Fix some typos.

Author: lohedges

python/BioSimSpace/Align/_align.py

@@ -967,7 +967,7 @@ def rmsdAlign(molecule0, molecule1, mapping=None, property_map0={}, property_map
     except Exception as e:
         msg = "Failed to align molecules based on mapping: %r" % mapping
         if "Could not calculate the single value decomposition" in str(e):
-            msg += ". Try minimising your molecular coordinates prior to aligment."
+            msg += ". Try minimising your molecular coordinates prior to alignment."
         if _isVerbose():
             raise _AlignmentError(msg) from e
         else:

python/BioSimSpace/Gateway/_resources.py

@@ -47,9 +47,9 @@ def __init__(self):
                                                 add_help=False, allow_abbrev=False)
 
         # Add the arguments.
-        self._parser.add_argument("--nodes", type=int, help="The number of harwdare nodes.")
-        self._parser.add_argument("--cpus", type=int, help="The number of harwdare central processing units.")
-        self._parser.add_argument("--gpus", type=int, help="The number of harwdare graphics processors.")
+        self._parser.add_argument("--nodes", type=int, help="The number of hardware nodes.")
+        self._parser.add_argument("--cpus", type=int, help="The number of hardware central processing units.")
+        self._parser.add_argument("--gpus", type=int, help="The number of hardware graphics processors.")
 
     def _initialise(self):
         """Initialise the resource manager."""

python/BioSimSpace/IO/_io.py

@@ -595,7 +595,7 @@ def saveMolecules(filebase, system, fileformat, property_map={}):
                 # Write the default file to get the full path.
                 file = _SireIO.MoleculeParser.save(system._sire_object, filebase, _property_map)
 
-                # Now overwite the file the PDB file with the updated records.
+                # Now overwrite the file the PDB file with the updated records.
                 with open(file[0], "w") as pdb_file:
                     pdb_file.write(pdb_records)
 

python/BioSimSpace/Process/_amber.py

@@ -838,7 +838,7 @@ def getSystem(self, block="AUTO"):
             # Create a copy of the existing system object.
             old_system = self._system.copy()
 
-            # Udpate the coordinates and velocities and return a mapping between
+            # Update the coordinates and velocities and return a mapping between
             # the molecule indices in the two systems.
             sire_system, mapping = _SireIO.updateCoordinatesAndVelocities(
                     old_system._sire_object,
@@ -948,7 +948,7 @@ def getFrame(self, index):
             # Create a copy of the existing system object.
             old_system = self._system.copy()
 
-            # Udpate the coordinates and velocities and return a mapping between
+            # Update the coordinates and velocities and return a mapping between
             # the molecule indices in the two systems.
             sire_system, mapping = _SireIO.updateCoordinatesAndVelocities(
                     old_system._sire_object,

python/BioSimSpace/Process/_gromacs.py

@@ -2479,7 +2479,7 @@ def _getFrame(self, time):
                 # Create a copy of the existing system object.
                 old_system = self._system.copy()
 
-                # Udpate the coordinates and velocities and return a mapping between
+                # Update the coordinates and velocities and return a mapping between
                 # the molecule indices in the two systems.
                 sire_system, mapping = _SireIO.updateCoordinatesAndVelocities(
                         old_system._sire_object,

python/BioSimSpace/Process/_namd.py

@@ -692,7 +692,7 @@ def getSystem(self, block="AUTO"):
                 # Create a copy of the existing system object.
                 old_system = self._system.copy()
 
-                # Udpate the coordinates and velocities and return a mapping between
+                # Update the coordinates and velocities and return a mapping between
                 # the molecule indices in the two systems.
                 sire_system, mapping = _SireIO.updateCoordinatesAndVelocities(
                         old_system._sire_object,
@@ -804,7 +804,7 @@ def getFrame(self, index):
             # Create a copy of the existing system object.
             old_system = self._system.copy()
 
-            # Udpate the coordinates and velocities and return a mapping between
+            # Update the coordinates and velocities and return a mapping between
             # the molecule indices in the two systems.
             sire_system, mapping = _SireIO.updateCoordinatesAndVelocities(
                     old_system._sire_object,

python/BioSimSpace/Process/_openmm.py

@@ -1087,7 +1087,7 @@ def getSystem(self, block="AUTO"):
                 # Make a copy of the existing molecular system.
                 old_system = self._system.copy()
 
-                # Udpate the coordinates and velocities and return a mapping between
+                # Update the coordinates and velocities and return a mapping between
                 # the molecule indices in the two systems.
                 sire_system, mapping = _SireIO.updateCoordinatesAndVelocities(
                         old_system._sire_object,
@@ -1223,7 +1223,7 @@ def getFrame(self, index):
                                                self._top_file,
                                                index)
 
-            # Udpate the coordinates and velocities and return a mapping between
+            # Update the coordinates and velocities and return a mapping between
             # the molecule indices in the two systems.
             sire_system, mapping = _SireIO.updateCoordinatesAndVelocities(
                     old_system._sire_object,

python/BioSimSpace/Process/_somd.py

@@ -672,7 +672,7 @@ def getSystem(self, block="AUTO"):
             # coordinates back into the original system.
             old_system = self._system.copy()
 
-            # Udpate the coordinates and velocities and return a mapping between
+            # Update the coordinates and velocities and return a mapping between
             # the molecule indices in the two systems.
             sire_system, mapping = _SireIO.updateCoordinatesAndVelocities(
                     old_system._sire_object,
@@ -781,7 +781,7 @@ def getFrame(self, index):
             # Copy the new coordinates back into the original system.
             old_system = self._system.copy()
 
-            # Udpate the coordinates and velocities and return a mapping between
+            # Update the coordinates and velocities and return a mapping between
             # the molecule numbers in the two systems.
             sire_system, mapping = _SireIO.updateCoordinatesAndVelocities(
                     old_system._sire_object,
@@ -1070,7 +1070,7 @@ def _to_pert_file(molecule, filename="MORPH.pert", zero_dummy_dihedrals=False,
     # that the names must be unique. As such we need to count the number of
     # atoms with a particular name, then append an index to their name.
 
-    # Loop over all atoms in the molecule and tally the occurence of each
+    # Loop over all atoms in the molecule and tally the occurrence of each
     # name.
     atom_names = {}
     for atom in mol.atoms():

python/BioSimSpace/_SireWrappers/_system.py

@@ -612,7 +612,7 @@ def updateMolecules(self, molecules):
                     system = _SireIO.updateAndPreserveOrder(
                             system, mol._sire_object, idx)
 
-        # Udpate the Sire object.
+        # Update the Sire object.
         self._sire_object = system
 
         # Reset the index mappings.