def testVec3Addition(self):
vec1 = Vec3(1, 2, 3)
vec2 = Vec3(4, 5, 6)
vec2_tup = (4, 5, 6)
result = Vec3(5, 7, 9)
self.assertEqual(vec1 + vec2, result)
self.assertEqual(vec1 + vec2_tup, result)
def testVec3Division(self):
vec1 = Vec3(4, 5, 6)
factor = 2
result = Vec3(2, 2.5, 3)
self.assertEqual(vec1 / factor, result)
with self.assertRaises(TypeError):
2 / vec1
def testVec3Subtraction(self):
vec1 = Vec3(1, 2, 3)
vec2 = Vec3(3, 2, 1)
vec2_tup = (3, 2, 1)
result = Vec3(-2, 0, 2)
self.assertEqual(vec1 - vec2, result)
self.assertEqual(vec1 - vec2_tup, result)
self.assertEqual(vec2_tup - vec1, -result)
def reducePeriodicBoxVectors(periodicBoxVectors):
""" Reduces the representation of the PBC. periodicBoxVectors is expected to
be an unpackable iterable of length-3 iterables
"""
if is_quantity(periodicBoxVectors):
a, b, c = periodicBoxVectors.value_in_unit(nanometers)
else:
a, b, c = periodicBoxVectors
a = Vec3(*a)
b = Vec3(*b)
c = Vec3(*c)
c = c - b * round(c[1] / b[1])
c = c - a * round(c[0] / a[0])
b = b - a * round(b[0] / a[0])
return (a, b, c) * nanometers
def testReducePBCVectors(self):
""" Checks that reducePeriodicBoxVectors properly reduces vectors """
a = Vec3(4.24388485, 0.0, 0.0)
b = Vec3(-1.4146281691908937, 4.001173048368583, 0.0)
c = Vec3(-1.4146281691908937, -2.0005862820516203, 3.4651176446201674)
vecs = reducePeriodicBoxVectors((a, b, c)*nanometers)
vecs2 = computePeriodicBoxVectors(4.24388485, 4.24388485, 4.24388485,
109.4712190*degrees, 109.4712190*degrees, 109.4712190*degrees)
# Check that the vectors are the same
a1, a2, a3 = vecs
b1, b2, b3 = vecs2
for x, y in zip(a1, b1):
self.assertAlmostEqual(strip_units(x), strip_units(y))
for x, y in zip(a2, b2):
self.assertAlmostEqual(strip_units(x), strip_units(y))
for x, y in zip(a3, b3):
self.assertAlmostEqual(strip_units(x), strip_units(y))
def computePeriodicBoxVectors(a_length, b_length, c_length, alpha, beta,
gamma):
"""Convert lengths and angles to periodic box vectors.
Lengths should be given in nanometers and angles in radians (or as Quantity
instances)
"""
if is_quantity(a_length): a_length = a_length.value_in_unit(nanometers)
if is_quantity(b_length): b_length = b_length.value_in_unit(nanometers)
if is_quantity(c_length): c_length = c_length.value_in_unit(nanometers)
if is_quantity(alpha): alpha = alpha.value_in_unit(radians)
if is_quantity(beta): beta = beta.value_in_unit(radians)
if is_quantity(gamma): gamma = gamma.value_in_unit(radians)
# Compute the vectors.
a = [a_length, 0, 0]
b = [b_length * math.cos(gamma), b_length * math.sin(gamma), 0]
cx = c_length * math.cos(beta)
cy = c_length * (math.cos(alpha) -
math.cos(beta) * math.cos(gamma)) / math.sin(gamma)
cz = math.sqrt(c_length * c_length - cx * cx - cy * cy)
c = [cx, cy, cz]
# If any elements are very close to 0, set them to exactly 0.
for i in range(3):
if abs(a[i]) < 1e-6:
a[i] = 0.0
if abs(b[i]) < 1e-6:
b[i] = 0.0
if abs(c[i]) < 1e-6:
c[i] = 0.0
a = Vec3(*a)
b = Vec3(*b)
c = Vec3(*c)
# Make sure they're in the reduced form required by OpenMM.
c = c - b * round(c[1] / b[1])
c = c - a * round(c[0] / a[0])
b = b - a * round(b[0] / a[0])
return (a, b, c) * nanometers
def _prep_sim(self, coords, external_forces=[]):
try:
from openmm import Platform, LangevinIntegrator, Vec3
from openmm.app import Modeller, ForceField, \
CutoffNonPeriodic, PME, Simulation, HBonds
from openmm.unit import angstrom, nanometers, picosecond, \
kelvin, Quantity, molar
except ImportError:
raise ImportError('Please install PDBFixer and OpenMM 7.6 in order to use ClustENM.')
