def test_read_pdb():
"""Tests that pdb files are read correctly."""
with open(local("test.pos_0.pdb"), "r") as f:
atoms, cell = io_pdb.read_pdb(f)
assert(len(atoms) == 3)
assert_equal(pos, atoms.q)
def init_pdb(filename):
"""Reads an pdb file and returns the data contained in it.
Args:
filename: A string giving the name of the pdb file to be read from.
Returns:
A list of Atoms objects as read from each frame of the pdb file, and
a Cell object as read from the final pdb frame.
"""
rfile = open(filename, "r")
ratoms = []
while True:
#while loop, so that more than one configuration can be given
#so multiple beads can be initialized at once.
try:
myatoms, rcell = read_pdb(rfile)
except EOFError:
break
ratoms.append(myatoms)
return (ratoms, rcell) # if multiple frames, the last cell is returned
def init_pdb(filename):
"""Reads an pdb file and returns the data contained in it.
Args:
filename: A string giving the name of the pdb file to be read from.
Returns:
A list of Atoms objects as read from each frame of the pdb file, and
a Cell object as read from the final pdb frame.
"""
rfile = open(filename,"r")
ratoms = []
while True:
#while loop, so that more than one configuration can be given
#so multiple beads can be initialized at once.
try:
myatoms, rcell = read_pdb(rfile)
except EOFError:
break
ratoms.append(myatoms)
return ( ratoms, rcell ) # if multiple frames, the last cell is returned
def step(self):
"""Does one simulation time step."""
self.ptime = self.ttime = 0
self.qtime = -time.time()
try:
if (self.intraj.mode == "xyz"):
for b in self.beads:
myatoms = read_xyz(self.rfile)
myatoms.q *= unit_to_internal("length", self.intraj.units,
1.0)
b.q[:] = myatoms.q
elif (self.intraj.mode == "pdb"):
for b in self.beads:
myatoms, mycell = read_pdb(self.rfile)
myatoms.q *= unit_to_internal("length", self.intraj.units,
1.0)
mycell.h *= unit_to_internal("length", self.intraj.units,
1.0)
b.q[:] = myatoms.q
self.cell.h[:] = mycell.h
elif (self.intraj.mode == "chk"
or self.intraj.mode == "checkpoint"):
# reads configuration from a checkpoint file
xmlchk = xml_parse_file(self.rfile) # Parses the file.
from ipi.inputs.simulation import InputSimulation
simchk = InputSimulation()
simchk.parse(xmlchk.fields[0][1])
mycell = simchk.cell.fetch()
mybeads = simchk.beads.fetch()
self.cell.h[:] = mycell.h
self.beads.q[:] = mybeads.q
softexit.trigger(" # Read single checkpoint")
except EOFError:
softexit.trigger(" # Finished reading re-run trajectory")
self.qtime += time.time()
def step(self):
"""Does one simulation time step."""
self.ptime = self.ttime = 0
self.qtime = -time.time()
try:
if self.intraj.mode == "xyz":
for b in self.beads:
myatoms = read_xyz(self.rfile)
myatoms.q *= unit_to_internal("length", self.intraj.units, 1.0)
b.q[:] = myatoms.q
elif self.intraj.mode == "pdb":
for b in self.beads:
myatoms, mycell = read_pdb(self.rfile)
myatoms.q *= unit_to_internal("length", self.intraj.units, 1.0)
mycell.h *= unit_to_internal("length", self.intraj.units, 1.0)
b.q[:] = myatoms.q
self.cell.h[:] = mycell.h
elif self.intraj.mode == "chk" or self.intraj.mode == "checkpoint":
# reads configuration from a checkpoint file
xmlchk = xml_parse_file(self.rfile) # Parses the file.
from ipi.inputs.simulation import InputSimulation
simchk = InputSimulation()
simchk.parse(xmlchk.fields[0][1])
mycell = simchk.cell.fetch()
mybeads = simchk.beads.fetch()
self.cell.h[:] = mycell.h
self.beads.q[:] = mybeads.q
softexit.trigger(" # Read single checkpoint")
except EOFError:
softexit.trigger(" # Finished reading re-run trajectory")
self.qtime += time.time()