def _load_final_fe(final_results_dir, ref_ligands, weight_scheme,
combining_rule, FF):
"""
:param final_results_dir: str
:param ref_ligands: list of str
:param weight_scheme: str
:param combining_rule: str
:param score_file: str
:return final_fes: dict {ref_ligand (str): {ligand (str): fe (float)}}
"""
final_fes = {}
for ref_ligand in ref_ligands:
fe_file = os.path.join(final_results_dir, ref_ligand + weight_scheme,
combining_rule, FF + ".score")
print("Loading file for final fes:", fe_file)
fes, _ = load_scores(fe_file, 0, 1, 2, exclude_ligands=[])
fes.pop(ref_ligand)
final_fes[ref_ligand] = fes
return final_fes
parser.add_argument("--ligands_to_scale_error", type=str, default="")
parser.add_argument("--error_scale_factor", type=float, default=1.)
args = parser.parse_args()
exclude_ligands_from_scatter_plots = args.exclude_ligands_from_scatter_plots.split(
)
print("exclude_ligands_from_scatter_plots ",
exclude_ligands_from_scatter_plots)
print("subtract_self_rbfe ", args.subtract_self_rbfe)
print("compare_absolute ", args.compare_absolute)
ligands_to_scale_error = args.ligands_to_scale_error.split()
yank_scores, yank_stds = load_scores(args.yank_results, 0, 1, 2, [])
weighting_schemes_ref_ligands = glob.glob(
os.path.join(args.algdock_results_dir, "*", args.averaging_rule,
args.algdock_score_file))
weighting_schemes_ref_ligands = [
file_name.split("/")[-3] for file_name in weighting_schemes_ref_ligands
]
weighting_schemes = []
for scheme_ligand in weighting_schemes_ref_ligands:
for ligand in SIX_YANK_SYSTEMS:
if ligand in scheme_ligand:
scheme = scheme_ligand.split(ligand)[-1]
weighting_schemes.append(scheme)
print("Ref ligands:\n" + "\n".join(ref_ligands))
error_scales = [float(s) for s in args.error_scales.split()]
print("error_scales", error_scales)
ylims = args.ylims.split()
if len(ylims) == 0:
ylims = [None for _ in ref_ligands]
assert len(ref_ligands) == len(error_scales) == len(ylims), "wrong length"
target_ligands = [lig for lig in exper_bfes.keys() if lig not in ref_ligands]
print("Target ligands:\n" + "\n".join(target_ligands))
# load yank results
yank_bfes, _ = load_scores(args.yank_results, 0, 1, 2, exclude_ligands=[])
# rbfe WITH CV
if args.control_variate == "with":
algdock_bfes = {} # algdock_bfes[ref_ligand][target_ligand] -> float
algdock_errors = {}
for ref_ligand in ref_ligands:
infile = os.path.join(args.algdock_dir,
ref_ligand + args.result_dir_suffix,
args.combining_rule, args.rel_bfe_file)
print("Loading", infile)
bfes, errors = load_scores(infile,
0,
1,
2,
exclude_ligands=ref_ligands)
default="convergence_relative_est_1")
#parser.add_argument( "--out_prefix", type=str, default = "convergence_relative_not_convert_2_abs_est_1")
args = parser.parse_args()
sample_sizes = np.array([5] + range(10, 101, 10) + range(150, 551, 50) + [576],
dtype=int)
#sample_sizes = np.array( range(5, 51, 5) + range(60, 91, 10) + [96], dtype=int)
print sample_sizes
block_weights, state_weights, single_snap_weights, stru_group_weights_equal_sys, stru_group_weights_ub_weighted = load_mbar_weights(
)
yank_interaction_energies = load_interaction_energies(
path=args.interaction_energies_dir)
yank_fes, yank_fe_stds = load_scores(args.yank_results, 0, 1, 2,
args.exclude_ligands)
if args.yank_systems == "all":
yank_systems = SIX_YANK_SYSTEMS
elif args.yank_systems == "actives":
yank_systems = FOUR_ACTIVE_YANK_SYSTEMS
elif args.yank_systems == "read":
yank_systems = [os.path.basename(os.getcwd())]
else:
raise Exception("Unknown yank systems")
if len(yank_systems) > 1:
if args.yank_systems != "all":
raise Exception("More than one yank systems but not all 6")
else:
print "Loading " + args.file_to_take_all_ligands
ref_ligands = [
ligand for ligand in single_snap_weights.keys() if ligand != "systems"
]
print("ref_ligands:", ref_ligands)
target_ligands = YANK_LIGANDS.keys()
print("target_ligands:", target_ligands)
yank_interaction_energies = load_interaction_energies(
path=args.interaction_energies_dir)
final_rel_fes = _load_final_fe(args.final_results_dir, ref_ligands,
args.weight_scheme, args.combining_rule,
args.FF)
yank_abs_fes, _ = load_scores(args.yank_results_file, 0, 1, 2, [])
for ref_ligand in ref_ligands:
print("Processing ref ligand:", ref_ligand)
out_dir = ref_ligand
if not os.path.isdir(out_dir):
os.makedirs(out_dir)
out_file_final = open(os.path.join(out_dir, "r_rmse_wrt_final.dat"), "w")
out_file_final.write(
"# sample_size r r_std rmse rmse_std\n")
out_file_yank = open(os.path.join(out_dir, "r_rmse_wrt_yank.dat"), "w")
out_file_yank.write(
"# sample_size r r_std rmse rmse_std\n")