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Commit a8a78957 authored by peastman's avatar peastman
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Fixed incorrectly formatted comments that caused problems in the API docs

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wrappers/python/simtk/openmm/app/desmonddmsfile.py
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'''
"""
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()
......
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