def testComputePBCVectors(self):
""" Tests computing periodic box vectors """
deg90 = 90 * degrees
vecs = computePeriodicBoxVectors(1, 2, 3, deg90, deg90, deg90)
a, b, c = vecs
self.assertAlmostEqual(a[0]/nanometers, 1)
self.assertAlmostEqual(a[1]/nanometers, 0)
self.assertAlmostEqual(a[2]/nanometers, 0)
self.assertAlmostEqual(b[0]/nanometers, 0)
self.assertAlmostEqual(b[1]/nanometers, 2)
self.assertAlmostEqual(b[2]/nanometers, 0)
self.assertAlmostEqual(c[0]/nanometers, 0)
self.assertAlmostEqual(c[1]/nanometers, 0)
self.assertAlmostEqual(c[2]/nanometers, 3)
# Make sure round-trip works
la, lb, lc, al, be, ga = computeLengthsAndAngles(vecs)
self.assertAlmostEqual(la, 1)
self.assertAlmostEqual(lb, 2)
self.assertAlmostEqual(lc, 3)
self.assertAlmostEqual(al, math.pi / 2)
self.assertAlmostEqual(be, math.pi / 2)
self.assertAlmostEqual(ga, math.pi / 2)
# Now test a truncated octahedron. Can't do a simple round-trip though,
# due to the reduced form. So test the *second* round-trip, which should
# yield the same measurements
vecs = computePeriodicBoxVectors(4.24388485, 4.24388485, 4.24388485,
109.4712190*degrees, 109.4712190*degrees, 109.4712190*degrees)
la, lb, lc, al, be, ga = computeLengthsAndAngles(vecs)
vecs2 = computePeriodicBoxVectors(la, lb, lc, al, be, ga)
la2, lb2, lc2, al2, be2, ga2 = computeLengthsAndAngles(vecs2)
# Now make sure that the round-trip worked
self.assertAlmostEqual(strip_units(la), strip_units(la2))
self.assertAlmostEqual(strip_units(lb), strip_units(lb2))
self.assertAlmostEqual(strip_units(lc), strip_units(lc2))
self.assertAlmostEqual(strip_units(al), strip_units(al2))
self.assertAlmostEqual(strip_units(be), strip_units(be2))
self.assertAlmostEqual(strip_units(ga), strip_units(ga2))
# 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 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 __init__(self, file):
"""Load a prmtop file."""
## The Topology read from the prmtop file
self.topology = top = Topology()
self.elements = []
# Load the prmtop file
prmtop = amber_file_parser.PrmtopLoader(file)
self._prmtop = prmtop
# Add atoms to the topology
PDBFile._loadNameReplacementTables()
lastResidue = None
c = top.addChain()
for index in range(prmtop.getNumAtoms()):
resNumber = prmtop.getResidueNumber(index)
if resNumber != lastResidue:
lastResidue = resNumber
resName = prmtop.getResidueLabel(iAtom=index).strip()
if resName in PDBFile._residueNameReplacements:
resName = PDBFile._residueNameReplacements[resName]
r = top.addResidue(resName, c)
if resName in PDBFile._atomNameReplacements:
atomReplacements = PDBFile._atomNameReplacements[resName]
else:
atomReplacements = {}
atomName = prmtop.getAtomName(index).strip()
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
# Get the element from the prmtop file if available
if prmtop.has_atomic_number:
try:
element = elem.Element.getByAtomicNumber(
int(prmtop._raw_data['ATOMIC_NUMBER'][index]))
except KeyError:
element = None
else:
# Try to guess the element from the atom name.
upper = atomName.upper()
if upper.startswith('CL'):
element = elem.chlorine
elif upper.startswith('NA'):
element = elem.sodium
elif upper.startswith('MG'):
element = elem.magnesium
elif upper.startswith('ZN'):
element = elem.zinc
else:
try:
element = elem.get_by_symbol(atomName[0])
except KeyError:
element = None
top.addAtom(atomName, element, r)
self.elements.append(element)
# 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():
box = prmtop.getBoxBetaAndDimensions()
top.setPeriodicBoxVectors(
computePeriodicBoxVectors(*(box[1:4] + box[0:1] * 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)