_molecule/extract_molecule_log.out:cmd_wrapper.py:33 check_structure -i /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb -o /tmp/biobb/unitests_13/extract_molecule/output_molecule_path.pdb --force_save --non_interactive command_list --list 7d1a565a-3b0f-410e-b073-15015683be21/extract_prot.lst\n\nINFO     /tmp/biobb/unitests_13/extract_molecule/extract_molecule_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_13/extract_molecule/extract_molecule_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb loaded\n PDB id: 1G54 \n Title: carbonic anhydrase ii complexed with 4-(aminosulfonyl)-n-[(2,3,4,5,6- pentafluorophenyl)methyl]-benzamide\n Experimental method: x-ray diffraction\n Keywords: carbonic anhydrase ii, 4-(aminosulfonyl)-n-[(2, 3, 4, 5, 6- pentafluorophenyl)methyl]-benzamide, lyase\n Resolution (A): 1.86\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  332\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  74\n Num. ligands or modified residues:  3\n Num. water mol.:  71\n Num. atoms:  2156\nMetal/Ion residues found\n ZN A262\n HG A263\nSmall mol ligands found\nFFB A555\n\nStep 1: ligands --remove All\n\nRunning ligands. Options: --remove All\nDetected 3 Ligands\n  ZN A262\n  HG A263\n FFB A555\nLigands removed All (3)\n\nStep 2: water --remove Yes\n\nRunning water. Options: --remove Yes\nDetected 71 Water molecules\nRemoved 71 Water molecules\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  258\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  2058\nStructure saved on /tmp/biobb/unitests_13/extract_molecule/output_molecule_path.pdb\n\nINFO     /tmp/biobb/unitests_13/extract_molecule/extract_molecule_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_molecule/5e013476-8fd5-4229-9883-127be60e8f4a&amp;#x27;, &amp;#x27;7d1a565a-3b0f-410e-b073-15015683be21&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_residues.py::TestExtractResidues::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_residues.py::TestExtractResidues::test_launch&#34;, &#34;duration&#34;: &#34;679 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_residues.py::TestExtractResidues::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;679 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:41:45,290 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.extract_residues Version: 4.1.0\n2024-03-12 16:41:45,292 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/extract_residues/025b2eef-65a9-4b52-b5b1-0fd6d4ef9afe\n2024-03-12 16:41:45,934 [MainThread  ] [INFO ]  Writting pdb to: /tmp/biobb/unitests_13/extract_residues/025b2eef-65a9-4b52-b5b1-0fd6d4ef9afe/output_residues_path.pdb\n2024-03-12 16:41:45,936 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_residues/025b2eef-65a9-4b52-b5b1-0fd6d4ef9afe&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/extract_residues/output_residues_path.pdb\nComparing: \n        File_A: /tmp/biobb/unitests_13/extract_residues/output_residues_path.pdb\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_extract_residues.pdb\n        File_A hash: b&amp;#x27;\\xf0\\x84\\xb8D\\x90whe\\xc3T\\xe2\\xf3\\\\\\xd72\\xfaT\\x9d\\x19\\x88\\xab\\x03\\xbe\\xf6\\x9a\\x81\\xec\\x15tx`D&amp;#x27;\n        File_B hash: b&amp;#x27;\\xf0\\x84\\xb8D\\x90whe\\xc3T\\xe2\\xf3\\\\\\xd72\\xfaT\\x9d\\x19\\x88\\xab\\x03\\xbe\\xf6\\x9a\\x81\\xec\\x15tx`D&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/extract_residues/extract_residues_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.extract_residues Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/extract_residues/extract_residues_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/extract_residues/025b2eef-65a9-4b52-b5b1-0fd6d4ef9afe\nINFO     /tmp/biobb/unitests_13/extract_residues/extract_residues_log.out:file_utils.py:390 Writting pdb to: /tmp/biobb/unitests_13/extract_residues/025b2eef-65a9-4b52-b5b1-0fd6d4ef9afe/output_residues_path.pdb\nINFO     /tmp/biobb/unitests_13/extract_residues/extract_residues_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_residues/025b2eef-65a9-4b52-b5b1-0fd6d4ef9afe&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_gro.py::TestRemoveLigandGro::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_gro.py::TestRemoveLigandGro::test_launch&#34;, &#34;duration&#34;: &#34;482 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_gro.py::TestRemoveLigandGro::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;482 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:41:45,971 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.remove_ligand Version: 4.1.0\n2024-03-12 16:41:45,974 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.gro to /tmp/biobb/unitests_13/remove_ligand_gro/e9a5a210-508a-4429-87c8-9dde929fd64d\n2024-03-12 16:41:45,974 [MainThread  ] [INFO ]  GRO format detected, removing all atoms from residues named AQ4\n2024-03-12 16:41:46,379 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/remove_ligand_gro/e9a5a210-508a-4429-87c8-9dde929fd64d&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/remove_ligand_gro/output_structure_path.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_13/remove_ligand_gro/output_structure_path.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/WT_apo_md_1.gro\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/remove_ligand_gro/remove_ligand_gro_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.remove_ligand Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/remove_ligand_gro/remove_ligand_gro_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.gro to /tmp/biobb/unitests_13/remove_ligand_gro/e9a5a210-508a-4429-87c8-9dde929fd64d\nINFO     /tmp/biobb/unitests_13/remove_ligand_gro/remove_ligand_gro_log.out:file_utils.py:390 GRO format detected, removing all atoms from residues named AQ4\nINFO     /tmp/biobb/unitests_13/remove_ligand_gro/remove_ligand_gro_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/remove_ligand_gro/e9a5a210-508a-4429-87c8-9dde929fd64d&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_pdb.py::TestRemoveLigandPDB::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_pdb.py::TestRemoveLigandPDB::test_launch&#34;, &#34;duration&#34;: &#34;00:00:03&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_pdb.py::TestRemoveLigandPDB::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:03&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:41:46,492 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.remove_ligand Version: 4.1.0\n2024-03-12 16:41:46,495 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.pdb to /tmp/biobb/unitests_13/remove_ligand/e99b7b16-c780-4a72-9dcd-a5bac4422773\n2024-03-12 16:41:46,495 [MainThread  ] [INFO ]  PDB format detected, removing all atoms from residues named AQ4\n2024-03-12 16:41:46,542 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/remove_ligand/e99b7b16-c780-4a72-9dcd-a5bac4422773&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/remove_ligand/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_13/remove_ligand/output_structure_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/WT_apo_md_1.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 12872\n     Atoms ALIGNED in PDB_B: 12872\n     RMS: 1.549802168438611e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/remove_ligand/remove_ligand_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.remove_ligand Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/remove_ligand/remove_ligand_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.pdb to /tmp/biobb/unitests_13/remove_ligand/e99b7b16-c780-4a72-9dcd-a5bac4422773\nINFO     /tmp/biobb/unitests_13/remove_ligand/remove_ligand_log.out:file_utils.py:390 PDB format detected, removing all atoms from residues named AQ4\nINFO     /tmp/biobb/unitests_13/remove_ligand/remove_ligand_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/remove_ligand/e99b7b16-c780-4a72-9dcd-a5bac4422773&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_molecules.py::TestRemoveMolecules::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_molecules.py::TestRemoveMolecules::test_launch&#34;, &#34;duration&#34;: &#34;00:00:06&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_remove_molecules.py::TestRemoveMolecules::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:06&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:41:49,423 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.remove_molecules Version: 4.1.0\n2024-03-12 16:41:49,424 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/remove_molecules/4a4202df-464f-40f0-9cdd-4e7b251254f6\n2024-03-12 16:41:55,066 [MainThread  ] [INFO ]  Writting pdb to: /tmp/biobb/unitests_13/remove_molecules/4a4202df-464f-40f0-9cdd-4e7b251254f6/output_molecules_path.pdb\n2024-03-12 16:41:55,073 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/remove_molecules/4a4202df-464f-40f0-9cdd-4e7b251254f6&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/remove_molecules/output_molecules_path.pdb\nComparing: \n        File_A: /tmp/biobb/unitests_13/remove_molecules/output_molecules_path.pdb\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_remove_molecules.pdb\n        File_A hash: b&amp;#x27;q$\\x11\\xa5u\\xca5\\xc0\\x90\\xd8\\x1bB&amp;amp;{\\xfcNm\\x85\\xb5(\\x8f\\x13\\xf0\\xef,\\xe6\\x8c\\x0ftV}\\x1d&amp;#x27;\n        File_B hash: b&amp;#x27;q$\\x11\\xa5u\\xca5\\xc0\\x90\\xd8\\x1bB&amp;amp;{\\xfcNm\\x85\\xb5(\\x8f\\x13\\xf0\\xef,\\xe6\\x8c\\x0ftV}\\x1d&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/remove_molecules/remove_molecules_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.remove_molecules Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/remove_molecules/remove_molecules_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/remove_molecules/4a4202df-464f-40f0-9cdd-4e7b251254f6\nINFO     /tmp/biobb/unitests_13/remove_molecules/remove_molecules_log.out:file_utils.py:390 Writting pdb to: /tmp/biobb/unitests_13/remove_molecules/4a4202df-464f-40f0-9cdd-4e7b251254f6/output_molecules_path.pdb\nINFO     /tmp/biobb/unitests_13/remove_molecules/remove_molecules_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/remove_molecules/4a4202df-464f-40f0-9cdd-4e7b251254f6&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_pdb_water.py::TestRemovePDBWater::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_pdb_water.py::TestRemovePDBWater::test_launch&#34;, &#34;duration&#34;: &#34;827 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_remove_pdb_water.py::TestRemovePDBWater::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;827 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:41:55,114 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.remove_pdb_water Version: 4.1.0\n2024-03-12 16:41:55,115 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_WAT.pdb to /tmp/biobb/unitests_13/remove_pdb_water/58d58fc7-c783-4d37-823f-36fa84517e50\n2024-03-12 16:41:55,115 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_13/remove_pdb_water/58d58fc7-c783-4d37-823f-36fa84517e50/WT_aq4_md_WAT.pdb -o /tmp/biobb/unitests_13/remove_pdb_water/58d58fc7-c783-4d37-823f-36fa84517e50/output_pdb_path.pdb --force_save water --remove yes\n\n2024-03-12 16:41:55,700 [MainThread  ] [INFO ]  Exit code 0\n\n2024-03-12 16:41:55,700 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_13/remove_pdb_water/58d58fc7-c783-4d37-823f-36fa84517e50/WT_aq4_md_WAT.pdb loaded\n PDB id:  \n Title: protein in water\n Experimental method: unknown\n Resolution (A): N.A.\n\n Num. models: 1\n Num. chains: 3 ( : Unknown, A: Protein, B: Unknown)\n Num. residues:  397\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 294 (total 2404 H atoms)\n Num. HETATM residues:  2\n Num. ligands or modified residues:  0\n Num. water mol.:  2\n Num. atoms:  4858\nRunning water. Options: --remove yes\nDetected 2 Water molecules\nRemoved 2 Water molecules\nFinal Num. models: 1\nFinal Num. chains: 3 ( : Unknown, A: Protein, B: Unknown)\nFinal Num. residues:  395\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 292 (total 2401 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  4853\nStructure saved on /tmp/biobb/unitests_13/remove_pdb_water/58d58fc7-c783-4d37-823f-36fa84517e50/output_pdb_path.pdb\n\n2024-03-12 16:41:55,701 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/remove_pdb_water/58d58fc7-c783-4d37-823f-36fa84517e50&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/remove_pdb_water/output_pdb_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_13/remove_pdb_water/output_pdb_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/WT_apo_no_wat.