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Commit 74415dd9 authored by Lee-Ping Wang's avatar Lee-Ping Wang
Browse files

Merge branch 'master' of https://github.com/SimTk/openmm

parents 25c22045 6701dacc
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wrappers/python/simtk/openmm/__init__.py
View file @ 74415dd9
......@@ -35,4 +35,4 @@ else:
from simtk.openmm.openmm import *
from simtk.openmm.vec3 import Vec3
pluginLoadedLibNames = Platform.loadPluginsFromDirectory(Platform.getDefaultPluginsDirectory())
\ No newline at end of file
pluginLoadedLibNames = Platform.loadPluginsFromDirectory(Platform.getDefaultPluginsDirectory())
wrappers/python/simtk/openmm/app/amberinpcrdfile.py
View file @ 74415dd9
......@@ -10,7 +10,7 @@ Portions copyright (c) 2012 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
Permission is hereby granted, free of charge, to any person obtaining a
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, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
......@@ -40,15 +40,15 @@ except:
class AmberInpcrdFile(object):
"""AmberInpcrdFile parses an AMBER inpcrd file and loads the data stored in it."""
def __init__(self, file, loadVelocities=False, loadBoxVectors=False):
"""Load an inpcrd file.
An inpcrd file contains atom positions and, optionally, velocities and periodic box dimensions.
Unfortunately, it is sometimes impossible to determine from the file itself exactly what data
it contains. You therefore must specify in advance what data to load. It is stored into this
object's "positions", "velocities", and "boxVectors" fields.
Parameters:
- file (string) the name of the file to load
- loadVelocities (boolean=False) whether to load velocities from the file
......@@ -78,7 +78,7 @@ class AmberInpcrdFile(object):
def getPositions(self, asNumpy=False):
"""Get the atomic positions.
Parameters:
- asNumpy (boolean=False) if true, the values are returned as a numpy array instead of a list of Vec3s
"""
......@@ -87,10 +87,10 @@ class AmberInpcrdFile(object):
self._numpyPositions = Quantity(numpy.array(self.positions.value_in_unit(nanometers)), nanometers)
return self._numpyPositions
return self.positions
def getVelocities(self, asNumpy=False):
"""Get the atomic velocities.
Parameters:
- asNumpy (boolean=False) if true, the vectors are returned as numpy arrays instead of Vec3s
"""
......@@ -99,10 +99,10 @@ class AmberInpcrdFile(object):
self._numpyVelocities = Quantity(numpy.array(self.velocities.value_in_unit(nanometers/picoseconds)), nanometers/picoseconds)
return self._numpyVelocities
return self.velocities
def getBoxVectors(self, asNumpy=False):
"""Get the periodic box vectors.
Parameters:
- asNumpy (boolean=False) if true, the values are returned as a numpy array instead of a list of Vec3s
"""
......@@ -114,4 +114,4 @@ class AmberInpcrdFile(object):
self._numpyBoxVectors.append(Quantity(numpy.array(self.boxVectors[2].value_in_unit(nanometers)), nanometers))
return self._numpyBoxVectors
return self.boxVectors
wrappers/python/simtk/openmm/app/amberprmtopfile.py
View file @ 74415dd9
......@@ -10,7 +10,7 @@ Portions copyright (c) 2012 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
Permission is hereby granted, free of charge, to any person obtaining a
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, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
......@@ -48,15 +48,15 @@ GBn = object()
class AmberPrmtopFile(object):
"""AmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it."""
def __init__(self, file):
"""Load a prmtop file."""
top = Topology()
## The Topology read from the prmtop file
self.topology = top
# Load the prmtop file
prmtop = amber_file_parser.PrmtopLoader(file)
self._prmtop = prmtop
......@@ -82,7 +82,7 @@ class AmberPrmtopFile(object):
atomName = atomReplacements[atomName]
# Try to guess the element.
upper = atomName.upper()
if upper.startswith('CL'):
element = elem.chlorine
......@@ -96,17 +96,17 @@ class AmberPrmtopFile(object):
except KeyError:
element = None
top.addAtom(atomName, element, r)
# Add bonds to the topology
atoms = list(top.atoms())
for bond in prmtop.getBondsWithH():
top.addBond(atoms[bond[0]], atoms[bond[1]])
for bond in prmtop.getBondsNoH():
top.addBond(atoms[bond[0]], atoms[bond[1]])
# Set the periodic box size.
if prmtop.getIfBox():
top.setUnitCellDimensions(tuple(x.value_in_unit(unit.nanometer) for x in prmtop.getBoxBetaAndDimensions()[1:4])*unit.nanometer)
......@@ -114,7 +114,7 @@ class AmberPrmtopFile(object):
constraints=None, rigidWater=True, implicitSolvent=None, soluteDielectric=1.0, solventDielectric=78.5, removeCMMotion=True,
ewaldErrorTolerance=0.0005):
"""Construct an OpenMM System representing the topology described by this prmtop file.
Parameters:
- nonbondedMethod (object=NoCutoff) The method to use for nonbonded interactions. Allowed values are
NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
......@@ -168,4 +168,4 @@ class AmberPrmtopFile(object):
force.setEwaldErrorTolerance(ewaldErrorTolerance)
if removeCMMotion:
sys.addForce(mm.CMMotionRemover())
return sys
\ No newline at end of file
return sys
wrappers/python/simtk/openmm/app/dcdfile.py
View file @ 74415dd9
......@@ -10,7 +10,7 @@ Portions copyright (c) 2012 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
Permission is hereby granted, free of charge, to any person obtaining a
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, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
......@@ -40,18 +40,18 @@ from simtk.unit import picoseconds, nanometers, angstroms, is_quantity, norm
class DCDFile(object):
"""DCDFile provides methods for creating DCD files.
DCD is a file format for storing simulation trajectories. It is supported by many programs, such
as CHARMM, NAMD, and X-PLOR. Note, however, that different programs produce subtly different
versions of the format. This class generates the CHARMM version. Also note that there is no
standard byte ordering (big-endian or little-endian) for this format. This class always generates
files with little-endian ordering.
To use this class, create a DCDFile object, then call writeModel() once for each model in the file."""
def __init__(self, file, topology, dt, firstStep=0, interval=1):
"""Create a DCD file and write out the header.
Parameters:
- file (file) A file to write to
- topology (Topology) The Topology defining the molecular system being written
......@@ -76,10 +76,10 @@ class DCDFile(object):
header += struct.pack('<80s', 'Created '+time.asctime(time.localtime(time.time())))
header += struct.pack('<4i', 164, 4, len(list(topology.atoms())), 4)
file.write(header)
def writeModel(self, positions, unitCellDimensions=None):
"""Write out a model to the DCD file.
Parameters:
- positions (list) The list of atomic positions to write
- unitCellDimensions (Vec3=None) The dimensions of the crystallographic unit cell. If None, the dimensions specified in
......@@ -87,7 +87,7 @@ class DCDFile(object):
represent a periodic system.
"""
if len(list(self._topology.atoms())) != len(positions):
raise ValueError('The number of positions must match the number of atoms')
raise ValueError('The number of positions must match the number of atoms')
if is_quantity(positions):
positions = positions.value_in_unit(nanometers)
if any(math.isnan(norm(pos)) for pos in positions):
......@@ -95,17 +95,17 @@ class DCDFile(object):
if any(math.isinf(norm(pos)) for pos in positions):
raise ValueError('Particle position is infinite')
file = self._file
# Update the header.
self._modelCount += 1
file.seek(8, os.SEEK_SET)
file.write(struct.pack('<i', self._modelCount))
file.seek(20, os.SEEK_SET)
file.write(struct.pack('<i', self._firstStep+self._modelCount*self._interval))
# Write the data.
file.seek(0, os.SEEK_END)
boxSize = self._topology.getUnitCellDimensions()
if boxSize is not None:
......
wrappers/python/simtk/openmm/app/dcdreporter.py
View file @ 74415dd9
......@@ -10,7 +10,7 @@ Portions copyright (c) 2012 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
Permission is hereby granted, free of charge, to any person obtaining a
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, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
......@@ -34,16 +34,16 @@ __version__ = "1.0"
import simtk.openmm as mm
from simtk.openmm.app import DCDFile
from simtk.unit import nanometer
class DCDReporter(object):
"""DCDReporter outputs a series of frames from a Simulation to a DCD file.
To use it, create a DCDReporter, then add it to the Simulation's list of reporters.
"""
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
......@@ -51,10 +51,10 @@ class DCDReporter(object):
self._reportInterval = reportInterval
self._out = open(file, 'wb')
self._dcd = None
def describeNextReport(self, simulation):
"""Get information about the next report this object will generate.
Parameters:
- simulation (Simulation) The Simulation to generate a report for
Returns: A five element tuple. The first element is the number of steps until the
......@@ -63,10 +63,10 @@ class DCDReporter(object):
"""
steps = self._reportInterval - simulation.currentStep%self._reportInterval
return (steps, True, False, False, False)
def report(self, simulation, state):
"""Generate a report.
Parameters:
- simulation (Simulation) The Simulation to generate a report for
- state (State) The current state of the simulation
......@@ -75,6 +75,6 @@ class DCDReporter(object):
self._dcd = DCDFile(self._out, simulation.topology, simulation.integrator.getStepSize(), 0, self._reportInterval)
a,b,c = state.getPeriodicBoxVectors()
self._dcd.writeModel(state.getPositions(), mm.Vec3(a[0].value_in_unit(nanometer), b[1].value_in_unit(nanometer), c[2].value_in_unit(nanometer))*nanometer)
def __del__(self):
self._out.close()
wrappers/python/simtk/openmm/app/element.py
View file @ 74415dd9
......@@ -12,7 +12,7 @@ Portions copyright (c) 2012 Stanford University and the Authors.
Authors: Christopher M. Bruns
Contributors:
Permission is hereby granted, free of charge, to any person obtaining a
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, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
......@@ -38,13 +38,13 @@ from simtk.unit import daltons
class Element:
"""An Element represents a chemical element.
The simtk.openmm.app.element module contains objects for all the standard chemical elements,
such as element.hydrogen or element.carbon. You can also call the static method Element.getBySymbol() to
look up the Element with a particular chemical symbol."""
