def make_res(iter_index, json_file):
fp = open(json_file, 'r')
jdata = json.load(fp)
numb_walkers = jdata["numb_walkers"]
template_dir = jdata["template_dir"]
bias_nsteps = jdata["bias_nsteps"]
bias_frame_freq = jdata["bias_frame_freq"]
nsteps = jdata["res_nsteps"]
frame_freq = jdata["res_frame_freq"]
sel_threshold = jdata["sel_threshold"]
max_sel = jdata["max_sel"]
cluster_threshold = jdata["cluster_threshold"]
base_path = os.getcwd() + "/"
iter_name = make_iter_name(iter_index)
enhc_path = iter_name + "/" + enhc_name + "/"
os.chdir(enhc_path)
enhc_path = os.getcwd() + "/"
os.chdir(base_path)
templ_mol_path = template_dir + "/" + mol_name + "/"
templ_res_path = template_dir + "/" + res_name + "/"
res_path = iter_name + "/" + res_name + "/"
create_path(res_path)
ret_list = [True for ii in range(numb_walkers)]
# sel angles
## check if we have graph in enhc
for walker_idx in range(numb_walkers):
walker_path = enhc_path + walker_format % walker_idx + "/"
graph_files = glob.glob(walker_path + "/*.pb")
if len(graph_files) != 0:
os.chdir(walker_path)
sel_cmd = "python3 test.std.py -m *.pb -t %f -d %s --output sel.out --output-angle sel.angle.out" % (
sel_threshold, enhc_out_angle)
sel_cmd = cmd_append_log(sel_cmd, "sel.log")
log_task("select with threshold %f" % sel_threshold)
log_task(sel_cmd)
sp.check_call(sel_cmd, shell=True)
os.chdir(base_path)
sel_idx = []
sel_angles = np.array([])
with open(walker_path + "sel.out") as fp:
for line in fp:
sel_idx += [int(x) for x in line.split()]
if len(sel_idx) != 0:
sel_angles = np.reshape(
np.loadtxt(walker_path + 'sel.angle.out'), [-1, cv_dim])
elif len(sel_idx) == 0:
np.savetxt(walker_path + 'num_of_cluster.dat', [0], fmt='%d')
np.savetxt(walker_path + 'cls.sel.out', [], fmt='%d')
continue
else:
sel_idx = range(
len(glob.glob(walker_path + enhc_out_conf + "conf*gro")))
sel_angles = np.loadtxt(walker_path + enhc_out_angle)
sel_angles = np.reshape(sel_angles, [-1, cv_dim])
np.savetxt(walker_path + 'sel.out', sel_idx, fmt='%d')
np.savetxt(walker_path + 'sel.angle.out', sel_angles, fmt='%.6f')
conf_start = 0
conf_every = 1
sel_idx = np.array(sel_idx, dtype=np.int)
assert (len(sel_idx) == sel_angles.shape[0])
if shell_clustering and len(sel_idx) > 1:
cmd_sel_from_cluster = (
base_path +
"template/tools/cluster_cv.py -i %s -c %s -t %f --output-idx %s --output-cv %s"
% (walker_path + 'sel.out', walker_path + 'sel.angle.out',
cluster_threshold, walker_path + 'cls.sel.out',
walker_path + 'cls.sel.angle.out'))
sp.check_call(cmd_sel_from_cluster, shell=True)
sel_idx = np.loadtxt(walker_path + 'cls.sel.out', dtype=np.int)
elif shell_clustering == False and len(sel_idx) > 1:
cls_sel = sel_from_cluster(sel_angles, cluster_threshold)
##############################################################################################
np.savetxt(walker_path + 'num_of_cluster.dat', [len(set(cls_sel))],
fmt='%d')
if len(cls_sel) > max_sel:
cls_sel = cls_sel[-max_sel:]
sel_idx = sel_idx[cls_sel]
np.savetxt(walker_path + 'cls.sel.angle.0.out',
sel_angles[cls_sel],
fmt='%.6f')
elif len(sel_idx) == 1:
np.savetxt(walker_path + 'num_of_cluster.dat', [1], fmt='%d')
res_angles = np.loadtxt(walker_path + enhc_out_angle)
res_angles = np.reshape(res_angles, [-1, cv_dim])
