def main():
options = options_desc.parse_args(sys.argv)[0]
pool = Pool()
choice = "state in ('converged', 'refined')"
if(options.ignore_convergence):
choice = "state in ('converged', 'not-converged', 'refined')"
needy_nodes = NodeList([n for n in pool.where(choice) if not n == pool.root]) # we won't touch the root
if not(len(needy_nodes)):
sys.exit("Nothing to do.")
if not(userinput("Once the solvent has been removed, further refinement of the pool is not possible. This includes the generation of unrestrained transition nodes! Continue?", "bool")):
sys.exit("Quit by user.")
assert(len(needy_nodes) == len(needy_nodes.multilock())) # make sure we lock ALL nodes
try:
for n in needy_nodes:
discard_solvent(n, "pdb")
discard_solvent(n, "trr")
for n in needy_nodes:
n.unlock()
except:
traceback.print_exc()
def main():
options = options_desc.parse_args(sys.argv)[0]
pool = Pool()
choice = "state in ('converged', 'refined')"
if (options.ignore_convergence):
choice = "state in ('converged', 'not-converged', 'refined')"
needy_nodes = NodeList([
n for n in pool.where(choice) if not n == pool.root
]) # we won't touch the root
if not (len(needy_nodes)):
sys.exit("Nothing to do.")
if not (userinput(
"Once the solvent has been removed, further refinement of the pool is not possible. This includes the generation of unrestrained transition nodes! Continue?",
"bool")):
sys.exit("Quit by user.")
assert (len(needy_nodes) == len(needy_nodes.multilock())
) # make sure we lock ALL nodes
try:
for n in needy_nodes:
discard_solvent(n, "pdb")
discard_solvent(n, "trr")
for n in needy_nodes:
n.unlock()
except:
traceback.print_exc()
def main():
options = options_desc.parse_args(sys.argv)[0]
#TODO put somehow into Options, e.g. min_value=1 or required=True
if(not options.doomed_nodes):
sys.exit("Option --doomed_nodes is required.")
pool = Pool()
old_pool_size = len(pool)
old_alpha = pool.alpha
doomed_nodes = NodeList()
#TODO: maybe this code should go into ZIBMolPy.ui
for name in options.doomed_nodes.split(","):
found = [n for n in pool if n.name == name]
if(len(found) != 1):
sys.exit("Coult not find node '%s'"%(name))
doomed_nodes.append(found[0])
for n in doomed_nodes:
if(n == pool.root):
sys.exit("Node %s is the root. Removal not allowed."%(n.name))
#if(len(n.children) > 0):
# sys.exit("Node %s has children. Removal not allowed."%(n.name)) #TODO why should we forbid this?
if not(userinput("The selected node(s) will be removed permanently. Continue?", "bool")):
sys.exit("Quit by user.")
assert(len(doomed_nodes) == len(doomed_nodes.multilock()))
for n in doomed_nodes:
print("Removing directory: "+n.dir)
shutil.rmtree(n.dir)
pool.reload_nodes()
#TODO: this code-block also exists in zgf_create_node
if(len(pool.where("isa_partition")) < 2):
pool.alpha = None
elif(options.methodalphas == "theta"):
pool.alpha = zgf_create_nodes.calc_alpha_theta(pool)
elif(options.methodalphas == "user"):
pool.alpha = userinput("Please enter a value for alpha", "float")
else:
raise(Exception("Method unkown: "+options.methodalphas))
pool.history.append({'removed_nodes': [(n.name, n.state) for n in doomed_nodes], 'size':old_pool_size, 'alpha':old_alpha, 'timestamp':datetime.now()})
pool.save()
#TODO: deal with analysis dir and dependencies
zgf_cleanup.main()
def main():
options = options_desc.parse_args(sys.argv)[0]
#TODO put somehow into Options, e.g. min_value=1 or required=True
if(not options.doomed_nodes):
sys.exit("Option --doomed_nodes is required.")
pool = Pool()
old_pool_size = len(pool)
old_alpha = pool.alpha
doomed_nodes = NodeList()
#TODO: maybe this code should go into ZIBMolPy.ui
for name in options.doomed_nodes.split(","):
found = [n for n in pool if n.name == name]
if(len(found) != 1):
sys.exit("Coult not find node '%s'"%(name))
doomed_nodes.append(found[0])
for n in doomed_nodes:
if(n == pool.root):
sys.exit("Node %s is the root. Removal not allowed."%(n.name))
#if(len(n.children) > 0):
# sys.exit("Node %s has children. Removal not allowed."%(n.name)) #TODO why should we forbid this?
if not(userinput("The selected node(s) will be removed permanently. Continue?", "bool")):
sys.exit("Quit by user.")
assert(len(doomed_nodes) == len(doomed_nodes.multilock()))
for n in doomed_nodes:
print("Removing directory: "+n.dir)
shutil.rmtree(n.dir)
pool.reload_nodes()
#TODO: this code-block also exists in zgf_create_node
if(len(pool.where("isa_partition")) < 2):
pool.alpha = None
elif(options.methodalphas == "theta"):
pool.alpha = zgf_create_nodes.calc_alpha_theta(pool)
elif(options.methodalphas == "user"):
pool.alpha = userinput("Please enter a value for alpha", "float")
else:
raise(Exception("Method unkown: "+options.methodalphas))
pool.history.append({'removed_nodes': [(n.name, n.state) for n in doomed_nodes], 'size':old_pool_size, 'alpha':old_alpha, 'timestamp':datetime.now()})
pool.save()
#TODO: deal with analysis dir and dependencies
zgf_cleanup.main()