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 3004\n     Atoms ALIGNED in PDB_B: 3004\n     RMS: 1.3997192439430224e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/remove_pdb_water/remove_pdb_water_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.remove_pdb_water Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/remove_pdb_water/remove_pdb_water_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_WAT.pdb to /tmp/biobb/unitests_13/remove_pdb_water/58d58fc7-c783-4d37-823f-36fa84517e50\nINFO     /tmp/biobb/unitests_13/remove_pdb_water/remove_pdb_water_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_13/remove_pdb_water/58d58fc7-c783-4d37-823f-36fa84517e50/WT_aq4_md_WAT.pdb -o /tmp/biobb/unitests_13/remove_pdb_water/58d58fc7-c783-4d37-823f-36fa84517e50/output_pdb_path.pdb --force_save water --remove yes\n\nINFO     /tmp/biobb/unitests_13/remove_pdb_water/remove_pdb_water_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_13/remove_pdb_water/remove_pdb_water_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_13/remove_pdb_water/58d58fc7-c783-4d37-823f-36fa84517e50/WT_aq4_md_WAT.pdb loaded\n PDB id:  \n Title: protein in water\n Experimental method: unknown\n Resolution (A): N.A.\n\n Num. models: 1\n Num. chains: 3 ( : Unknown, A: Protein, B: Unknown)\n Num. residues:  397\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 294 (total 2404 H atoms)\n Num. HETATM residues:  2\n Num. ligands or modified residues:  0\n Num. water mol.:  2\n Num. atoms:  4858\nRunning water. Options: --remove yes\nDetected 2 Water molecules\nRemoved 2 Water molecules\nFinal Num. models: 1\nFinal Num. chains: 3 ( : Unknown, A: Protein, B: Unknown)\nFinal Num. residues:  395\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 292 (total 2401 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  4853\nStructure saved on /tmp/biobb/unitests_13/remove_pdb_water/58d58fc7-c783-4d37-823f-36fa84517e50/output_pdb_path.pdb\n\nINFO     /tmp/biobb/unitests_13/remove_pdb_water/remove_pdb_water_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/remove_pdb_water/58d58fc7-c783-4d37-823f-36fa84517e50&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_2vgb.py::TestRenumberStructure2VGB::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_2vgb.py::TestRenumberStructure2VGB::test_launch&#34;, &#34;duration&#34;: &#34;952 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_2vgb.py::TestRenumberStructure2VGB::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;952 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:41:56,000 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.renumber_structure Version: 4.1.0\n2024-03-12 16:41:56,002 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/renumber_structure_2vgb/3596b78e-6903-49bf-9113-b9a80f662709\n2024-03-12 16:41:56,002 [MainThread  ] [INFO ]  PDB format detected, reenumerating atoms\n2024-03-12 16:41:56,070 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/renumber_structure_2vgb/3596b78e-6903-49bf-9113-b9a80f662709&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/renumber_structure_2vgb/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_13/renumber_structure_2vgb/output_structure_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_2vgb.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 15488\n     Atoms ALIGNED in PDB_B: 15488\n     RMS: 1.871093208699659e-14\n     RMS_CUTOFF: 1\nChecking if empty file: /tmp/biobb/unitests_13/renumber_structure_2vgb/output_mapping_json_path.json\nComparing: \n        File_A: /tmp/biobb/unitests_13/renumber_structure_2vgb/output_mapping_json_path.json\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/2vgb_output_mapping_json_path.json\n        File_A hash: b&amp;#x27;F\\xbe!`V\\xdb.\\x99\\xfb\\xda\\x94\\xb1\\xa8\\xdf6\\xbcJ\\\\\\\\\\xc7k\\xb6\\xe9\\xc1I\\nm\\xc1\\xe4:v\\x15&amp;#x27;\n        File_B hash: b&amp;#x27;F\\xbe!`V\\xdb.\\x99\\xfb\\xda\\x94\\xb1\\xa8\\xdf6\\xbcJ\\\\\\\\\\xc7k\\xb6\\xe9\\xc1I\\nm\\xc1\\xe4:v\\x15&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/renumber_structure_2vgb/renumber_structure_2vgb_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.renumber_structure Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/renumber_structure_2vgb/renumber_structure_2vgb_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/renumber_structure_2vgb/3596b78e-6903-49bf-9113-b9a80f662709\nINFO     /tmp/biobb/unitests_13/renumber_structure_2vgb/renumber_structure_2vgb_log.out:file_utils.py:390 PDB format detected, reenumerating atoms\nINFO     /tmp/biobb/unitests_13/renumber_structure_2vgb/renumber_structure_2vgb_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/renumber_structure_2vgb/3596b78e-6903-49bf-9113-b9a80f662709&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_gro.py::TestRenumberStructureGRO::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_gro.py::TestRenumberStructureGRO::test_launch&#34;, &#34;duration&#34;: &#34;154 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_gro.py::TestRenumberStructureGRO::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;154 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:41:56,898 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.renumber_structure Version: 4.1.0\n2024-03-12 16:41:56,899 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/pyruvate.gro to /tmp/biobb/unitests_13/renumber_structure_gro/820bf1f9-79bf-49d6-98f3-8b9632225da5\n2024-03-12 16:41:56,899 [MainThread  ] [INFO ]  GRO format detected, reenumerating atoms\n2024-03-12 16:41:57,011 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/renumber_structure_gro/820bf1f9-79bf-49d6-98f3-8b9632225da5&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/renumber_structure_gro/output_structure_path.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_13/renumber_structure_gro/output_structure_path.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/renum_pyruvate.gro\nChecking if empty file: /tmp/biobb/unitests_13/renumber_structure_gro/output_mapping_json_path.json\nComparing: \n        File_A: /tmp/biobb/unitests_13/renumber_structure_gro/output_mapping_json_path.json\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/pyruvate_output_mapping_json_path.json\n        File_A hash: b&amp;#x27;/\\xa1\\xe9\\x19X\\xe3\\xb5\\x15R \\x81\\x02\\xc4PX\\x11h\\x08\\x83\\xdb\\r\\xf9j\\xebP\\xe9\\\\\\x1eT#A\\r&amp;#x27;\n        File_B hash: b&amp;#x27;/\\xa1\\xe9\\x19X\\xe3\\xb5\\x15R \\x81\\x02\\xc4PX\\x11h\\x08\\x83\\xdb\\r\\xf9j\\xebP\\xe9\\\\\\x1eT#A\\r&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/renumber_structure_gro/renumber_structure_gro_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.renumber_structure Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/renumber_structure_gro/renumber_structure_gro_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/pyruvate.gro to /tmp/biobb/unitests_13/renumber_structure_gro/820bf1f9-79bf-49d6-98f3-8b9632225da5\nINFO     /tmp/biobb/unitests_13/renumber_structure_gro/renumber_structure_gro_log.out:file_utils.py:390 GRO format detected, reenumerating atoms\nINFO     /tmp/biobb/unitests_13/renumber_structure_gro/renumber_structure_gro_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/renumber_structure_gro/820bf1f9-79bf-49d6-98f3-8b9632225da5&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_pdb.py::TestRenumberStructurePDB::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_pdb.py::TestRenumberStructurePDB::test_launch&#34;, &#34;duration&#34;: &#34;35 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_pdb.py::TestRenumberStructurePDB::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;35 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:41:57,052 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.renumber_structure Version: 4.1.0\n2024-03-12 16:41:57,053 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cl3.noH.pdb to /tmp/biobb/unitests_13/renumber_structure/09150834-bb17-4bb1-a028-0d25eccee5df\n2024-03-12 16:41:57,053 [MainThread  ] [INFO ]  PDB format detected, reenumerating atoms\n2024-03-12 16:41:57,054 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/renumber_structure/09150834-bb17-4bb1-a028-0d25eccee5df&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/renumber_structure/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_13/renumber_structure/output_structure_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/renum_cl3_noH.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 28\n     Atoms ALIGNED in PDB_B: 28\n     RMS: 1.89900533991096e-15\n     RMS_CUTOFF: 1\nChecking if empty file: /tmp/biobb/unitests_13/renumber_structure/output_mapping_json_path.json\nComparing: \n        File_A: /tmp/biobb/unitests_13/renumber_structure/output_mapping_json_path.json\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/cl3_output_mapping_json_path.json\n        File_A hash: b&amp;#x27;\\xe5\\xbc\\xaf\\xec\\xc4\\x1a\\x14\\x1d&amp;gt;\\x1f\\xe1\\x1a\\xbe_\\xd5g\\xb6\\xac\\xeb\\xce\\x9a\\xa4\\x9f\\xa7\\xf9\\x98\\xc7\\x00\\xaa\\xa2\\t\\x13&amp;#x27;\n        File_B hash: b&amp;#x27;\\xe5\\xbc\\xaf\\xec\\xc4\\x1a\\x14\\x1d&amp;gt;\\x1f\\xe1\\x1a\\xbe_\\xd5g\\xb6\\xac\\xeb\\xce\\x9a\\xa4\\x9f\\xa7\\xf9\\x98\\xc7\\x00\\xaa\\xa2\\t\\x13&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/renumber_structure/renumber_structure_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.renumber_structure Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/renumber_structure/renumber_structure_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cl3.noH.pdb to /tmp/biobb/unitests_13/renumber_structure/09150834-bb17-4bb1-a028-0d25eccee5df\nINFO     /tmp/biobb/unitests_13/renumber_structure/renumber_structure_log.out:file_utils.py:390 PDB format detected, reenumerating atoms\nINFO     /tmp/biobb/unitests_13/renumber_structure/renumber_structure_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/renumber_structure/09150834-bb17-4bb1-a028-0d25eccee5df&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_smallgro.py::TestRenumberStructureSMALLGRO::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_smallgro.py::TestRenumberStructureSMALLGRO::test_launch&#34;, &#34;duration&#34;: &#34;34 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_smallgro.py::TestRenumberStructureSMALLGRO::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;34 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:41:57,089 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.renumber_structure Version: 4.1.0\n2024-03-12 16:41:57,090 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/smallgro.gro to /tmp/biobb/unitests_13/renumber_structure_smallgro/83653e03-cd31-470d-86db-4c2279da83c5\n2024-03-12 16:41:57,090 [MainThread  ] [INFO ]  GRO format detected, reenumerating atoms\n2024-03-12 16:41:57,091 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/renumber_structure_smallgro/83653e03-cd31-470d-86db-4c2279da83c5&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/renumber_structure_smallgro/output_structure_path.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_13/renumber_structure_smallgro/output_structure_path.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/renum_smallgro.gro\nChecking if empty file: /tmp/biobb/unitests_13/renumber_structure_smallgro/output_mapping_json_path.json\nComparing: \n        File_A: /tmp/biobb/unitests_13/renumber_structure_smallgro/output_mapping_json_path.json\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/smallgro_output_mapping_json_path.json\n        File_A hash: b&amp;#x27;\\x8a\\t\\xfd\\xe8\\x8f@K\\xafz\\xd2\\x8dO\\xed[\\xe0\\xcchg\\xda\\xd7\\x13\\xb4\\x0c\\xcf3\\rNRg,\\xaf\\xf4&amp;#x27;\n        File_B hash: b&amp;#x27;\\x8a\\t\\xfd\\xe8\\x8f@K\\xafz\\xd2\\x8dO\\xed[\\xe0\\xcchg\\xda\\xd7\\x13\\xb4\\x0c\\xcf3\\rNRg,\\xaf\\xf4&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/renumber_structure_smallgro/renumber_structure_smallgro_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.renumber_structure Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/renumber_structure_smallgro/renumber_structure_smallgro_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/smallgro.gro to /tmp/biobb/unitests_13/renumber_structure_smallgro/83653e03-cd31-470d-86db-4c2279da83c5\nINFO     /tmp/biobb/unitests_13/renumber_structure_smallgro/renumber_structure_smallgro_log.out:file_utils.py:390 GRO format detected, reenumerating atoms\nINFO     /tmp/biobb/unitests_13/renumber_structure_smallgro/renumber_structure_smallgro_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/renumber_structure_smallgro/83653e03-cd31-470d-86db-4c2279da83c5&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_sort_gro_residues.py::TestSortGroResidues::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_sort_gro_residues.py::TestSortGroResidues::test_launch&#34;, &#34;duration&#34;: &#34;00:00:05&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_sort_gro_residues.py::TestSortGroResidues::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:05&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:41:57,124 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.sort_gro_residues Version: 4.1.0\n2024-03-12 16:41:57,127 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.gro to /tmp/biobb/unitests_13/sort_gro_residues/638a58e5-8407-4191-afdf-3c5dabc22842\n2024-03-12 16:42:01,844 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/sort_gro_residues/638a58e5-8407-4191-afdf-3c5dabc22842&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/sort_gro_residues/output_gro_path.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_13/sort_gro_residues/output_gro_path.