positions = Quantity([Vec3(*xyz) for xyz in coords], angstrom)
modeller = Modeller(self._topology, positions)
if self._sol == 'imp':
forcefield = ForceField(*self._force_field)
system = forcefield.createSystem(modeller.topology,
nonbondedMethod=CutoffNonPeriodic,
nonbondedCutoff=1.0*nanometers,
constraints=HBonds)
if self._sol == 'exp':
forcefield = ForceField(*self._force_field)
modeller.addSolvent(forcefield,
padding=self._padding*nanometers,
ionicStrength=self._ionicStrength*molar)
system = forcefield.createSystem(modeller.topology,
nonbondedMethod=PME,
nonbondedCutoff=1.0*nanometers,
constraints=HBonds)
for force in external_forces:
system.addForce(force)
integrator = LangevinIntegrator(self._temp*kelvin,
1/picosecond,
0.002*picosecond)
# precision could be mixed, but single is okay.
platform = self._platform if self._platform is None else Platform.getPlatformByName(self._platform)
properties = None
if self._platform is None:
properties = {'Precision': 'single'}
elif self._platform in ['CUDA', 'OpenCL']:
properties = {'Precision': 'single'}
simulation = Simulation(modeller.topology, system, integrator,
platform, properties)
simulation.context.setPositions(modeller.positions)
return simulation
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
"""
xsize = self._periodicBoxVectors[frame][0][0].value_in_unit(nanometers)
ysize = self._periodicBoxVectors[frame][1][1].value_in_unit(nanometers)
zsize = self._periodicBoxVectors[frame][2][2].value_in_unit(nanometers)
return Vec3(xsize, ysize, zsize) * nanometers
def _construct_box_vectors(line):
"""Create the periodic box vectors based on the values stored in the file.
@param[in] line The line containing the description
"""
sline = line.split()
values = [float(i) for i in sline]
if len(sline) == 3:
return (Vec3(values[0], 0, 0), Vec3(
0, values[1], 0), Vec3(0, 0, values[2])) * nanometers
return reducePeriodicBoxVectors(
(Vec3(values[0], values[3],
values[4]), Vec3(values[5], values[1], values[6]),
Vec3(values[7], values[8], values[2])) * nanometers)
def testVec3Attributes(self):
vec1 = Vec3(1, 2, 3)
self.assertEqual(vec1.x, 1)
self.assertEqual(vec1.y, 2)
self.assertEqual(vec1.z, 3)
def __init__(self, file):
"""Load a PDBx/mmCIF file.
The atom positions and Topology can be retrieved by calling
getPositions() and getTopology().
Parameters
----------
file : string
the name of the file to load. Alternatively you can pass an open
file object.
"""
top = Topology()
## The Topology read from the PDBx/mmCIF file
self.topology = top
self._positions = []
PDBFile._loadNameReplacementTables()
# Load the file.
inputFile = file
ownHandle = False
if isinstance(file, str):
inputFile = open(file)
ownHandle = True
reader = PdbxReader(inputFile)
data = []
reader.read(data)
if ownHandle:
inputFile.close()
block = data[0]
# Build the topology.
atomData = block.getObj('atom_site')
atomNameCol = atomData.getAttributeIndex('auth_atom_id')
if atomNameCol == -1:
atomNameCol = atomData.getAttributeIndex('label_atom_id')
atomIdCol = atomData.getAttributeIndex('id')
resNameCol = atomData.getAttributeIndex('auth_comp_id')
if resNameCol == -1:
resNameCol = atomData.getAttributeIndex('label_comp_id')
resNumCol = atomData.getAttributeIndex('auth_seq_id')
if resNumCol == -1:
resNumCol = atomData.getAttributeIndex('label_seq_id')
resInsertionCol = atomData.getAttributeIndex('pdbx_PDB_ins_code')
chainIdCol = atomData.getAttributeIndex('auth_asym_id')
if chainIdCol == -1:
chainIdCol = atomData.getAttributeIndex('label_asym_id')
altChainIdCol = -1
else:
altChainIdCol = atomData.getAttributeIndex('label_asym_id')
if altChainIdCol != -1:
# Figure out which column is best to use for chain IDs.
idSet = set(row[chainIdCol] for row in atomData.getRowList())
altIdSet = set(row[altChainIdCol] for row in atomData.getRowList())
if len(altIdSet) > len(idSet):
chainIdCol, altChainIdCol = (altChainIdCol, chainIdCol)
elementCol = atomData.getAttributeIndex('type_symbol')
altIdCol = atomData.getAttributeIndex('label_alt_id')
modelCol = atomData.getAttributeIndex('pdbx_PDB_model_num')
xCol = atomData.getAttributeIndex('Cartn_x')
yCol = atomData.getAttributeIndex('Cartn_y')
zCol = atomData.getAttributeIndex('Cartn_z')
lastChainId = None
lastAltChainId = None
lastResId = None
lastInsertionCode = ''
atomTable = {}
atomsInResidue = set()
models = []
for row in atomData.getRowList():
atomKey = ((row[resNumCol], row[chainIdCol], row[atomNameCol]))
model = ('1' if modelCol == -1 else row[modelCol])
if model not in models:
models.append(model)
self._positions.append([])
modelIndex = models.index(model)
if row[altIdCol] != '.' and atomKey in atomTable and len(
self._positions[modelIndex]) > atomTable[atomKey].index:
# This row is an alternate position for an existing atom, so ignore it.
continue
if modelIndex == 0:
# This row defines a new atom.
if resInsertionCol == -1:
insertionCode = ''
else:
insertionCode = row[resInsertionCol]
if insertionCode in ('.', '?'):
insertionCode = ''
if lastChainId != row[chainIdCol] or (
altChainIdCol != -1
and lastAltChainId != row[altChainIdCol]):
# The start of a new chain.
chain = top.addChain(row[chainIdCol])
lastChainId = row[chainIdCol]
lastResId = None
if altChainIdCol != -1:
lastAltChainId = row[altChainIdCol]
if lastResId != row[resNumCol] or lastChainId != row[
chainIdCol] or lastInsertionCode != insertionCode or (
lastResId == '.'
and row[atomNameCol] in atomsInResidue):
# The start of a new residue.
resId = (None if resNumCol == -1 else row[resNumCol])
resIC = insertionCode
resName = row[resNameCol]
if resName in PDBFile._residueNameReplacements:
resName = PDBFile._residueNameReplacements[resName]
res = top.addResidue(resName, chain, resId, resIC)
if resName in PDBFile._atomNameReplacements:
atomReplacements = PDBFile._atomNameReplacements[
resName]
else:
atomReplacements = {}
lastResId = row[resNumCol]
lastInsertionCode = insertionCode
atomsInResidue.clear()
element = None
try:
element = elem.get_by_symbol(row[elementCol])
except KeyError:
pass
atomName = row[atomNameCol]
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
atom = top.addAtom(atomName, element, res, row[atomIdCol])
atomTable[atomKey] = atom
atomsInResidue.add(atomName)
else:
# This row defines coordinates for an existing atom in one of the later models.
try:
atom = atomTable[atomKey]
except KeyError:
raise ValueError(
'Unknown atom %s in residue %s %s for model %s' %
(row[atomNameCol], row[resNameCol], row[resNumCol],
model))
if atom.index != len(self._positions[modelIndex]):
raise ValueError(
'Atom %s for model %s does not match the order of atoms for model %s'
% (row[atomIdCol], model, models[0]))
self._positions[modelIndex].append(
Vec3(float(row[xCol]), float(row[yCol]), float(row[zCol])) *
0.1)
for i in range(len(self._positions)):
self._positions[i] = self._positions[i] * nanometers
## The atom positions read from the PDBx/mmCIF file. If the file contains multiple frames, these are the positions in the first frame.