_elements_by_symbol = {}
def __init__(self, number, name, symbol, mass):
## The atomic number of the element
self.atomic_number = number
......
wrappers/python/simtk/openmm/app/gromacsgrofile.py
View file @ 74415dd9
......@@ -10,7 +10,7 @@ Portions copyright (c) 2012 Stanford University and the Authors.
Authors: Lee-Ping Wang, Peter Eastman
Contributors:
Permission is hereby granted, free of charge, to any person obtaining a
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, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
......@@ -47,7 +47,7 @@ def _isint(word):
@param[in] word String (for instance, '123', '153.0', '2.', '-354')
@return answer Boolean which specifies whether the string is an integer (only +/- sign followed by digits)
"""
return match('^[-+]?[0-9]+$',word)
......@@ -57,7 +57,7 @@ def _isfloat(word):
@param[in] word String (for instance, '123', '153.0', '2.', '-354')
@return answer Boolean which specifies whether the string is any number
"""
return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word)
......@@ -65,7 +65,7 @@ def _is_gro_coord(line):
""" Determines whether a line contains GROMACS data or not
@param[in] line The line to be tested
"""
sline = line.split()
if len(sline) == 6 or len(sline) == 9:
......@@ -79,7 +79,7 @@ def _is_gro_box(line):
""" Determines whether a line contains a GROMACS box vector or not
@param[in] line The line to be tested
"""
sline = line.split()
if len(sline) == 9 and all([_isfloat(i) for i in sline]):
......@@ -91,16 +91,16 @@ def _is_gro_box(line):
class GromacsGroFile(object):
"""GromacsGroFile parses a Gromacs .gro file and constructs a set of atom positions from it.
A .gro file also contains some topological information, such as elements and residue names,
but not enough to construct a full Topology object. This information is recorded and stored
in the object's public fields."""
def __init__(self, file):
"""Load a .gro file.
The atom positions can be retrieved by calling getPositions().
Parameters:
- file (string) the name of the file to load
"""
......@@ -145,7 +145,7 @@ class GromacsGroFile(object):
else:
raise Exception("Unexpected line in .gro file: "+line)
ln += 1
## The atom positions read from the file. If the file contains multiple frames, these are the positions in the first frame.
self.positions = xyzs[0]
## A list containing the element of each atom stored in the file
......@@ -159,14 +159,14 @@ class GromacsGroFile(object):
self._positions = xyzs
self._unitCellDimensions = boxes
self._numpyPositions = None
def getNumFrames(self):
"""Get the number of frames stored in the file."""
return len(self._positions)
def getPositions(self, asNumpy=False, frame=0):
"""Get the atomic positions.
Parameters:
- asNumpy (boolean=False) if true, the values are returned as a numpy array instead of a list of Vec3s
- frame (int=0) the index of the frame for which to get positions
......@@ -178,10 +178,10 @@ class GromacsGroFile(object):
self._numpyPositions[frame] = Quantity(numpy.array(self._positions[frame].value_in_unit(nanometers)), nanometers)
return self._numpyPositions[frame]
return self._positions[frame]
def getUnitCellDimensions(self, frame=0):
"""Get the dimensions of the crystallographic unit cell.
Parameters:
- frame (int=0) the index of the frame for which to get the unit cell dimensions
"""
......
wrappers/python/simtk/openmm/app/gromacstopfile.py
View file @ 74415dd9
......@@ -10,7 +10,7 @@ Portions copyright (c) 2012-2013 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
Permission is hereby granted, free of charge, to any person obtaining a
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, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
......@@ -49,7 +49,7 @@ OBC2 = prmtop.OBC2
class GromacsTopFile(object):
"""GromacsTopFile parses a Gromacs top file and constructs a Topology and (optionally) an OpenMM System from it."""
class _MoleculeType(object):
"""Inner class to store information about a molecule type."""
def __init__(self):
......@@ -60,7 +60,7 @@ class GromacsTopFile(object):
self.exclusions = []
self.pairs = []
self.cmaps = []
def _processFile(self, file):
append = ''
for line in open(file):
......@@ -69,7 +69,7 @@ class GromacsTopFile(object):
else:
self._processLine(append+' '+line, file)
append = ''
def _processLine(self, line, file):
"""Process one line from a file."""
if ';' in line:
......@@ -79,13 +79,13 @@ class GromacsTopFile(object):
if stripped.startswith('*') or len(stripped) == 0:
# A comment or empty line.
return
elif stripped.startswith('[') and not ignore:
# The start of a category.
if not stripped.endswith(']'):
raise ValueError('Illegal line in .top file: '+line)
self._currentCategory = stripped[1:-1].strip()
elif stripped.startswith('#'):
# A preprocessor command.
fields = stripped.split()
......@@ -127,7 +127,7 @@ class GromacsTopFile(object):
if len(self._ifStack) == 0:
raise ValueError('Unexpected line in .top file: '+line)
del(self._ifStack[-1])
elif not ignore:
# A line of data for the current category
if self._currentCategory is None:
......@@ -166,7 +166,7 @@ class GromacsTopFile(object):
self._processPairType(line)
elif self._currentCategory == 'cmaptypes':
self._processCmapType(line)
def _processDefaults(self, line):
"""Process the [ defaults ] line."""
fields = line.split()
......@@ -179,7 +179,7 @@ class GromacsTopFile(object):
if fields[2].lower() == 'no':
raise ValueError('gen_pairs=no is not supported')
self._defaults = fields
def _processMoleculeType(self, line):
"""Process a line in the [ moleculetypes ] category."""
fields = line.split()
......@@ -188,14 +188,14 @@ class GromacsTopFile(object):
type = GromacsTopFile._MoleculeType()
self._moleculeTypes[fields[0]] = type
self._currentMoleculeType = type
def _processMolecule(self, line):
"""Process a line in the [ molecules ] category."""
fields = line.split()
if len(fields) < 2:
raise ValueError('Too few fields in [ molecules ] line: '+line);
self._molecules.append((fields[0], int(fields[1])))
def _processAtom(self, line):
"""Process a line in the [ atoms ] category."""
if self._currentMoleculeType is None:
......@@ -204,7 +204,7 @@ class GromacsTopFile(object):
if len(fields) < 5:
raise ValueError('Too few fields in [ atoms ] line: '+line);
self._currentMoleculeType.atoms.append(fields)
def _processBond(self, line):
"""Process a line in the [ bonds ] category."""
if self._currentMoleculeType is None:
......@@ -215,7 +215,7 @@ class GromacsTopFile(object):
if fields[2] != '1':
raise ValueError('Unsupported function type in [ bonds ] line: '+line);
self._currentMoleculeType.bonds.append(fields)
def _processAngle(self, line):
"""Process a line in the [ angles ] category."""
if self._currentMoleculeType is None:
......@@ -226,7 +226,7 @@ class GromacsTopFile(object):
if fields[3] not in ('1', '5'):
raise ValueError('Unsupported function type in [ angles ] line: '+line);
self._currentMoleculeType.angles.append(fields)
def _processDihedral(self, line):
"""Process a line in the [ dihedrals ] category."""
if self._currentMoleculeType is None:
......@@ -237,7 +237,7 @@ class GromacsTopFile(object):
if fields[4] not in ('1', '2', '3', '4', '9'):
raise ValueError('Unsupported function type in [ dihedrals ] line: '+line);
self._currentMoleculeType.dihedrals.append(fields)
def _processExclusion(self, line):
"""Process a line in the [ exclusions ] category."""
if self._currentMoleculeType is None:
......@@ -246,7 +246,7 @@ class GromacsTopFile(object):
if len(fields) < 2:
raise ValueError('Too few fields in [ exclusions ] line: '+line);
self._currentMoleculeType.exclusions.append(fields)
def _processPair(self, line):
"""Process a line in the [ pairs ] category."""
if self._currentMoleculeType is None:
......@@ -257,7 +257,7 @@ class GromacsTopFile(object):
if fields[2] != '1':
raise ValueError('Unsupported function type in [ pairs ] line: '+line);
self._currentMoleculeType.pairs.append(fields)
def _processCmap(self, line):
"""Process a line in the [ cmaps ] category."""
if self._currentMoleculeType is None:
......@@ -266,14 +266,14 @@ class GromacsTopFile(object):
if len(fields) < 6:
raise ValueError('Too few fields in [ pairs ] line: '+line);
self._currentMoleculeType.cmaps.append(fields)
def _processAtomType(self, line):
"""Process a line in the [ atomtypes ] category."""
fields = line.split()
if len(fields) < 7:
raise ValueError('Too few fields in [ atomtypes ] line: '+line);
self._atomTypes[fields[0]] = fields
def _processBondType(self, line):
"""Process a line in the [ bondtypes ] category."""
fields = line.split()
......@@ -282,7 +282,7 @@ class GromacsTopFile(object):
if fields[2] != '1':
raise ValueError('Unsupported function type in [ bondtypes ] line: '+line);
self._bondTypes[tuple(fields[:2])] = fields
def _processAngleType(self, line):
"""Process a line in the [ angletypes ] category."""
fields = line.split()
......@@ -291,7 +291,7 @@ class GromacsTopFile(object):
if fields[3] not in ('1', '5'):
raise ValueError('Unsupported function type in [ angletypes ] line: '+line);
self._angleTypes[tuple(fields[:3])] = fields
def _processDihedralType(self, line):
"""Process a line in the [ dihedraltypes ] category."""
fields = line.split()
......@@ -305,14 +305,14 @@ class GromacsTopFile(object):
self._dihedralTypes[key].append(fields)
else:
self._dihedralTypes[key] = [fields]
def _processImplicitType(self, line):
"""Process a line in the [ implicit_genborn_params ] category."""
fields = line.split()
if len(fields) < 6:
raise ValueError('Too few fields in [ implicit_genborn_params ] line: '+line);
self._implicitTypes[fields[0]] = fields
def _processPairType(self, line):
"""Process a line in the [ pairtypes ] category."""
fields = line.split()
......@@ -321,7 +321,7 @@ class GromacsTopFile(object):
if fields[2] != '1':
raise ValueError('Unsupported function type in [ pairtypes ] line: '+line);
self._pairTypes[tuple(fields[:2])] = fields
def _processCmapType(self, line):
"""Process a line in the [ cmaptypes ] category."""
fields = line.split()
......@@ -330,10 +330,10 @@ class GromacsTopFile(object):
if fields[5] != '1':
raise ValueError('Unsupported function type in [ cmaptypes ] line: '+line);
self._cmapTypes[tuple(fields[:5])] = fields
def __init__(self, file, unitCellDimensions=None, includeDir='/usr/local/gromacs/share/gromacs/top', defines={}):
"""Load a top file.