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/WT_aq4_md_sorted.gro\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/sort_gro_residues/sort_gro_residues_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.sort_gro_residues Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/sort_gro_residues/sort_gro_residues_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.gro to /tmp/biobb/unitests_13/sort_gro_residues/638a58e5-8407-4191-afdf-3c5dabc22842\nINFO     /tmp/biobb/unitests_13/sort_gro_residues/sort_gro_residues_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/sort_gro_residues/638a58e5-8407-4191-afdf-3c5dabc22842&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_str_check_add_hydrogens.py::TestStrCheckAddHydrogens::test_str_check_add_hydrogens&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_str_check_add_hydrogens.py::TestStrCheckAddHydrogens::test_str_check_add_hydrogens&#34;, &#34;duration&#34;: &#34;988 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_str_check_add_hydrogens.py::TestStrCheckAddHydrogens::test_str_check_add_hydrogens&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;988 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:42:01,916 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.str_check_add_hydrogens Version: 4.1.0\n2024-03-12 16:42:01,917 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/str_no_H.pdb to /tmp/biobb/unitests_13/str_check_add_hydrogens/3c2c17c4-38bc-4d14-90f7-03e8c59087ba\n2024-03-12 16:42:01,917 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_13/str_check_add_hydrogens/3c2c17c4-38bc-4d14-90f7-03e8c59087ba/str_no_H.pdb -o /tmp/biobb/unitests_13/str_check_add_hydrogens/3c2c17c4-38bc-4d14-90f7-03e8c59087ba/output_structure_path.pdbqt --non_interactive --force_save --keep_canonical_resnames command_list --list &amp;#x27;add_hydrogen --add_charges ADT --add_mode auto &amp;#x27;\n\n2024-03-12 16:42:02,840 [MainThread  ] [INFO ]  Exit code 0\n\n2024-03-12 16:42:02,840 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_13/str_check_add_hydrogens/3c2c17c4-38bc-4d14-90f7-03e8c59087ba/str_no_H.pdb loaded\n PDB id:  \n Title: \n Experimental method: unknown\n Resolution (A): N.A.\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  532\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  15\n Num. ligands or modified residues:  3\n Num. water mol.:  12\n Num. atoms:  3946\nMetal/Ion residues found\n  K A582\n MN A583\nSmall mol ligands found\nFBP A580\n\nStep 1: add_hydrogen --add_charges ADT --add_mode auto \nRunning add_hydrogen. Options: --add_charges ADT --add_mode auto\nFound 143 Residues requiring selection on adding H atoms\nWARNING: fixing side chains, override with --no_fix_side\nRunning fixside. Options: --fix all\nFound no residues with missing or unknown side chain atoms\nSelection: auto\nReplacing HIS A72 by HIE\nReplacing HIS A121 by HIE\nReplacing HIS A124 by HIE\nReplacing HIS A127 by HIE\nReplacing HIS A278 by HIE\nReplacing HIS A306 by HIE\nReplacing HIS A317 by HIE\nReplacing HIS A422 by HIE\nReplacing HIS A434 by HIE\nReplacing HIS A507 by HIE\nUpdating partial charges and atom types\nWarning: OXT atom missing in CILE A573. Run backbone --fix_atoms first\nWarning: FBP not found in residue library atom, charges set to 0.\nWarning: K not found in residue library atom, charges set to 0.\nWarning: MN not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nTotal assigned charge:      -1.25\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  532\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 517 (total 3995 H atoms)\nFinal Num. HETATM residues:  15\nFinal Num. ligands or modified residues:  3\nFinal Num. water mol.:  12\nFinal Num. atoms:  7941\nMetal/Ion residues found\n  K A582\n MN A583\nSmall mol ligands found\nFBP A580\nWarning: reverting residue names to canonical on output\nStructure saved on /tmp/biobb/unitests_13/str_check_add_hydrogens/3c2c17c4-38bc-4d14-90f7-03e8c59087ba/output_structure_path.pdbqt\n\n2024-03-12 16:42:02,845 [MainThread  ] [INFO ]  /tmp/biobb/unitests_13/str_check_add_hydrogens/output_structure_path.pdbqt file ends with END, cleaning\n2024-03-12 16:42:02,849 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/str_check_add_hydrogens/3c2c17c4-38bc-4d14-90f7-03e8c59087ba&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/str_check_add_hydrogens/output_structure_path.pdbqt\nComparing: \n        File_A: /tmp/biobb/unitests_13/str_check_add_hydrogens/output_structure_path.pdbqt\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_str_H.pdbqt\n        File_A hash: b&amp;quot;U\\xd1\\xc0c\\xb8\\xe3(\\xac\\xf0&amp;#x27;\\xc0\\xc4P\\xd6\\x1f\\x08\\xd1\\xa2\\xd5j\\xa5\\xef\\xc9&amp;amp;\\xedoq\\x9fM\\xa0\\x88F&amp;quot;\n        File_B hash: b&amp;quot;U\\xd1\\xc0c\\xb8\\xe3(\\xac\\xf0&amp;#x27;\\xc0\\xc4P\\xd6\\x1f\\x08\\xd1\\xa2\\xd5j\\xa5\\xef\\xc9&amp;amp;\\xedoq\\x9fM\\xa0\\x88F&amp;quot;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/str_check_add_hydrogens/str_check_add_hydrogens_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.str_check_add_hydrogens Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/str_check_add_hydrogens/str_check_add_hydrogens_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/str_no_H.pdb to /tmp/biobb/unitests_13/str_check_add_hydrogens/3c2c17c4-38bc-4d14-90f7-03e8c59087ba\nINFO     /tmp/biobb/unitests_13/str_check_add_hydrogens/str_check_add_hydrogens_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_13/str_check_add_hydrogens/3c2c17c4-38bc-4d14-90f7-03e8c59087ba/str_no_H.pdb -o /tmp/biobb/unitests_13/str_check_add_hydrogens/3c2c17c4-38bc-4d14-90f7-03e8c59087ba/output_structure_path.pdbqt --non_interactive --force_save --keep_canonical_resnames command_list --list &amp;#x27;add_hydrogen --add_charges ADT --add_mode auto &amp;#x27;\n\nINFO     /tmp/biobb/unitests_13/str_check_add_hydrogens/str_check_add_hydrogens_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_13/str_check_add_hydrogens/str_check_add_hydrogens_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_13/str_check_add_hydrogens/3c2c17c4-38bc-4d14-90f7-03e8c59087ba/str_no_H.pdb loaded\n PDB id:  \n Title: \n Experimental method: unknown\n Resolution (A): N.A.\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  532\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  15\n Num. ligands or modified residues:  3\n Num. water mol.:  12\n Num. atoms:  3946\nMetal/Ion residues found\n  K A582\n MN A583\nSmall mol ligands found\nFBP A580\n\nStep 1: add_hydrogen --add_charges ADT --add_mode auto \nRunning add_hydrogen. Options: --add_charges ADT --add_mode auto\nFound 143 Residues requiring selection on adding H atoms\nWARNING: fixing side chains, override with --no_fix_side\nRunning fixside. Options: --fix all\nFound no residues with missing or unknown side chain atoms\nSelection: auto\nReplacing HIS A72 by HIE\nReplacing HIS A121 by HIE\nReplacing HIS A124 by HIE\nReplacing HIS A127 by HIE\nReplacing HIS A278 by HIE\nReplacing HIS A306 by HIE\nReplacing HIS A317 by HIE\nReplacing HIS A422 by HIE\nReplacing HIS A434 by HIE\nReplacing HIS A507 by HIE\nUpdating partial charges and atom types\nWarning: OXT atom missing in CILE A573. Run backbone --fix_atoms first\nWarning: FBP not found in residue library atom, charges set to 0.\nWarning: K not found in residue library atom, charges set to 0.\nWarning: MN not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nTotal assigned charge:      -1.25\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  532\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 517 (total 3995 H atoms)\nFinal Num. HETATM residues:  15\nFinal Num. ligands or modified residues:  3\nFinal Num. water mol.:  12\nFinal Num. atoms:  7941\nMetal/Ion residues found\n  K A582\n MN A583\nSmall mol ligands found\nFBP A580\nWarning: reverting residue names to canonical on output\nStructure saved on /tmp/biobb/unitests_13/str_check_add_hydrogens/3c2c17c4-38bc-4d14-90f7-03e8c59087ba/output_structure_path.pdbqt\n\nINFO     /tmp/biobb/unitests_13/str_check_add_hydrogens/str_check_add_hydrogens_log.out:file_utils.py:390 /tmp/biobb/unitests_13/str_check_add_hydrogens/output_structure_path.pdbqt file ends with END, cleaning\nINFO     /tmp/biobb/unitests_13/str_check_add_hydrogens/str_check_add_hydrogens_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/str_check_add_hydrogens/3c2c17c4-38bc-4d14-90f7-03e8c59087ba&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_structure_check.py::TestStructureCheck::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_structure_check.py::TestStructureCheck::test_launch&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_structure_check.py::TestStructureCheck::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:42:02,907 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.structure_check Version: 4.1.0\n2024-03-12 16:42:02,909 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/structure_check/6f7693b3-5023-42a4-88ba-03874ca7b3ef\n2024-03-12 16:42:02,909 [MainThread  ] [INFO ]  Computing features: chains, models\n2024-03-12 16:42:02,909 [MainThread  ] [INFO ]  Creating db2f043b-c229-4b86-ab01-156ba34588be temporary folder\n2024-03-12 16:42:02,909 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_13/structure_check/6f7693b3-5023-42a4-88ba-03874ca7b3ef/2vgb.pdb --json /tmp/biobb/unitests_13/structure_check/6f7693b3-5023-42a4-88ba-03874ca7b3ef/output_summary_path.json --check_only --non_interactive command_list --list db2f043b-c229-4b86-ab01-156ba34588be/command_list.lst\n\n2024-03-12 16:42:03,989 [MainThread  ] [INFO ]  Exit code 0\n\n2024-03-12 16:42:03,989 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_13/structure_check/6f7693b3-5023-42a4-88ba-03874ca7b3ef/2vgb.pdb loaded\n PDB id: 2VGB \n Title: human erythrocyte pyruvate kinase\n Experimental method: x-ray diffraction\n Keywords: metal-binding, phosphorylation, pyruvate kinase in the active r- state, kinase, pyruvate, magnesium, glycolysis, transferase, disease mutation\n Resolution (A): 2.73\n\n Num. models: 1\n Num. chains: 4 (A: Protein, B: Protein, C: Protein, D: Protein)\n Num. residues:  2118\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  81\n Num. ligands or modified residues:  16\n Num. water mol.:  65\n Num. atoms:  15612\nMetal/Ion residues found\n  K A582\n MN A583\n  K B586\n MN B587\n  K C590\n MN C591\n  K D594\n MN D595\nSmall mol ligands found\nFBP A580\nPGA A581\nFBP B580\nPGA B581\nFBP C580\nPGA C581\nFBP D580\nPGA D581\n\nStep 1: chains\n\nRunning chains.\nDetected 4 Chain(s)\n A: Protein\n B: Protein\n C: Protein\n D: Protein\n\nStep 2: models\n\nRunning models.\nDetected 1 Model(s)\nFound Single model\nCommand list completed\nSummary data saved on /tmp/biobb/unitests_13/structure_check/6f7693b3-5023-42a4-88ba-03874ca7b3ef/output_summary_path.json\n\n2024-03-12 16:42:03,990 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/structure_check/6f7693b3-5023-42a4-88ba-03874ca7b3ef&amp;#x27;, &amp;#x27;db2f043b-c229-4b86-ab01-156ba34588be&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/structure_check/output_summary_path.json\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/structure_check/structure_check_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.structure_check Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/structure_check/structure_check_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/structure_check/6f7693b3-5023-42a4-88ba-03874ca7b3ef\nINFO     /tmp/biobb/unitests_13/structure_check/structure_check_log.out:file_utils.py:390 Computing features: chains, models\nINFO     /tmp/biobb/unitests_13/structure_check/structure_check_log.out:file_utils.py:390 Creating db2f043b-c229-4b86-ab01-156ba34588be temporary folder\nINFO     /tmp/biobb/unitests_13/structure_check/structure_check_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_13/structure_check/6f7693b3-5023-42a4-88ba-03874ca7b3ef/2vgb.pdb --json /tmp/biobb/unitests_13/structure_check/6f7693b3-5023-42a4-88ba-03874ca7b3ef/output_summary_path.json --check_only --non_interactive command_list --list db2f043b-c229-4b86-ab01-156ba34588be/command_list.lst\n\nINFO     /tmp/biobb/unitests_13/structure_check/structure_check_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_13/structure_check/structure_check_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_13/structure_check/6f7693b3-5023-42a4-88ba-03874ca7b3ef/2vgb.pdb loaded\n PDB id: 2VGB \n Title: human erythrocyte pyruvate kinase\n Experimental method: x-ray diffraction\n Keywords: metal-binding, phosphorylation, pyruvate kinase in the active r- state, kinase, pyruvate, magnesium, glycolysis, transferase, disease mutation\n Resolution (A): 2.73\n\n Num. models: 1\n Num. chains: 4 (A: Protein, B: Protein, C: Protein, D: Protein)\n Num. residues:  2118\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  81\n Num. ligands or modified residues:  16\n Num. water mol.:  65\n Num. atoms:  15612\nMetal/Ion residues found\n  K A582\n MN A583\n  K B586\n MN B587\n  K C590\n MN C591\n  K D594\n MN D595\nSmall mol ligands found\nFBP A580\nPGA A581\nFBP B580\nPGA B581\nFBP C580\nPGA C581\nFBP D580\nPGA D581\n\nStep 1: chains\n\nRunning chains.\nDetected 4 Chain(s)\n A: Protein\n B: Protein\n C: Protein\n D: Protein\n\nStep 2: models\n\nRunning models.\nDetected 1 Model(s)\nFound Single model\nCommand list completed\nSummary data saved on /tmp/biobb/unitests_13/structure_check/6f7693b3-5023-42a4-88ba-03874ca7b3ef/output_summary_path.json\n\nINFO     /tmp/biobb/unitests_13/structure_check/structure_check_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/structure_check/6f7693b3-5023-42a4-88ba-03874ca7b3ef&amp;#x27;, &amp;#x27;db2f043b-c229-4b86-ab01-156ba34588be&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