self.positions = self._positions[0]
self.topology.createStandardBonds()
self._numpyPositions = None
# Record unit cell information, if present.
cell = block.getObj('cell')
if cell is not None and cell.getRowCount() > 0:
row = cell.getRow(0)
(a, b, c) = [
float(row[cell.getAttributeIndex(attribute)]) * 0.1
for attribute in ('length_a', 'length_b', 'length_c')
]
(alpha, beta, gamma) = [
float(row[cell.getAttributeIndex(attribute)]) * math.pi / 180.0
for attribute in ('angle_alpha', 'angle_beta', 'angle_gamma')
]
self.topology.setPeriodicBoxVectors(
computePeriodicBoxVectors(a, b, c, alpha, beta, gamma))
# Add bonds based on struct_conn records.
connectData = block.getObj('struct_conn')
if connectData is not None:
res1Col = connectData.getAttributeIndex('ptnr1_label_seq_id')
res2Col = connectData.getAttributeIndex('ptnr2_label_seq_id')
atom1Col = connectData.getAttributeIndex('ptnr1_label_atom_id')
atom2Col = connectData.getAttributeIndex('ptnr2_label_atom_id')
asym1Col = connectData.getAttributeIndex('ptnr1_label_asym_id')
asym2Col = connectData.getAttributeIndex('ptnr2_label_asym_id')
typeCol = connectData.getAttributeIndex('conn_type_id')
connectBonds = []
for row in connectData.getRowList():
type = row[typeCol][:6]
if type in ('covale', 'disulf', 'modres'):
key1 = (row[res1Col], row[asym1Col], row[atom1Col])
key2 = (row[res2Col], row[asym2Col], row[atom2Col])
if key1 in atomTable and key2 in atomTable:
connectBonds.append((atomTable[key1], atomTable[key2]))
if len(connectBonds) > 0:
# Only add bonds that don't already exist.
existingBonds = set(top.bonds())
for bond in connectBonds:
if bond not in existingBonds and (
bond[1], bond[0]) not in existingBonds:
top.addBond(bond[0], bond[1])
existingBonds.add(bond)
def __init__(self, file, extraParticleIdentifier='EP'):
"""Load a PDB file.
The atom positions and Topology can be retrieved by calling getPositions() and getTopology().
Parameters
----------
file : string or file
the name of the file to load. Alternatively you can pass an open file object.
extraParticleIdentifier : string='EP'
if this value appears in the element column for an ATOM record, the Atom's element will be set to None to mark it as an extra particle
"""
metalElements = [
'Al', 'As', 'Ba', 'Ca', 'Cd', 'Ce', 'Co', 'Cs', 'Cu', 'Dy', 'Fe',
'Gd', 'Hg', 'Ho', 'In', 'Ir', 'K', 'Li', 'Mg', 'Mn', 'Mo', 'Na',
'Ni', 'Pb', 'Pd', 'Pt', 'Rb', 'Rh', 'Sm', 'Sr', 'Te', 'Tl', 'V',
'W', 'Yb', 'Zn'
]
top = Topology()
## The Topology read from the PDB file
self.topology = top
# Load the PDB file
if isinstance(file, PdbStructure):
pdb = file
else:
inputfile = file
own_handle = False
if isinstance(file, str):
inputfile = open(file)
own_handle = True
pdb = PdbStructure(inputfile,
load_all_models=True,
extraParticleIdentifier=extraParticleIdentifier)
if own_handle:
inputfile.close()
PDBFile._loadNameReplacementTables()
# Build the topology
atomByNumber = {}
for chain in pdb.iter_chains():
c = top.addChain(chain.chain_id)
for residue in chain.iter_residues():
resName = residue.get_name()
if resName in PDBFile._residueNameReplacements:
resName = PDBFile._residueNameReplacements[resName]
r = top.addResidue(resName, c, str(residue.number),
residue.insertion_code)
if resName in PDBFile._atomNameReplacements:
atomReplacements = PDBFile._atomNameReplacements[resName]
else:
atomReplacements = {}
for atom in residue.iter_atoms():
atomName = atom.get_name()
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
atomName = atomName.strip()
element = atom.element
if element == 'EP':
element = None
elif element is None:
# Try to guess the element.
upper = atomName.upper()
while len(upper) > 1 and upper[0].isdigit():
upper = upper[1:]
if upper.startswith('CL'):
element = elem.chlorine
elif upper.startswith('NA'):
element = elem.sodium
elif upper.startswith('MG'):
element = elem.magnesium
elif upper.startswith('BE'):
element = elem.beryllium
elif upper.startswith('LI'):
element = elem.lithium
elif upper.startswith('K'):
element = elem.potassium
elif upper.startswith('ZN'):
element = elem.zinc
elif len(residue) == 1 and upper.startswith('CA'):
element = elem.calcium
elif upper.startswith('D') and any(
a.name == atomName[1:]
for a in residue.iter_atoms()):
pass # A Drude particle
else:
try:
element = elem.get_by_symbol(upper[0])
except KeyError:
pass
newAtom = top.addAtom(atomName, element, r,
str(atom.serial_number))
atomByNumber[atom.serial_number] = newAtom
self._positions = []
for model in pdb.iter_models(True):
coords = []
for chain in model.iter_chains():
for residue in chain.iter_residues():
for atom in residue.iter_atoms():
pos = atom.get_position().value_in_unit(nanometers)
coords.append(Vec3(pos[0], pos[1], pos[2]))
self._positions.append(coords * nanometers)
## The atom positions read from the PDB file. If the file contains multiple frames, these are the positions in the first frame.
self.positions = self._positions[0]
self.topology.setPeriodicBoxVectors(pdb.get_periodic_box_vectors())
self.topology.createStandardBonds()
self.topology.createDisulfideBonds(self.positions)
self._numpyPositions = None
# Add bonds based on CONECT records. Bonds between metals of elements specified in metalElements and residues in standardResidues are not added.
connectBonds = []
for connect in pdb.models[-1].connects:
i = connect[0]
for j in connect[1:]:
if i in atomByNumber and j in atomByNumber:
if atomByNumber[i].element is not None and atomByNumber[
j].element is not None:
if atomByNumber[
i].element.symbol not in metalElements and atomByNumber[
j].element.symbol not in metalElements:
connectBonds.append(
(atomByNumber[i], atomByNumber[j]))
elif atomByNumber[
i].element.symbol in metalElements and atomByNumber[
j].residue.name not in PDBFile._standardResidues:
connectBonds.append(
(atomByNumber[i], atomByNumber[j]))
elif atomByNumber[
j].element.symbol in metalElements and atomByNumber[
i].residue.name not in PDBFile._standardResidues:
connectBonds.append(
(atomByNumber[i], atomByNumber[j]))
else:
connectBonds.append((atomByNumber[i], atomByNumber[j]))
if len(connectBonds) > 0:
# Only add bonds that don't already exist.
existingBonds = set(top.bonds())
for bond in connectBonds:
if bond not in existingBonds and (
bond[1], bond[0]) not in existingBonds:
top.addBond(bond[0], bond[1])
existingBonds.add(bond)
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
"""
xyzs = []
elements = [
] # The element, most useful for quantum chemistry calculations
atomname = [] # The atom name, for instance 'HW1'
comms = []
resid = []
resname = []
boxes = []
xyz = []
ln = 0
frame = 0
with open(file) as grofile:
for line in grofile:
if ln == 0:
comms.append(line.strip())
elif ln == 1:
na = int(line.strip())
elif _is_gro_coord(line):
if frame == 0: # Create the list of residues, atom names etc. only if it's the first frame.
(thisresnum, thisresname, thisatomname) = [
line[i * 5:i * 5 + 5].strip() for i in range(3)
]
resname.append(thisresname)
resid.append(int(thisresnum))
atomname.append(thisatomname)
thiselem = thisatomname
if len(thiselem) > 1:
thiselem = thiselem[0] + sub(
'[A-Z0-9]', '', thiselem[1:])
try:
elements.append(elem.get_by_symbol(thiselem))
except KeyError:
elements.append(None)
firstDecimalPos = line.index('.', 20)
secondDecimalPos = line.index('.', firstDecimalPos + 1)
digits = secondDecimalPos - firstDecimalPos
pos = [
float(line[20 + i * digits:20 + (i + 1) * digits])
for i in range(3)
]
xyz.append(Vec3(pos[0], pos[1], pos[2]))
elif _is_gro_box(line) and ln == na + 2:
boxes.append(_construct_box_vectors(line))
xyzs.append(xyz * nanometers)
xyz = []
ln = -1
frame += 1
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
self.elements = elements
## A list containing the name of each atom stored in the file
self.atomNames = atomname
## A list containing the ID of the residue that each atom belongs to
self.residueIds = resid
## A list containing the name of the residue that each atom belongs to
self.residueNames = resname
self._positions = xyzs
self._periodicBoxVectors = boxes
self._numpyPositions = None
def writeModel(self, positions, unitCellDimensions=None, periodicBoxVectors=None):
"""Write out a model to the DCD file.