Parameters:
- file (string) the name of the file to load
- unitCellDimensions (Vec3=None) the dimensions of the crystallographic unit cell
......@@ -343,9 +343,9 @@ class GromacsTopFile(object):
"""
self._includeDirs = (os.path.dirname(file), includeDir)
self._defines = defines
# Parse the file.
self._currentCategory = None
self._ifStack = []
self._moleculeTypes = {}
......@@ -359,9 +359,9 @@ class GromacsTopFile(object):
self._pairTypes = {}
self._cmapTypes = {}
self._processFile(file)
# Create the Topology from it.
top = Topology()
## The Topology read from the prmtop file
self.topology = top
......@@ -371,9 +371,9 @@ class GromacsTopFile(object):
if moleculeName not in self._moleculeTypes:
raise ValueError("Unknown molecule type: "+moleculeName)
moleculeType = self._moleculeTypes[moleculeName]
# Create the specified number of molecules of this type.
for i in range(moleculeCount):
atoms = []
lastResidue = None
......@@ -393,9 +393,9 @@ class GromacsTopFile(object):
atomName = fields[4]
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
# Try to guess the element.
upper = atomName.upper()
if upper.startswith('CL'):
element = elem.chlorine
......@@ -409,16 +409,16 @@ class GromacsTopFile(object):
except KeyError:
element = None
atoms.append(top.addAtom(atomName, element, r))
# Add bonds to the topology
for fields in moleculeType.bonds:
top.addBond(atoms[int(fields[0])-1], atoms[int(fields[1])-1])
def createSystem(self, nonbondedMethod=ff.NoCutoff, nonbondedCutoff=1.0*unit.nanometer,
constraints=None, rigidWater=True, implicitSolvent=None, soluteDielectric=1.0, solventDielectric=78.5, ewaldErrorTolerance=0.0005, removeCMMotion=True):
"""Construct an OpenMM System representing the topology described by this prmtop file.
Parameters:
- nonbondedMethod (object=NoCutoff) The method to use for nonbonded interactions. Allowed values are
NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
......@@ -434,7 +434,7 @@ class GromacsTopFile(object):
Returns: the newly created System
"""
# Create the System.
sys = mm.System()
boxSize = self.topology.getUnitCellDimensions()
if boxSize is not None:
......@@ -462,33 +462,33 @@ class GromacsTopFile(object):
topologyAtoms = list(self.topology.atoms())
exceptions = []
fudgeQQ = float(self._defaults[4])
# Loop over molecules and create the specified number of each type.
for moleculeName, moleculeCount in self._molecules:
moleculeType = self._moleculeTypes[moleculeName]
for i in range(moleculeCount):
# Record the types of all atoms.
baseAtomIndex = sys.getNumParticles()
atomTypes = [atom[1] for atom in moleculeType.atoms]
try:
[self._atomTypes[t][1] for t in atomTypes]
except KeyError as e:
raise ValueError('Unknown atom type: '+e.message)
# Add atoms.
for fields in moleculeType.atoms:
if len(fields) >= 8:
mass = float(fields[7])
else:
mass = float(self._atomTypes[fields[1]][2])
sys.addParticle(mass)
# Add bonds.
atomBonds = [{} for x in range(len(moleculeType.atoms))]
for fields in moleculeType.bonds:
atoms = [int(x)-1 for x in fields[:2]]
......@@ -523,9 +523,9 @@ class GromacsTopFile(object):
# Record information that will be needed for constraining angles.
atomBonds[atoms[0]][atoms[1]] = length
atomBonds[atoms[1]][atoms[0]] = length
# Add angles.
degToRad = math.pi/180
for fields in moleculeType.angles:
atoms = [int(x)-1 for x in fields[:3]]
......@@ -572,7 +572,7 @@ class GromacsTopFile(object):
bonds.addBond(baseAtomIndex+atoms[0], baseAtomIndex+atoms[2], float(params[2]), k)
# Add torsions.
for fields in moleculeType.dihedrals:
atoms = [int(x)-1 for x in fields[:4]]
types = tuple(atomTypes[i] for i in atoms)
......@@ -618,7 +618,7 @@ class GromacsTopFile(object):
rb = mm.RBTorsionForce()
sys.addForce(rb)
rb.addTorsion(baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], baseAtomIndex+atoms[3], c[0], c[1], c[2], c[3], c[4], c[5])
# Add CMAP terms.
for fields in moleculeType.cmaps:
......@@ -649,7 +649,7 @@ class GromacsTopFile(object):
baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], baseAtomIndex+atoms[3], baseAtomIndex+atoms[4])
# Set nonbonded parameters for particles.
for fields in moleculeType.atoms:
params = self._atomTypes[fields[1]]
if len(fields) > 6:
......@@ -665,9 +665,9 @@ class GromacsTopFile(object):
for fields in moleculeType.bonds:
atoms = [int(x)-1 for x in fields[:2]]
bondIndices.append((baseAtomIndex+atoms[0], baseAtomIndex+atoms[1]))
# Record nonbonded exceptions.
for fields in moleculeType.pairs:
atoms = [int(x)-1 for x in fields[:2]]
types = tuple(atomTypes[i] for i in atoms)
......@@ -682,15 +682,15 @@ class GromacsTopFile(object):
atom1params = nb.getParticleParameters(baseAtomIndex+atoms[0])
atom2params = nb.getParticleParameters(baseAtomIndex+atoms[1])
exceptions.append((baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], atom1params[0]*atom2params[0]*fudgeQQ, params[0], params[1]))
# Create nonbonded exceptions.
nb.createExceptionsFromBonds(bondIndices, fudgeQQ, float(self._defaults[3]))
for exception in exceptions:
nb.addException(exception[0], exception[1], exception[2], float(exception[3]), float(exception[4]), True)
# Finish configuring the NonbondedForce.
methodMap = {ff.NoCutoff:mm.NonbondedForce.NoCutoff,
ff.CutoffNonPeriodic:mm.NonbondedForce.CutoffNonPeriodic,
ff.CutoffPeriodic:mm.NonbondedForce.CutoffPeriodic,
......
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
View file @ 74415dd9
......@@ -16,7 +16,7 @@ Portions copyright (c) 2012-2013 Stanford University and the Authors.
Authors: Randall J. Radmer, John D. Chodera, Peter Eastman
Contributors: Christoph Klein, Michael R. Shirts
Permission is hereby granted, free of charge, to any person obtaining a
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, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
......@@ -92,7 +92,7 @@ class PrmtopLoader(object):
>>> import os, os.path
>>> directory = os.path.join(os.getenv('YANK_INSTALL_DIR'), 'test', 'systems', 'alanine-dipeptide-explicit')
>>> prmtop_filename = os.path.join(directory, 'alanine-dipeptide.prmtop')
>>> prmtop = PrmtopLoader(prmtop_filename)
>>> prmtop = PrmtopLoader(prmtop_filename)
"""
def __init__(self, inFilename):
......@@ -101,7 +101,7 @@ class PrmtopLoader(object):
ARGUMENTS
inFilename (string) - AMBER 'new-style' prmtop file, probably generated with one of the AMBER tleap/xleap/sleap
inFilename (string) - AMBER 'new-style' prmtop file, probably generated with one of the AMBER tleap/xleap/sleap
"""
......@@ -152,7 +152,7 @@ class PrmtopLoader(object):
Parameter:
- pointerLabel: a string matching one of the following:
NATOM : total number of atoms
NATOM : total number of atoms
NTYPES : total number of distinct atom types
NBONH : number of bonds containing hydrogen
MBONA : number of bonds not containing hydrogen
......@@ -183,7 +183,7 @@ class PrmtopLoader(object):
NMXRS : number of atoms in the largest residue
IFCAP : set to 1 if the CAP option from edit was specified
"""
index = POINTER_LABEL_LIST.index(pointerLabel)
index = POINTER_LABEL_LIST.index(pointerLabel)
return float(self._raw_data['POINTERS'][index])
def getNumAtoms(self):
......@@ -350,7 +350,7 @@ class PrmtopLoader(object):
bondPointers=self._raw_data["BONDS_INC_HYDROGEN"]
self._bondListWithH = self._getBonds(bondPointers)
return self._bondListWithH
def getBondsNoH(self):
"""Return list of bonded atom pairs, K, and Rmin for each bond with no hydrogen"""
......@@ -509,11 +509,11 @@ class PrmtopLoader(object):
def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmodel=None, soluteDielectric=1.0, solventDielectric=78.5, nonbondedCutoff=None, nonbondedMethod='NoCutoff', scee=1.2, scnb=2.0, mm=None, verbose=False, EwaldErrorTolerance=None, flexibleConstraints=True, rigidWater=True):
"""
Create an OpenMM System from an Amber prmtop file.
