def testNoGrowth(self):
# Here, all the monomers are available at the beginning of the simulation
try:
# minimize random calls by providing set list of monomer types
mono_type_list = [
S, S, S, S, G, S, S, S, S, S, S, G, S, S, S, S, S, S, S, S, S,
S, S, S
]
random_num = 24
initial_monomers = [
Monomer(mono_type, i)
for i, mono_type in enumerate(mono_type_list)
]
initial_events = create_initial_events(initial_monomers,
DEF_RXN_RATES)
initial_state = create_initial_state(initial_events,
initial_monomers)
# since GROW is not added to event_dict, no additional monomers will be added
result = run_kmc(DEF_RXN_RATES,
initial_state,
sorted(initial_events),
t_max=0.0001,
random_seed=random_num)
gen_tcl(result[ADJ_MATRIX],
result[MONO_LIST],
tcl_fname=TCL_FNAME,
chain_id="L",
out_dir=SUB_DATA_DIR)
self.assertFalse(diff_lines(TCL_FILE_LOC, GOOD_TCL_NO_GROW_OUT))
finally:
silent_remove(TCL_FILE_LOC, disable=DISABLE_REMOVE)
pass
def testMakeTCL(self):
try:
silent_remove(TCL_FILE_LOC)
result = create_sample_kmc_result()
gen_tcl(result[ADJ_MATRIX], result[MONO_LIST], tcl_fname=TCL_FNAME, chain_id="L",
toppar_dir='toppar', out_dir=SUB_DATA_DIR)
self.assertFalse(diff_lines(TCL_FILE_LOC, GOOD_TCL_OUT))
finally:
silent_remove(TCL_FILE_LOC, disable=DISABLE_REMOVE)
pass
def testMakeTCLCLignin(self):
# Only adds 3 lines to coverage... oh well! At least it's quick.
try:
seed = 1
monos = 7
silent_remove(TCL_FILE_LOC)
result = create_sample_kmc_result_c_lignin(num_monos=monos, max_monos=monos*2, seed=seed)
good_last_time = 0.004474718478040326
self.assertAlmostEqual(result[TIME][-1], good_last_time)
gen_tcl(result[ADJ_MATRIX], result[MONO_LIST], tcl_fname=TCL_FNAME, chain_id="L", toppar_dir=None,
out_dir=SUB_DATA_DIR)
self.assertFalse(diff_lines(TCL_FILE_LOC, GOOD_TCL_C_LIGNIN_OUT))
finally:
silent_remove(TCL_FILE_LOC, disable=DISABLE_REMOVE)
pass
def produce_output(adj_matrix, mono_list, cfg):
if cfg[SUPPRESS_SMI] and not (cfg[SAVE_JSON] or cfg[SAVE_PNG] or cfg[SAVE_SVG]):
format_list = [SAVE_TCL]
mol = None # Make IDE happy
else:
# Default out is SMILES, which requires getting an rdKit molecule object; also required for everything
# except the TCL format
format_list = [SAVE_TCL, SAVE_JSON, SAVE_PNG, SAVE_SVG]
block = generate_mol(adj_matrix, mono_list)
mol = MolFromMolBlock(block)
try:
smi_str = MolToSmiles(mol) + '\n'
except:
raise InvalidDataError("Error in producing SMILES string.")
# if SMI is to be saved, don't output to stdout
if cfg[SAVE_SMI]:
fname = create_out_fname(cfg[BASENAME], base_dir=cfg[OUT_DIR], ext=SAVE_SMI)
str_to_file(smi_str, fname, print_info=True)
else:
print("\nSMILES representation: \n", MolToSmiles(mol), "\n")
if cfg[SAVE_PNG] or cfg[SAVE_SVG] or cfg[SAVE_JSON]:
# PNG and SVG make 2D images and thus need coordinates
# JSON will save coordinates--zero's if not computed; might as well compute and save non-zero values
Compute2DCoords(mol)
for save_format in format_list:
if cfg[save_format]:
fname = create_out_fname(cfg[BASENAME], base_dir=cfg[OUT_DIR], ext=save_format)
if save_format == SAVE_TCL:
gen_tcl(adj_matrix, mono_list, tcl_fname=fname, chain_id=cfg[CHAIN_ID],
psf_fname=cfg[PSF_FNAME], toppar_dir=cfg[TOPPAR_DIR], out_dir=cfg[OUT_DIR])
if save_format == SAVE_JSON:
json_str = MolToJSON(mol)
str_to_file(json_str + '\n', fname)
elif save_format == SAVE_PNG or save_format == SAVE_SVG:
MolToFile(mol, fname, size=cfg[IMAGE_SIZE])
print(f"Wrote file: {fname}")
initial_monomers = create_initial_monomers(pct_s, monomer_draw)
# Initially allow only oxidation events. After they are used to determine the initial state, add
# GROW to the events, which allows additional monomers to be added to the reaction at the
# specified rate and with the specified ratio
initial_events = create_initial_events(initial_monomers, rxn_rates)
initial_state = create_initial_state(initial_events, initial_monomers)
initial_events.append(Event(GROW, [], rate=mono_add_rate))
result = run_kmc(rxn_rates,
initial_state,
initial_events,
n_max=max_num_monos,
t_max=t_max,
sg_ratio=sg_ratio)
# Convert the sparse matrix to a full array before printing
print("The adjacency matrix for the simulated lignin is:")
print(result[ADJ_MATRIX].toarray())
# From the list of monomers and the adjacency matrix, we can use LigninKMC to write out a tcl script for psfgen to
# turn into a .psf file.
# fname and sgnames are things that we'd want to change; file name always the same as the segname
gen_tcl(result[ADJ_MATRIX],
result[MONO_LIST],
toppar_dir="../smilesdemo/toppar/",
tcl_fname="psfgen.tcl",
psf_fname="L",
chain_id="L")
# Now we switch over into vmd...