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Commit 895f9a6f authored by Jason Swails's avatar Jason Swails
Browse files

Update the CHARMM API to be consistent with the rest of OpenMM.

parent 2e927a35
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Showing with 58 additions and 58 deletions
wrappers/python/simtk/openmm/app/charmmparameterset.py
View file @ 895f9a6f
......@@ -220,7 +220,7 @@ class CharmmParameterSet(object):
atomic_number = get_by_symbol(elem).atomic_number
except (IndexError, KeyError):
# Figure it out from the mass
atomic_number = element_by_mass(mass).atomic_number
atomic_number = Element.getByMass(mass).atomic_number
atype = AtomType(name=name, number=idx, mass=mass,
atomic_number=atomic_number)
self.atom_types_str[atype.name] = atype
......@@ -441,7 +441,7 @@ class CharmmParameterSet(object):
atomic_number = get_by_symbol(elem).atomic_number
except (IndexError, KeyError):
# Figure it out from the mass
atomic_number = element_by_mass(mass).atomic_number
atomic_number = Element.getByMass(mass).atomic_number
atype = AtomType(name=name, number=idx, mass=mass,
atomic_number=atomic_number)
self.atom_types_str[atype.name] = atype
......@@ -488,7 +488,7 @@ class CharmmParameterSet(object):
time.
Example:
>>> params = CharmmParameterSet.loadSet(pfile='charmm.prm').condense()
>>> params = CharmmParameterSet('charmm.prm').condense()
"""
# First scan through all of the bond types
self._condense_types(self.bond_types)
......@@ -529,18 +529,3 @@ class CharmmParameterSet(object):
typedict[key2] = typedict[key1]
# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
def element_by_mass(mass):
""" Determines what element the given atom is based on its mass """
diff = mass
best_guess = 'EP'
for key in Element._elements_by_atomic_number:
element = Element._elements_by_atomic_number[key]
massdiff = abs(element.mass.value_in_unit(u.daltons) - mass)
if massdiff < diff:
best_guess = element
diff = massdiff
return best_guess
wrappers/python/simtk/openmm/app/charmmpsffile.py
View file @ 895f9a6f
......@@ -53,7 +53,7 @@ def _catchindexerror(func):
class CharmmPsfFile(object):
"""
A chemical structure instantiated from CHARMM files. You can instantiate a
ProteinStructure from a PSF file using the load_from_psf constructor
CharmmPsfFile from a PSF file using the load_from_psf constructor
Example:
>>> cs = CharmmPsfFile("testfiles/test.psf")
......@@ -80,7 +80,7 @@ class CharmmPsfFile(object):
etc.)
Example:
>>> cs = ProteinStructure.load_from_psf("testfiles/test.psf")
>>> cs = CharmmPsfFile("testfiles/test.psf")
>>> len(cs.atom_list)
33
>>> len(cs.bond_list)
......@@ -102,8 +102,8 @@ class CharmmPsfFile(object):
@_catchindexerror
def __init__(self, psf_name):
"""
Opens and parses a PSF file, then instantiates a ProteinStructure
instance from the data.
Opens and parses a PSF file, then instantiates a CharmmPsfFile instance
from the data.
Parameters:
psf_name (str) : Name of the PSF file (it must exist)
......@@ -112,7 +112,7 @@ class CharmmPsfFile(object):
IOError : If file "psf_name" does not exist
CharmmPSFError: If any parsing errors are encountered
"""
conv = ProteinStructure._convert
conv = CharmmPsfFile._convert
# Make sure the file exists
if not os.path.exists(psf_name):
raise IOError('Could not find PSF file %s' % psf_name)
......@@ -164,7 +164,7 @@ class CharmmPsfFile(object):
# Eat the next line
psf.readline()
# Now get the number of bonds
nbond, holder = ProteinStructure._parse_psf_section(psf, int)
nbond, holder = CharmmPsfFile._parse_psf_section(psf, int)
bond_list = TrackedList()
if len(holder) != nbond * 2:
raise CharmmPSFError('Got %d indexes for %d bonds' %
......@@ -175,7 +175,7 @@ class CharmmPsfFile(object):
bond_list.append(Bond(atom_list[id1], atom_list[id2]))
bond_list.changed = False
# Now get the number of angles and the angle list
ntheta, holder = ProteinStructure._parse_psf_section(psf, int)
ntheta, holder = CharmmPsfFile._parse_psf_section(psf, int)
angle_list = TrackedList()
if len(holder) != ntheta * 3:
raise CharmmPSFError('Got %d indexes for %d angles' %
......@@ -189,7 +189,7 @@ class CharmmPsfFile(object):
)
angle_list.changed = False
# Now get the number of torsions and the torsion list
nphi, holder = ProteinStructure._parse_psf_section(psf, int)
nphi, holder = CharmmPsfFile._parse_psf_section(psf, int)
dihedral_list = TrackedList()
if len(holder) != nphi * 4:
raise CharmmPSFError('Got %d indexes for %d torsions' %
......@@ -205,7 +205,7 @@ class CharmmPsfFile(object):
)
dihedral_list.changed = False
# Now get the number of improper torsions
nimphi, holder = ProteinStructure._parse_psf_section(psf, int)
nimphi, holder = CharmmPsfFile._parse_psf_section(psf, int)
improper_list = TrackedList()
if len(holder) != nimphi * 4:
raise CharmmPSFError('Got %d indexes for %d impropers' %
......@@ -221,7 +221,7 @@ class CharmmPsfFile(object):
)