res_angles = res_angles[sel_idx]
np.savetxt(walker_path + 'cls.sel.out', sel_idx, fmt='%d')
np.savetxt(walker_path + 'cls.sel.angle.out', res_angles, fmt='%.6f')
res_confs = []
for ii in sel_idx:
res_confs.append(walker_path + enhc_out_conf + ("conf%d.gro" % ii))
assert (len(res_confs) == res_angles.shape[0]
), "number of enhc out conf does not match out angle"
assert (len(sel_idx) == res_angles.shape[0]
), "number of enhc out conf does not numb sel"
nconf = len(res_confs)
if nconf == 0:
ret_list[walker_idx] = False
continue
sel_list = ""
for ii in range(nconf):
if ii == 0: sel_list = str(sel_idx[ii])
else: sel_list += "," + str(sel_idx[ii])
log_task("selected %d confs, indexes: %s" % (nconf, sel_list))
for ii in range(conf_start, nconf, conf_every):
# print (ii, sel_idx[ii])
work_path = res_path + ((walker_format + ".%06d") %
(walker_idx, sel_idx[ii])) + "/"
os.makedirs(work_path)
copy_file_list(mol_files, templ_mol_path, work_path)
copy_file_list(res_files, templ_res_path, work_path)
conf_file = walker_path + enhc_out_conf + ("conf%d.gro" %
sel_idx[ii])
if os.path.exists(work_path + "conf.gro"):
os.remove(work_path + "conf.gro")
conf_file = os.path.abspath(conf_file)
tmp_cwd = os.getcwd()
os.chdir(work_path)
os.symlink(os.path.relpath(conf_file), "conf.gro")
os.chdir(tmp_cwd)
task_dirs = []
task_args = []
for ii in range(conf_start, nconf, conf_every):
dir_str = ((walker_format + ".%06d") % (walker_idx, sel_idx[ii]))
arg_str = np.array2string(res_angles[ii],
formatter={
'float_kind': lambda x: "%.6f" % x
}).replace("[",
"").replace("]", "").replace(
"\n", " ")
task_dirs.append(dir_str)
task_args.append(arg_str)
log_task(task_dirs[-1] + ": " + task_args[-1])
os.chdir(res_path)
exec_hosts(MachineLocal, "./general_mkres.sh", 1, task_dirs, task_args)
os.chdir(base_path)
for ii in range(conf_start, nconf, conf_every):
work_path = res_path + ((walker_format + ".%06d") %
(walker_idx, sel_idx[ii])) + "/"
mol_conf_file = work_path + "grompp.mdp"
make_grompp_res(mol_conf_file, nsteps, frame_freq)
replace(work_path + res_plm, "STRIDE=[^ ]* ",
"STRIDE=%d " % frame_freq)
if any(ret_list):
return True
else:
return False
def make_res(iter_index, json_file):
fp = open(json_file, 'r')
jdata = json.load(fp)
cmd_env = jdata.get("cmd_sources", [])
sits_param = jdata.get("sits_settings", None)
if sits_param is not None:
sits_param["nst-sits-enerd-out"] = jdata["res_frame_freq"]
bPosre = jdata.get("gmx_posre", False)
bPosre_res = jdata.get("gmx_posre_res", False)
numb_walkers = jdata["numb_walkers"]
template_dir = jdata["template_dir"]
bias_nsteps = jdata["bias_nsteps"]
bias_frame_freq = jdata["bias_frame_freq"]
nsteps = jdata["res_nsteps"]
frame_freq = jdata["res_frame_freq"]
sel_threshold = jdata["sel_threshold"]
max_sel = jdata["max_sel"]
cluster_threshold = jdata["cluster_threshold"]
init_numb_cluster = [22, 30]
base_path = os.getcwd()
iter_name = make_iter_name(iter_index)
enhc_path = join(base_path, iter_name, enhc_name)
templ_mol_path = join(template_dir, mol_name)
templ_res_path = join(template_dir, res_name)
res_path = join(iter_name, res_name) + "/"
create_path(res_path)
ret_list = [True for ii in range(numb_walkers)]
# sel angles
# check if we have graph in enhc
for walker_idx in range(numb_walkers):