+    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.10.13&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-159-generic-x86_64-with-glibc2.31&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.1.1&#34;, &#34;pluggy&#34;: &#34;1.4.0&#34;}, &#34;Plugins&#34;: {&#34;cov&#34;: &#34;4.1.0&#34;, &#34;metadata&#34;: &#34;3.1.1&#34;, &#34;html&#34;: &#34;4.1.1&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_structure_utils/test/unitests/test_utils/test_cat_pdb.py::TestCatPDB::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_cat_pdb.py::TestCatPDB::test_launch&#34;, &#34;duration&#34;: &#34;125 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_cat_pdb.py::TestCatPDB::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;125 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:43:41,342 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.cat_pdb Version: 4.1.0\n2024-03-12 16:43:41,343 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cat_protein.pdb to /tmp/biobb/unitests_13/cat_pdb/c692938a-5434-40f9-a64a-e1d7ba121da6\n2024-03-12 16:43:41,343 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cat_ligand.pdb to /tmp/biobb/unitests_13/cat_pdb/c692938a-5434-40f9-a64a-e1d7ba121da6\n2024-03-12 16:43:41,345 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/cat_pdb/c692938a-5434-40f9-a64a-e1d7ba121da6&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/cat_pdb/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_13/cat_pdb/output_structure_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_cat_pdb.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 2058\n     Atoms ALIGNED in PDB_B: 2058\n     RMS: 6.579094722437545e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/cat_pdb/cat_pdb_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.cat_pdb Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/cat_pdb/cat_pdb_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cat_protein.pdb to /tmp/biobb/unitests_13/cat_pdb/c692938a-5434-40f9-a64a-e1d7ba121da6\nINFO     /tmp/biobb/unitests_13/cat_pdb/cat_pdb_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cat_ligand.pdb to /tmp/biobb/unitests_13/cat_pdb/c692938a-5434-40f9-a64a-e1d7ba121da6\nINFO     /tmp/biobb/unitests_13/cat_pdb/cat_pdb_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/cat_pdb/c692938a-5434-40f9-a64a-e1d7ba121da6&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_closest_residues.py::TestClosestResidues::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_closest_residues.py::TestClosestResidues::test_launch&#34;, &#34;duration&#34;: &#34;00:00:02&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_closest_residues.py::TestClosestResidues::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:02&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:43:41,476 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.closest_residues Version: 4.1.0\n2024-03-12 16:43:41,477 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/closest_residues/9af41662-4162-4c36-86e3-c82bcc4c2ac2\n2024-03-12 16:43:41,855 [MainThread  ] [INFO ]  Found 548 nearby residues\n2024-03-12 16:43:43,264 [MainThread  ] [INFO ]  Writting pdb to: /tmp/biobb/unitests_13/closest_residues/9af41662-4162-4c36-86e3-c82bcc4c2ac2/output_residues_path.pdb\n2024-03-12 16:43:43,267 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/closest_residues/9af41662-4162-4c36-86e3-c82bcc4c2ac2&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/closest_residues/output_residues_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_13/closest_residues/output_residues_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_closest_residues.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 4251\n     Atoms ALIGNED in PDB_B: 4251\n     RMS: 1.931680690520553e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/closest_residues/closest_residues_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.closest_residues Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/closest_residues/closest_residues_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/closest_residues/9af41662-4162-4c36-86e3-c82bcc4c2ac2\nINFO     /tmp/biobb/unitests_13/closest_residues/closest_residues_log.out:file_utils.py:390 Found 548 nearby residues\nINFO     /tmp/biobb/unitests_13/closest_residues/closest_residues_log.out:file_utils.py:390 Writting pdb to: /tmp/biobb/unitests_13/closest_residues/9af41662-4162-4c36-86e3-c82bcc4c2ac2/output_residues_path.pdb\nINFO     /tmp/biobb/unitests_13/closest_residues/closest_residues_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/closest_residues/9af41662-4162-4c36-86e3-c82bcc4c2ac2&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_gro.py::TestExtractAtomsGRO::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_gro.py::TestExtractAtomsGRO::test_launch&#34;, &#34;duration&#34;: &#34;00:00:05&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_gro.py::TestExtractAtomsGRO::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:05&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:43:43,519 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.extract_atoms Version: 4.1.0\n2024-03-12 16:43:43,523 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/G2S_stateA_frame92.sorted.gro to /tmp/biobb/unitests_13/extract_atoms_gro/ec23d332-3283-41d4-8c79-532c43ade15a\n2024-03-12 16:43:43,523 [MainThread  ] [INFO ]  GRO format detected, extracting all atoms matching ^D\n2024-03-12 16:43:48,845 [MainThread  ] [INFO ]  4 atoms found writting GRO file\n2024-03-12 16:43:48,846 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_atoms_gro/ec23d332-3283-41d4-8c79-532c43ade15a&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/extract_atoms_gro/output_structure_path.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_13/extract_atoms_gro/output_structure_path.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/dummy_atoms.gro\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.extract_atoms Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/G2S_stateA_frame92.sorted.gro to /tmp/biobb/unitests_13/extract_atoms_gro/ec23d332-3283-41d4-8c79-532c43ade15a\nINFO     /tmp/biobb/unitests_13/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:390 GRO format detected, extracting all atoms matching ^D\nINFO     /tmp/biobb/unitests_13/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:390 4 atoms found writting GRO file\nINFO     /tmp/biobb/unitests_13/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_atoms_gro/ec23d332-3283-41d4-8c79-532c43ade15a&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_pdb.py::TestExtractAtomsPDB::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_pdb.py::TestExtractAtomsPDB::test_launch&#34;, &#34;duration&#34;: &#34;75 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_pdb.py::TestExtractAtomsPDB::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;75 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:43:48,882 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.extract_atoms Version: 4.1.0\n2024-03-12 16:43:48,884 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/extract_atoms/06f9894c-5109-434a-aeae-18c4fd277087\n2024-03-12 16:43:48,884 [MainThread  ] [INFO ]  PDB format detected, extracting all atoms matching OE2\n2024-03-12 16:43:48,914 [MainThread  ] [INFO ]  141 atoms found writting PDB file\n2024-03-12 16:43:48,914 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_atoms/06f9894c-5109-434a-aeae-18c4fd277087&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/extract_atoms/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_13/extract_atoms/output_structure_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/OE2_atoms.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 141\n     Atoms ALIGNED in PDB_B: 141\n     RMS: 1.3133613935773403e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/extract_atoms/extract_atoms_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.extract_atoms Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/extract_atoms/extract_atoms_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/extract_atoms/06f9894c-5109-434a-aeae-18c4fd277087\nINFO     /tmp/biobb/unitests_13/extract_atoms/extract_atoms_log.out:file_utils.py:390 PDB format detected, extracting all atoms matching OE2\nINFO     /tmp/biobb/unitests_13/extract_atoms/extract_atoms_log.out:file_utils.py:390 141 atoms found writting PDB file\nINFO     /tmp/biobb/unitests_13/extract_atoms/extract_atoms_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_atoms/06f9894c-5109-434a-aeae-18c4fd277087&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_chain.py::TestExtractChain::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_chain.py::TestExtractChain::test_launch&#34;, &#34;duration&#34;: &#34;395 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_chain.py::TestExtractChain::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;395 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:43:48,957 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.extract_chain Version: 4.1.0\n2024-03-12 16:43:48,958 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_chain.pdb to /tmp/biobb/unitests_13/extract_chain/bfff54f1-aad5-4402-9b01-c7999548e598\n2024-03-12 16:43:48,958 [MainThread  ] [INFO ]  Selected Chains: B,C\n2024-03-12 16:43:48,958 [MainThread  ] [INFO ]  Warning: Use permissive=True is a risky option use it under your own responsability\n2024-03-12 16:43:48,972 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_chain/bfff54f1-aad5-4402-9b01-c7999548e598&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/extract_chain/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_13/extract_chain/output_structure_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_extract_chain.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 7893\n     Atoms ALIGNED in PDB_B: 7893\n     RMS: 1.6129351886983116e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/extract_chain/extract_chain_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.extract_chain Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/extract_chain/extract_chain_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_chain.pdb to /tmp/biobb/unitests_13/extract_chain/bfff54f1-aad5-4402-9b01-c7999548e598\nINFO     /tmp/biobb/unitests_13/extract_chain/extract_chain_log.out:file_utils.py:390 Selected Chains: B,C\nINFO     /tmp/biobb/unitests_13/extract_chain/extract_chain_log.out:file_utils.py:390 Warning: Use permissive=True is a risky option use it under your own responsability\nINFO     /tmp/biobb/unitests_13/extract_chain/extract_chain_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_chain/bfff54f1-aad5-4402-9b01-c7999548e598&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_heteroatom.py::TestExtractHeteroAtoms::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_heteroatom.py::TestExtractHeteroAtoms::test_launch&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_heteroatom.py::TestExtractHeteroAtoms::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:43:49,355 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.extract_heteroatoms Version: 4.1.0\n2024-03-12 16:43:49,358 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_heteroatom.pdb to /tmp/biobb/unitests_13/extract_heteroatoms/654ebac7-09f7-4814-b2f7-43a25361d2ae\n2024-03-12 16:43:50,431 [MainThread  ] [INFO ]  Writting pdb to: /tmp/biobb/unitests_13/extract_heteroatoms/654ebac7-09f7-4814-b2f7-43a25361d2ae/output_heteroatom_path.pdb\n2024-03-12 16:43:50,432 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_heteroatoms/654ebac7-09f7-4814-b2f7-43a25361d2ae&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/extract_heteroatoms/output_heteroatom_path.pdb\nComparing: \n        File_A: /tmp/biobb/unitests_13/extract_heteroatoms/output_heteroatom_path.pdb\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_extract_heteroatom.pdb\n        File_A hash: b&amp;#x27;\\x1e\\x83\\x13\\xbd\\xed\\xd0\\xcb0J\\xed\\x0eCp\\xe8\\xe2\\x91\\xf0w~x\\xd5\\x95\\xfc^9\\x83J\\x00\\x0f!^\\x04&amp;#x27;\n        File_B hash: b&amp;#x27;\\x1e\\x83\\x13\\xbd\\xed\\xd0\\xcb0J\\xed\\x0eCp\\xe8\\xe2\\x91\\xf0w~x\\xd5\\x95\\xfc^9\\x83J\\x00\\x0f!