improper_list.changed = False
# Now handle the donors (what is this used for??)
ndon, holder = ProteinStructure._parse_psf_section(psf, int)
ndon, holder = CharmmPsfFile._parse_psf_section(psf, int)
donor_list = TrackedList()
if len(holder) != ndon * 2:
raise CharmmPSFError('Got %d indexes for %d donors' %
......@@ -232,7 +232,7 @@ class CharmmPsfFile(object):
donor_list.append(AcceptorDonor(atom_list[id1], atom_list[id2]))
donor_list.changed = False
# Now handle the acceptors (what is this used for??)
nacc, holder = ProteinStructure._parse_psf_section(psf, int)
nacc, holder = CharmmPsfFile._parse_psf_section(psf, int)
acceptor_list = TrackedList()
if len(holder) != nacc * 2:
raise CharmmPSFError('Got %d indexes for %d acceptors' %
......@@ -244,9 +244,9 @@ class CharmmPsfFile(object):
acceptor_list.changed = False
# Now get the NNB section. Not sure what this section is for or what it
# does...
nnb, holder = ProteinStructure._parse_psf_section(psf, int)
nnb, holder = CharmmPsfFile._parse_psf_section(psf, int)
# Now get the group sections
pointers, holder = ProteinStructure._parse_psf_section(psf, int)
pointers, holder = CharmmPsfFile._parse_psf_section(psf, int)
group_list = TrackedList()
try:
ngrp, nst2 = pointers
......@@ -273,7 +273,7 @@ class CharmmPsfFile(object):
# and the number of entries in the group. If the # of entries is
# NATOM, assume we have MOLNT section. Warn if the MOLNT section is
# 'wrong'...
pointer, holder = ProteinStructure._parse_psf_section(psf, int)
pointer, holder = CharmmPsfFile._parse_psf_section(psf, int)
# Assign all of the atoms to molecules recursively
set_molecules(atom_list)
......@@ -292,7 +292,7 @@ class CharmmPsfFile(object):
'section.')
psf.readline() # blank
# Now we get to the cross-term section
ncrterm, holder = ProteinStructure._parse_psf_section(psf, int)
ncrterm, holder = CharmmPsfFile._parse_psf_section(psf, int)
else:
ncrterm = pointer
# At this point, ncrterm and holder are both set to the CMAP list for
......@@ -370,7 +370,7 @@ class CharmmPsfFile(object):
- data (list) : A list of all data in the parsed section converted
to `dtype'
"""
conv = ProteinStructure._convert
conv = CharmmPsfFile._convert
words = psf.readline().split()
if len(words) == 1:
pointers = conv(words[0], int, 'pointer')
......@@ -400,7 +400,7 @@ class CharmmPsfFile(object):
- vmd (bool) : If True, it will write out a PSF in the format that
VMD prints it in (i.e., no NUMLP/NUMLPH or MOLNT sections)
Example:
>>> cs = ProteinStructure.load_from_psf('testfiles/test.psf')
>>> cs = CharmmPsfFile.load_from_psf('testfiles/test.psf')
>>> cs.write_psf('testfiles/test2.psf')
"""
# See if this is an extended format
......@@ -769,8 +769,13 @@ class CharmmPsfFile(object):
if atom.residue.idx != last_residue:
last_residue = atom.residue.idx
residue = topology.addResidue(atom.residue.resname, chain)
atomic_num = atom.type.atomic_number
elem = element.Element.getByAtomicNumber(atomic_num)
if atom.type is not None:
# This is the most reliable way of determining the element
atomic_num = atom.type.atomic_number
elem = element.Element.getByAtomicNumber(atomic_num)
else:
# If we didn't load a parameter set yet, try based on mass
elem = element.Element.getByMass(atom.mass)
topology.addAtom(atom.name, elem, residue)
# Add all of the bonds
......@@ -933,7 +938,7 @@ class CharmmPsfFile(object):
# back up the dihedral list
dihedral_list = self.dihedral_list
# Load the parameter set
self.load_parameters(params)
self.load_parameters(params.condense())
hasbox = self.topology.getUnitCellDimensions() is not None
# Set the cutoff distance in nanometers
cutoff = None
......
