def parse(self, files = None):
if files is None:
if len(self.files) <= 0:
# Error("Attempted to parse without files available", type="Fatal")
files = dircache.listdir("data")
print "Using all files found in data/ directory"
print "%s" % (", ".join(files))
else:
files = self.files
badfiles = []
for file in files:
try:
_f = open("data/%s" % (file), "r")
_chain = Chain(file)
_nodes = []
for line in _f:
if line.strip():
try:
name, x, y, z = line.split()
except:
print "Error in line: '%s'" % (line)
globals.shutdown()
x = float(x)
y = float(y)
z = float(z)
_nodes.append(Node(name, x, y, z))
if len(_nodes) == 2:
_bond = Bond(_nodes[0], _nodes[1])
_chain.add_bond(_bond)
_nodes = []
globals.chains.append(_chain)
except IOError as (no, err):
badfiles.append("data/%s" % (file))
def parse(self, files=None):
if files is None:
if len(self.files) <= 0:
# Error("Attempted to parse without files available", type="Fatal")
files = dircache.listdir("data")
print "Using all files found in data/ directory"
print "%s" % (", ".join(files))
else:
files = self.files
badfiles = []
for file in files:
try:
_f = open("data/%s" % (file), "r")
_chain = Chain(file)
_nodes = []
for line in _f:
if line.strip():
try:
name, x, y, z = line.split()
except:
print "Error in line: '%s'" % (line)
globals.shutdown()
x = float(x)
y = float(y)
z = float(z)
_nodes.append(Node(name, x, y, z))
if len(_nodes) == 2:
_bond = Bond(_nodes[0], _nodes[1])
_chain.add_bond(_bond)
_nodes = []
globals.chains.append(_chain)
except IOError as (no, err):
badfiles.append("data/%s" % (file))
def start():
# The tasks for this function are as follows
# @TODO: This is being updated regularly and is not in a final form
#
# - setup and manage the process pool for the head-node that has
# the following responsibilities
# - user-interface activity (responsiveness and display real-time data)
# - receive MPI messages passed from the child-nodes
# - send MPI messages to the child-nodes
# - manage appropriate actions through the logic controller
# - manage the database interface (as a sub-process)
# @TODO: tbc...
# start the dispatcher process
# it is accessible from here on out in globals manager and can be accessed by name
globals.manager.new_process(run=com.dispatcher, name="dispatcher")
# start the service that will be listening for the reports from the child nodes
globals.manager.new_process(run=com.publisher, name="publisher")
# Error("The size of the graph of nodes is %d" % (globals.comm.size))
# need to set the chains object in the global namespace (head-only)
globals.chains = []
# need to set the parser object
globals.parser = parser()
# Need to start the GUI
# TEMPORARY !--------------------------------
# READ FILENAMES ONE AT A TIME UNTIL BLANK
print "Please enter filenames space-delimited then press enter,"
print "or press enter to use all available chains in the data/ directory"
files = raw_input("\r: ")
if files == "":
globals.parser.parse()
else:
globals.parser.set_files(files, True)
#--------------------------------------------
print "Done parsing"
print "Printing chains:"
for chain in globals.chains:
print ""
print "Name: %s" % (chain.name)
for bond in chain.bonds:
print bond
print ""
# globals.manager.close()
# exit
globals.shutdown()
def Error(message, type = "Debug"):
stack = traceback.extract_stack(limit=2)
caller = stack[0][2]
file = stack[0][0]
line = stack[0][1]
print "Caught : %s => %s" % (type, message)
print "\t["
print "\t node => %s" % globals.name
print "\t process => %s" % globals.rank
print "\t pid => %d" % os.getpid()
print "\t caller => %s" % caller
print "\t file => %s" % file
print "\t line => %s" % line
print "\t]"
if type == "Fatal":
globals.shutdown()