def unzip_to_tempresults(self):
temp_results = path.join(self.bigtraj_folder, 'temp_results')
temp_host_folder = path.join(temp_results, self.host)
f_zip = path.join(self.bigtraj_folder, f'{self.host}_results.zip')
check_dir_exist_and_make(temp_host_folder)
with zipfile.ZipFile(f_zip, 'r') as zip_ref:
zip_ref.extractall(temp_host_folder)
info = f'Unzip {f_zip} into {temp_host_folder}'
print(info)
def initialize_folders(self):
for folder in [
self.host_folder, self.na_folder, self.input_folder,
self.charmminp_folder, self.charmmdat_folder,
self.mode_traj_folder, self.ic_folder, self.mat_folder,
self.rtficstr_folder, self.datafolder, self.backupfolder,
self.scratchfolder
]:
check_dir_exist_and_make(folder)
def make_qsub_file(self, path_to_pythonexec):
check_dir_exist_and_make(self.qsub_folder)
jobname = f'{self.host}_{self.time_label}'
wtime = '48:00:00'
run_n_node = 1
run_n_cpu = 16
p_agent = PBSAgent(self.qsub_file, jobname, wtime, run_n_node, run_n_cpu, path_to_pythonexec)
p_agent.open_file()
p_agent.pbssuffix()
p_agent.set_pythonexec()
p_agent.cutomize_part(self.pyfile)
p_agent.close_file()
def make_folders(self):
folders = [self.host_folder, self.na_folder, self.input_folder, self.aa_folder, self.heavy_folder,
self.inp_folder, self.dat_folder, self.mkcrd_folder]
for folder in folders:
check_dir_exist_and_make(folder)
def fluct_match(host, type_na, time_label, start, end, cutoff, icfluct_0,
icavg_0, scratchfolder, charmm, rootfolder):
# Backup Folder
backupfolder = path.join(scratchfolder, 'backup')
check_dir_exist_and_make(backupfolder)
# Set initial variables
avg_file = path.join(scratchfolder, 'average_{0:.2f}.ic'.format(cutoff))
fluct_file = path.join(scratchfolder, 'fluct_{0:.2f}.ic'.format(cutoff))
prmfile = path.join(scratchfolder, 'na_enm_{0:.2f}.prm'.format(cutoff))
prm_backup = path.join(backupfolder,
'na_enm_{0:.2f}.backup.prm'.format(cutoff))
prm_backup_0 = path.join(backupfolder,
'na_enm_{0:.2f}.backup.0.prm'.format(cutoff))
err_file = path.join(scratchfolder, 'error_{0:.2f}.txt'.format(cutoff))
copyfile(prmfile, prm_backup_0)
# Read icavg, icfluct, set k and target
icavg = ic_table.ICTable(avg_file)
icfluct = ic_table.ICTable(fluct_file)
kbpair = ic_table.KBPair(read_from_prm=False,
icavg=icavg,
icfluct=icfluct,
rt=RT)
k = kbpair.d['k']
target = np.reciprocal(np.square(icfluct_0.values))
# Write Error
f = open(err_file, 'w')
f.write('Created at {0}\n'.format(datetime.datetime.now()))
f.write('{0:<5} {1:8}\n'.format('n_iter', 'error'))
f.close()
# Iteration and Do NMA
for i in range(start, end):
print("IterNum: {0}".format(i))
nma_inp = path.join(scratchfolder, 'nma.inp')
nma_dat = path.join(scratchfolder, 'nma.dat')
if i == 0:
write_nmainit_inp(nma_inp, host, type_na, time_label, cutoff,
rootfolder, scratchfolder)
exec_charmm(charmm, nma_inp, nma_dat)
time.sleep(2)
# Read icavg, icfluct
new_icavg = ic_table.ICTable(avg_file)
new_icfluct = ic_table.ICTable(fluct_file)
optimized = np.reciprocal(np.square(new_icfluct.values))
# Be Careful, b0 is from icavg_0, which is the average structure of MD, it should be kept fix
new_kbpair = ic_table.KBPair(read_from_prm=False,
icavg=icavg_0,
icfluct=new_icfluct,
rt=RT)
# Update k
k -= alpha * (optimized - target)
k[np.where(k < 0.)] = 0. # Make all negative values zero
new_kbpair.d['k'] = k
