Fix typos discovered by codespell in Python files (#5173)

devtools/forcefield-scripts/processTinkerForceField.py

@@ -293,7 +293,7 @@ def buildResidueDict( residueXmlFileName ):
         atoms       = getXmlAtoms( residue.findall('Atom') ) 
         bondInfo    = getXmlBonds( residue.findall('Bond') ) 
 
-        # if residue is an amino acid, then create CALA and NALA residues, in addition to non-termianal residue, and include approriate atoms
+        # if residue is an amino acid, then create CALA and NALA residues, in addition to non-termianal residue, and include appropriate atoms
         # HXT is excluded from all residues
 
         if( isWater ):

devtools/run-ctest.py

@@ -2,7 +2,7 @@
 Run test suite through CTest, with some options set for the CI environment.
 
 - Runs with a per-test and overall timeout which can be governed by the
-  avialable time on the CI system.
+  available time on the CI system.
 - Reruns tests which fail (does not rerun tests which merely timeout).
 
 """

examples/benchmarks/benchmark.py

@@ -34,7 +34,7 @@ def appendTestResult(filename=None, test_result=None, system_info=None):
         The filename to append a result to, ending either in .yaml or .json
         If None, no result is written
     test_result : dict, optional, default=None
-        The test result to append to the 'benchmarks' blcok
+        The test result to append to the 'benchmarks' block
     system_info : dict, optional, default=None
         System info to append to the 'system' block
     """

examples/extras/rigid.py

@@ -52,7 +52,7 @@ def createRigidBodies(system, positions, bodies):
     
     Care is needed when using constraints, since virtual particles cannot participate in constraints.  If the
     input system includes any constraints, this function will automatically remove ones that connect two
-    particles in the same rigid body.  But if there is a constraint beween a particle in a rigid body and
+    particles in the same rigid body.  But if there is a constraint between a particle in a rigid body and
     another particle not in that body, it will likely lead to an exception when you try to create a context.
     
     Parameters:

wrappers/python/openmm/app/desmonddmsfile.py

@@ -60,7 +60,7 @@ class DesmondDMSFile(object):
 
         # sqlite3 is included in the standard lib, but at python
         # compile time, you can disable support (I think), so it's
-        # not *guarenteed* to be available. Doing the import here
+        # not *guaranteed* to be available. Doing the import here
         # means we only raise an ImportError if people try to use
         # this class, so the module can be safely imported
         import sqlite3
@@ -90,7 +90,7 @@ class DesmondDMSFile(object):
             self._open[fcounter] = True
             tables = self._readSchemas(conn)
             if len(tables) == 0:
-                raise IOError('DMS file %s was not loaded sucessfully. No tables found' % str(f))
+                raise IOError('DMS file %s was not loaded successfully. No tables found' % str(f))
             if 'nbtype' not in tables['particle']:
                 raise ValueError('No nonbonded parameters associated with '
                                  'DMS file %s. You can add a forcefield with the '
@@ -882,7 +882,7 @@ class DesmondDMSFile(object):
 
 
     def _checkForUnsupportedTerms(self):
-        """Check the file for forcefield terms that are not currenty supported,
+        """Check the file for forcefield terms that are not currently supported,
         raising a NotImplementedError
         """
         flat_bottom_potential_terms = ['stretch_fbhw_term', 'angle_fbhw_term',

wrappers/python/openmm/app/internal/amber_file_parser.py

@@ -697,7 +697,7 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
       scee (float) - 1-4 electrostatics scaling factor (default: taken from prmtop or 2.0 if not present there)
       mm - if specified, this module will be used in place of pyopenmm (default: None)
       verbose (boolean) - if True, print out information on progress (default: False)
-      flexibleConstraints (boolean) - if True, flexible bonds will be added in addition ot constrained bonds
+      flexibleConstraints (boolean) - if True, flexible bonds will be added in addition to constrained bonds
       rigidWater (boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the shake argument
       sasaMethod (str='ACE') The string representing the SA model to use for GB calculations. Must be 'ACE', 'LCPO', or None
 