The periodic box can be specified either by the unit cell dimensions
(for a rectangular box), or the full set of box vectors (for an
arbitrary triclinic box). If neither is specified, the box vectors
specified in the Topology will be used. Regardless of the value
specified, no dimensions will be written if the Topology does not
represent a periodic system.
Parameters
----------
positions : list
The list of atomic positions to write
unitCellDimensions : Vec3=None
The dimensions of the crystallographic unit cell.
periodicBoxVectors : tuple of Vec3=None
The vectors defining the periodic box.
"""
if len(list(self._topology.atoms())) != len(positions):
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):
raise ValueError('Particle position is NaN')
if any(math.isinf(norm(pos)) for pos in positions):
raise ValueError('Particle position is infinite')
file = self._file
self._modelCount += 1
if self._interval > 1 and self._firstStep+self._modelCount*self._interval > 1<<31:
# This will exceed the range of a 32 bit integer. To avoid crashing or producing a corrupt file,
# update the header to say the trajectory consisted of a smaller number of larger steps (so the
# total trajectory length remains correct).
self._firstStep //= self._interval
self._dt *= self._interval
self._interval = 1
file.seek(0, os.SEEK_SET)
file.write(struct.pack('<i4c9if', 84, b'C', b'O', b'R', b'D', 0, self._firstStep, self._interval, 0, 0, 0, 0, 0, 0, self._dt))
# Update the header.
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)
boxVectors = self._topology.getPeriodicBoxVectors()
if boxVectors is not None:
if periodicBoxVectors is not None:
boxVectors = periodicBoxVectors
elif unitCellDimensions is not None:
if is_quantity(unitCellDimensions):
unitCellDimensions = unitCellDimensions.value_in_unit(nanometers)
boxVectors = (Vec3(unitCellDimensions[0], 0, 0), Vec3(0, unitCellDimensions[1], 0), Vec3(0, 0, unitCellDimensions[2]))*nanometers
(a_length, b_length, c_length, alpha, beta, gamma) = computeLengthsAndAngles(boxVectors)
a_length = a_length * 10. # computeLengthsAndAngles returns unitless nanometers, but need angstroms here.
b_length = b_length * 10. # computeLengthsAndAngles returns unitless nanometers, but need angstroms here.
c_length = c_length * 10. # computeLengthsAndAngles returns unitless nanometers, but need angstroms here.
