Fix more python docstrings, especially __init__ functions

wrappers/python/simtk/openmm/app/charmmpsffile.py

@@ -591,13 +591,22 @@ class CharmmPsfFile(object):
 
     def setBox(self, a, b, c, alpha=90.0*u.degrees, beta=90.0*u.degrees,
                gamma=90.0*u.degrees):
-        """
-        Sets the periodic box boundary conditions.
+        """Sets the periodic box boundary conditions.
 
-        Parameters:
-            - a, b, c (floats) : Lengths of the periodic cell
-            - alpha, beta, gamma (floats, optional) : Angles between the
-                periodic cell vectors.
+        Parameters
+        ----------
+        a : length
+            Lengths of the periodic cell
+        b : length
+            Lengths of the periodic cell
+        c : length
+            Lengths of the periodic cell
+        alpha : floats, optional
+            Angles between the periodic cell vectors.
+        beta : floats, optional
+            Angles between the periodic cell vectors.
+        gamma : floats, optional
+            Angles between the periodic cell vectors.
         """
         try:
             # Since we are setting the box, delete the cached box lengths if we

wrappers/python/simtk/openmm/app/dcdreporter.py

@@ -45,9 +45,12 @@ class DCDReporter(object):
     def __init__(self, file, reportInterval):
         """Create a DCDReporter.
 
-        Parameters:
-         - file (string) The file to write to
-         - reportInterval (int) The interval (in time steps) at which to write frames
+        Parameters
+        ----------
+        file : string
+            The file to write to
+        reportInterval : int
+            The interval (in time steps) at which to write frames
         """
         self._reportInterval = reportInterval
         self._out = open(file, 'wb')

wrappers/python/simtk/openmm/app/desmonddmsfile.py

@@ -46,10 +46,11 @@ class DesmondDMSFile(object):
     def __init__(self, file):
         """Load a DMS file
 
-        Parameters:
-         - file (string) the name of the file to load
+        Parameters
+        ----------
+        file : string
+            the name of the file to load
         """
-
         # 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

wrappers/python/simtk/openmm/app/element.py

@@ -58,11 +58,16 @@ class Element(object):
     def __init__(self, number, name, symbol, mass):
         """Create a new element
 
-        Parameters:
-        number (int) The atomic number of the element
-        name (string) The name of the element
-        symbol (string) The chemical symbol of the element
-        mass (float) The atomic mass of the element
+        Parameters
+        ----------
+        number : int
+            The atomic number of the element
+        name : string
+            The name of the element
+        symbol : string
+            The chemical symbol of the element
+        mass : float
+            The atomic mass of the element
         """
         ## The atomic number of the element
         self._atomic_number = number

wrappers/python/simtk/openmm/app/gromacsgrofile.py

@@ -114,10 +114,11 @@ class GromacsGroFile(object):
 
         The atom positions can be retrieved by calling getPositions().
 
-        Parameters:
-         - file (string) the name of the file to load
+        Parameters
+        ----------
+        file : string
+            the name of the file to load
         """
-
         xyzs     = []
         elements = [] # The element, most useful for quantum chemistry calculations
         atomname = [] # The atom name, for instance 'HW1'

wrappers/python/simtk/openmm/app/gromacstopfile.py

@@ -433,16 +433,22 @@ class GromacsTopFile(object):
     def __init__(self, file, periodicBoxVectors=None, unitCellDimensions=None, includeDir=None, defines=None):
         """Load a top file.
 
-        Parameters:
-         - file (string) the name of the file to load
-         - periodicBoxVectors (tuple of Vec3=None) the vectors defining the periodic box
-         - unitCellDimensions (Vec3=None) the dimensions of the crystallographic unit cell.  For
-           non-rectangular unit cells, specify periodicBoxVectors instead.
-         - includeDir (string=None) A directory in which to look for other files
-           included from the top file. If not specified, we will attempt to locate a gromacs
-           installation on your system. When gromacs is installed in /usr/local, this will resolve
-           to  /usr/local/gromacs/share/gromacs/top
-         - defines (dict={}) preprocessor definitions that should be predefined when parsing the file
+        Parameters
+        ----------
+        file : str
+            the name of the file to load
+        periodicBoxVectors : tuple of Vec3=None
+            the vectors defining the periodic box
+        unitCellDimensions : Vec3=None
+            the dimensions of the crystallographic unit cell.  For
+            non-rectangular unit cells, specify periodicBoxVectors instead.
+        includeDir : string=None
+            A directory in which to look for other files included from the
+            top file. If not specified, we will attempt to locate a gromacs
+            installation on your system. When gromacs is installed in
+            /usr/local, this will resolve to /usr/local/gromacs/share/gromacs/top
+        defines : dict={}
+            preprocessor definitions that should be predefined when parsing the file
          """
         if includeDir is None:
             includeDir = _defaultGromacsIncludeDir()

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

@@ -123,15 +123,18 @@ class PdbStructure(object):
     """
 
 
-    def __init__(self, input_stream, load_all_models = False):
+    def __init__(self, input_stream, load_all_models=False):
         """Create a PDB model from a PDB file stream.
 
