def testUndoAfterRemoveAtomOnDiscrete(self, discr):
cmd.set('suspend_undo', 0)
cmd.load(self.datafile('ligs3d.sdf'), discrete=discr)
natms = cmd.count_atoms()
cmd.remove("index 1")
cmd.undo()
self.assertEqual(natms, cmd.count_atoms())
def testUndoAfterRemoveAtomOnDiscrete(self, discr):
cmd.set('suspend_undo', 0)
cmd.load(self.datafile('ligs3d.sdf'), discrete=discr)
natms = cmd.count_atoms()
cmd.remove("index 1")
cmd.undo()
self.assertEqual(natms, cmd.count_atoms())
def test(self):
if cmd.get_setting_int('suspend_undo'):
self.skipTest("need suspend_undo=0")
cmd.fragment('gly', 'm1')
cmd.create('m2', 'm1')
cmd.edit('m1 & name N')
cmd.replace('I', 1, 1)
self.assertEqual(cmd.count_atoms('m1 in m2'), 5)
cmd.undo()
self.assertEqual(cmd.count_atoms('m1 in m2'), 7)
def test(self):
if cmd.get_setting_int('suspend_undo'):
self.skipTest("need suspend_undo=0")
cmd.fragment('gly', 'm1')
cmd.create('m2', 'm1')
cmd.edit('m1 & name N')
cmd.replace('I', 1, 1)
self.assertEqual(cmd.count_atoms('m1 in m2'), 5)
cmd.undo()
self.assertEqual(cmd.count_atoms('m1 in m2'), 7)
def testAtomLevelSettingsOnRemove2(self):
if cmd.get_setting_int('suspend_undo'):
self.skipTest("need suspend_undo=0")
cmd.load(self.datafile("1molecule.mae"))
cmd.load(self.datafile("1molecule.mae"))
cmd.label("index 10", "'Test Label'")
plv = [ 5., 0., 0.]
cmd.alter("index 10", "s.label_placement_offset = %s" % plv)
cmd.remove("index 10")
cmd.undo()
stored.offset = None
cmd.iterate("index 10", "stored.offset = list(s.label_placement_offset)")
self.assertEqual(stored.offset, plv)
def generate(dihedrals,
directory="temp",
setup_path="default",
verbose="False"):
# dihedrals = [[atom a, atom b, atom c, atom d]]
# Log generation
log = Log()
log.write(
"\n\n########################################\n########### G E N E R A T E ############\n########################################\n\n"
)
#verbose
if verbose.lower() in ['true', '1', 't', 'y', 'yes']: verbose = True
else: verbose = False
# dihedrals: auto?
if dihedrals.lower() in ['auto']:
dihedrals = 'auto' #To DO: generate dihedrals automatically
# get setup.ini
setup = Setup(log, setup_path)
if setup.isLoaded() == True:
angle_step = 360 / setup.angle_count
dihedrals = dihedrals.strip(' []').split(',')
for i in range(0, len(dihedrals)):
dihedrals[i] = dihedrals[i].strip(' []')
if len(dihedrals) % 4 != 0 and len(dihedrals) != 1:
log.write(
"Error: Problem in dihedral selection. 4 selections are needed for each dihedral. [%s] "
% dihedrals)
return False
dihedral_count = int(len(dihedrals) / 4)
combination_count = int(setup.angle_count**dihedral_count)
log.write("Number of dihedrals: %s" % dihedral_count)
log.write("For each dihedral: %s steps of %s degree" %
(setup.angle_count, angle_step))
log.write("That represents %s combinations" % combination_count)
result = backup_generate(directory) # create backup
if result: log.write("Making archives: %s" % result, verbose)
else: log.write("Making directory: %s" % directory, verbose)
if combination_count == 0:
path = "%s/%s_0.pdb" % (directory, cmd.get_object_list()[0])
try:
cmd.set("retain_order", 1)
cmd.save(path)
except:
log.write(
"Error: Can't save %s first conformer. One conformer will be missing!"
% path, verbose)
else:
# Generate all the combinations
combination_list = [{} for k in range(0, combination_count)]
for i in range(0, combination_count
): # iterate all the combinations of dihedrals
dihedrals_curr_cbn = [{} for k in range(dihedral_count)]
count = i
for j in range(
0, dihedral_count
): # modify the dihedral according to the combination
dihedrals_curr_cbn[j] = int(count % setup.angle_count)
count = int(count / setup.angle_count)
log.write("Combination %s : %s " % (i, dihedrals_curr_cbn),
verbose)
combination_list[i] = dihedrals_curr_cbn
# Too many combinations?
if combination_count > setup.combination_limit:
todestroy_count = combination_count - setup.combination_limit
log.write(
"The amount of possibility is %s. The limit is set at %s. %s combinations will be deleted to go down to the limit using %s algorithm."
% (combination_count, setup.combination_limit,
todestroy_count, setup.combination_remove_algorithm))
if setup.combination_remove_algorithm == "random":
for i in range(
0, todestroy_count
): # loop as many time as the amount to randomly destroy
del combination_list[random.randint(
0, len(combination_list))]
log.write(
"%s combinations. Limit is %s. Reduction of combinations done."
% (len(combination_list), setup.combination_limit),
verbose)
# Generate the files
for i in range(
len(combination_list)): # going through each combination
for j in range(
len(combination_list[i])
): # going through each dihedral of the combination
try:
cmd.set_dihedral(dihedrals[j * 4],
dihedrals[j * 4 + 1],
dihedrals[j * 4 + 2],
dihedrals[j * 4 + 3],
combination_list[i][j] * angle_step)
except:
log.write(
"Error: Can't set the dihedrals. cmd.set_dihedrals failed."
)
log.write(
"Writing Combination %s : %s " % (i, combination_list[i]),
verbose)
path = "%s/%s_%s.pdb" % (directory, cmd.get_object_list()[0],
str(i))
try:
cmd.set("retain_order", 1)
cmd.save(path)
except:
log.write(
"Error: Can't save %s. One conformer will be missing!"
% path)
for j in range(0, dihedral_count):
cmd.undo()
log.write(
"----------------------------\n---- Normal Termination ----\n----------------------------\n"
)
log.finalize()
return True
else:
log.write(
"Error: Failed to load setup.ini in [%s]. Fix it to continue." %
setup_path)
return False
