Merge pull request #356 from peastman/master

Fixed incorrectly formatted comments that caused problems in the API docs

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

-'''
+"""
 desmonddmsfile.py: Load Desmond dms files
 
 Portions copyright (c) 2013 Stanford University and the Authors
@@ -23,7 +23,7 @@ THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
 DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
-'''
+"""
 
 import os
 import math
@@ -38,16 +38,16 @@ from simtk.unit import (nanometer, angstrom, dalton, radian,
 
 
 class DesmondDMSFile(object):
-    '''DesmondDMSFile parses a Desmond DMS (desmond molecular system) and
+    """DesmondDMSFile parses a Desmond DMS (desmond molecular system) and
     constructs a topology and (optionally) an OpenMM System from it
-    '''
+    """
 
     def __init__(self, file):
-        '''Load a DMS file
+        """Load a DMS file
 
         Parameters:
-        - file (string) the name of the file to load
-        '''
+         - 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
@@ -73,8 +73,8 @@ class DesmondDMSFile(object):
 
         # build the provenance string
         provenance = []
-        q = '''SELECT id, user, timestamp, version, workdir, cmdline, executable
-        FROM provenance'''
+        q = """SELECT id, user, timestamp, version, workdir, cmdline, executable
+        FROM provenance"""
         #for id, user, timestamp, version, workdir, cmdline, executable in self._conn.execute(q):
         for row in self._conn.execute('SELECT * FROM provenance'):
             rowdict = dict(zip(self._tables['provenance'], row))
@@ -89,23 +89,23 @@ class DesmondDMSFile(object):
         self._angleConstraints = [{} for x in range(len(self._topologyAtoms))]
 
     def getPositions(self):
-        '''Get the positions of each atom in the system
-        '''
+        """Get the positions of each atom in the system
+        """
         return self.positions
 
     def getTopology(self):
-        '''Get the topology of the system
-        '''
+        """Get the topology of the system
+        """
         return self.topology
 
     def getProvenance(self):
-        '''Get the provenance string of this system
-        '''
+        """Get the provenance string of this system
+        """
         return self.provenance
 
     def _createTopology(self):
-        '''Build the topology of the system
-        '''
+        """Build the topology of the system
+        """
         top = Topology()
         positions = []
 
@@ -119,8 +119,8 @@ class DesmondDMSFile(object):
         lastChain = None
         lastResId = None
         c = top.addChain()
-        q = '''SELECT id, name, anum, resname, resid, chain, x, y, z
-        FROM particle'''
+        q = """SELECT id, name, anum, resname, resid, chain, x, y, z
+        FROM particle"""
         for (atomId, atomName, atomNumber, resName, resId, chain, x, y, z) in self._conn.execute(q):
             newChain = False
             if chain != lastChain:
@@ -156,17 +156,17 @@ class DesmondDMSFile(object):
 
     def createSystem(self, nonbondedMethod=ff.NoCutoff, nonbondedCutoff=1.0*nanometer,
                      ewaldErrorTolerance=0.0005, removeCMMotion=True, hydrogenMass=None):
-        '''Construct an OpenMM System representing the topology described by this dms file
+        """Construct an OpenMM System representing the topology described by this dms file
 
         Parameters:
-        - nonbondedMethod (object=NoCutoff) The method to use for nonbonded interactions.  Allowed values are
-          NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
-        - nonbondedCutoff (distance=1*nanometer) The cutoff distance to use for nonbonded interactions
-        - ewaldErrorTolerance (float=0.0005) The error tolerance to use if nonbondedMethod is Ewald or PME.
-        - removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System
-        - hydrogenMass (mass=None) The mass to use for hydrogen atoms bound to heavy atoms.  Any mass added to a hydrogen is
-          subtracted from the heavy atom to keep their total mass the same.
-        '''
+         - nonbondedMethod (object=NoCutoff) The method to use for nonbonded interactions.  Allowed values are
+           NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
+         - nonbondedCutoff (distance=1*nanometer) The cutoff distance to use for nonbonded interactions
+         - ewaldErrorTolerance (float=0.0005) The error tolerance to use if nonbondedMethod is Ewald or PME.
+         - removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System
+         - hydrogenMass (mass=None) The mass to use for hydrogen atoms bound to heavy atoms.  Any mass added to a hydrogen is
+           subtracted from the heavy atom to keep their total mass the same.
+        """
         self._checkForUnsupportedTerms()
         sys = mm.System()
 