wrappers/python/openmm/app/internal/amoebaforces.py

@@ -280,7 +280,7 @@ class AmoebaBondForceBuilder(BaseAmoebaForceBuilder):
         bonds : list
             List of bonds indices as tuples of (atom1, atom2).
         isConstrained : list
-            List of flags indicating if a given bond is constrainted.
+            List of flags indicating if a given bond is constrained.
         flexibleConstraints : bool
             If True, constrained bonds will still be added to the system.
         """   
@@ -426,7 +426,7 @@ class AmoebaAngleForceBuilder(BaseAmoebaForceBuilder):
         angles : List[Tuple[int, int, int]]
             List of angle indices as tuples of (atom1, atom2, atom3).
         anglesConstraints : Optional[list]
-            List of flags indicating if a given angle is constrainted.
+            List of flags indicating if a given angle is constrained.
         flexibleConstraints : bool
             If True, constrained angles will still be added to the system.
         """
@@ -545,7 +545,7 @@ class AmoebaInPlaneAngleForceBuilder(BaseAmoebaForceBuilder):
         inPlaneAngles : List[Tuple[int, int, int, int]]
             List of in-plane angle indices as tuples of (atom1, atom2, atom3, atom4).
         anglesConstraints : Optional[list]
-            List of flags indicating if a given angle is constrainted.
+            List of flags indicating if a given angle is constrained.
         flexibleConstraints : bool
             If True, constrained angles will still be added to the system.
         """

wrappers/python/openmm/app/internal/pdbstructure.py

 """
-pdbstructure.py: Used for managing PDB formated files.
+pdbstructure.py: Used for managing PDB formatted files.
 
 This is part of the OpenMM molecular simulation toolkit.
 See https://openmm.org/development.
@@ -890,7 +890,7 @@ class Atom(object):
         if alternate_location_indicator is None:
             alternate_location_indicator = self.alternate_location_indicator
         # produce PDB line in three parts: names, numbers, and end
-        # Accomodate 4-character residue names that use column 21
+        # Accommodate 4-character residue names that use column 21
         long_res_name = self.residue_name_with_spaces
         if len(long_res_name) == 3:
             long_res_name += " "

wrappers/python/openmm/app/internal/pdbx/reader/PdbxContainers.py

@@ -23,7 +23,7 @@ A base container class is defined which supports common features of
 data and definition containers.   PDBx data files are organized in
 sections called data blocks which are mapped to data containers.
 PDBx dictionaries contain definition sections and data sections
-which are mapped to definition and data containes respectively.
+which are mapped to definition and data containers respectively.
 
 Data in both PDBx data files and dictionaries are organized in
 data categories. In the PDBx syntax individual items or data

wrappers/python/openmm/app/internal/pdbx/reader/PdbxParser.py

@@ -6,7 +6,7 @@
 #
 # 2009-11-05 - (jdw) Change table storage architecture for list of
 #                   dictionaries to list of lists.
-# 2012-01-09 - (jdw) This module now obsolted by PdbxReader/PdbxWriter
+# 2012-01-09 - (jdw) This module now obsoleted by PdbxReader/PdbxWriter
 #                   modules.  APIs are preserved.
 #
 # 2012-09-01 - (jdw) Revise tokenizer to better handle embedded quoting.
@@ -334,7 +334,7 @@ class PdbxReader(object):
                 curCatName,curAttName,curQuotedString,curWord = next(tokenizer)
 
             elif state == "ST_UNKNOWN":
-                self.__syntaxError("Unrecogized syntax element: " + str(curWord))
+                self.__syntaxError("Unrecognized syntax element: " + str(curWord))
                 return
                 
 
@@ -532,7 +532,7 @@ class PdbxWriter(object):
             if len(objL) == 0:
                 continue
 
-            # Item - value formattting 
+            # Item - value formatting 
             elif len(objL) == 1:
                 self.__writeItemValueFormat(obj)
 

wrappers/python/openmm/app/internal/pdbx/reader/PdbxReader.py

@@ -323,7 +323,7 @@ class PdbxReader(object):
                 curCatName,curAttName,curQuotedString,curWord = next(tokenizer)
 
             elif state == "ST_UNKNOWN":
-                self.__syntaxError("Unrecogized syntax element: " + str(curWord))
+                self.__syntaxError("Unrecognized syntax element: " + str(curWord))
                 return
                 
 

wrappers/python/openmm/app/internal/pdbx/writer/PdbxWriter.py

@@ -75,7 +75,7 @@ class PdbxWriter(object):
             if len(objL) == 0:
                 continue
 