ARGUMENTS (specify one or the other, but not both)
prmtop_filename (String) - name of Amber prmtop file (new-style only)
prmtop_loader (PrmtopLoader) - the loaded prmtop file
OPTIONAL ARGUMENTS
shake (String) - if 'h-bonds', will SHAKE all bonds to hydrogen and water; if 'all-bonds', will SHAKE all bonds and water (default: None)
gbmodel (String) - if 'OBC', OBC GBSA will be used; if 'GBVI', GB/VI will be used (default: None)
......@@ -547,10 +547,10 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
>>> directory = os.path.join(os.getenv('YANK_INSTALL_DIR'), 'test', 'systems', 'alanine-dipeptide-explicit')
>>> prmtop_filename = os.path.join(directory, 'alanine-dipeptide.prmtop')
>>> system = readAmberSystem(prmtop_filename)
>>> system = readAmberSystem(prmtop_filename)
"""
if prmtop_filename is None and prmtop_loader is None:
raise Exception("Must specify a filename or loader")
if prmtop_filename is not None and prmtop_loader is not None:
......@@ -567,7 +567,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
if prmtop.getIfPert()>0:
raise Exception("perturbation not currently supported")
if prmtop.getIfBox()>1:
raise Exception("only standard periodic boxes are currently supported")
......@@ -596,9 +596,9 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
for (iAtom, jAtom, k, rMin) in prmtop.getBondsWithH():
if isWater[iAtom] and isWater[jAtom]:
system.addConstraint(iAtom, jAtom, rMin)
# Add harmonic bonds.
if verbose: print "Adding bonds..."
if verbose: print "Adding bonds..."
force = mm.HarmonicBondForce()
if flexibleConstraints or (shake not in ('h-bonds', 'all-bonds', 'h-angles')):
for (iAtom, jAtom, k, rMin) in prmtop.getBondsWithH():
......@@ -610,7 +610,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
system.addForce(force)
# Add harmonic angles.
if verbose: print "Adding angles..."
if verbose: print "Adding angles..."
force = mm.HarmonicAngleForce()
if shake == 'h-angles':
numConstrainedBonds = system.getNumConstraints()
......@@ -638,7 +638,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
l1 = bond[1]
elif bond[0] == kAtom:
l2 = bond[1]
# Compute the distance between atoms and add a constraint
length = math.sqrt(l1*l1 + l2*l2 - 2*l1*l2*math.cos(aMin))
system.addConstraint(iAtom, kAtom, length)
......@@ -647,14 +647,14 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
system.addForce(force)
# Add torsions.
if verbose: print "Adding torsions..."
if verbose: print "Adding torsions..."
force = mm.PeriodicTorsionForce()
for (iAtom, jAtom, kAtom, lAtom, forceConstant, phase, periodicity) in prmtop.getDihedrals():
force.addTorsion(iAtom, jAtom, kAtom, lAtom, periodicity, phase, forceConstant)
system.addForce(force)
# Add nonbonded interactions.
if verbose: print "Adding nonbonded interactions..."
if verbose: print "Adding nonbonded interactions..."
force = mm.NonbondedForce()
if (prmtop.getIfBox() == 0):
# System is non-periodic.
......@@ -663,12 +663,12 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
elif nonbondedMethod == 'CutoffNonPeriodic':
if nonbondedCutoff is None:
raise Exception("No cutoff value specified")
force.setNonbondedMethod(mm.NonbondedForce.CutoffNonPeriodic)
force.setNonbondedMethod(mm.NonbondedForce.CutoffNonPeriodic)
force.setCutoffDistance(nonbondedCutoff)
else:
raise Exception("Illegal nonbonded method for a non-periodic system")
else:
# System is periodic.
# System is periodic.
# Set periodic box vectors for periodic system
(boxBeta, boxX, boxY, boxZ) = prmtop.getBoxBetaAndDimensions()
d0 = units.Quantity(0.0, units.angstroms)
......@@ -676,16 +676,16 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
yVec = units.Quantity((d0, boxY, d0))
zVec = units.Quantity((d0, d0, boxZ))
system.setDefaultPeriodicBoxVectors(xVec, yVec, zVec)
# Set cutoff.
if nonbondedCutoff is None:
# Compute cutoff automatically.
min_box_width = min([boxX / units.nanometers, boxY / units.nanometers, boxZ / units.nanometers])
CLEARANCE_FACTOR = 0.97 # reduce the cutoff to be a bit smaller than 1/2 smallest box length
CLEARANCE_FACTOR = 0.97 # reduce the cutoff to be a bit smaller than 1/2 smallest box length
nonbondedCutoff = units.Quantity((min_box_width * CLEARANCE_FACTOR) / 2.0, units.nanometers)
if nonbondedMethod != 'NoCutoff':
force.setCutoffDistance(nonbondedCutoff)
# Set nonbonded method.
if nonbondedMethod == 'NoCutoff':
force.setNonbondedMethod(mm.NonbondedForce.NoCutoff)
......@@ -724,7 +724,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
excludeParams = (0.0, 0.1, 0.0)
for iAtom in range(prmtop.getNumAtoms()):
for jAtom in excludedAtoms[iAtom]:
if min((iAtom, jAtom), (jAtom, iAtom)) in excludedAtomPairs: continue
if min((iAtom, jAtom), (jAtom, iAtom)) in excludedAtomPairs: continue
force.addException(iAtom, jAtom, excludeParams[0], excludeParams[1], excludeParams[2])
system.addForce(force)
......@@ -812,7 +812,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
if gbmodel == 'OBC2':
gb.addParticle(charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1])
else:
gb.addParticle([charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1]])
gb.addParticle([charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1]])
system.addForce(gb)
if nonbondedMethod == 'NoCutoff':
gb.setNonbondedMethod(mm.NonbondedForce.NoCutoff)
......@@ -836,7 +836,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
def readAmberCoordinates(filename, read_box=False, read_velocities=False, verbose=False, asNumpy=False):
"""
Read atomic coordinates (and optionally, box vectors) from Amber formatted coordinate file.
Read atomic coordinates (and optionally, box vectors) from Amber formatted coordinate file.
ARGUMENTS
......@@ -853,13 +853,13 @@ def readAmberCoordinates(filename, read_box=False, read_velocities=False, verbos
Read coordinates in vacuum.
>>> directory = os.path.join(os.getenv('YANK_INSTALL_DIR'), 'test', 'systems', 'alanine-dipeptide-gbsa')
>>> crd_filename = os.path.join(directory, 'alanine-dipeptide.inpcrd')
>>> crd_filename = os.path.join(directory, 'alanine-dipeptide.inpcrd')
>>> coordinates = readAmberCoordinates(crd_filename)
Read coordinates in solvent.
>>> directory = os.path.join(os.getenv('YANK_INSTALL_DIR'), 'test', 'systems', 'alanine-dipeptide-explicit')
>>> crd_filename = os.path.join(directory, 'alanine-dipeptide.inpcrd')
>>> crd_filename = os.path.join(directory, 'alanine-dipeptide.inpcrd')
>>> [coordinates, box_vectors] = readAmberCoordinates(crd_filename, read_box=True)
"""
......@@ -922,7 +922,7 @@ def readAmberCoordinates(filename, read_box=False, read_velocities=False, verbos
velocities = newvel
# Assign units.
velocities = units.Quantity(velocities, units.angstroms/units.picoseconds)
# Read box size if present
box_vectors = None
if (read_box):
......@@ -944,20 +944,20 @@ def readAmberCoordinates(filename, read_box=False, read_velocities=False, verbos
else:
a = units.Quantity(mm.Vec3(box_dimensions[0], 0.0, 0.0), units.angstroms)
b = units.Quantity(mm.Vec3(0.0, box_dimensions[1], 0.0), units.angstroms)
c = units.Quantity(mm.Vec3(0.0, 0.0, box_dimensions[2]), units.angstroms)
c = units.Quantity(mm.Vec3(0.0, 0.0, box_dimensions[2]), units.angstroms)
box_vectors = [a,b,c]
else:
raise Exception("Don't know what to do with box vectors: %s" % line)
# Close file
infile.close()
if box_vectors and velocities:
return (coordinates, box_vectors, velocities)
if box_vectors:
return (coordinates, box_vectors)
if velocities:
return (coordinates, velocities)
return (coordinates, velocities)
return coordinates
#=============================================================================================
......
wrappers/python/simtk/openmm/app/internal/customgbforces.py
View file @ 74415dd9
......@@ -10,7 +10,7 @@ Portions copyright (c) 2012 University of Virginia and the Authors.