@@ -219,14 +219,14 @@ class DesmondDMSFile(object):
         return sys
 
     def _addBondsToSystem(self, sys):
-        '''Create the harmonic bonds
-        '''
+        """Create the harmonic bonds
+        """
         bonds = mm.HarmonicBondForce()
         sys.addForce(bonds)
 
-        q = '''SELECT p0, p1, r0, fc, constrained
+        q = """SELECT p0, p1, r0, fc, constrained
         FROM stretch_harm_term INNER JOIN stretch_harm_param
-        ON stretch_harm_term.param=stretch_harm_param.id'''
+        ON stretch_harm_term.param=stretch_harm_param.id"""
         for p0, p1, r0, fc, constrained in self._conn.execute(q):
             if constrained:
                 sys.addConstraint(p0, p1, r0*angstrom)
@@ -242,15 +242,15 @@ class DesmondDMSFile(object):
         return bonds
 
     def _addAnglesToSystem(self, sys):
-        '''Create the harmonic angles
-        '''
+        """Create the harmonic angles
+        """
         angles = mm.HarmonicAngleForce()
         sys.addForce(angles)
         degToRad = math.pi/180
 
-        q = '''SELECT p0, p1, p2, theta0, fc, constrained
+        q = """SELECT p0, p1, p2, theta0, fc, constrained
         FROM angle_harm_term INNER JOIN angle_harm_param
-        ON angle_harm_term.param=angle_harm_param.id'''
+        ON angle_harm_term.param=angle_harm_param.id"""
         for p0, p1, p2, theta0, fc, constrained in self._conn.execute(q):
             if constrained:
                 l1 = self._atomBonds[p1][p0]
@@ -267,15 +267,15 @@ class DesmondDMSFile(object):
         return angles
 
     def _addConstraintsToSystem(self, sys):
-        '''Add constraints to system. Normally these should already be
+        """Add constraints to system. Normally these should already be
         added by the bonds table, but we want to make sure that there's
         no extra information in the constraints table that we're not
-        including in the system'''
+        including in the system"""
         for term_table in [n for n in self._tables.keys() if n.startswith('constraint_a') and n.endswith('term')]:
             param_table = term_table.replace('term', 'param')
-            q = '''SELECT p0, p1, r1
+            q = """SELECT p0, p1, r1
             FROM %(term)s INNER JOIN %(param)s
-            ON %(term)s.param=%(param)s.id''' % \
+            ON %(term)s.param=%(param)s.id""" % \
                 {'term': term_table, 'param': param_table}
             for p0, p1, r1 in self._conn.execute(q):
                 if not p1 in self._atomBonds[p0]:
@@ -285,9 +285,9 @@ class DesmondDMSFile(object):
 
         if 'constraint_hoh_term' in self._tables:
             degToRad = math.pi/180
-            q = '''SELECT p0, p1, p2, r1, r2, theta
+            q = """SELECT p0, p1, p2, r1, r2, theta
             FROM constraint_hoh_term INNER JOIN constraint_hoh_param
-            ON constraint_hoh_term.param=constraint_hoh_param.id'''
+            ON constraint_hoh_term.param=constraint_hoh_param.id"""
             for p0, p1, p2, r1, r2, theta in self._conn.execute(q):
                 # Here, p0 is the heavy atom and p1 and p2 are the H1 and H2
                 # wihth O-H1 and O-H2 distances r1 and r2
@@ -296,14 +296,14 @@ class DesmondDMSFile(object):
                     sys.addConstraint(p1, p2, length)
 
     def _addPeriodicTorsionsToSystem(self, sys):
-        '''Create the torsion terms
-        '''
+        """Create the torsion terms
+        """
         periodic = mm.PeriodicTorsionForce()
         sys.addForce(periodic)
 
