Fixed verion settings

Author: Steven Ayoub

blues/integrators.py

@@ -99,7 +99,7 @@ class AlchemicalExternalLangevinIntegrator(AlchemicalNonequilibriumLangevinInteg
 
     def __init__(self,
                  alchemical_functions,
-                 splitting="R V O H O V R",
+                 splitting="H V R O V R H",
                  temperature=298.0 * openmm.unit.kelvin,
                  collision_rate=1.0 / openmm.unit.picoseconds,
                  timestep=1.0 * openmm.unit.femtoseconds,

blues/moves.py

@@ -195,12 +195,12 @@ def __init__(self, structure, resname='LIG', random_state=None):
         self.resname = resname
         self.random_state = random_state
         self.atom_indices = self.getAtomIndices(structure, self.resname)
-        atom_indices_1based = [i + 1 for i in self.atom_indices]
-        self.topology = structure[atom_indices_1based].topology
+        #atom_indices_1based = [i + 1 for i in self.atom_indices]
+        self.topology = structure[self.atom_indices].topology
         self.totalmass = 0
         self.masses = []
         self.center_of_mass = None
-        self.positions = structure[atom_indices_1based].positions
+        self.positions = structure[self.atom_indices].positions
         self._calculateProperties()
 
     def getAtomIndices(self, structure, resname):

setup.py

@@ -82,4 +82,4 @@ def find_package_data(data_root, package_root):
         'tox',
     ],
     zip_safe=False,
-    include_package_data=True)
+    include_package_data=True)

versioneer.py

@@ -336,9 +336,9 @@ def get_config_from_root(root):
     # configparser.NoOptionError (if it lacks "VCS="). See the docstring at
     # the top of versioneer.py for instructions on writing your setup.cfg .
     setup_cfg = os.path.join(root, "setup.cfg")
-    parser = configparser.SafeConfigParser()
+    parser = configparser.ConfigParser()
     with open(setup_cfg, "r") as f:
-        parser.readfp(f)
+        parser.read_file(f)
     VCS = parser.get("versioneer", "VCS")  # mandatory
 
     def get(parser, name):
@@ -1834,4 +1834,4 @@ def scan_setup_py():
         errors = do_setup()
         errors += scan_setup_py()
         if errors:
-            sys.exit(1)
+            sys.exit(1)