Authors: Christoph Klein, Michael R. Shirts
Contributors:
Permission is hereby granted, free of charge, to any person obtaining a
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, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
......@@ -35,15 +35,15 @@ import sys, pdb, pickle
d0=[2.26685,2.32548,2.38397,2.44235,2.50057,2.55867,2.61663,2.67444,
2.73212,2.78965,2.84705,2.9043,2.96141,3.0184,3.07524,3.13196,
3.18854,3.24498,3.30132,3.35752,3.4136,
2.31191,2.37017,2.4283,2.48632,2.5442,2.60197,2.65961,2.71711,
2.77449,2.83175,2.88887,2.94586,3.00273,3.05948,3.1161,3.1726,
3.22897,3.28522,3.34136,3.39738,3.45072,
2.35759,2.41549,2.47329,2.53097,2.58854,2.646,2.70333,2.76056,
2.31191,2.37017,2.4283,2.48632,2.5442,2.60197,2.65961,2.71711,
2.77449,2.83175,2.88887,2.94586,3.00273,3.05948,3.1161,3.1726,
3.22897,3.28522,3.34136,3.39738,3.45072,
2.35759,2.41549,2.47329,2.53097,2.58854,2.646,2.70333,2.76056,
2.81766,2.87465,2.93152,2.98827,3.0449,3.10142,3.15782,3.21411,
3.27028,3.32634,3.3823,3.43813,3.49387,
2.4038,2.46138,2.51885,2.57623,2.63351,2.69067,2.74773,2.80469,
2.86152,2.91826,2.97489,3.0314,3.08781,3.1441,3.20031,3.25638,
3.31237,3.36825,3.42402,3.4797,3.53527,
3.31237,3.36825,3.42402,3.4797,3.53527,
2.45045,2.50773,2.56492,2.62201,2.679,2.7359,2.7927,2.8494,2.90599,
2.9625,3.0189,3.07518,3.13138,3.18748,3.24347,3.29937,3.35515,
3.41085,3.46646,3.52196,3.57738,
......@@ -53,134 +53,134 @@ d0=[2.26685,2.32548,2.38397,2.44235,2.50057,2.55867,2.61663,2.67444,
2.54489,2.60164,2.6583,2.71488,2.77134,2.8278,2.88412,2.94034,
2.9965,3.05256,3.10853,3.16442,3.22021,3.27592,3.33154,3.38707,
3.44253,3.49789,3.55316,3.60836,3.66348,
2.59259,2.6491,2.70553,2.76188,2.81815,2.87434,2.93044,2.98646,
3.04241,3.09827,3.15404,3.20974,3.26536,3.32089,3.37633,3.4317,
3.48699,3.54219,3.59731,3.65237,3.70734,
2.59259,2.6491,2.70553,2.76188,2.81815,2.87434,2.93044,2.98646,
3.04241,3.09827,3.15404,3.20974,3.26536,3.32089,3.37633,3.4317,
3.48699,3.54219,3.59731,3.65237,3.70734,
2.64054,2.69684,2.75305,2.80918,2.86523,2.92122,2.97712,3.03295,
3.0887,3.14437,3.19996,3.25548,3.31091,3.36627,3.42156,3.47677,
3.5319,3.58695,3.64193,3.69684,3.75167,
2.68873,2.74482,2.80083,2.85676,2.91262,2.96841,3.02412,3.07976,
3.13533,3.19082,3.24623,3.30157,3.35685,3.41205,3.46718,3.52223,
3.57721,3.63213,3.68696,3.74174,3.79644,
2.73713,2.79302,2.84884,2.90459,2.96027,3.01587,3.0714,3.12686,
3.0887,3.14437,3.19996,3.25548,3.31091,3.36627,3.42156,3.47677,
3.5319,3.58695,3.64193,3.69684,3.75167,
2.68873,2.74482,2.80083,2.85676,2.91262,2.96841,3.02412,3.07976,
3.13533,3.19082,3.24623,3.30157,3.35685,3.41205,3.46718,3.52223,
3.57721,3.63213,3.68696,3.74174,3.79644,
2.73713,2.79302,2.84884,2.90459,2.96027,3.01587,3.0714,3.12686,
3.18225,3.23757,3.29282,3.34801,3.40313,3.45815,3.51315,3.56805,
3.6229,3.67767,3.73237,3.78701,3.84159,
3.6229,3.67767,3.73237,3.78701,3.84159,
2.78572,2.84143,2.89707,2.95264,3.00813,3.06356,3.11892,3.17422,
3.22946,3.28462,3.33971,3.39474,3.44971,3.5046,3.55944,3.61421,
3.66891,3.72356,3.77814,3.83264,3.8871,
2.83446,2.89,2.94547,3.00088,3.05621,3.11147,3.16669,3.22183,
3.27689,3.33191,3.38685,3.44174,3.49656,3.55132,3.60602,3.66066,
3.71523,3.76975,3.82421,3.8786,3.93293,
2.88335,2.93873,2.99404,3.04929,3.10447,3.15959,3.21464,3.26963,
3.32456,3.37943,3.43424,3.48898,3.54366,3.5983,3.65287,3.70737,
3.76183,3.81622,3.87056,3.92484,3.97905,
2.93234,2.9876,3.04277,3.09786,3.15291,3.20787,3.26278,3.31764,
3.37242,3.42716,3.48184,3.53662,3.591,3.64551,3.69995,3.75435,
3.80867,3.86295,3.91718,3.97134,4.02545,
2.98151,3.0366,3.09163,3.14659,3.20149,3.25632,3.3111,3.36581,
3.42047,3.47507,3.52963,3.58411,3.63855,3.69293,3.74725,3.80153,
3.85575,3.90991,3.96403,4.01809,4.07211,
3.03074,3.08571,3.14061,3.19543,3.25021,3.30491,3.35956,3.41415,
3.46869,3.52317,3.57759,3.63196,3.68628,3.74054,3.79476,3.84893,
3.90303,3.95709,4.01111,4.06506,4.11897,
3.08008,3.13492,3.1897,3.2444,3.29905,3.35363,3.40815,3.46263,
3.22946,3.28462,3.33971,3.39474,3.44971,3.5046,3.55944,3.61421,
3.66891,3.72356,3.77814,3.83264,3.8871,
2.83446,2.89,2.94547,3.00088,3.05621,3.11147,3.16669,3.22183,
3.27689,3.33191,3.38685,3.44174,3.49656,3.55132,3.60602,3.66066,
3.71523,3.76975,3.82421,3.8786,3.93293,
2.88335,2.93873,2.99404,3.04929,3.10447,3.15959,3.21464,3.26963,
3.32456,3.37943,3.43424,3.48898,3.54366,3.5983,3.65287,3.70737,
3.76183,3.81622,3.87056,3.92484,3.97905,
2.93234,2.9876,3.04277,3.09786,3.15291,3.20787,3.26278,3.31764,
3.37242,3.42716,3.48184,3.53662,3.591,3.64551,3.69995,3.75435,
3.80867,3.86295,3.91718,3.97134,4.02545,
2.98151,3.0366,3.09163,3.14659,3.20149,3.25632,3.3111,3.36581,
3.42047,3.47507,3.52963,3.58411,3.63855,3.69293,3.74725,3.80153,
3.85575,3.90991,3.96403,4.01809,4.07211,
3.03074,3.08571,3.14061,3.19543,3.25021,3.30491,3.35956,3.41415,
3.46869,3.52317,3.57759,3.63196,3.68628,3.74054,3.79476,3.84893,
3.90303,3.95709,4.01111,4.06506,4.11897,
3.08008,3.13492,3.1897,3.2444,3.29905,3.35363,3.40815,3.46263,
3.51704,3.57141,3.62572,3.67998,3.73418,3.78834,3.84244,3.8965,
3.95051,4.00447,4.05837,4.11224,4.16605,
3.95051,4.00447,4.05837,4.11224,4.16605,
3.12949,3.18422,3.23888,3.29347,3.348,3.40247,3.45688,3.51124,
3.56554,3.6198,3.674,3.72815,3.78225,3.83629,3.8903,3.94425,
3.99816,4.05203,4.10583,4.15961,4.21333,
3.56554,3.6198,3.674,3.72815,3.78225,3.83629,3.8903,3.94425,
3.99816,4.05203,4.10583,4.15961,4.21333,
3.17899,3.23361,3.28815,3.34264,3.39706,3.45142,3.50571,3.55997,
3.61416,3.66831,3.72241,3.77645,3.83046,3.8844,3.93831,3.99216,
4.04598,4.09974,4.15347,4.20715,4.26078,
3.22855,3.28307,3.33751,3.39188,3.4462,3.50046,3.55466,3.6088,
3.6629,3.71694,3.77095,3.82489,3.8788,3.93265,3.98646,4.04022,
3.61416,3.66831,3.72241,3.77645,3.83046,3.8844,3.93831,3.99216,
4.04598,4.09974,4.15347,4.20715,4.26078,
3.22855,3.28307,3.33751,3.39188,3.4462,3.50046,3.55466,3.6088,
3.6629,3.71694,3.77095,3.82489,3.8788,3.93265,3.98646,4.04022,
4.09395,4.14762,4.20126,4.25485,4.3084]
m0=[0.0381511,0.0338587,0.0301776,0.027003,0.0242506,0.0218529,
0.0197547,0.0179109,0.0162844,0.0148442,0.0135647,0.0124243,
0.0114047,0.0104906,0.00966876,0.008928,0.0082587,0.00765255,
0.00710237,0.00660196,0.00614589,
0.0396198,0.0351837,0.0313767,0.0280911,0.0252409,0.0227563,
0.0205808,0.0186681,0.0169799,0.0154843,0.014155,0.0129696,
0.0119094,0.0109584,0.0101031,0.00933189,0.0086348,0.00800326,
0.00742986,0.00690814,0.00643255,
0.041048,0.0364738,0.0325456,0.0291532,0.0262084,0.0236399,
0.0213897,0.0194102,0.0176622,0.0161129,0.0147351,0.0135059,
0.0124061,0.0114192,0.0105312,0.00973027,0.00900602,0.00834965,
0.0077535,0.00721091,0.00671609,
0.0424365,0.0377295,0.0336846,0.0301893,0.0271533,0.0245038,
0.0221813,0.0201371,0.018331,0.0167295,0.0153047,0.014033,
0.0128946,0.0118727,0.0109529,0.0101229,0.00937212,0.00869147,
0.00807306,0.00751003,0.00699641,
m0=[0.0381511,0.0338587,0.0301776,0.027003,0.0242506,0.0218529,
0.0197547,0.0179109,0.0162844,0.0148442,0.0135647,0.0124243,
0.0114047,0.0104906,0.00966876,0.008928,0.0082587,0.00765255,
0.00710237,0.00660196,0.00614589,
0.0396198,0.0351837,0.0313767,0.0280911,0.0252409,0.0227563,
0.0205808,0.0186681,0.0169799,0.0154843,0.014155,0.0129696,
0.0119094,0.0109584,0.0101031,0.00933189,0.0086348,0.00800326,
0.00742986,0.00690814,0.00643255,
0.041048,0.0364738,0.0325456,0.0291532,0.0262084,0.0236399,
0.0213897,0.0194102,0.0176622,0.0161129,0.0147351,0.0135059,
0.0124061,0.0114192,0.0105312,0.00973027,0.00900602,0.00834965,
0.0077535,0.00721091,0.00671609,
0.0424365,0.0377295,0.0336846,0.0301893,0.0271533,0.0245038,
0.0221813,0.0201371,0.018331,0.0167295,0.0153047,0.014033,
0.0128946,0.0118727,0.0109529,0.0101229,0.00937212,0.00869147,
0.00807306,0.00751003,0.00699641,
0.0437861,0.0389516,0.0347944,0.0311998,0.0280758,0.0253479,
0.0229555,0.0208487,0.0189864,0.0173343,0.0158637,0.0145507,
0.0133748,0.0123188,0.0113679,0.0105096,0.0097329,0.00902853,
0.00838835,0.00780533,0.0072733,
0.0450979,0.0401406,0.0358753,0.0321851,0.0289761,0.0261726,
0.0237125,0.0215451,0.0196282,0.017927,0.0164121,0.0150588,
0.0138465,0.0127573,0.0117761,0.0108902,0.0100882,0.00936068,
0.00869923,0.00809665,0.00754661,
0.0463729,0.0412976,0.0369281,0.0331456,0.0298547,0.026978,
0.0244525,0.0222264,0.0202567,0.0185078,0.0169498,0.0155575,
0.0143096,0.0131881,0.0121775,0.0112646,0.010438,0.00968781,
0.0229555,0.0208487,0.0189864,0.0173343,0.0158637,0.0145507,
0.0133748,0.0123188,0.0113679,0.0105096,0.0097329,0.00902853,
0.00838835,0.00780533,0.0072733,
0.0450979,0.0401406,0.0358753,0.0321851,0.0289761,0.0261726,
0.0237125,0.0215451,0.0196282,0.017927,0.0164121,0.0150588,
