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MolBioMedUAB · Nov 23, 2022 · 0520627 · 0520627
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commit 0520627
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Showing 3 changed files with 10 additions and 12 deletions.
diff --git a/RCBS/md_analyser/measurements.py b/RCBS/md_analyser/measurements.py
@@ -314,16 +314,13 @@ def add_RMSD(self, name, sel, ref=None, superposition=True):
         elif isinstance(ref, AtomGroup):
             ref = ref.positions - ref.center_of_mass()
 
-
         self.measurements.append(
             {
                 "name": name,
                 "type": "rmsd",
                 "sel": sel,
                 "ref": ref,
-                "options": {
-                    "superposition" : superposition
-                },
+                "options": {"superposition": superposition},
             }
         )
 
@@ -725,22 +722,24 @@ def run_measure(self, save_output=False, verbose=True):
 
                         self.results[measurement["name"]].append(
                             rms.rmsd(
-                                measurement["sel"].positions - measurement["sel"].center_of_mass(),
+                                measurement["sel"].positions
+                                - measurement["sel"].center_of_mass(),
                                 measurement["ref"],
-                                center=True, superposition=True
+                                center=True,
+                                superposition=True,
                             )
                         )
 
                     elif measurement["options"]["superposition"] == False:
 
                         self.results[measurement["name"]].append(
                             rms.rmsd(
-                                measurement["sel"].positions - measurement["sel"].center_of_mass(),
-                                measurement["ref"]
+                                measurement["sel"].positions
+                                - measurement["sel"].center_of_mass(),
+                                measurement["ref"],
                             )
                         )
 
-
         if save_output != False:
 
             if save_output.split(".")[-1] in ("json", "jsn"):

diff --git a/RCBS/md_analyser/selections.py b/RCBS/md_analyser/selections.py
@@ -21,7 +21,7 @@ def selection(u, sel_input, sel_type=None, return_atomic_sel_string=False):
         - MDAnalysis selection as AtomGroup
     """
 
-    if sel_type == None or sel_type.lower() in ('none', 'pipe'):
+    if sel_type == None or sel_type.lower() in ("none", "pipe"):
         sel_string = sel_input
 
     elif isinstance(sel_input, list):
@@ -70,7 +70,6 @@ def selection(u, sel_input, sel_type=None, return_atomic_sel_string=False):
         elif sel_type.lower() == "res_name":
             sel_string = " ".join(["resname", str(sel_input)])
 
-
     if return_atomic_sel_string == False:
         return u.select_atoms(sel_string)
 

diff --git a/setup.py b/setup.py
@@ -6,7 +6,7 @@
 
 setup(
     name="RCBS.py",
-    version='0.1.0b',
+    version="0.1.0",
     description="Python package useful for analysing MD trajectories and creating QMMM models built on top of MDAnalysis.",
     long_description=long_description,
     long_description_content_type="text/markdown",