-        q = '''SELECT p0, p1, p2, p3, phi0, fc0, fc1, fc2, fc3, fc4, fc5, fc6
+        q = """SELECT p0, p1, p2, p3, phi0, fc0, fc1, fc2, fc3, fc4, fc5, fc6
         FROM dihedral_trig_term INNER JOIN dihedral_trig_param
-        ON dihedral_trig_term.param=dihedral_trig_param.id'''
+        ON dihedral_trig_term.param=dihedral_trig_param.id"""
         for p0, p1, p2, p3, phi0, fc0, fc1, fc2, fc3, fc4, fc5, fc6 in self._conn.execute(q):
             for order, fc in enumerate([fc0, fc1, fc2, fc3, fc4, fc5, fc6]):
                 if fc == 0:
@@ -312,8 +312,8 @@ class DesmondDMSFile(object):
 
 
     def _addImproperHarmonicTorsionsToSystem(self, sys):
-        '''Create the improper harmonic torsion terms
-        '''
+        """Create the improper harmonic torsion terms
+        """
         if not self._hasTable('improper_harm_term'):
             return
 
@@ -322,15 +322,15 @@ class DesmondDMSFile(object):
         harmonicTorsion.addPerTorsionParameter('k')
         sys.addForce(harmonicTorsion)
 
-        q = '''SELECT p0, p1, p2, p3, phi0, fc
+        q = """SELECT p0, p1, p2, p3, phi0, fc
         FROM improper_harm_term INNER JOIN improper_harm_param
-        ON improper_harm_term.param=improper_harm_param.id'''
+        ON improper_harm_term.param=improper_harm_param.id"""
         for p0, p1, p2, p3, phi0, fc in self._conn.execute(q):
             harmonicTorsion.addTorsion(p0, p1, p2, p3, [phi0*degree, fc*kilocalorie_per_mole])
 
     def _addCMAPToSystem(self, sys):
-        '''Create the CMAP terms
-        '''
+        """Create the CMAP terms
+        """
         if not self._hasTable('torsiontorsion_cmap_term'):
             return
 
@@ -354,30 +354,30 @@ class DesmondDMSFile(object):
             index = cmap.addMap(size, map*kilocalorie_per_mole)
             cmap_indices[name] = index
 
-        q = '''SELECT p0, p1, p2, p3, p4, p5, p6, p7, cmapid
+        q = """SELECT p0, p1, p2, p3, p4, p5, p6, p7, cmapid
         FROM torsiontorsion_cmap_term INNER JOIN torsiontorsion_cmap_param
-        ON torsiontorsion_cmap_term.param=torsiontorsion_cmap_param.id'''
+        ON torsiontorsion_cmap_term.param=torsiontorsion_cmap_param.id"""
         for p0, p1, p2, p3, p4, p5, p6, p7, cmapid in self._conn.execute(q):
             cmap.addTorsion(cmap_indices[cmapid], p0, p1, p2, p3, p4, p5, p6, p7)
 
     def _addNonbondedForceToSystem(self, sys):
-        '''Create the nonbonded force
-        '''
+        """Create the nonbonded force
+        """
         nb = mm.NonbondedForce()
         sys.addForce(nb)
 
-        q = '''SELECT charge, sigma, epsilon
+        q = """SELECT charge, sigma, epsilon
         FROM particle INNER JOIN nonbonded_param
-        ON particle.nbtype=nonbonded_param.id'''
+        ON particle.nbtype=nonbonded_param.id"""
         for charge, sigma, epsilon in self._conn.execute(q):
             nb.addParticle(charge, sigma*angstrom, epsilon*kilocalorie_per_mole)
 
         for p0, p1 in self._conn.execute('SELECT p0, p1 FROM exclusion'):
             nb.addException(p0, p1, 0.0, 1.0, 0.0)
 
-        q = '''SELECT p0, p1, aij, bij, qij
+        q = """SELECT p0, p1, aij, bij, qij
         FROM pair_12_6_es_term INNER JOIN pair_12_6_es_param
-        ON pair_12_6_es_term.param=pair_12_6_es_param.id;'''
+        ON pair_12_6_es_term.param=pair_12_6_es_param.id;"""
         for p0, p1, a_ij, b_ij, q_ij in self._conn.execute(q):
             a_ij = (a_ij*kilocalorie_per_mole*(angstrom**12)).in_units_of(kilojoule_per_mole*(nanometer**12))
             b_ij = (b_ij*kilocalorie_per_mole*(angstrom**6)).in_units_of(kilojoule_per_mole*(nanometer**6))
@@ -391,41 +391,41 @@ class DesmondDMSFile(object):
                 new_sigma = (a_ij / b_ij)**(1.0/6.0)
             nb.addException(p0, p1, q_ij, new_sigma, new_epsilon, True)
 