wrappers/python/simtk/openmm/app/element.py
View file @ 895f9a6f
......@@ -34,7 +34,7 @@ __author__ = "Christopher M. Bruns"
__version__ = "1.0"
from simtk.unit import daltons
from simtk.unit import daltons, is_quantity
import copy_reg
class Element(object):
......@@ -93,6 +93,23 @@ class Element(object):
def getByAtomicNumber(atomic_number):
return Element._elements_by_atomic_number[atomic_number]
@staticmethod
def getByMass(mass):
# Assume masses are in daltons if they are not units
if not is_quantity(mass):
mass = mass * daltons
diff = mass
best_guess = 'EP'
for key in Element._elements_by_atomic_number:
element = Element._elements_by_atomic_number[key]
massdiff = abs(element.mass - mass)
if massdiff < diff:
best_guess = element
diff = massdiff
return best_guess
@property
def atomic_number(self):
return self._atomic_number
......
wrappers/python/tests/TestCharmmFiles.py
View file @ 895f9a6f
......@@ -13,20 +13,13 @@ class TestCharmmFiles(unittest.TestCase):
"""Set up the tests by loading the input files."""
# alanine tripeptide; no waters
self.psf_c = CharmmPSF.load_from_psf('systems/ala_ala_ala.psf')
self.psf_x = CharmmPSF.load_from_psf('systems/ala_ala_ala.xpsf')
self.psf_v = CharmmPSF.load_from_psf('systems/ala_ala_ala.vpsf')
params = CharmmParameterSet.load_set(
tfile='systems/charmm22.rtf',
pfile='systems/charmm22.par',
).condense()
self.psf_c = CharmmPsfFile('systems/ala_ala_ala.psf')
self.psf_x = CharmmPsfFile('systems/ala_ala_ala.xpsf')
self.psf_v = CharmmPsfFile('systems/ala_ala_ala.vpsf')
self.params = CharmmParameterSet(
'systems/charmm22.rtf', 'systems/charmm22.par')
self.pdb = PDBFile('systems/ala_ala_ala.pdb')
# Load parameters
self.psf_c.load_parameters(params)
self.psf_x.load_parameters(params)
self.psf_v.load_parameters(params)
def test_NonbondedMethod(self):
"""Test both non-periodic methods for the systems"""
......@@ -34,7 +27,7 @@ class TestCharmmFiles(unittest.TestCase):
CutoffNonPeriodic:NonbondedForce.CutoffNonPeriodic}
for top in (self.psf_c, self.psf_x, self.psf_v):
for method in methodMap:
system = top.createSystem(nonbondedMethod=method)
system = top.createSystem(self.params, nonbondedMethod=method)
forces = system.getForces()
self.assertTrue(any(isinstance(f, NonbondedForce) and
f.getNonbondedMethod()==methodMap[method]
......@@ -45,7 +38,7 @@ class TestCharmmFiles(unittest.TestCase):
for top in (self.psf_c, self.psf_x, self.psf_v):
for method in [CutoffNonPeriodic]:
system = top.createSystem(nonbondedMethod=method,
system = top.createSystem(self.params, nonbondedMethod=method,
nonbondedCutoff=2*nanometer,
constraints=HBonds)
cutoff_distance = 0.0*nanometer
......@@ -59,21 +52,21 @@ class TestCharmmFiles(unittest.TestCase):
"""Test both options (True and False) for the removeCMMotion parameter."""
for b in [True, False]:
system = self.psf_c.createSystem(removeCMMotion=b)
system = self.psf_c.createSystem(self.params, removeCMMotion=b)
self.assertEqual(any(isinstance(f, CMMotionRemover) for f in system.getForces()), b)
def test_ImplicitSolvent(self):
"""Test implicit solvent using the implicitSolvent parameter.
"""
system = self.psf_v.createSystem(implicitSolvent=OBC2)
system = self.psf_v.createSystem(self.params, implicitSolvent=OBC2)
self.assertTrue(any(isinstance(f, CustomGBForce) for f in system.getForces()))
def test_ImplicitSolventParameters(self):
"""Test that solventDielectric and soluteDielectric are passed correctly.
"""
system = self.psf_x.createSystem(implicitSolvent=GBn,
system = self.psf_x.createSystem(self.params, implicitSolvent=GBn,
solventDielectric=50.0,
soluteDielectric = 0.9)
found_matching_solvent_dielectric=False
......@@ -97,8 +90,8 @@ class TestCharmmFiles(unittest.TestCase):
topology = self.psf_v.topology
hydrogenMass = 4*amu
system1 = self.psf_v.createSystem()
system2 = self.psf_v.createSystem(hydrogenMass=hydrogenMass)
system1 = self.psf_v.createSystem(self.params)
system2 = self.psf_v.createSystem(self.params, hydrogenMass=hydrogenMass)
for atom in topology.atoms():
if atom.element == elem.hydrogen:
self.assertNotEqual(hydrogenMass, system1.getParticleMass(atom.index))
......
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