-        Parameters:
-         - self (PdbStructure) The new object that is created.
-         - input_stream (stream) An input file stream, probably created with
-             open().
-         - load_all_models (bool) Whether to load every model of an NMR
-             structure or trajectory, or just load the first model, to save memory.
+        Parameters
+        ----------
+        self : PdbStructure
+            The new object that is created.
+        input_stream : stream
+            An input file stream, probably created with open().
+        load_all_models : bool
+            Whether to load every model of an NMR structure or trajectory, or
+            just load the first model, to save memory.
         """
         # initialize models
         self.load_all_models = load_all_models
@@ -201,7 +204,7 @@ class PdbStructure(object):
     def _reset_atom_numbers(self):
         self._atom_numbers_are_hex = False
         self._next_atom_number = 1
-    
+
     def _reset_residue_numbers(self):
         self._residue_numbers_are_hex = False
         self._next_residue_number = 1
@@ -269,8 +272,11 @@ class PdbStructure(object):
         Iterate over atomic positions.
 
         Parameters
-         - use_all_models (bool=False) Get positions from all models or just the first one.
-         - include_alt_loc (bool=False) Get all positions for each atom, or just the first one.
+        ----------
+        use_all_models : bool=False
+            Get positions from all models or just the first one.
+        include_alt_loc : bool=False
+            Get all positions for each atom, or just the first one.
         """
         for model in self.iter_models(use_all_models):
             for loc in model.iter_positions(include_alt_loc):
@@ -711,7 +717,7 @@ class Atom(object):
         self.is_first_atom_in_chain = False
         self.is_final_atom_in_chain = False
         self.is_first_residue_in_chain = False
-        self.is_final_residue_in_chain = False 
+        self.is_final_residue_in_chain = False
         # Start parsing fields from pdb line
         self.record_name = pdb_line[0:6].strip()
         if pdbstructure is not None and pdbstructure._atom_numbers_are_hex:

wrappers/python/simtk/openmm/app/modeller.py

@@ -186,10 +186,15 @@ class Modeller(object):
     def convertWater(self, model='tip3p'):
         """Convert all water molecules to a different water model.
 
-        Parameters:
-         - model (string='tip3p') the water model to convert to.  Supported values are 'tip3p', 'spce', 'tip4pew', and 'tip5p'.
+        Parameters
+        ----------
+        model : string='tip3p'
+            the water model to convert to.  Supported values are 'tip3p',
+            'spce', 'tip4pew', and 'tip5p'.
+
 
-        @deprecated Use addExtraParticles() instead.  It performs the same function but in a more general way.
+        @deprecated Use addExtraParticles() instead.  It performs the same
+        function but in a more general way.
         """
         if model in ('tip3p', 'spce'):
             sites = 3

wrappers/python/simtk/openmm/app/pdbfile.py

@@ -64,8 +64,10 @@ class PDBFile(object):
 
         The atom positions and Topology can be retrieved by calling getPositions() and getTopology().
 
-        Parameters:
-         - file (string) the name of the file to load
+        Parameters
+        ----------
+        file : string
+            the name of the file to load
         """
         top = Topology()
         ## The Topology read from the PDB file

wrappers/python/simtk/openmm/app/pdbreporter.py

@@ -44,9 +44,12 @@ class PDBReporter(object):
     def __init__(self, file, reportInterval):
         """Create a PDBReporter.
 
-        Parameters:
-         - file (string) The file to write to
-         - reportInterval (int) The interval (in time steps) at which to write frames
+        Parameters
+        ----------
+        file : string
+            The file to write to
+        reportInterval : int
+            The interval (in time steps) at which to write frames
         """
         self._reportInterval = reportInterval
         self._out = open(file, 'w')

wrappers/python/simtk/openmm/app/pdbxfile.py

@@ -53,10 +53,14 @@ class PDBxFile(object):
     def __init__(self, file):
         """Load a PDBx/mmCIF file.
 
-        The atom positions and Topology can be retrieved by calling getPositions() and getTopology().
+        The atom positions and Topology can be retrieved by calling
+        getPositions() and getTopology().
 
-        Parameters:
-         - file (string) the name of the file to load.  Alternatively you can pass an open file object.
+        Parameters
+        ----------
+        file : string
+            the name of the file to load.  Alternatively you can pass an open
+            file object.
         """
         top = Topology()
         ## The Topology read from the PDBx/mmCIF file

wrappers/python/simtk/openmm/app/simulation.py

@@ -55,13 +55,19 @@ class Simulation(object):
     def __init__(self, topology, system, integrator, platform=None, platformProperties=None):
         """Create a Simulation.
 