angle1 = math.sin(math.pi/2-gamma)
angle2 = math.sin(math.pi/2-beta)
angle3 = math.sin(math.pi/2-alpha)
file.write(struct.pack('<i6di', 48, a_length, angle1, b_length, angle2, angle3, c_length, 48))
length = struct.pack('<i', 4*len(positions))
for i in range(3):
file.write(length)
data = array.array('f', (10*x[i] for x in positions))
data.tofile(file)
file.write(length)
try:
file.flush()
except AttributeError:
pass
def solvate(molecular_system,
box_geometry="truncated octahedral",
clearance='14.0 angstroms',
anion='Cl-',
num_anions="neutralize",
cation='Na+',
num_cations="neutralize",
ionic_strength='0.0 molar',
engine="LEaP",
to_form=None,
logfile=False,
verbose=False):
"""solvate(item, geometry=None, water=None, engine=None)
Methods and wrappers to create and solvate boxes
Parameters
----------
anion: 'Cl-', 'Br-', 'F-', and 'I-'
num_anions: number of cations to add. integer or "neutralize"
cation: "NA" 'Cs+', 'K+', 'Li+', 'Na+', and 'Rb+'
num_cations: number of cations to add. integer or "neutralize"
box_geometry: "cubic", "truncated_octahedral" or "rhombic_dodecahedron" (Default: "truncated_octahedral")
Returns
-------
item : bla bla
bla bla
Examples
--------
See Also
--------
Notes
-----
"""
from molsysmt.basic import get_form, convert
engine = digest_engine(engine)
to_form = digest_to_form(to_form)
if to_form is None:
to_form = get_form(molecular_system)
if engine == "OpenMM":
from openmm import Vec3
clearance = puw.convert(clearance, to_form='openmm.unit')
ionic_strength = puw.convert(ionic_strength, to_form='openmm.unit')
modeller = convert(molecular_system, to_form='openmm.Modeller')
molecular_mechanics = convert(molecular_system,
to_form='molsysmt.MolecularMechanics')
parameters = molecular_mechanics.get_openmm_System_parameters()
forcefield = molecular_mechanics.to_openmm_ForceField()
solvent_model = None
if molecular_mechanics.water_model == 'SPC':
solvent_model = 'tip3p'
elif molecular_mechanics.water_model in [
'TIP3P', 'TIP3PFB', 'SPCE', 'TIP4PEW', 'TIP4PFB', 'TIP5P'
]:
solvent_model = molecular_mechanics.water_model.lower()
else:
raise NotImplementedError()
if box_geometry == "truncated octahedral":
max_size = max(
max((pos[i] for pos in modeller.positions)) -
min((pos[i] for pos in modeller.positions)) for i in range(3))
vectors = Vec3(1.0, 0,
0), Vec3(1.0 / 3.0, 2.0 * np.sqrt(2.0) / 3.0,
0.0), Vec3(-1.0 / 3.0,
np.sqrt(2.0) / 3.0,
np.sqrt(6.0) / 3.0)
box_vectors = [(max_size + clearance) * v for v in vectors]
modeller.addSolvent(forcefield,
model=solvent_model,
boxVectors=box_vectors,
ionicStrength=ionic_strength,
positiveIon=cation,
negativeIon=anion)
elif box_geometry == "rhombic dodecahedral":
max_size = max(
max((pos[i] for pos in modeller.positions)) -
min((pos[i] for pos in modeller.positions)) for i in range(3))
vectors = Vec3(1.0, 0.0,
0.0), Vec3(0.0, 1.0,
0.0), Vec3(0.5, 0.5,
np.sqrt(2) / 2)
box_vectors = [(max_size + clearance) * v for v in vectors]
modeller.addSolvent(forcefield,
model=solvent_model,
boxVectors=box_vectors,
ionicStrength=ionic_strength,
positiveIon=cation,
negativeIon=anion)
else:
modeller.addSolvent(forcefield,
model=solvent_model,
padding=clearance,
ionicStrength=ionic_strength,
positiveIon=cation,
negativeIon=anion)
tmp_item = convert(modeller, to_form=to_form)
del (modeller)
return tmp_item
elif engine == "PDBFixer":
from openmm import Vec3
clearance = puw.convert(clearance, to_form='openmm.unit')
ionic_strength = puw.convert(ionic_strength, to_form='openmm.unit')
pdbfixer = convert(molecular_system, to_form='pdbfixer.PDBFixer')
max_size = max(
max((pos[i] for pos in pdbfixer.positions)) -
min((pos[i] for pos in pdbfixer.positions)) for i in range(3))
box_size = None
box_vectors = None
if box_geometry == "truncated octahedral":
vectors = Vec3(1.0, 0,
0), Vec3(1.0 / 3.0, 2.0 * np.sqrt(2.0) / 3.0,
0.0), Vec3(-1.0 / 3.0,
np.sqrt(2.0) / 3.0,
np.sqrt(6.0) / 3.0)
elif box_geometry == "rhombic dodecahedral":
vectors = Vec3(1.0, 0.0,
0.0), Vec3(0.0, 1.0,
0.0), Vec3(0.5, 0.5,
np.sqrt(2) / 2)
elif box_geometry == "cubic":
vectors = Vec3(1.0, 0.0, 0.0), Vec3(0.0, 1.0,
0.0), Vec3(0.0, 0.0, 1.0)
box_vectors = [(max_size + clearance) * v for v in vectors]
pdbfixer.addSolvent(boxVectors=box_vectors,
ionicStrength=ionic_strength,
positiveIon=cation,
negativeIon=anion)
tmp_item = convert(pdbfixer, to_form=to_form)
del (pdbfixer)
return tmp_item
elif engine == "LEaP":
from molsysmt.thirds.tleap import TLeap
from molsysmt._private.files_and_directories import temp_directory, temp_filename
from molsysmt.tools.file_pdb import replace_HETATM_by_ATOM_in_terminal_cappings
from shutil import rmtree, copyfile
from os import getcwd, chdir
from molsysmt.basic import set as _set, select
from molsysmt.build import has_hydrogens, remove_hydrogens
if has_hydrogens(molecular_system):
raise ValueError(
"A molecular system without hydrogen atoms is needed.")