^\\x04&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/extract_heteroatoms/extract_heteroatoms_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.extract_heteroatoms Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/extract_heteroatoms/extract_heteroatoms_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_heteroatom.pdb to /tmp/biobb/unitests_13/extract_heteroatoms/654ebac7-09f7-4814-b2f7-43a25361d2ae\nINFO     /tmp/biobb/unitests_13/extract_heteroatoms/extract_heteroatoms_log.out:file_utils.py:390 Writting pdb to: /tmp/biobb/unitests_13/extract_heteroatoms/654ebac7-09f7-4814-b2f7-43a25361d2ae/output_heteroatom_path.pdb\nINFO     /tmp/biobb/unitests_13/extract_heteroatoms/extract_heteroatoms_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_heteroatoms/654ebac7-09f7-4814-b2f7-43a25361d2ae&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_model.py::TestExtractModel::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_model.py::TestExtractModel::test_launch&#34;, &#34;duration&#34;: &#34;00:00:03&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_model.py::TestExtractModel::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:03&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:43:50,467 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.extract_model Version: 4.1.0\n2024-03-12 16:43:50,469 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_model.pdb to /tmp/biobb/unitests_13/extract_model/52c4ca31-be1f-45da-ad59-a57be16462a7\n2024-03-12 16:43:50,469 [MainThread  ] [INFO ]  Creating cd43a9b8-e919-450e-8a12-4d5ac9bf7862 temporary folder\n2024-03-12 16:43:50,469 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_13/extract_model/52c4ca31-be1f-45da-ad59-a57be16462a7/extract_model.pdb -o cd43a9b8-e919-450e-8a12-4d5ac9bf7862/model1.pdb --force_save models --select 1\n\n2024-03-12 16:43:52,040 [MainThread  ] [INFO ]  Exit code 0\n\n2024-03-12 16:43:52,040 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_13/extract_model/52c4ca31-be1f-45da-ad59-a57be16462a7/extract_model.pdb loaded\n PDB id: 1NMR \n Title: solution structure of c-terminal domain from trypanosoma cruzi poly(a)-binding protein\n Experimental method: solution nmr\n Keywords: all helical domain, peptide binding protein\n Resolution (A): N.A.\n\n Num. models: 20 (type: Ensembl/NMR,    6.831 A)\n Num. chains: 20 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein|A/15: Protein|A/16: Protein|A/17: Protein|A/18: Protein|A/19: Protein)\n Num. residues:  1700\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 1700 (total 13080 H atoms)\n Num. HETATM residues:  0\n Num. ligands or modified residues:  0\n Num. water mol.:  0\n Num. atoms:  25800\nRunning models. Options: --select 1\nDetected 20 Model(s)\nModels  superimpose, RMSd:    6.831 A, guessed as Ensembl/NMR \nSelecting model num. 1\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  85\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 85 (total 654 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1290\nStructure saved on cd43a9b8-e919-450e-8a12-4d5ac9bf7862/model1.pdb\n\n2024-03-12 16:43:52,040 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_13/extract_model/52c4ca31-be1f-45da-ad59-a57be16462a7/extract_model.pdb -o cd43a9b8-e919-450e-8a12-4d5ac9bf7862/model4.pdb --force_save models --select 4\n\n2024-03-12 16:43:53,598 [MainThread  ] [INFO ]  Exit code 0\n\n2024-03-12 16:43:53,598 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_13/extract_model/52c4ca31-be1f-45da-ad59-a57be16462a7/extract_model.pdb loaded\n PDB id: 1NMR \n Title: solution structure of c-terminal domain from trypanosoma cruzi poly(a)-binding protein\n Experimental method: solution nmr\n Keywords: all helical domain, peptide binding protein\n Resolution (A): N.A.\n\n Num. models: 20 (type: Ensembl/NMR,    6.831 A)\n Num. chains: 20 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein|A/15: Protein|A/16: Protein|A/17: Protein|A/18: Protein|A/19: Protein)\n Num. residues:  1700\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 1700 (total 13080 H atoms)\n Num. HETATM residues:  0\n Num. ligands or modified residues:  0\n Num. water mol.:  0\n Num. atoms:  25800\nRunning models. Options: --select 4\nDetected 20 Model(s)\nModels  superimpose, RMSd:    6.831 A, guessed as Ensembl/NMR \nSelecting model num. 4\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  85\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 85 (total 654 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1290\nStructure saved on cd43a9b8-e919-450e-8a12-4d5ac9bf7862/model4.pdb\n\n2024-03-12 16:43:53,601 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_model/52c4ca31-be1f-45da-ad59-a57be16462a7&amp;#x27;, &amp;#x27;cd43a9b8-e919-450e-8a12-4d5ac9bf7862&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/extract_model/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_13/extract_model/output_structure_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_extract_model.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 636\n     Atoms ALIGNED in PDB_B: 636\n     RMS: 5.262008214811879e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/extract_model/extract_model_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.extract_model Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/extract_model/extract_model_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_model.pdb to /tmp/biobb/unitests_13/extract_model/52c4ca31-be1f-45da-ad59-a57be16462a7\nINFO     /tmp/biobb/unitests_13/extract_model/extract_model_log.out:file_utils.py:390 Creating cd43a9b8-e919-450e-8a12-4d5ac9bf7862 temporary folder\nINFO     /tmp/biobb/unitests_13/extract_model/extract_model_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_13/extract_model/52c4ca31-be1f-45da-ad59-a57be16462a7/extract_model.pdb -o cd43a9b8-e919-450e-8a12-4d5ac9bf7862/model1.pdb --force_save models --select 1\n\nINFO     /tmp/biobb/unitests_13/extract_model/extract_model_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_13/extract_model/extract_model_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_13/extract_model/52c4ca31-be1f-45da-ad59-a57be16462a7/extract_model.pdb loaded\n PDB id: 1NMR \n Title: solution structure of c-terminal domain from trypanosoma cruzi poly(a)-binding protein\n Experimental method: solution nmr\n Keywords: all helical domain, peptide binding protein\n Resolution (A): N.A.\n\n Num. models: 20 (type: Ensembl/NMR,    6.831 A)\n Num. chains: 20 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein|A/15: Protein|A/16: Protein|A/17: Protein|A/18: Protein|A/19: Protein)\n Num. residues:  1700\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 1700 (total 13080 H atoms)\n Num. HETATM residues:  0\n Num. ligands or modified residues:  0\n Num. water mol.:  0\n Num. atoms:  25800\nRunning models. Options: --select 1\nDetected 20 Model(s)\nModels  superimpose, RMSd:    6.831 A, guessed as Ensembl/NMR \nSelecting model num. 1\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  85\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 85 (total 654 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1290\nStructure saved on cd43a9b8-e919-450e-8a12-4d5ac9bf7862/model1.pdb\n\nINFO     /tmp/biobb/unitests_13/extract_model/extract_model_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_13/extract_model/52c4ca31-be1f-45da-ad59-a57be16462a7/extract_model.pdb -o cd43a9b8-e919-450e-8a12-4d5ac9bf7862/model4.pdb --force_save models --select 4\n\nINFO     /tmp/biobb/unitests_13/extract_model/extract_model_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_13/extract_model/extract_model_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_13/extract_model/52c4ca31-be1f-45da-ad59-a57be16462a7/extract_model.pdb loaded\n PDB id: 1NMR \n Title: solution structure of c-terminal domain from trypanosoma cruzi poly(a)-binding protein\n Experimental method: solution nmr\n Keywords: all helical domain, peptide binding protein\n Resolution (A): N.A.\n\n Num. models: 20 (type: Ensembl/NMR,    6.831 A)\n Num. chains: 20 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein|A/15: Protein|A/16: Protein|A/17: Protein|A/18: Protein|A/19: Protein)\n Num. residues:  1700\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 1700 (total 13080 H atoms)\n Num. HETATM residues:  0\n Num. ligands or modified residues:  0\n Num. water mol.:  0\n Num. atoms:  25800\nRunning models. Options: --select 4\nDetected 20 Model(s)\nModels  superimpose, RMSd:    6.831 A, guessed as Ensembl/NMR \nSelecting model num. 4\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  85\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 85 (total 654 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1290\nStructure saved on cd43a9b8-e919-450e-8a12-4d5ac9bf7862/model4.pdb\n\nINFO     /tmp/biobb/unitests_13/extract_model/extract_model_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_model/52c4ca31-be1f-45da-ad59-a57be16462a7&amp;#x27;, &amp;#x27;cd43a9b8-e919-450e-8a12-4d5ac9bf7862&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_molecule.py::TestExtractMolecule::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_molecule.py::TestExtractMolecule::test_launch&#34;, &#34;duration&#34;: &#34;703 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_molecule.py::TestExtractMolecule::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;703 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:43:53,726 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.extract_molecule Version: 4.1.0\n2024-03-12 16:43:53,727 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb to /tmp/biobb/unitests_13/extract_molecule/50090d2e-b564-4911-873f-ce8063634abb\n2024-03-12 16:43:53,727 [MainThread  ] [INFO ]  Creating 1447d48d-dd15-49e3-b626-873addb42034 temporary folder\n2024-03-12 16:43:53,727 [MainThread  ] [INFO ]  check_structure -i /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb -o /tmp/biobb/unitests_13/extract_molecule/output_molecule_path.pdb --force_save --non_interactive command_list --list 1447d48d-dd15-49e3-b626-873addb42034/extract_prot.lst\n\n2024-03-12 16:43:54,311 [MainThread  ] [INFO ]  Exit code 0\n\n2024-03-12 16:43:54,312 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb loaded\n PDB id: 1G54 \n Title: carbonic anhydrase ii complexed with 4-(aminosulfonyl)-n-[(2,3,4,5,6- pentafluorophenyl)methyl]-benzamide\n Experimental method: x-ray diffraction\n Keywords: carbonic anhydrase ii, 4-(aminosulfonyl)-n-[(2, 3, 4, 5, 6- pentafluorophenyl)methyl]-benzamide, lyase\n Resolution (A): 1.86\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  332\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  74\n Num. ligands or modified residues:  3\n Num. water mol.:  71\n Num. atoms:  2156\nMetal/Ion residues found\n ZN A262\n HG A263\nSmall mol ligands found\nFFB A555\n\nStep 1: ligands --remove All\n\nRunning ligands. Options: --remove All\nDetected 3 Ligands\n  ZN A262\n  HG A263\n FFB A555\nLigands removed All (3)\n\nStep 2: water --remove Yes\n\nRunning water. Options: --remove Yes\nDetected 71 Water molecules\nRemoved 71 Water molecules\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  258\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  2058\nStructure saved on /tmp/biobb/unitests_13/extract_molecule/output_molecule_path.pdb\n\n2024-03-12 16:43:54,312 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_molecule/50090d2e-b564-4911-873f-ce8063634abb&amp;#x27;, &amp;#x27;1447d48d-dd15-49e3-b626-873addb42034&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/extract_molecule/output_molecule_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_13/extract_molecule/output_molecule_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_extract_molecule.