walker_path = join(enhc_path, walker_format % walker_idx) + "/"
if sits_param is not None:
if os.path.exists(join("sits", "log_nk.dat")):
shutil.copyfile(join("sits", "log_nk.dat"),
join(walker_path, "log_nk.dat"))
if os.path.exists(join("sits", "log_norm.dat")):
shutil.copyfile(join("sits", "log_norm.dat"),
join(walker_path, "log_norm.dat"))
os.chdir(walker_path)
graph_files = glob.glob("*.pb")
if len(graph_files) != 0:
cluster_threshold = np.loadtxt(
join(base_path, "cluster_threshold.dat"))
sel_cmd = "python3 test.std.py -m *.pb -t %f -d %s --output sel.out --output-angle sel.angle.out" % \
(sel_threshold, enhc_out_angle)
sel_cmd = cmd_append_log(sel_cmd, "sel.log")
log_task("select with threshold %f" % sel_threshold)
log_task(sel_cmd)
sp.check_call(sel_cmd, shell=True)
sel_idx = []
sel_angles = np.array([])
with open("sel.out") as fp:
for line in fp:
sel_idx += [int(x) for x in line.split()]
if len(sel_idx) != 0:
sel_angles = np.reshape(np.loadtxt('sel.angle.out'),
[-1, cv_dim])
elif len(sel_idx) == 0:
np.savetxt('num_of_cluster.dat', [0], fmt='%d')
np.savetxt('cls.sel.out', [], fmt='%d')
continue
else:
cluster_threshold = jdata["cluster_threshold"]
conf_files = glob.glob(join(enhc_out_conf, "conf*gro"))
sel_idx = range(len(conf_files))
sel_angles = np.loadtxt(enhc_out_angle)
sel_angles = np.reshape(sel_angles, [-1, cv_dim])
np.savetxt('sel.out', sel_idx, fmt='%d')
np.savetxt('sel.angle.out', sel_angles, fmt='%.6f')
if walker_idx == 0:
cls_sel = sel_from_cluster(sel_angles, cluster_threshold)
test_numb_cluster = len(set(cls_sel))
print(test_numb_cluster)
for test_iter in range(500):
if test_numb_cluster < init_numb_cluster[0]:
cluster_threshold = cluster_threshold * 0.95
cls_sel = sel_from_cluster(sel_angles,
cluster_threshold)
test_numb_cluster = len(set(cls_sel))
print(cluster_threshold)
print(test_numb_cluster)
elif test_numb_cluster > init_numb_cluster[1]:
cluster_threshold = cluster_threshold * 1.05
cls_sel = sel_from_cluster(sel_angles,
cluster_threshold)
test_numb_cluster = len(set(cls_sel))
print(cluster_threshold)
print(test_numb_cluster)
else:
print(cluster_threshold)
np.savetxt(join(base_path, 'cluster_threshold.dat'),
[cluster_threshold],
fmt='%f')
np.savetxt('cluster_threshold.dat',
[cluster_threshold],
fmt='%f')
break
else:
cluster_threshold = np.loadtxt(
join(base_path, "cluster_threshold.dat"))
conf_start = 0
conf_every = 1
sel_idx = np.array(sel_idx, dtype=np.int)
assert (len(sel_idx) == sel_angles.shape[0])
if shell_clustering and len(sel_idx) > 1:
cmd_sel_from_cluster = (
base_path +
"/template/tools/cluster_cv.py -i %s -c %s -t %f --output-idx %s --output-cv %s"
% ('sel.out', 'sel.angle.out', cluster_threshold,
'cls.sel.out', 'cls.sel.angle.out'))
sp.check_call(cmd_sel_from_cluster, shell=True)
sel_idx = np.loadtxt('cls.sel.out', dtype=np.int)
elif shell_clustering == False and len(sel_idx) > 1:
cls_sel = sel_from_cluster(sel_angles, cluster_threshold)
##############################################################################################
np.savetxt('num_of_cluster.dat', [len(set(cls_sel))], fmt='%d')
np.savetxt('cluster_threshold.dat', [cluster_threshold], fmt='%f')
if len(cls_sel) > max_sel:
cls_sel = cls_sel[-max_sel:]
sel_idx = sel_idx[cls_sel]
np.savetxt('cls.sel.angle.0.out', sel_angles[cls_sel], fmt='%.6f')
elif len(sel_idx) == 1:
np.savetxt('num_of_cluster.dat', [1], fmt='%d')
res_angles = np.loadtxt(enhc_out_angle)
res_angles = np.reshape(res_angles, [-1, cv_dim])
res_angles = res_angles[sel_idx]
np.savetxt('cls.sel.out', sel_idx, fmt='%d')
np.savetxt('cls.sel.angle.out', res_angles, fmt='%.6f')
res_confs = []
for ii in sel_idx:
res_confs.append(walker_path + enhc_out_conf + ("conf%d.gro" % ii))
assert (len(res_confs) == res_angles.shape[0]
), "number of enhc out conf does not match out angle"
assert (len(sel_idx) == res_angles.shape[0]
), "number of enhc out conf does not numb sel"
nconf = len(res_confs)
if nconf == 0:
ret_list[walker_idx] = False
continue
sel_list = ""
for ii in range(nconf):
if ii == 0:
sel_list = str(sel_idx[ii])
else:
sel_list += "," + str(sel_idx[ii])
log_task("selected %d confs, indexes: %s" % (nconf, sel_list))
os.chdir(base_path)
for ii in range(conf_start, nconf, conf_every):
# print (ii, sel_idx[ii])
work_path = join(res_path, (walker_format + ".%06d") %
(walker_idx, sel_idx[ii])) + "/"
os.makedirs(work_path)
copy_file_list(mol_files, templ_mol_path, work_path)
copy_file_list(res_files, templ_res_path, work_path)
if sits_param is not None:
if os.path.exists(join("sits", "log_nk.dat")):
shutil.copyfile(join("sits", "log_nk.dat"),
join(work_path, "log_nk.dat"))
if os.path.exists(join("sits", "log_norm.dat")):
shutil.copyfile(join("sits", "log_norm.dat"),
join(work_path, "log_norm.dat"))
mol_conf_file = join(work_path, "grompp_sits.mdp")
if bPosre_res:
mol_conf_file = join(work_path,
"grompp_sits_restraint.mdp")
make_grompp_sits(mol_conf_file,
sits_param,
sits_iter=False,
iter_index=iter_index)
conf_file = walker_path + enhc_out_conf + ("conf%d.gro" %
sel_idx[ii])
if os.path.exists(work_path + "conf.gro"):
os.remove(work_path + "conf.gro")
conf_file = os.path.abspath(conf_file)
conf_init_file = walker_path + "conf_init.gro"
if os.path.exists(work_path + "conf_init.gro"):
os.remove(work_path + "conf_init.gro")
conf_init_file = os.path.abspath(conf_init_file)
tmp_cwd = os.getcwd()
os.chdir(work_path)
os.symlink(os.path.relpath(conf_file), "conf.gro")
os.symlink(os.path.relpath(conf_init_file), "conf_init.gro")
os.chdir(tmp_cwd)
task_dirs = []
task_args = []
for ii in range(conf_start, nconf, conf_every):
dir_str = ((walker_format + ".%06d") % (walker_idx, sel_idx[ii]))
arg_str = np.array2string(res_angles[ii],
formatter={
'float_kind': lambda x: "%.6f" % x
}).replace("[",
"").replace("]", "").replace(
"\n", " ")
task_dirs.append(dir_str)
task_args.append(arg_str)
log_task(task_dirs[-1] + ": " + task_args[-1])
os.chdir(base_path)
os.chdir(res_path)
exec_hosts(MachineLocal, "./general_mkres.sh", 1, task_dirs, task_args)
os.chdir(base_path)
for ii in range(conf_start, nconf, conf_every):
work_path = res_path + ((walker_format + ".%06d") %
(walker_idx, sel_idx[ii])) + "/"
mol_conf_files = glob.glob(work_path + "*.mdp")
for mol_conf_file in mol_conf_files:
make_grompp_res(mol_conf_file, nsteps, frame_freq)
replace(work_path + res_plm, "STRIDE=[^ ]* ",
"STRIDE=%d " % frame_freq)
os.chdir(base_path)
if any(ret_list):
return True
else:
return False