0.0138465,0.0127573,0.0117761,0.0108902,0.0100882,0.00936068,
0.00869923,0.00809665,0.00754661,
0.0463729,0.0412976,0.0369281,0.0331456,0.0298547,0.026978,
0.0244525,0.0222264,0.0202567,0.0185078,0.0169498,0.0155575,
0.0143096,0.0131881,0.0121775,0.0112646,0.010438,0.00968781,
0.00900559,0.00838388,0.00781622,
0.0476123,0.0424233,0.0379534,0.034082,0.0307118,0.0277645,
0.0476123,0.0424233,0.0379534,0.034082,0.0307118,0.0277645,
0.0251757,0.0228927,0.0208718,0.0190767,0.0174768,0.0160466,
0.0147642,0.0136112,0.0125719,0.0116328,0.0107821,0.0100099,
0.00930735,0.00866695,0.00808206,
0.0488171,0.0435186,0.038952,0.0349947,0.0315481,0.0285324,
0.0258824,0.0235443,0.0214738,0.0196339,0.0179934,0.0165262,
0.0152103,0.0140267,0.0129595,0.0119947,0.0111206,0.0103268,
0.00960445,0.00894579,0.00834405,
0.0499883,0.0445845,0.0399246,0.0358844,0.032364,0.0292822,
0.0265729,0.0241815,0.0220629,0.0201794,0.0184994,0.0169964,
0.0156479,0.0144345,0.0133401,0.0123504,0.0114534,0.0106386,
0.00989687,0.00922037,0.00860216,
0.0511272,0.0456219,0.040872,0.0367518,0.0331599,0.0300142,
0.0147642,0.0136112,0.0125719,0.0116328,0.0107821,0.0100099,
0.00930735,0.00866695,0.00808206,
0.0488171,0.0435186,0.038952,0.0349947,0.0315481,0.0285324,
0.0258824,0.0235443,0.0214738,0.0196339,0.0179934,0.0165262,
0.0152103,0.0140267,0.0129595,0.0119947,0.0111206,0.0103268,
0.00960445,0.00894579,0.00834405,
0.0499883,0.0445845,0.0399246,0.0358844,0.032364,0.0292822,
0.0265729,0.0241815,0.0220629,0.0201794,0.0184994,0.0169964,
0.0156479,0.0144345,0.0133401,0.0123504,0.0114534,0.0106386,
0.00989687,0.00922037,0.00860216,
0.0511272,0.0456219,0.040872,0.0367518,0.0331599,0.0300142,
0.0272475,0.0248045,0.0226392,0.0207135,0.0189952,0.0174574,
0.0160771,0.0148348,0.0137138,0.0126998,0.0117805,0.0109452,
0.0101846,0.00949067,0.00885636,
0.0522348,0.0466315,0.0417948,0.0375973,0.0339365,0.030729,
0.0160771,0.0148348,0.0137138,0.0126998,0.0117805,0.0109452,
0.0101846,0.00949067,0.00885636,
0.0522348,0.0466315,0.0417948,0.0375973,0.0339365,0.030729,
0.0279067,0.0254136,0.023203,0.0212363,0.0194809,0.0179092,
0.016498,0.0152275,0.0140807,0.013043,0.012102,0.0112466,
0.0104676,0.00975668,0.00910664,
0.016498,0.0152275,0.0140807,0.013043,0.012102,0.0112466,
0.0104676,0.00975668,0.00910664,
0.0533123,0.0476145,0.042694,0.0384218,0.0346942,0.0314268,
0.0285507,0.026009,0.0237547,0.0217482,0.0199566,0.018352,
0.0169108,0.0156128,0.0144408,0.0133801,0.0124179,0.011543,
0.010746,0.0100184,0.00935302,
0.0285507,0.026009,0.0237547,0.0217482,0.0199566,0.018352,
0.0169108,0.0156128,0.0144408,0.0133801,0.0124179,0.011543,
0.010746,0.0100184,0.00935302,
0.0543606,0.0485716,0.04357,0.0392257,0.0354335,0.0321082,
0.02918,0.0265913,0.0242943,0.0222492,0.0204225,0.0187859,
0.0173155,0.0159908,0.0147943,0.0137111,0.0127282,0.0118343,
0.0110197,0.0102759,0.00959549,
0.0553807,0.0495037,0.0444239,0.0400097,0.0361551,0.0327736,
0.0297949,0.0271605,0.0248222,0.0227396,0.0208788,0.0192111,
0.0177122,0.0163615,0.0151413,0.0140361,0.013033,0.0121206,
0.0112888,0.0105292,0.00983409,
0.0563738,0.0504116,0.0452562,0.0407745,0.0368593,0.0334235,
0.0303958,0.0277171,0.0253387,0.0232197,0.0213257,0.0196277,
0.0181013,0.0167252,0.0154817,0.0143552,0.0133325,0.0124019,
0.0115534,0.0107783,0.0100688,
0.0573406,0.0512963,0.0460676,0.0415206,0.0375468,0.0340583,
0.030983,0.0282614,0.0258441,0.0236896,0.0217634,0.020036,
0.0184826,0.017082,0.0158158,0.0146685,0.0136266,0.0126783,
0.0118135,0.0110232,0.0102998,
0.0582822,0.0521584,0.0468589,0.0422486,0.038218,0.0346784,
0.02918,0.0265913,0.0242943,0.0222492,0.0204225,0.0187859,
0.0173155,0.0159908,0.0147943,0.0137111,0.0127282,0.0118343,
0.0110197,0.0102759,0.00959549,
0.0553807,0.0495037,0.0444239,0.0400097,0.0361551,0.0327736,
0.0297949,0.0271605,0.0248222,0.0227396,0.0208788,0.0192111,
0.0177122,0.0163615,0.0151413,0.0140361,0.013033,0.0121206,
0.0112888,0.0105292,0.00983409,
0.0563738,0.0504116,0.0452562,0.0407745,0.0368593,0.0334235,
0.0303958,0.0277171,0.0253387,0.0232197,0.0213257,0.0196277,
0.0181013,0.0167252,0.0154817,0.0143552,0.0133325,0.0124019,
0.0115534,0.0107783,0.0100688,
0.0573406,0.0512963,0.0460676,0.0415206,0.0375468,0.0340583,
0.030983,0.0282614,0.0258441,0.0236896,0.0217634,0.020036,
0.0184826,0.017082,0.0158158,0.0146685,0.0136266,0.0126783,
0.0118135,0.0110232,0.0102998,
0.0582822,0.0521584,0.0468589,0.0422486,0.038218,0.0346784,
0.0315571,0.0287938,0.0263386,0.0241497,0.0221922,0.0204362,
0.0188566,0.0174319,0.0161437,0.0149761,0.0139154,0.0129499,
0.0120691,0.0112641,0.0105269,
0.0591994,0.0529987,0.0476307,0.042959,0.0388734,0.0352843,
0.0188566,0.0174319,0.0161437,0.0149761,0.0139154,0.0129499,
0.0120691,0.0112641,0.0105269,
0.0591994,0.0529987,0.0476307,0.042959,0.0388734,0.0352843,
0.0321182,0.0293144,0.0268225,0.0246002,0.0226121,0.0208283,
0.0192232,0.0177751,0.0164654,0.015278,0.0141991,0.0132167,
0.0123204,0.0115009,0.0107504,
0.0600932,0.053818,0.0483836,0.0436525,0.0395136,0.0358764,
0.0192232,0.0177751,0.0164654,0.015278,0.0141991,0.0132167,
0.0123204,0.0115009,0.0107504,
0.0600932,0.053818,0.0483836,0.0436525,0.0395136,0.0358764,
0.0326669,0.0298237,0.0272961,0.0250413,0.0230236,0.0212126,
0.0195826,0.0181118,0.0167811,0.0155744,0.0144778,0.0134789,
0.0125673,0.0117338,0.0109702,
0.0609642,0.0546169,0.0491183,0.0443295,0.0401388,0.036455,
0.0332033,0.030322,0.0277596,0.0254732,0.0234266,0.0215892,
0.0199351,0.018442,0.0170909,0.0158654,0.0147514,0.0137365,
0.0195826,0.0181118,0.0167811,0.0155744,0.0144778,0.0134789,
0.0125673,0.0117338,0.0109702,
0.0609642,0.0546169,0.0491183,0.0443295,0.0401388,0.036455,
0.0332033,0.030322,0.0277596,0.0254732,0.0234266,0.0215892,
0.0199351,0.018442,0.0170909,0.0158654,0.0147514,0.0137365,
0.0128101,0.0119627,0.0111863]
# Rescale to nm
for i in range (len(d0)):
......@@ -196,7 +196,7 @@ Amber Equivalent: igb = 1
def GBSAHCTForce(solventDielectric=78.5, soluteDielectric=1, SA=None):
custom = CustomGBForce()
custom.addPerParticleParameter("q");
custom.addPerParticleParameter("radius");
custom.addPerParticleParameter("scale");
......@@ -213,7 +213,7 @@ def GBSAHCTForce(solventDielectric=78.5, soluteDielectric=1, SA=None):
custom.addComputedValue("B", "1/(1/or-I);"
"or=radius-offset", CustomGBForce.SingleParticle)
custom.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce.SingleParticle)
if SA=='ACE':
custom.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6", CustomGBForce.SingleParticle)
......@@ -225,7 +225,7 @@ def GBSAHCTForce(solventDielectric=78.5, soluteDielectric=1, SA=None):
return custom
"""
Amber Equivalents: igb = 2
Amber Equivalents: igb = 2
"""
def GBSAOBC1Force(solventDielectric=78.5, soluteDielectric=1, SA=None):
......@@ -258,7 +258,7 @@ def GBSAOBC1Force(solventDielectric=78.5, soluteDielectric=1, SA=None):
return custom
"""
Amber Equivalents: igb = 5
Amber Equivalents: igb = 5
"""
def GBSAOBC2Force(solventDielectric=78.5, soluteDielectric=1, SA=None):
......@@ -295,27 +295,27 @@ Amber Equivalents: igb = 7
"""
def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None):
"""
Indexing for tables:
input: radius1, radius2
index = (radius2*200-20)*21 + (radius1*200-20)
output: index of desired value in row-by-row, 1D version of Tables 3 & 4
"""
custom = CustomGBForce()
custom.addPerParticleParameter("q");
custom.addPerParticleParameter("radius");
custom.addPerParticleParameter("scale");
custom.addGlobalParameter("solventDielectric", solventDielectric);
custom.addGlobalParameter("soluteDielectric", soluteDielectric);
custom.addGlobalParameter("offset", 0.009)
custom.addGlobalParameter("neckScale", 0.361825)
custom.addGlobalParameter("neckCut", 0.68)
custom.addFunction("getd0", d0, 0, 440)
custom.addFunction("getm0", m0, 0, 440)
......@@ -328,10 +328,10 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None):
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-tanh(1.09511284*psi-1.907992938*psi^2+2.50798245*psi^3)/radius);"
"psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
custom.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce.SingleParticle)
if SA=='ACE':
custom.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6", CustomGBForce.SingleParticle)
......@@ -340,4 +340,4 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None):
custom.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)
return custom
\ No newline at end of file
return custom
wrappers/python/simtk/openmm/app/internal/pdbstructure.py
View file @ 74415dd9
......@@ -12,7 +12,7 @@ Portions copyright (c) 2012 Stanford University and the Authors.