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 2058\n     Atoms ALIGNED in PDB_B: 2058\n     RMS: 6.579094722437545e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/extract_molecule/extract_molecule_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.extract_molecule Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/extract_molecule/extract_molecule_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb to /tmp/biobb/unitests_13/extract_molecule/50090d2e-b564-4911-873f-ce8063634abb\nINFO     /tmp/biobb/unitests_13/extract_molecule/extract_molecule_log.out:file_utils.py:390 Creating 1447d48d-dd15-49e3-b626-873addb42034 temporary folder\nINFO     /tmp/biobb/unitests_13/extract_molecule/extract_molecule_log.out:cmd_wrapper.py:33 check_structure -i /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb -o /tmp/biobb/unitests_13/extract_molecule/output_molecule_path.pdb --force_save --non_interactive command_list --list 1447d48d-dd15-49e3-b626-873addb42034/extract_prot.lst\n\nINFO     /tmp/biobb/unitests_13/extract_molecule/extract_molecule_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_13/extract_molecule/extract_molecule_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb loaded\n PDB id: 1G54 \n Title: carbonic anhydrase ii complexed with 4-(aminosulfonyl)-n-[(2,3,4,5,6- pentafluorophenyl)methyl]-benzamide\n Experimental method: x-ray diffraction\n Keywords: carbonic anhydrase ii, 4-(aminosulfonyl)-n-[(2, 3, 4, 5, 6- pentafluorophenyl)methyl]-benzamide, lyase\n Resolution (A): 1.86\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  332\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  74\n Num. ligands or modified residues:  3\n Num. water mol.:  71\n Num. atoms:  2156\nMetal/Ion residues found\n ZN A262\n HG A263\nSmall mol ligands found\nFFB A555\n\nStep 1: ligands --remove All\n\nRunning ligands. Options: --remove All\nDetected 3 Ligands\n  ZN A262\n  HG A263\n FFB A555\nLigands removed All (3)\n\nStep 2: water --remove Yes\n\nRunning water. Options: --remove Yes\nDetected 71 Water molecules\nRemoved 71 Water molecules\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  258\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  2058\nStructure saved on /tmp/biobb/unitests_13/extract_molecule/output_molecule_path.pdb\n\nINFO     /tmp/biobb/unitests_13/extract_molecule/extract_molecule_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_molecule/50090d2e-b564-4911-873f-ce8063634abb&amp;#x27;, &amp;#x27;1447d48d-dd15-49e3-b626-873addb42034&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_residues.py::TestExtractResidues::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_residues.py::TestExtractResidues::test_launch&#34;, &#34;duration&#34;: &#34;581 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_residues.py::TestExtractResidues::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;581 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:43:54,430 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.extract_residues Version: 4.1.0\n2024-03-12 16:43:54,431 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/extract_residues/a0107edf-bc93-4644-b66a-8117a9f902bb\n2024-03-12 16:43:54,978 [MainThread  ] [INFO ]  Writting pdb to: /tmp/biobb/unitests_13/extract_residues/a0107edf-bc93-4644-b66a-8117a9f902bb/output_residues_path.pdb\n2024-03-12 16:43:54,979 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_residues/a0107edf-bc93-4644-b66a-8117a9f902bb&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/extract_residues/output_residues_path.pdb\nComparing: \n        File_A: /tmp/biobb/unitests_13/extract_residues/output_residues_path.pdb\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_extract_residues.pdb\n        File_A hash: b&amp;#x27;\\xf0\\x84\\xb8D\\x90whe\\xc3T\\xe2\\xf3\\\\\\xd72\\xfaT\\x9d\\x19\\x88\\xab\\x03\\xbe\\xf6\\x9a\\x81\\xec\\x15tx`D&amp;#x27;\n        File_B hash: b&amp;#x27;\\xf0\\x84\\xb8D\\x90whe\\xc3T\\xe2\\xf3\\\\\\xd72\\xfaT\\x9d\\x19\\x88\\xab\\x03\\xbe\\xf6\\x9a\\x81\\xec\\x15tx`D&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/extract_residues/extract_residues_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.extract_residues Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/extract_residues/extract_residues_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/extract_residues/a0107edf-bc93-4644-b66a-8117a9f902bb\nINFO     /tmp/biobb/unitests_13/extract_residues/extract_residues_log.out:file_utils.py:390 Writting pdb to: /tmp/biobb/unitests_13/extract_residues/a0107edf-bc93-4644-b66a-8117a9f902bb/output_residues_path.pdb\nINFO     /tmp/biobb/unitests_13/extract_residues/extract_residues_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/extract_residues/a0107edf-bc93-4644-b66a-8117a9f902bb&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_gro.py::TestRemoveLigandGro::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_gro.py::TestRemoveLigandGro::test_launch&#34;, &#34;duration&#34;: &#34;486 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_gro.py::TestRemoveLigandGro::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;486 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:43:55,013 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.remove_ligand Version: 4.1.0\n2024-03-12 16:43:55,016 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.gro to /tmp/biobb/unitests_13/remove_ligand_gro/751ccaaa-0ed1-4f7b-8b44-64cf48b57748\n2024-03-12 16:43:55,017 [MainThread  ] [INFO ]  GRO format detected, removing all atoms from residues named AQ4\n2024-03-12 16:43:55,430 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/remove_ligand_gro/751ccaaa-0ed1-4f7b-8b44-64cf48b57748&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/remove_ligand_gro/output_structure_path.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_13/remove_ligand_gro/output_structure_path.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/WT_apo_md_1.gro\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/remove_ligand_gro/remove_ligand_gro_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.remove_ligand Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/remove_ligand_gro/remove_ligand_gro_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.gro to /tmp/biobb/unitests_13/remove_ligand_gro/751ccaaa-0ed1-4f7b-8b44-64cf48b57748\nINFO     /tmp/biobb/unitests_13/remove_ligand_gro/remove_ligand_gro_log.out:file_utils.py:390 GRO format detected, removing all atoms from residues named AQ4\nINFO     /tmp/biobb/unitests_13/remove_ligand_gro/remove_ligand_gro_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/remove_ligand_gro/751ccaaa-0ed1-4f7b-8b44-64cf48b57748&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_pdb.py::TestRemoveLigandPDB::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_pdb.py::TestRemoveLigandPDB::test_launch&#34;, &#34;duration&#34;: &#34;00:00:03&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_pdb.py::TestRemoveLigandPDB::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:03&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:43:55,501 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.remove_ligand Version: 4.1.0\n2024-03-12 16:43:55,504 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.pdb to /tmp/biobb/unitests_13/remove_ligand/0d6b3cf5-fa8c-4804-a529-525108eafd33\n2024-03-12 16:43:55,505 [MainThread  ] [INFO ]  PDB format detected, removing all atoms from residues named AQ4\n2024-03-12 16:43:55,554 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/remove_ligand/0d6b3cf5-fa8c-4804-a529-525108eafd33&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/remove_ligand/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_13/remove_ligand/output_structure_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/WT_apo_md_1.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 12872\n     Atoms ALIGNED in PDB_B: 12872\n     RMS: 1.549802168438611e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/remove_ligand/remove_ligand_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.remove_ligand Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/remove_ligand/remove_ligand_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.pdb to /tmp/biobb/unitests_13/remove_ligand/0d6b3cf5-fa8c-4804-a529-525108eafd33\nINFO     /tmp/biobb/unitests_13/remove_ligand/remove_ligand_log.out:file_utils.py:390 PDB format detected, removing all atoms from residues named AQ4\nINFO     /tmp/biobb/unitests_13/remove_ligand/remove_ligand_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/remove_ligand/0d6b3cf5-fa8c-4804-a529-525108eafd33&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_molecules.py::TestRemoveMolecules::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_molecules.py::TestRemoveMolecules::test_launch&#34;, &#34;duration&#34;: &#34;00:00:05&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_remove_molecules.py::TestRemoveMolecules::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:05&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:43:58,203 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.remove_molecules Version: 4.1.0\n2024-03-12 16:43:58,205 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/remove_molecules/3b3971dc-5b64-414b-a084-cb1828a63ad8\n2024-03-12 16:44:03,612 [MainThread  ] [INFO ]  Writting pdb to: /tmp/biobb/unitests_13/remove_molecules/3b3971dc-5b64-414b-a084-cb1828a63ad8/output_molecules_path.pdb\n2024-03-12 16:44:03,620 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/remove_molecules/3b3971dc-5b64-414b-a084-cb1828a63ad8&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/remove_molecules/output_molecules_path.pdb\nComparing: \n        File_A: /tmp/biobb/unitests_13/remove_molecules/output_molecules_path.pdb\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_remove_molecules.pdb\n        File_A hash: b&amp;#x27;q$\\x11\\xa5u\\xca5\\xc0\\x90\\xd8\\x1bB&amp;amp;{\\xfcNm\\x85\\xb5(\\x8f\\x13\\xf0\\xef,\\xe6\\x8c\\x0ftV}\\x1d&amp;#x27;\n        File_B hash: b&amp;#x27;q$\\x11\\xa5u\\xca5\\xc0\\x90\\xd8\\x1bB&amp;amp;{\\xfcNm\\x85\\xb5(\\x8f\\x13\\xf0\\xef,\\xe6\\x8c\\x0ftV}\\x1d&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/remove_molecules/remove_molecules_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.remove_molecules Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/remove_molecules/remove_molecules_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/remove_molecules/3b3971dc-5b64-414b-a084-cb1828a63ad8\nINFO     /tmp/biobb/unitests_13/remove_molecules/remove_molecules_log.out:file_utils.py:390 Writting pdb to: /tmp/biobb/unitests_13/remove_molecules/3b3971dc-5b64-414b-a084-cb1828a63ad8/output_molecules_path.pdb\nINFO     /tmp/biobb/unitests_13/remove_molecules/remove_molecules_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/remove_molecules/3b3971dc-5b64-414b-a084-cb1828a63ad8&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_pdb_water.py::TestRemovePDBWater::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_pdb_water.py::TestRemovePDBWater::test_launch&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_remove_pdb_water.py::TestRemovePDBWater::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:44:03,661 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.remove_pdb_water Version: 4.1.0\n2024-03-12 16:44:03,662 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_WAT.pdb to /tmp/biobb/unitests_13/remove_pdb_water/8d55f394-d901-45d9-b3c7-d7ec09a408ec\n2024-03-12 16:44:03,662 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_13/remove_pdb_water/8d55f394-d901-45d9-b3c7-d7ec09a408ec/WT_aq4_md_WAT.pdb -o /tmp/biobb/unitests_13/remove_pdb_water/8d55f394-d901-45d9-b3c7-d7ec09a408ec/output_pdb_path.pdb --force_save water --remove yes\n\n2024-03-12 16:44:04,359 [MainThread  ] [INFO ]  Exit code 0\n\n2024-03-12 16:44:04,359 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_13/remove_pdb_water/8d55f394-d901-45d9-b3c7-d7ec09a408ec/WT_aq4_md_WAT.pdb loaded\n PDB id:  \n Title: protein in water\n Experimental method: unknown\n Resolution (A): N.A.\n\n Num. models: 1\n Num. chains: 3 ( : Unknown, A: Protein, B: Unknown)\n Num. residues:  397\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 294 (total 2404 H atoms)\n Num. HETATM residues:  2\n Num. ligands or modified residues:  0\n Num. water mol.:  2\n Num. atoms:  4858\nRunning water. Options: --remove yes\nDetected 2 Water molecules\nRemoved 2 Water molecules\nFinal Num. models: 1\nFinal Num. chains: 3 ( : Unknown, A: Protein, B: Unknown)\nFinal Num. residues:  395\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 292 (total 2401 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  4853\nStructure saved on /tmp/biobb/unitests_13/remove_pdb_water/8d55f394-d901-45d9-b3c7-d7ec09a408ec/output_pdb_path.pdb\n\n2024-03-12 16:44:04,360 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/remove_pdb_water/8d55f394-d901-45d9-b3c7-d7ec09a408ec&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/remove_pdb_water/output_pdb_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_13/remove_pdb_water/output_pdb_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/WT_apo_no_wat.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 3004\n     Atoms ALIGNED in PDB_B: 3004\n     RMS: 1.3997192439430224e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/remove_pdb_water/remove_pdb_water_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.remove_pdb_water Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/remove_pdb_water/remove_pdb_water_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_WAT.pdb to /tmp/biobb/unitests_13/remove_pdb_water/8d55f394-d901-45d9-b3c7-d7ec09a408ec\nINFO     /tmp/biobb/unitests_13/remove_pdb_water/remove_pdb_water_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_13/remove_pdb_water/8d55f394-d901-45d9-b3c7-d7ec09a408ec/WT_aq4_md_WAT.pdb -o /tmp/biobb/unitests_13/remove_pdb_water/8d55f394-d901-45d9-b3c7-d7ec09a408ec/output_pdb_path.pdb --force_save water --remove yes\n\nINFO     /tmp/biobb/unitests_13/remove_pdb_water/remove_pdb_water_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_13/remove_pdb_water/remove_pdb_water_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_13/remove_pdb_water/8d55f394-d901-45d9-b3c7-d7ec09a408ec/WT_aq4_md_WAT.pdb loaded\n PDB id:  \n Title: protein in water\n Experimental method: unknown\n Resolution (A): N.A.