-        n_total = self._conn.execute('''SELECT COUNT(*) FROM pair_12_6_es_term''').fetchone()
-        n_in_exclusions = self._conn.execute('''SELECT COUNT(*)
+        n_total = self._conn.execute("""SELECT COUNT(*) FROM pair_12_6_es_term""").fetchone()
+        n_in_exclusions = self._conn.execute("""SELECT COUNT(*)
         FROM exclusion INNER JOIN pair_12_6_es_term
-        ON exclusion.p0==pair_12_6_es_term.p0 AND exclusion.p1==pair_12_6_es_term.p1''').fetchone()
+        ON exclusion.p0==pair_12_6_es_term.p0 AND exclusion.p1==pair_12_6_es_term.p1""").fetchone()
         if not n_total == n_in_exclusions:
             raise NotImplementedError('All pair_12_6_es_terms must have a corresponding exclusion')
 
         return nb
 
     def _addVirtualSitesToSystem(self, sys):
-        '''Create any virtual sites in the systempy
-        '''
+        """Create any virtual sites in the systempy
+        """
         if not any(t.startswith('virtual_') for t in self._tables.keys()):
             return
 
         if 'virtual_lc2_term' in self._tables:
-            q = '''SELECT p0, p1, p2, c1
+            q = """SELECT p0, p1, p2, c1
             FROM virtual_lc2_term INNER JOIN virtual_lc2_param
-            ON virtual_lc2_term.param=virtual_lc2_param.id'''
+            ON virtual_lc2_term.param=virtual_lc2_param.id"""
             for p0, p1, p2, c1 in self._conn.execute(q):
                 vsite = mm.TwoParticleAverageSite(p1, p2, (1-c1), c1)
                 sys.setVirtualSite(p0, vsite)
 
         if 'virtual_lc3_term' in self._tables:
-            q = '''SELECT p0, p1, p2, p3, c1, c2
+            q = """SELECT p0, p1, p2, p3, c1, c2
             FROM virtual_lc3_term INNER JOIN virtual_lc3_param
-            ON virtual_lc3_term.param=virtual_lc3_param.id'''
+            ON virtual_lc3_term.param=virtual_lc3_param.id"""
             for p0, p1, p2, p3, c1, c2 in self._conn.execute(q):
                 vsite = mm.ThreeParticleAverageSite(p1, p2, p3, (1-c1-c2), c1, c2)
                 sys.setVirtualSite(p0, vsite)
 
         if 'virtual_out3_term' in self._tables:
-            q = '''SELECT p0, p1, p2, p3, c1, c2, c3
+            q = """SELECT p0, p1, p2, p3, c1, c2, c3
             FROM virtual_out3_term INNER JOIN virtual_out3_param
-            ON virtual_out3_term.param=virtual_out3_param.id'''
+            ON virtual_out3_term.param=virtual_out3_param.id"""
             for p0, p1, p2, p3, c1, c2, c3 in self._conn.execute(q):
                 vsite = mm.OutOfPlaneSite(p1, p2, p3, c1, c2, c3)
                 sys.setVirtualSite(p0, vsite)
@@ -436,14 +436,14 @@ class DesmondDMSFile(object):
 
 
     def _hasTable(self, table_name):
-        '''Does our DMS file contain this table?
-        '''
+        """Does our DMS file contain this table?
+        """
         return table_name in self._tables
 
     def _readSchemas(self):
-        '''Read the schemas of each of the tables in the dms file, populating
+        """Read the schemas of each of the tables in the dms file, populating
         the `_tables` instance attribute
-        '''
+        """
         tables = {}
         for table in self._conn.execute("SELECT name FROM sqlite_master WHERE type='table'"):
             names = []
@@ -453,9 +453,9 @@ class DesmondDMSFile(object):
         self._tables = tables
 
     def _checkForUnsupportedTerms(self):
-        '''Check the file for forcefield terms that are not currenty supported,
+        """Check the file for forcefield terms that are not currenty supported,
         raising a NotImplementedError
-        '''
+        """
         if 'posre_harm_term' in self._tables:
             raise NotImplementedError('Position restraints are not implemented.')
         flat_bottom_potential_terms = ['stretch_fbhw_term', 'angle_fbhw_term',
@@ -488,8 +488,8 @@ class DesmondDMSFile(object):
                 raise NotImplementedError('Drude particles are not currently supported')
 
     def close(self):
-        '''Close the SQL connection
-        '''
+        """Close the SQL connection
+        """
         if self._open:
             self._conn.close()