Authors: Christopher M. Bruns
Contributors: Peter Eastman
Permission is hereby granted, free of charge, to any person obtaining a
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, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
......@@ -260,7 +260,7 @@ class PdbStructure(object):
"""Establish first and last residues, atoms, etc."""
for model in self.models:
model._finalize()
def get_unit_cell_dimensions(self):
"""Get the dimensions of the crystallographic unit cell (may be None)."""
return self._unit_cell_dimensions
......@@ -547,12 +547,12 @@ class Residue(object):
...
>>> for atom in res:
... print atom
ATOM 188 N CYS A 42 40.714 -5.292 12.123 1.00 11.29 N
ATOM 189 CA CYS A 42 39.736 -5.883 12.911 1.00 10.01 C
ATOM 190 C CYS A 42 40.339 -6.654 14.087 1.00 22.28 C
ATOM 191 O CYS A 42 41.181 -7.530 13.859 1.00 13.70 O
ATOM 192 CB CYS A 42 38.949 -6.825 12.002 1.00 9.67 C
ATOM 193 SG CYS A 42 37.557 -7.514 12.922 1.00 20.12 S
ATOM 188 N CYS A 42 40.714 -5.292 12.123 1.00 11.29 N
ATOM 189 CA CYS A 42 39.736 -5.883 12.911 1.00 10.01 C
ATOM 190 C CYS A 42 40.339 -6.654 14.087 1.00 22.28 C
ATOM 191 O CYS A 42 41.181 -7.530 13.859 1.00 13.70 O
ATOM 192 CB CYS A 42 38.949 -6.825 12.002 1.00 9.67 C
ATOM 193 SG CYS A 42 37.557 -7.514 12.922 1.00 20.12 S
"""
for atom in self.iter_atoms():
yield atom
......
wrappers/python/simtk/openmm/app/pdbfile.py
View file @ 74415dd9
......@@ -10,7 +10,7 @@ Portions copyright (c) 2012 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
Permission is hereby granted, free of charge, to any person obtaining a
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, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
......@@ -48,28 +48,28 @@ except:
class PDBFile(object):
"""PDBFile parses a Protein Data Bank (PDB) file and constructs a Topology and a set of atom positions from it.
This class also provides methods for creating PDB files. To write a file containing a single model, call
writeFile(). You also can create files that contain multiple models. To do this, first call writeHeader(),
then writeModel() once for each model in the file, and finally writeFooter() to complete the file."""
_residueNameReplacements = {}
_atomNameReplacements = {}
def __init__(self, file):
"""Load a PDB file.
The atom positions and Topology can be retrieved by calling getPositions() and getTopology().
Parameters:
- file (string) the name of the file to load
"""
top = Topology()
## The Topology read from the PDB file
self.topology = top
# Load the PDB file
pdb = PdbStructure(open(file), load_all_models=True)
PDBFile._loadNameReplacementTables()
......@@ -95,7 +95,7 @@ class PDBFile(object):
element = atom.element
if element is None:
# Try to guess the element.
upper = atomName.upper()
if upper.startswith('CL'):
element = elem.chlorine
......@@ -133,9 +133,9 @@ class PDBFile(object):
self.topology.createStandardBonds()
self.topology.createDisulfideBonds(self.positions)
self._numpyPositions = None
# Add bonds based on CONECT records.
connectBonds = []
for connect in pdb.models[0].connects:
i = connect[0]
......@@ -152,14 +152,14 @@ class PDBFile(object):
def getTopology(self):
"""Get the Topology of the model."""
return self.topology
def getNumFrames(self):
"""Get the number of frames stored in the file."""
return len(self._positions)
def getPositions(self, asNumpy=False, frame=0):
"""Get the atomic positions.
Parameters:
- asNumpy (boolean=False) if true, the values are returned as a numpy array instead of a list of Vec3s
- frame (int=0) the index of the frame for which to get positions
......@@ -213,11 +213,11 @@ class PDBFile(object):
name = atom.attrib['name']
for id in atom.attrib:
map[atom.attrib[id]] = name
@staticmethod
def writeFile(topology, positions, file=sys.stdout, modelIndex=None):
"""Write a PDB file containing a single model.
Parameters:
- topology (Topology) The Topology defining the model to write
- positions (list) The list of atomic positions to write
......@@ -230,7 +230,7 @@ class PDBFile(object):
@staticmethod
def writeHeader(topology, file=sys.stdout):
"""Write out the header for a PDB file.
Parameters:
- topology (Topology) The Topology defining the molecular system being written
- file (file=stdout) A file to write the file to
......@@ -239,11 +239,11 @@ class PDBFile(object):
if boxSize is not None:
size = boxSize.value_in_unit(angstroms)
print >>file, "CRYST1%9.3f%9.3f%9.3f 90.00 90.00 90.00 P 1 1 " % size
@staticmethod
def writeModel(topology, positions, file=sys.stdout, modelIndex=None):
"""Write out a model to a PDB file.
Parameters:
- topology (Topology) The Topology defining the model to write
- positions (list) The list of atomic positions to write
......@@ -251,7 +251,7 @@ class PDBFile(object):
- modelIndex (int=None) If not None, the model will be surrounded by MODEL/ENDMDL records with this index
"""
if len(list(topology.atoms())) != len(positions):
raise ValueError('The number of positions must match the number of atoms')
raise ValueError('The number of positions must match the number of atoms')
if is_quantity(positions):
positions = positions.value_in_unit(angstroms)
if any(math.isnan(norm(pos)) for pos in positions):
......@@ -295,7 +295,7 @@ class PDBFile(object):
@staticmethod
def writeFooter(topology, file=sys.stdout):
"""Write out the footer for a PDB file.
Parameters:
- topology (Topology) The Topology defining the molecular system being written
- file (file=stdout) A file to write the file to
......
wrappers/python/simtk/openmm/app/pdbreporter.py
View file @ 74415dd9
......@@ -10,7 +10,7 @@ Portions copyright (c) 2012 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
Permission is hereby granted, free of charge, to any person obtaining a
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, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
......@@ -33,16 +33,16 @@ __version__ = "1.0"
import simtk.openmm as mm
from simtk.openmm.app import PDBFile
class PDBReporter(object):
"""PDBReporter outputs a series of frames from a Simulation to a PDB file.
To use it, create a PDBReporter, then add it to the Simulation's list of reporters.
"""
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
......@@ -51,10 +51,10 @@ class PDBReporter(object):
self._out = open(file, 'w')
self._topology = None
self._nextModel = 0
def describeNextReport(self, simulation):
"""Get information about the next report this object will generate.
Parameters:
- simulation (Simulation) The Simulation to generate a report for
Returns: A five element tuple. The first element is the number of steps until the
......@@ -63,10 +63,10 @@ class PDBReporter(object):
"""
steps = self._reportInterval - simulation.currentStep%self._reportInterval
return (steps, True, False, False, False)
def report(self, simulation, state):
"""Generate a report.
Parameters:
- simulation (Simulation) The Simulation to generate a report for
- state (State) The current state of the simulation
......@@ -77,7 +77,7 @@ class PDBReporter(object):
self._nextModel += 1
PDBFile.writeModel(simulation.topology, state.getPositions(), self._out, self._nextModel)
self._nextModel += 1
def __del__(self):
PDBFile.writeFooter(self._topology, self._out)
self._out.close()
wrappers/python/simtk/openmm/app/simulation.py
View file @ 74415dd9
......@@ -10,7 +10,7 @@ Portions copyright (c) 2012 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
Permission is hereby granted, free of charge, to any person obtaining a
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, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
......@@ -33,25 +33,25 @@ __version__ = "1.0"
import simtk.openmm as mm
import simtk.unit as unit
class Simulation(object):
"""Simulation provides a simplified API for running simulations with OpenMM and reporting results.
A Simulation ties together various objects used for running a simulation: a Topology, System,
Integrator, and Context. To use it, you provide the Topology, System, and Integrator, and it
creates the Context automatically.
Simulation also maintains a list of "reporter" objects that record or analyze data as the simulation
runs, such as writing coordinates to files or displaying structures on the screen. For example,
the following line will cause a file called "output.pdb" to be created, and a structure written to
it every 1000 time steps:
simulation.reporters.append(PDBReporter('output.pdb', 1000))
"""
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
......@@ -77,17 +77,17 @@ class Simulation(object):
self.context = mm.Context(system, integrator, platform)
else:
self.context = mm.Context(system, integrator, platform, platformProperties)
def minimizeEnergy(self, tolerance=1*unit.kilojoule/unit.mole, maxIterations=0):
"""Perform a local energy minimization on the system.