\n\n Num. models: 1\n Num. chains: 3 ( : Unknown, A: Protein, B: Unknown)\n Num. residues:  397\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 294 (total 2404 H atoms)\n Num. HETATM residues:  2\n Num. ligands or modified residues:  0\n Num. water mol.:  2\n Num. atoms:  4858\nRunning water. Options: --remove yes\nDetected 2 Water molecules\nRemoved 2 Water molecules\nFinal Num. models: 1\nFinal Num. chains: 3 ( : Unknown, A: Protein, B: Unknown)\nFinal Num. residues:  395\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 292 (total 2401 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  4853\nStructure saved on /tmp/biobb/unitests_13/remove_pdb_water/8d55f394-d901-45d9-b3c7-d7ec09a408ec/output_pdb_path.pdb\n\nINFO     /tmp/biobb/unitests_13/remove_pdb_water/remove_pdb_water_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/remove_pdb_water/8d55f394-d901-45d9-b3c7-d7ec09a408ec&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_2vgb.py::TestRenumberStructure2VGB::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_2vgb.py::TestRenumberStructure2VGB::test_launch&#34;, &#34;duration&#34;: &#34;850 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_2vgb.py::TestRenumberStructure2VGB::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;850 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:44:04,742 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.renumber_structure Version: 4.1.0\n2024-03-12 16:44:04,744 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/renumber_structure_2vgb/93b9e787-0f41-47e6-8d06-64a5f347c67c\n2024-03-12 16:44:04,744 [MainThread  ] [INFO ]  PDB format detected, reenumerating atoms\n2024-03-12 16:44:04,812 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/renumber_structure_2vgb/93b9e787-0f41-47e6-8d06-64a5f347c67c&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/renumber_structure_2vgb/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_13/renumber_structure_2vgb/output_structure_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_2vgb.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 15488\n     Atoms ALIGNED in PDB_B: 15488\n     RMS: 1.871093208699659e-14\n     RMS_CUTOFF: 1\nChecking if empty file: /tmp/biobb/unitests_13/renumber_structure_2vgb/output_mapping_json_path.json\nComparing: \n        File_A: /tmp/biobb/unitests_13/renumber_structure_2vgb/output_mapping_json_path.json\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/2vgb_output_mapping_json_path.json\n        File_A hash: b&amp;#x27;F\\xbe!`V\\xdb.\\x99\\xfb\\xda\\x94\\xb1\\xa8\\xdf6\\xbcJ\\\\\\\\\\xc7k\\xb6\\xe9\\xc1I\\nm\\xc1\\xe4:v\\x15&amp;#x27;\n        File_B hash: b&amp;#x27;F\\xbe!`V\\xdb.\\x99\\xfb\\xda\\x94\\xb1\\xa8\\xdf6\\xbcJ\\\\\\\\\\xc7k\\xb6\\xe9\\xc1I\\nm\\xc1\\xe4:v\\x15&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/renumber_structure_2vgb/renumber_structure_2vgb_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.renumber_structure Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/renumber_structure_2vgb/renumber_structure_2vgb_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/renumber_structure_2vgb/93b9e787-0f41-47e6-8d06-64a5f347c67c\nINFO     /tmp/biobb/unitests_13/renumber_structure_2vgb/renumber_structure_2vgb_log.out:file_utils.py:390 PDB format detected, reenumerating atoms\nINFO     /tmp/biobb/unitests_13/renumber_structure_2vgb/renumber_structure_2vgb_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/renumber_structure_2vgb/93b9e787-0f41-47e6-8d06-64a5f347c67c&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_gro.py::TestRenumberStructureGRO::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_gro.py::TestRenumberStructureGRO::test_launch&#34;, &#34;duration&#34;: &#34;157 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_gro.py::TestRenumberStructureGRO::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;157 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:44:05,593 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.renumber_structure Version: 4.1.0\n2024-03-12 16:44:05,594 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/pyruvate.gro to /tmp/biobb/unitests_13/renumber_structure_gro/2713ae5e-6524-4274-8124-d70d2e915f59\n2024-03-12 16:44:05,595 [MainThread  ] [INFO ]  GRO format detected, reenumerating atoms\n2024-03-12 16:44:05,711 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/renumber_structure_gro/2713ae5e-6524-4274-8124-d70d2e915f59&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/renumber_structure_gro/output_structure_path.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_13/renumber_structure_gro/output_structure_path.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/renum_pyruvate.gro\nChecking if empty file: /tmp/biobb/unitests_13/renumber_structure_gro/output_mapping_json_path.json\nComparing: \n        File_A: /tmp/biobb/unitests_13/renumber_structure_gro/output_mapping_json_path.json\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/pyruvate_output_mapping_json_path.json\n        File_A hash: b&amp;#x27;/\\xa1\\xe9\\x19X\\xe3\\xb5\\x15R \\x81\\x02\\xc4PX\\x11h\\x08\\x83\\xdb\\r\\xf9j\\xebP\\xe9\\\\\\x1eT#A\\r&amp;#x27;\n        File_B hash: b&amp;#x27;/\\xa1\\xe9\\x19X\\xe3\\xb5\\x15R \\x81\\x02\\xc4PX\\x11h\\x08\\x83\\xdb\\r\\xf9j\\xebP\\xe9\\\\\\x1eT#A\\r&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/renumber_structure_gro/renumber_structure_gro_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.renumber_structure Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/renumber_structure_gro/renumber_structure_gro_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/pyruvate.gro to /tmp/biobb/unitests_13/renumber_structure_gro/2713ae5e-6524-4274-8124-d70d2e915f59\nINFO     /tmp/biobb/unitests_13/renumber_structure_gro/renumber_structure_gro_log.out:file_utils.py:390 GRO format detected, reenumerating atoms\nINFO     /tmp/biobb/unitests_13/renumber_structure_gro/renumber_structure_gro_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/renumber_structure_gro/2713ae5e-6524-4274-8124-d70d2e915f59&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_pdb.py::TestRenumberStructurePDB::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_pdb.py::TestRenumberStructurePDB::test_launch&#34;, &#34;duration&#34;: &#34;35 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_pdb.py::TestRenumberStructurePDB::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;35 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:44:05,753 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.renumber_structure Version: 4.1.0\n2024-03-12 16:44:05,753 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cl3.noH.pdb to /tmp/biobb/unitests_13/renumber_structure/fb373cba-4dbd-487b-b728-8e4e0faba37d\n2024-03-12 16:44:05,754 [MainThread  ] [INFO ]  PDB format detected, reenumerating atoms\n2024-03-12 16:44:05,754 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/renumber_structure/fb373cba-4dbd-487b-b728-8e4e0faba37d&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/renumber_structure/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_13/renumber_structure/output_structure_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/renum_cl3_noH.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 28\n     Atoms ALIGNED in PDB_B: 28\n     RMS: 1.89900533991096e-15\n     RMS_CUTOFF: 1\nChecking if empty file: /tmp/biobb/unitests_13/renumber_structure/output_mapping_json_path.json\nComparing: \n        File_A: /tmp/biobb/unitests_13/renumber_structure/output_mapping_json_path.json\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/cl3_output_mapping_json_path.json\n        File_A hash: b&amp;#x27;\\xe5\\xbc\\xaf\\xec\\xc4\\x1a\\x14\\x1d&amp;gt;\\x1f\\xe1\\x1a\\xbe_\\xd5g\\xb6\\xac\\xeb\\xce\\x9a\\xa4\\x9f\\xa7\\xf9\\x98\\xc7\\x00\\xaa\\xa2\\t\\x13&amp;#x27;\n        File_B hash: b&amp;#x27;\\xe5\\xbc\\xaf\\xec\\xc4\\x1a\\x14\\x1d&amp;gt;\\x1f\\xe1\\x1a\\xbe_\\xd5g\\xb6\\xac\\xeb\\xce\\x9a\\xa4\\x9f\\xa7\\xf9\\x98\\xc7\\x00\\xaa\\xa2\\t\\x13&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/renumber_structure/renumber_structure_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.renumber_structure Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/renumber_structure/renumber_structure_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cl3.noH.pdb to /tmp/biobb/unitests_13/renumber_structure/fb373cba-4dbd-487b-b728-8e4e0faba37d\nINFO     /tmp/biobb/unitests_13/renumber_structure/renumber_structure_log.out:file_utils.py:390 PDB format detected, reenumerating atoms\nINFO     /tmp/biobb/unitests_13/renumber_structure/renumber_structure_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/renumber_structure/fb373cba-4dbd-487b-b728-8e4e0faba37d&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_smallgro.py::TestRenumberStructureSMALLGRO::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_smallgro.py::TestRenumberStructureSMALLGRO::test_launch&#34;, &#34;duration&#34;: &#34;33 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_smallgro.py::TestRenumberStructureSMALLGRO::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;33 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:44:05,789 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.renumber_structure Version: 4.1.0\n2024-03-12 16:44:05,789 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/smallgro.gro to /tmp/biobb/unitests_13/renumber_structure_smallgro/dcc03017-c020-4c4d-bd32-17d2c382d73c\n2024-03-12 16:44:05,789 [MainThread  ] [INFO ]  GRO format detected, reenumerating atoms\n2024-03-12 16:44:05,790 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/renumber_structure_smallgro/dcc03017-c020-4c4d-bd32-17d2c382d73c&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/renumber_structure_smallgro/output_structure_path.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_13/renumber_structure_smallgro/output_structure_path.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/renum_smallgro.gro\nChecking if empty file: /tmp/biobb/unitests_13/renumber_structure_smallgro/output_mapping_json_path.json\nComparing: \n        File_A: /tmp/biobb/unitests_13/renumber_structure_smallgro/output_mapping_json_path.json\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/smallgro_output_mapping_json_path.json\n        File_A hash: b&amp;#x27;\\x8a\\t\\xfd\\xe8\\x8f@K\\xafz\\xd2\\x8dO\\xed[\\xe0\\xcchg\\xda\\xd7\\x13\\xb4\\x0c\\xcf3\\rNRg,\\xaf\\xf4&amp;#x27;\n        File_B hash: b&amp;#x27;\\x8a\\t\\xfd\\xe8\\x8f@K\\xafz\\xd2\\x8dO\\xed[\\xe0\\xcchg\\xda\\xd7\\x13\\xb4\\x0c\\xcf3\\rNRg,\\xaf\\xf4&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/renumber_structure_smallgro/renumber_structure_smallgro_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.renumber_structure Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/renumber_structure_smallgro/renumber_structure_smallgro_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/smallgro.gro to /tmp/biobb/unitests_13/renumber_structure_smallgro/dcc03017-c020-4c4d-bd32-17d2c382d73c\nINFO     /tmp/biobb/unitests_13/renumber_structure_smallgro/renumber_structure_smallgro_log.out:file_utils.py:390 GRO format detected, reenumerating atoms\nINFO     /tmp/biobb/unitests_13/renumber_structure_smallgro/renumber_structure_smallgro_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/renumber_structure_smallgro/dcc03017-c020-4c4d-bd32-17d2c382d73c&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_sort_gro_residues.py::TestSortGroResidues::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_sort_gro_residues.py::TestSortGroResidues::test_launch&#34;, &#34;duration&#34;: &#34;00:00:05&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_sort_gro_residues.py::TestSortGroResidues::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:05&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:44:05,823 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.sort_gro_residues Version: 4.1.0\n2024-03-12 16:44:05,826 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.gro to /tmp/biobb/unitests_13/sort_gro_residues/396390f2-7a5f-4e95-84f0-a9008e8fd649\n2024-03-12 16:44:10,622 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/sort_gro_residues/396390f2-7a5f-4e95-84f0-a9008e8fd649&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/sort_gro_residues/output_gro_path.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_13/sort_gro_residues/output_gro_path.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/WT_aq4_md_sorted.gro\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/sort_gro_residues/sort_gro_residues_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.sort_gro_residues Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/sort_gro_residues/sort_gro_residues_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.gro to /tmp/biobb/unitests_13/sort_gro_residues/396390f2-7a5f-4e95-84f0-a9008e8fd649\nINFO     /tmp/biobb/unitests_13/sort_gro_residues/sort_gro_residues_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/sort_gro_residues/396390f2-7a5f-4e95-84f0-a9008e8fd649&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_str_check_add_hydrogens.py::TestStrCheckAddHydrogens::test_str_check_add_hydrogens&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_str_check_add_hydrogens.py::TestStrCheckAddHydrogens::test_str_check_add_hydrogens&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_str_check_add_hydrogens.py::TestStrCheckAddHydrogens::test_str_check_add_hydrogens&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:44:10,695 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.str_check_add_hydrogens Version: 4.1.0\n2024-03-12 16:44:10,696 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/str_no_H.pdb to /tmp/biobb/unitests_13/str_check_add_hydrogens/4cc2cd6e-4c9f-4212-95dc-629e5790891b\n2024-03-12 16:44:10,696 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_13/str_check_add_hydrogens/4cc2cd6e-4c9f-4212-95dc-629e5790891b/str_no_H.pdb -o /tmp/biobb/unitests_13/str_check_add_hydrogens/4cc2cd6e-4c9f-4212-95dc-629e5790891b/output_structure_path.pdbqt --non_interactive --force_save --keep_canonical_resnames command_list --list &amp;#x27;add_hydrogen --add_charges ADT --add_mode auto &amp;#x27;\n\n2024-03-12 16:44:11,633 [MainThread  ] [INFO ]  Exit code 0\n\n2024-03-12 16:44:11,633 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_13/str_check_add_hydrogens/4cc2cd6e-4c9f-4212-95dc-629e5790891b/str_no_H.pdb loaded\n PDB id:  \n Title: \n Experimental method: unknown\n Resolution (A): N.A.