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