Parameters:
- tolerance (energy=1*kilojoule/mole) The energy tolerance to which the system should be minimized
- maxIterations (int=0) The maximum number of iterations to perform. If this is 0, minimization is continued
until the results converge without regard to how many iterations it takes.
"""
mm.LocalEnergyMinimizer.minimize(self.context, tolerance, maxIterations)
def step(self, steps):
"""Advance the simulation by integrating a specified number of time steps."""
stepTo = self.currentStep+steps
......
wrappers/python/simtk/openmm/app/statedatareporter.py
View file @ 74415dd9
......@@ -10,7 +10,7 @@ Portions copyright (c) 2012-2013 Stanford University and the Authors.
Authors: Peter Eastman
Contributors: Robert McGibbon
Permission is hereby granted, free of charge, to any person obtaining a
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, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
......@@ -35,7 +35,7 @@ import simtk.openmm as mm
import simtk.unit as unit
from simtk.openmm.app import PDBFile
import math
class StateDataReporter(object):
"""StateDataReporter outputs information about a simulation, such as energy and temperature, to a file.
......
wrappers/python/simtk/openmm/app/topology.py
View file @ 74415dd9
......@@ -10,7 +10,7 @@ Portions copyright (c) 2012-2013 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
Permission is hereby granted, free of charge, to any person obtaining a
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, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
......@@ -37,18 +37,18 @@ from simtk.unit import nanometers, sqrt
class Topology(object):
"""Topology stores the topological information about a system.
The structure of a Topology object is similar to that of a PDB file. It consists of a set of Chains
(often but not always corresponding to polymer chains). Each Chain contains a set of Residues,
and each Residue contains a set of Atoms. In addition, the Topology stores a list of which atom
pairs are bonded to each other, and the dimensions of the crystallographic unit cell.
Atom and residue names should follow the PDB 3.0 nomenclature for all molecules for which one exists.
"""
_standardBonds = {}
_hasLoadedStandardBonds = False
def __init__(self):
"""Create a new Topology object"""
self._chains = []
......@@ -56,19 +56,19 @@ class Topology(object):
self._numAtoms = 0
self._bonds = []
self._unitCellDimensions = None
def addChain(self):
"""Create a new Chain and add it to the Topology.
Returns: the newly created Chain
"""
chain = Chain(len(self._chains), self)
self._chains.append(chain)
return chain
def addResidue(self, name, chain):
"""Create a new Residue and add it to the Topology.
Parameters:
- name (string) The name of the residue to add
- chain (Chain) The Chain to add it to
......@@ -78,10 +78,10 @@ class Topology(object):
self._numResidues += 1
chain._residues.append(residue)
return residue
def addAtom(self, name, element, residue):
"""Create a new Atom and add it to the Topology.
Parameters:
- name (string) The name of the atom to add
- element (Element) The element of the atom to add
......@@ -92,52 +92,52 @@ class Topology(object):
self._numAtoms += 1
residue._atoms.append(atom)
return atom
def addBond(self, atom1, atom2):
"""Create a new bond and add it to the Topology.
Parameters:
- atom1 (Atom) The first Atom connected by the bond
- atom2 (Atom) The second Atom connected by the bond
"""
self._bonds.append((atom1, atom2))
def chains(self):
"""Iterate over all Chains in the Topology."""
return iter(self._chains)
def residues(self):
"""Iterate over all Residues in the Topology."""
for chain in self._chains:
for residue in chain._residues:
yield residue
def atoms(self):
"""Iterate over all Atoms in the Topology."""
for chain in self._chains:
for residue in chain._residues:
for atom in residue._atoms:
yield atom
def bonds(self):
"""Iterate over all bonds (each represented as a tuple of two Atoms) in the Topology."""
return iter(self._bonds)
def getUnitCellDimensions(self):
"""Get the dimensions of the crystallographic unit cell.
The return value may be None if this Topology does not represent a periodic structure.
"""
return self._unitCellDimensions
def setUnitCellDimensions(self, dimensions):
"""Set the dimensions of the crystallographic unit cell."""
self._unitCellDimensions = dimensions
@staticmethod
def loadBondDefinitions(file):
"""Load an XML file containing definitions of bonds that should be used by createStandardBonds().
The built in residues.xml file containing definitions for standard amino acids and nucleotides is loaded automatically.
This method can be used to load additional definitions for other residue types. They will then be used in subsequent
calls to createStandardBonds(). This is a static method, so it affects subsequent calls on all Topology objects.
......@@ -149,31 +149,31 @@ class Topology(object):
bonds = []
Topology._standardBonds[residue.attrib['name']] = bonds
for bond in residue.findall('Bond'):
bonds.append((bond.attrib['from'], bond.attrib['to']))
bonds.append((bond.attrib['from'], bond.attrib['to']))
def createStandardBonds(self):
"""Create bonds based on the atom and residue names for all standard residue types.
Definitions for standard amino acids and nucleotides are built in. You can call loadBondDefinitions() to load
additional definitions for other residue types.
"""
if not Topology._hasLoadedStandardBonds:
# Load the standard bond definitions.
Topology.loadBondDefinitions(os.path.join(os.path.dirname(__file__), 'data', 'residues.xml'))
Topology._hasLoadedStandardBonds = True
for chain in self._chains:
# First build a map of atom names to atoms.
atomMaps = []
for residue in chain._residues:
atomMap = {}
atomMaps.append(atomMap)
for atom in residue._atoms:
atomMap[atom.name] = atom
# Loop over residues and construct bonds.
for i in range(len(chain._residues)):
name = chain._residues[i].name
if name in Topology._standardBonds:
......@@ -198,17 +198,17 @@ class Topology(object):
toAtom = bond[1]
if fromAtom in atomMaps[fromResidue] and toAtom in atomMaps[toResidue]:
self.addBond(atomMaps[fromResidue][fromAtom], atomMaps[toResidue][toAtom])
def createDisulfideBonds(self, positions):
"""Identify disulfide bonds based on proximity and add them to the Topology.
Parameters:
- positions (list) The list of atomic positions based on which to identify bonded atoms
"""
def isCyx(res):
names = [atom.name for atom in res._atoms]
return 'SG' in names and 'HG' not in names
cyx = [res for res in self.residues() if res.name == 'CYS' and isCyx(res)]
atomNames = [[atom.name for atom in res._atoms] for res in cyx]
for i in range(len(cyx)):
......@@ -231,7 +231,7 @@ class Chain(object):
## The Topology this Chain belongs to
self.topology = topology
self._residues = []
def residues(self):
"""Iterate over all Residues in the Chain."""
return iter(self._residues)
......@@ -253,14 +253,14 @@ class Residue(object):
## The Chain this Residue belongs to
self.chain = chain
self._atoms = []
def atoms(self):
"""Iterate over all Atoms in the Residue."""
return iter(self._atoms)
class Atom(object):
"""An Atom object represents a residue within a Topology."""
def __init__(self, name, element, index, residue):
"""Construct a new Atom. You should call addAtom() on the Topology instead of calling this directly."""
## The name of the Atom
......
wrappers/python/simtk/openmm/vec3.py
View file @ 74415dd9
......@@ -10,7 +10,7 @@ Portions copyright (c) 2012 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
Permission is hereby granted, free of charge, to any person obtaining a
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, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
......@@ -35,43 +35,43 @@ import simtk.unit as unit
class Vec3(tuple):
"""Vec3 is a 3-element tuple that supports many math operations."""
def __new__(cls, x, y, z):
"""Create a new Vec3."""
return tuple.__new__(cls, (x, y, z))
def __add__(self, other):
"""Add two Vec3s."""
return Vec3(self[0]+other[0], self[1]+other[1], self[2]+other[2])
def __radd__(self, other):
"""Add two Vec3s."""
return Vec3(self[0]+other[0], self[1]+other[1], self[2]+other[2])
def __sub__(self, other):
"""Add two Vec3s."""
return Vec3(self[0]-other[0], self[1]-other[1], self[2]-other[2])
def __rsub__(self, other):
"""Add two Vec3s."""
return Vec3(other[0]-self[0], other[1]-self[1], other[2]-self[2])
def __mul__(self, other):
"""Multiply a Vec3 by a constant."""
if unit.is_unit(other):
return unit.Quantity(self, other)
return Vec3(other*self[0], other*self[1], other*self[2])
def __rmul__(self, other):
"""Multiply a Vec3 by a constant."""
if unit.is_unit(other):
return unit.Quantity(self, other)
return Vec3(other*self[0], other*self[1], other*self[2])
def __div__(self, other):
"""Divide a Vec3 by a constant."""
return Vec3(self[0]/other, self[1]/other, self[2]/other)
__truediv__ = __div__
def __deepcopy__(self, memo):
return Vec3(self[0], self[1], self[2])
wrappers/python/simtk/unit/basedimension.py
View file @ 74415dd9
......@@ -16,7 +16,7 @@ Portions copyright (c) 2012 Stanford University and the Authors.
Authors: Christopher M. Bruns
Contributors: Peter Eastman
Permission is hereby granted, free of charge, to any person obtaining a
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, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
......@@ -42,7 +42,7 @@ __version__ = "0.6"
class BaseDimension(object):
'''
A physical dimension such as length, mass, or temperature.
It is unlikely the user will need to create new ones.
'''
# Keep deterministic order of dimensions
......@@ -57,7 +57,7 @@ class BaseDimension(object):
'angle': 8,
}
_next_unused_index = 9
def __init__(self, name):
"""Create a new BaseDimension.
......@@ -70,17 +70,17 @@ class BaseDimension(object):
BaseDimension._index_by_name[name] = BaseDimension._next_unused_index
BaseDimension._next_unused_index += 1
self._index = BaseDimension._index_by_name[name]
def __lt__(self, other):
"""
The implicit order of BaseDimensions is the order in which they were created.
This method is used for using BaseDimensions as hash keys, and also affects
the order in which units appear in multi-dimensional Quantities.
Returns True if self < other, False otherwise.
"""
return self._index < other._index
def __hash__(self):
"""
Needed for using BaseDimensions as hash keys.
......
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