-        Parameters:
-         - topology (Topology) A Topology describing the the system to simulate
-         - system (System) The OpenMM System object to simulate
-         - integrator (Integrator) The OpenMM Integrator to use for simulating the System
-         - platform (Platform=None) If not None, the OpenMM Platform to use
-         - platformProperties (map=None) If not None, a set of platform-specific properties to pass
-           to the Context's constructor
+        Parameters
+        ----------
+        topology : Topology
+            A Topology describing the the system to simulate
+        system : System
+            The OpenMM System object to simulate
+        integrator : Integrator
+            The OpenMM Integrator to use for simulating the System
+        platform : Platform=None
+            If not None, the OpenMM Platform to use
+        platformProperties : map=None
+            If not None, a set of platform-specific properties to pass to the
+            Context's constructor
         """
         ## The Topology describing the system being simulated
         self.topology = topology

wrappers/python/simtk/openmm/app/statedatareporter.py

@@ -60,31 +60,54 @@ class StateDataReporter(object):
                  progress=False, remainingTime=False, speed=False, elapsedTime=False, separator=',', systemMass=None, totalSteps=None):
         """Create a StateDataReporter.
 
-        Parameters:
-         - file (string or file) The file to write to, specified as a file name or file object
-         - reportInterval (int) The interval (in time steps) at which to write frames
-         - step (boolean=False) Whether to write the current step index to the file
-         - time (boolean=False) Whether to write the current time to the file
-         - potentialEnergy (boolean=False) Whether to write the potential energy to the file
-         - kineticEnergy (boolean=False) Whether to write the kinetic energy to the file
-         - totalEnergy (boolean=False) Whether to write the total energy to the file
-         - temperature (boolean=False) Whether to write the instantaneous temperature to the file
-         - volume (boolean=False) Whether to write the periodic box volume to the file
-         - density (boolean=False) Whether to write the system density to the file
-         - progress (boolean=False) Whether to write current progress (percent completion) to the file.
-           If this is True, you must also specify totalSteps.
-         - remainingTime (boolean=False) Whether to write an estimate of the remaining clock time until
-           completion to the file.  If this is True, you must also specify totalSteps.
-         - speed (bool=False) Whether to write an estimate of the simulation speed in ns/day to the file
-         - elapsedTime (bool=False) Whether to write the elapsed time of the simulation in seconds to the file.
-         - separator (string=',') The separator to use between columns in the file
-         - systemMass (mass=None) The total mass to use for the system when reporting density.  If this is
-           None (the default), the system mass is computed by summing the masses of all particles.  This
-           parameter is useful when the particle masses do not reflect their actual physical mass, such as
-           when some particles have had their masses set to 0 to immobilize them.
-         - totalSteps (int=None) The total number of steps that will be included in the simulation.  This
-           is required if either progress or remainingTime is set to True, and defines how many steps will
-           indicate 100% completion.
+        Parameters
+        ----------
+        file : string or file
+            The file to write to, specified as a file name or file object
+        reportInterval : int
+            The interval (in time steps) at which to write frames
+        step : bool=False
+            Whether to write the current step index to the file
+        time : bool=False
+            Whether to write the current time to the file
+        potentialEnergy : bool=False
+            Whether to write the potential energy to the file
+        kineticEnergy : bool=False
+            Whether to write the kinetic energy to the file
+        totalEnergy : bool=False
+            Whether to write the total energy to the file
+        temperature : bool=False
+            Whether to write the instantaneous temperature to the file
+        volume : bool=False
+            Whether to write the periodic box volume to the file
+        density : bool=False
+            Whether to write the system density to the file
+        progress : bool=False
+            Whether to write current progress (percent completion) to the file.
+            If this is True, you must also specify totalSteps.
+        remainingTime : bool=False
+            Whether to write an estimate of the remaining clock time until
+            completion to the file.  If this is True, you must also specify
+            totalSteps.
+        speed : bool=False
+            Whether to write an estimate of the simulation speed in ns/day to
+            the file
+        elapsedTime : bool=False
+            Whether to write the elapsed time of the simulation in seconds to
+            the file.
+        separator : string=','
+            The separator to use between columns in the file
+        systemMass : mass=None
+            The total mass to use for the system when reporting density.  If
+            this is None (the default), the system mass is computed by summing
+            the masses of all particles.  This parameter is useful when the
+            particle masses do not reflect their actual physical mass, such as
+            when some particles have had their masses set to 0 to immobilize
+            them.
+        totalSteps : int=None
+            The total number of steps that will be included in the simulation.
+            This is required if either progress or remainingTime is set to True,
+            and defines how many steps will indicate 100% completion.
         """
         self._reportInterval = reportInterval
         self._openedFile = isinstance(file, str)
@@ -189,11 +212,16 @@ class StateDataReporter(object):
     def _constructReportValues(self, simulation, state):
         """Query the simulation for the current state of our observables of interest.
 
-        Parameters:
-         - simulation (Simulation) The Simulation to generate a report for
-         - state (State) The current state of the simulation
+        Parameters
+        ----------
+        simulation : Simulation
+            The Simulation to generate a report for
+        state : State
+            The current state of the simulation
 
-        Returns: A list of values summarizing the current state of
+        Returns
+        -------
+        A list of values summarizing the current state of
         the simulation, to be printed or saved. Each element in the list
         corresponds to one of the columns in the resulting CSV file.
         """