-            # Item - value formattting 
+            # Item - value formatting 
             elif len(objL) == 1:
                 self.__writeItemValueFormat(obj)
 

wrappers/python/openmm/app/tinkerfiles.py

@@ -10,7 +10,7 @@ Contributors: Peter Eastman
 
 Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),
-to deal in the Software without restriction, includ  ing without limitation
+to deal in the Software without restriction, including without limitation
 the rights to use, copy, modify, merge, publish, distribute, sublicense,
 and/or sell copies of the Software, and to permit persons to whom the
 Software is furnished to do so, subject to the following conditions:

wrappers/python/openmm/unit/mymatrix.py

@@ -223,7 +223,7 @@ class MyMatrix(MyVector):
         n = len(rhs[0])
         r = len(rhs)
         if self.numCols() != r:
-            raise ArithmeticError("Matrix multplication size mismatch (%d vs %d)" % (self.numCols(), r))
+            raise ArithmeticError("Matrix multiplication size mismatch (%d vs %d)" % (self.numCols(), r))
         result = zeros(m, n)
         for i in range(m):
             for j in range(n):

wrappers/python/openmm/unit/prefix.py

@@ -144,7 +144,7 @@ def define_prefixed_units(base_unit, module = sys.modules[__name__]):
         new_unit = Unit({new_base_unit: 1.0})
         # Create base_unit attribute, needed for creating UnitSystems
         module.__dict__[name + '_base_unit'] = new_base_unit # e.g. "kilometer_base_unit"
-        # Create attribue in this module
+        # Create attribute in this module
         module.__dict__[name] = new_unit # e.g. "kilometer"
         # And plural version
         module.__dict__[name + 's'] = new_unit # e.g. "kilometers"

wrappers/python/openmm/unit/quantity.py

@@ -151,10 +151,10 @@ class Quantity(object):
                         if isinstance(value, numpy.ndarray):
                             value = numpy.array(new_container._value)
                         else:
-                            # delegate contruction to container class from list
+                            # delegate construction to container class from list
                             value = value.__class__(new_container._value)
                     except ImportError:
-                        # delegate contruction to container class from list
+                        # delegate construction to container class from list
                         value = value.__class__(new_container._value)
                 else:
                     # Non-Quantity, non container

wrappers/python/openmm/unit/unit.py

@@ -91,7 +91,7 @@ class Unit(object):
                 if base_unit not in self._all_base_units[dim]:
                     self._all_base_units[dim][base_unit] = 0
                 self._all_base_units[dim][base_unit] += exponent1 * exponent2
-        # What about heterogenous units that cancel? --> leave them
+        # What about heterogeneous units that cancel? --> leave them
         self._scaled_units.sort()
 
     def create_unit(self, scale, name, symbol):
@@ -466,7 +466,7 @@ class Unit(object):
     def get_name(self):
         """
         Returns a unit name (string) for this Unit, composed of its various
-        BaseUnit symbols.  e.g. 'kilogram meter**2 secon**-1'.
+        BaseUnit symbols.  e.g. 'kilogram meter**2 second**-1'.
         """
         try:
             return self._name

wrappers/python/src/swig_doxygen/swigInputBuilder.py

 #!/usr/bin/env python
-"""Build swig imput file from xml encoded header files (see gccxml)."""
+"""Build swig input file from xml encoded header files (see gccxml)."""
 __author__ = "Randall J. Radmer"
 __version__ = "1.0"
 

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -4,7 +4,7 @@
 # Add base classes missing from the XML input file
 MISSING_BASE_CLASSES = {'OpenMMException':'std::exception'}
 
-# Doc strings to replace some fo the confusing ones generaged by swig
+# Doc strings to replace some of the confusing ones generated by swig
 # Indexed by (className, methodName)
 DOC_STRINGS = {("Context", "setPositions") :
                 "setPositions(self, positions)",

wrappers/python/tests/TestAPIUnits.py

@@ -1258,7 +1258,7 @@ class TestAPIUnits(unittest.TestCase):
         integrator.setRelativeCollisionFrequency(0.1/picosecond)
         self.assertEqual(integrator.getRelativeCollisionFrequency(), 0.1/picosecond)
 
-        # Test bare consructor and addThermostat
+        # Test bare constructor and addThermostat
         integrator = NoseHooverIntegrator(1*femtosecond)
         self.assertEqual(integrator.getStepSize(), 1*femtosecond)