def _createTopology(self):
"""Build the topology of the system
"""
top = Topology()
positions = []
velocities = []
boxVectors = []
for x, y, z in self._conn.execute('SELECT x, y, z FROM global_cell'):
boxVectors.append(mm.Vec3(x, y, z))
unitCellDimensions = [boxVectors[0][0], boxVectors[1][1], boxVectors[2][2]]
top.setUnitCellDimensions(unitCellDimensions*angstrom)
atoms = {}
lastChain = None
lastResId = None
c = top.addChain()
q = """SELECT id, name, anum, resname, resid, chain, x, y, z, vx, vy, vz
FROM particle ORDER BY id"""
for (atomId, atomName, atomNumber, resName, resId, chain, x, y, z, vx, vy, vz) in self._conn.execute(q):
newChain = False
if chain != lastChain:
lastChain = chain
c = top.addChain()
newChain = True
if resId != lastResId or newChain:
lastResId = resId
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 = {}
if atomNumber == 0 and atomName.startswith('Vrt'):
elem = None
else:
elem = Element.getByAtomicNumber(atomNumber)
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
atoms[atomId] = top.addAtom(atomName, elem, r)
positions.append(mm.Vec3(x, y, z))
velocities.append(mm.Vec3(vx, vy, vz))
for p0, p1 in self._conn.execute('SELECT p0, p1 FROM bond'):
top.addBond(atoms[p0], atoms[p1])
positions = positions*angstrom
velocities = velocities*angstrom/femtosecond
return top, positions, velocities
def _createTopology(self):
"""Build the topology of the system
"""
top = Topology()
positions = []
velocities = []
boxVectors = []
for x, y, z in self._conn.execute('SELECT x, y, z FROM global_cell'):
boxVectors.append(mm.Vec3(x, y, z))
unitCellDimensions = [boxVectors[0][0], boxVectors[1][1], boxVectors[2][2]]
top.setUnitCellDimensions(unitCellDimensions*angstrom)
atoms = {}
lastChain = None
lastResId = None
c = top.addChain()
q = """SELECT id, name, anum, resname, resid, chain, x, y, z, vx, vy, vz
FROM particle ORDER BY id"""
for (atomId, atomName, atomNumber, resName, resId, chain, x, y, z, vx, vy, vz) in self._conn.execute(q):
newChain = False
if chain != lastChain:
lastChain = chain
c = top.addChain()
newChain = True
if resId != lastResId or newChain:
lastResId = resId
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 = {}
if atomNumber == 0 and atomName.startswith('Vrt'):
elem = None
else:
elem = Element.getByAtomicNumber(atomNumber)
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
atoms[atomId] = top.addAtom(atomName, elem, r)
positions.append(mm.Vec3(x, y, z))
velocities.append(mm.Vec3(vx, vy, vz))
for p0, p1 in self._conn.execute('SELECT p0, p1 FROM bond'):
top.addBond(atoms[p0], atoms[p1])
positions = positions*angstrom
velocities = velocities*angstrom/femtosecond
return top, positions, velocities
def _createTopology(self):
'''Build the topology of the system
'''
top = Topology()
positions = []
boxVectors = []
for x, y, z in self._conn.execute('SELECT x, y, z FROM global_cell'):
boxVectors.append(mm.Vec3(x, y, z)*angstrom)
unitCellDimensions = [boxVectors[0][0], boxVectors[1][1], boxVectors[2][2]]
top.setUnitCellDimensions(unitCellDimensions)
atoms = {}
lastChain = None
lastResId = None
c = top.addChain()
q = '''SELECT id, name, anum, resname, resid, chain, x, y, z
FROM particle'''
for (atomId, atomName, atomNumber, resName, resId, chain, x, y, z) in self._conn.execute(q):
if chain != lastChain:
lastChain = chain
c = top.addChain()
if resId != lastResId:
lastResId = resId
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 = {}
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
elem = Element.getByAtomicNumber(atomNumber)
atoms[atomId] = top.addAtom(atomName, elem, r)
positions.append(mm.Vec3(x, y, z)*angstrom)
for p0, p1 in self._conn.execute('SELECT p0, p1 FROM bond'):
top.addBond(atoms[p0], atoms[p1])
return top, positions
def _createTopology(self):
"""Build the topology of the system
"""
top = Topology()
positions = []
velocities = []
boxVectors = []
#assume cell dimensions are set in the first file
#the other molecules inherit the same cell
conn = self._conn[0]
self.pbc = False
if self._hasTable('global_cell', self._tables[0]):
for x, y, z in conn.execute('SELECT x, y, z FROM global_cell'):
boxVectors.append(mm.Vec3(x, y, z))
unitCellDimensions = [boxVectors[0][0], boxVectors[1][1], boxVectors[2][2]]
top.setUnitCellDimensions(unitCellDimensions*angstrom)
self.pbc = True
#process each file
nfiles = len(self._conn)
for (fcounter, conn, tables) in zip(range(0,nfiles),self._conn,self._tables):
"""
resdb = {}
chaindb = {}
"""
atoms = {}
lastChain = None
lastResId = None
c = top.addChain()
q = """SELECT id, name, anum, resname, resid, chain, x, y, z, vx, vy, vz
FROM particle ORDER BY id"""
for (atomId, atomName, atomNumber, resName, resId, chain, x, y, z, vx, vy, vz) in conn.execute(q):
"""
#more elegant way to assign atoms to residues
#but it works only if atoms in residues are contiguous
#due to the fact that openmm does not support non-contiguous residues
resuid = "%s:%s:%s" % (resName, resId, chain)
if resuid in resdb.keys():
r = resdb[resuid]
c = chaindb[chain]
else:
if chain in chaindb.keys():
c = chaindb[chain]
else:
c = top.addChain()
chaindb[chain] = c
r = top.addResidue(resName, c)
resdb[resuid] = r
"""
newChain = False
if chain != lastChain:
lastChain = chain
c = top.addChain()
newChain = True
if resId != lastResId or newChain:
lastResId = resId
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 = {}
if atomNumber == 0 and atomName.startswith('Vrt'):
elem = None
else:
elem = Element.getByAtomicNumber(atomNumber)
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
atoms[atomId] = top.addAtom(atomName, elem, r)
positions.append(mm.Vec3(x, y, z))
velocities.append(mm.Vec3(vx, vy, vz))
self._natoms[fcounter] = len(atoms)
for p0, p1 in conn.execute('SELECT p0, p1 FROM bond'):
top.addBond(atoms[p0], atoms[p1])
positions = positions*angstrom
velocities = velocities*angstrom/picosecond
return top, positions, velocities