\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  532\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  15\n Num. ligands or modified residues:  3\n Num. water mol.:  12\n Num. atoms:  3946\nMetal/Ion residues found\n  K A582\n MN A583\nSmall mol ligands found\nFBP A580\n\nStep 1: add_hydrogen --add_charges ADT --add_mode auto \nRunning add_hydrogen. Options: --add_charges ADT --add_mode auto\nFound 143 Residues requiring selection on adding H atoms\nWARNING: fixing side chains, override with --no_fix_side\nRunning fixside. Options: --fix all\nFound no residues with missing or unknown side chain atoms\nSelection: auto\nReplacing HIS A72 by HIE\nReplacing HIS A121 by HIE\nReplacing HIS A124 by HIE\nReplacing HIS A127 by HIE\nReplacing HIS A278 by HIE\nReplacing HIS A306 by HIE\nReplacing HIS A317 by HIE\nReplacing HIS A422 by HIE\nReplacing HIS A434 by HIE\nReplacing HIS A507 by HIE\nUpdating partial charges and atom types\nWarning: OXT atom missing in CILE A573. Run backbone --fix_atoms first\nWarning: FBP not found in residue library atom, charges set to 0.\nWarning: K not found in residue library atom, charges set to 0.\nWarning: MN not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nTotal assigned charge:      -1.25\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  532\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 517 (total 3995 H atoms)\nFinal Num. HETATM residues:  15\nFinal Num. ligands or modified residues:  3\nFinal Num. water mol.:  12\nFinal Num. atoms:  7941\nMetal/Ion residues found\n  K A582\n MN A583\nSmall mol ligands found\nFBP A580\nWarning: reverting residue names to canonical on output\nStructure saved on /tmp/biobb/unitests_13/str_check_add_hydrogens/4cc2cd6e-4c9f-4212-95dc-629e5790891b/output_structure_path.pdbqt\n\n2024-03-12 16:44:11,638 [MainThread  ] [INFO ]  /tmp/biobb/unitests_13/str_check_add_hydrogens/output_structure_path.pdbqt file ends with END, cleaning\n2024-03-12 16:44:11,642 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/str_check_add_hydrogens/4cc2cd6e-4c9f-4212-95dc-629e5790891b&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/str_check_add_hydrogens/output_structure_path.pdbqt\nComparing: \n        File_A: /tmp/biobb/unitests_13/str_check_add_hydrogens/output_structure_path.pdbqt\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_str_H.pdbqt\n        File_A hash: b&amp;quot;U\\xd1\\xc0c\\xb8\\xe3(\\xac\\xf0&amp;#x27;\\xc0\\xc4P\\xd6\\x1f\\x08\\xd1\\xa2\\xd5j\\xa5\\xef\\xc9&amp;amp;\\xedoq\\x9fM\\xa0\\x88F&amp;quot;\n        File_B hash: b&amp;quot;U\\xd1\\xc0c\\xb8\\xe3(\\xac\\xf0&amp;#x27;\\xc0\\xc4P\\xd6\\x1f\\x08\\xd1\\xa2\\xd5j\\xa5\\xef\\xc9&amp;amp;\\xedoq\\x9fM\\xa0\\x88F&amp;quot;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/str_check_add_hydrogens/str_check_add_hydrogens_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.str_check_add_hydrogens Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/str_check_add_hydrogens/str_check_add_hydrogens_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/str_no_H.pdb to /tmp/biobb/unitests_13/str_check_add_hydrogens/4cc2cd6e-4c9f-4212-95dc-629e5790891b\nINFO     /tmp/biobb/unitests_13/str_check_add_hydrogens/str_check_add_hydrogens_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_13/str_check_add_hydrogens/4cc2cd6e-4c9f-4212-95dc-629e5790891b/str_no_H.pdb -o /tmp/biobb/unitests_13/str_check_add_hydrogens/4cc2cd6e-4c9f-4212-95dc-629e5790891b/output_structure_path.pdbqt --non_interactive --force_save --keep_canonical_resnames command_list --list &amp;#x27;add_hydrogen --add_charges ADT --add_mode auto &amp;#x27;\n\nINFO     /tmp/biobb/unitests_13/str_check_add_hydrogens/str_check_add_hydrogens_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_13/str_check_add_hydrogens/str_check_add_hydrogens_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_13/str_check_add_hydrogens/4cc2cd6e-4c9f-4212-95dc-629e5790891b/str_no_H.pdb loaded\n PDB id:  \n Title: \n Experimental method: unknown\n Resolution (A): N.A.\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  532\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  15\n Num. ligands or modified residues:  3\n Num. water mol.:  12\n Num. atoms:  3946\nMetal/Ion residues found\n  K A582\n MN A583\nSmall mol ligands found\nFBP A580\n\nStep 1: add_hydrogen --add_charges ADT --add_mode auto \nRunning add_hydrogen. Options: --add_charges ADT --add_mode auto\nFound 143 Residues requiring selection on adding H atoms\nWARNING: fixing side chains, override with --no_fix_side\nRunning fixside. Options: --fix all\nFound no residues with missing or unknown side chain atoms\nSelection: auto\nReplacing HIS A72 by HIE\nReplacing HIS A121 by HIE\nReplacing HIS A124 by HIE\nReplacing HIS A127 by HIE\nReplacing HIS A278 by HIE\nReplacing HIS A306 by HIE\nReplacing HIS A317 by HIE\nReplacing HIS A422 by HIE\nReplacing HIS A434 by HIE\nReplacing HIS A507 by HIE\nUpdating partial charges and atom types\nWarning: OXT atom missing in CILE A573. Run backbone --fix_atoms first\nWarning: FBP not found in residue library atom, charges set to 0.\nWarning: K not found in residue library atom, charges set to 0.\nWarning: MN not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nTotal assigned charge:      -1.25\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  532\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 517 (total 3995 H atoms)\nFinal Num. HETATM residues:  15\nFinal Num. ligands or modified residues:  3\nFinal Num. water mol.:  12\nFinal Num. atoms:  7941\nMetal/Ion residues found\n  K A582\n MN A583\nSmall mol ligands found\nFBP A580\nWarning: reverting residue names to canonical on output\nStructure saved on /tmp/biobb/unitests_13/str_check_add_hydrogens/4cc2cd6e-4c9f-4212-95dc-629e5790891b/output_structure_path.pdbqt\n\nINFO     /tmp/biobb/unitests_13/str_check_add_hydrogens/str_check_add_hydrogens_log.out:file_utils.py:390 /tmp/biobb/unitests_13/str_check_add_hydrogens/output_structure_path.pdbqt file ends with END, cleaning\nINFO     /tmp/biobb/unitests_13/str_check_add_hydrogens/str_check_add_hydrogens_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/str_check_add_hydrogens/4cc2cd6e-4c9f-4212-95dc-629e5790891b&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_structure_check.py::TestStructureCheck::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_structure_check.py::TestStructureCheck::test_launch&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_structure_check.py::TestStructureCheck::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-03-12 16:44:11,718 [MainThread  ] [INFO ]  Executing biobb_structure_utils.utils.structure_check Version: 4.1.0\n2024-03-12 16:44:11,720 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/structure_check/593340a0-6f89-4efd-8a06-af6ae9f32231\n2024-03-12 16:44:11,720 [MainThread  ] [INFO ]  Computing features: chains, models\n2024-03-12 16:44:11,720 [MainThread  ] [INFO ]  Creating d7e3182d-5761-49e6-ae18-ea9e87fe091c temporary folder\n2024-03-12 16:44:11,720 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_13/structure_check/593340a0-6f89-4efd-8a06-af6ae9f32231/2vgb.pdb --json /tmp/biobb/unitests_13/structure_check/593340a0-6f89-4efd-8a06-af6ae9f32231/output_summary_path.json --check_only --non_interactive command_list --list d7e3182d-5761-49e6-ae18-ea9e87fe091c/command_list.lst\n\n2024-03-12 16:44:12,823 [MainThread  ] [INFO ]  Exit code 0\n\n2024-03-12 16:44:12,823 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_13/structure_check/593340a0-6f89-4efd-8a06-af6ae9f32231/2vgb.pdb loaded\n PDB id: 2VGB \n Title: human erythrocyte pyruvate kinase\n Experimental method: x-ray diffraction\n Keywords: metal-binding, phosphorylation, pyruvate kinase in the active r- state, kinase, pyruvate, magnesium, glycolysis, transferase, disease mutation\n Resolution (A): 2.73\n\n Num. models: 1\n Num. chains: 4 (A: Protein, B: Protein, C: Protein, D: Protein)\n Num. residues:  2118\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  81\n Num. ligands or modified residues:  16\n Num. water mol.:  65\n Num. atoms:  15612\nMetal/Ion residues found\n  K A582\n MN A583\n  K B586\n MN B587\n  K C590\n MN C591\n  K D594\n MN D595\nSmall mol ligands found\nFBP A580\nPGA A581\nFBP B580\nPGA B581\nFBP C580\nPGA C581\nFBP D580\nPGA D581\n\nStep 1: chains\n\nRunning chains.\nDetected 4 Chain(s)\n A: Protein\n B: Protein\n C: Protein\n D: Protein\n\nStep 2: models\n\nRunning models.\nDetected 1 Model(s)\nFound Single model\nCommand list completed\nSummary data saved on /tmp/biobb/unitests_13/structure_check/593340a0-6f89-4efd-8a06-af6ae9f32231/output_summary_path.json\n\n2024-03-12 16:44:12,824 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/structure_check/593340a0-6f89-4efd-8a06-af6ae9f32231&amp;#x27;, &amp;#x27;d7e3182d-5761-49e6-ae18-ea9e87fe091c&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/structure_check/output_summary_path.json\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/structure_check/structure_check_log.out:file_utils.py:390 Executing biobb_structure_utils.utils.structure_check Version: 4.1.0\nINFO     /tmp/biobb/unitests_13/structure_check/structure_check_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_13/structure_check/593340a0-6f89-4efd-8a06-af6ae9f32231\nINFO     /tmp/biobb/unitests_13/structure_check/structure_check_log.out:file_utils.py:390 Computing features: chains, models\nINFO     /tmp/biobb/unitests_13/structure_check/structure_check_log.out:file_utils.py:390 Creating d7e3182d-5761-49e6-ae18-ea9e87fe091c temporary folder\nINFO     /tmp/biobb/unitests_13/structure_check/structure_check_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_13/structure_check/593340a0-6f89-4efd-8a06-af6ae9f32231/2vgb.pdb --json /tmp/biobb/unitests_13/structure_check/593340a0-6f89-4efd-8a06-af6ae9f32231/output_summary_path.json --check_only --non_interactive command_list --list d7e3182d-5761-49e6-ae18-ea9e87fe091c/command_list.lst\n\nINFO     /tmp/biobb/unitests_13/structure_check/structure_check_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_13/structure_check/structure_check_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_13/structure_check/593340a0-6f89-4efd-8a06-af6ae9f32231/2vgb.pdb loaded\n PDB id: 2VGB \n Title: human erythrocyte pyruvate kinase\n Experimental method: x-ray diffraction\n Keywords: metal-binding, phosphorylation, pyruvate kinase in the active r- state, kinase, pyruvate, magnesium, glycolysis, transferase, disease mutation\n Resolution (A): 2.73\n\n Num. models: 1\n Num. chains: 4 (A: Protein, B: Protein, C: Protein, D: Protein)\n Num. residues:  2118\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  81\n Num. ligands or modified residues:  16\n Num. water mol.:  65\n Num. atoms:  15612\nMetal/Ion residues found\n  K A582\n MN A583\n  K B586\n MN B587\n  K C590\n MN C591\n  K D594\n MN D595\nSmall mol ligands found\nFBP A580\nPGA A581\nFBP B580\nPGA B581\nFBP C580\nPGA C581\nFBP D580\nPGA D581\n\nStep 1: chains\n\nRunning chains.\nDetected 4 Chain(s)\n A: Protein\n B: Protein\n C: Protein\n D: Protein\n\nStep 2: models\n\nRunning models.\nDetected 1 Model(s)\nFound Single model\nCommand list completed\nSummary data saved on /tmp/biobb/unitests_13/structure_check/593340a0-6f89-4efd-8a06-af6ae9f32231/output_summary_path.json\n\nINFO     /tmp/biobb/unitests_13/structure_check/structure_check_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_13/structure_check/593340a0-6f89-4efd-8a06-af6ae9f32231&amp;#x27;, &amp;#x27;d7e3182d-5761-49e6-ae18-ea9e87fe091c&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
     <script>
       (function(){function r(e,n,t){function o(i,f){if(!n[i]){if(!e[i]){var c="function"==typeof require&&require;if(!f&&c)return c(i,!0);if(u)return u(i,!0);var a=new Error("Cannot find module '"+i+"'");throw a.code="MODULE_NOT_FOUND",a}var p=n[i]={exports:{}};e[i][0].call(p.exports,function(r){var n=e[i][1][r];return o(n||r)},p,p.exports,r,e,n,t)}return n[i].exports}for(var u="function"==typeof require&&require,i=0;i<t.length;i++)o(t[i]);return o}return r})()({1:[function(require,module,exports){
 const { getCollapsedCategory, setCollapsedIds } = require('./storage.js')