#molecular_system = remove_hydrogens(molecular_system)
#if verbose:
# print("All Hydrogen atoms were removed to be added by LEaP\n\n")
indices_NME_C = select(
molecular_system,
target='atom',
selection='group_name=="NME" and atom_name=="C"')
with_NME_C = (len(indices_NME_C) > 0)
if with_NME_C:
_set(molecular_system,
target='atom',
selection='group_name=="NME" and atom_name=="C"',
atom_name='CH3')
current_directory = getcwd()
working_directory = temp_directory()
pdbfile_in = temp_filename(dir=working_directory, extension='pdb')
_ = convert(molecular_system, to_form=pdbfile_in)
#replace_HETATM_from_capping_atoms(pdbfile_in)
tmp_prmtop = temp_filename(dir=working_directory, extension='prmtop')
tmp_inpcrd = tmp_prmtop.replace('prmtop', 'inpcrd')
tmp_logfile = tmp_prmtop.replace('prmtop', 'leap.log')
molecular_mechanics = convert(molecular_system,
to_form='molsysmt.MolecularMechanics')
parameters = molecular_mechanics.get_leap_parameters()
forcefield = parameters['forcefield']
water = parameters['water_model']
solvent_model = None
if water == 'SPC':
solvent_model = 'SPCBOX'
elif water == 'TIP3P':
solvent_model = 'TIP3PBOX'
elif water == 'TIP4P':
solvent_model = 'TIP4PBOX'
if verbose:
print('Working directory:', working_directory)
tleap = TLeap()
tleap.load_parameters(*forcefield)
tleap.load_unit('MolecularSystem', pdbfile_in)
tleap.check_unit('MolecularSystem')
tleap.get_total_charge('MolecularSystem')
tleap.solvate('MolecularSystem',
solvent_model,
clearance,
box_geometry=box_geometry)
if num_anions != 0:
if num_anions == 'neutralize':
num_anions = 0
tleap.add_ions('MolecularSystem',
anion,
num_ions=num_anions,
replace_solvent=True)
if num_cations != 0:
if num_cations == 'neutralize':
num_cations = 0
tleap.add_ions('MolecularSystem',
cation,
num_ions=num_cations,
replace_solvent=True)
tleap.save_unit('MolecularSystem', tmp_prmtop)
errors = tleap.run(working_directory=working_directory,
verbose=verbose)
del (tleap)
if logfile:
copyfile(tmp_logfile, current_directory + '/build_peptide.log')
tmp_item = convert([tmp_prmtop, tmp_inpcrd], to_form=to_form)
if with_NME_C:
_set(tmp_item,
target='atom',
selection='group_name=="NME" and atom_name=="CH3"',
atom_name='C')
rmtree(working_directory)
return tmp_item
else:
raise NotImplementedError
def testNegation(self):
vec1 = Vec3(1, 2, 3)
vec1_neg = Vec3(-1, -2, -3)
self.assertEqual(-vec1, vec1_neg)
def testVec3Equality(self):
vec1 = Vec3(1, 2, 3)
vec2 = Vec3(1, 2, 3)
self.assertEqual(vec1, vec2)
def testVec3Multiplication(self):
vec1 = Vec3(1, 2, 3)
factor = 2
result = Vec3(2, 4, 6)
self.assertEqual(vec1 * factor, result)
self.assertEqual(factor * vec1, result)