# Calculate RMSD error and Write
error = icfluct_0.values - new_icfluct.values
error = np.square(error).mean()
error = np.sqrt(error)
f = open(err_file, 'a')
f.write('{0:<5} {1:8.4f}\n'.format(i + 1, error))
f.close()
# Backup PRM
copyfile(prmfile, prm_backup)
# Update PRM
prm_agent = prm.PRM(host, type_na, new_kbpair, iternum=i)
prm_agent.write_prm(prmfile)
def main_split_window(rootfolder, host, type_na, time_label, cutoff, start,
end, charmm):
# Initialize
agent = SmallTrajAgent(rootfolder, host, type_na, time_label)
nadir = agent.time_folder
charmminpfolder = path.join(nadir, 'charmm_inp')
charmmdatfolder = path.join(nadir, 'charmm_dat')
icfolder = path.join(nadir, 'ic')
datafolder = path.join(nadir, 'data')
agent.initialize_scratch_folders()
scratchfolder = agent.scratchfolder
# IC fluct
icfluct_inp = path.join(charmminpfolder,
'ic_fluct_{0:.2f}.inp'.format(cutoff))
icfluct_dat = path.join(charmmdatfolder,
'ic_fluct_{0:.2f}.dat'.format(cutoff))
write_ic_fluct_inp(icfluct_inp, host, type_na, time_label, cutoff,
rootfolder)
exec_charmm(charmm, icfluct_inp, icfluct_dat)
mode0ic = path.join(icfolder, 'mode.0.{0:.2f}.ic'.format(cutoff))
nafluctic = path.join(datafolder, 'na.fluct.{0:.2f}.ic'.format(cutoff))
with open(mode0ic, 'r') as f:
context = f.read()
context = re.sub(r'-99 ', ' -99 ', context)
with open(nafluctic, 'w') as f:
f.write(context)
icfluct_0 = ic_table.ICTable(nafluctic, initial=True)
# IC Avg
icavg_inp = path.join(charmminpfolder, 'ic_avg_{0:.2f}.inp'.format(cutoff))
icavg_dat = path.join(charmmdatfolder, 'ic_avg_{0:.2f}.dat'.format(cutoff))
write_ic_avg_inp(icavg_inp,
host,
type_na,
time_label,
cutoff,
rootfolder,
distance_average=True) # Important! Check Fix b0
exec_charmm(charmm, icavg_inp, icavg_dat)
mode0avgic = path.join(icfolder, 'mode.0.avg.{0:.2f}.ic'.format(cutoff))
naavgic = path.join(datafolder, 'na.avg.{0:.2f}.ic'.format(cutoff))
with open(mode0avgic, 'r') as f:
context = f.read()
context = re.sub(r'-99 ', ' -99 ', context)
with open(naavgic, 'w') as f:
f.write(context)
icavg_0 = ic_table.ICTable(naavgic, initial=True)
# Get the initial equilibrium distance and force constant and write PRM
kbpair_0 = ic_table.KBPair(read_from_prm=False,
icavg=icavg_0,
icfluct=icfluct_0,
rt=RT)
scratch_prm = path.join(
scratchfolder,
'na_enm_{0:.2f}.prm'.format(cutoff)) #!!! Important File
prm_agent = prm.PRM(host, type_na, kbpair_0, iternum=0)
prm_agent.write_prm(scratch_prm)
# NMA Initialize
nma_init_inp = path.join(scratchfolder, 'nmainit.inp')
nma_init_dat = path.join(scratchfolder, 'nmainit.dat')
write_nmainit_inp(nma_init_inp, host, type_na, time_label, cutoff,
rootfolder, scratchfolder)
exec_charmm(charmm, nma_init_inp, nma_init_dat)
# Fluctuation-Matching
fluct_match(host, type_na, time_label, start, end, cutoff, icfluct_0,
icavg_0, scratchfolder, charmm, rootfolder)
# Copy Back to the folder
cutoffdatafolder = path.join(nadir, 'cutoffdata')
check_dir_exist_and_make(cutoffdatafolder)
lastprmfile = path.join(cutoffdatafolder,
'na_enm_{0:.2f}.prm'.format(cutoff))
copyfile(scratch_prm, lastprmfile)
print('cp {0} {1}'.format(scratch_prm, lastprmfile))
err_file = path.join(scratchfolder, 'error_{0:.2f}.txt'.format(cutoff))
lasterrfile = path.join(cutoffdatafolder,
'error_{0:.2f}.txt'.format(cutoff))
copyfile(err_file, lasterrfile)
print('cp {0} {1}'.format(err_file, lasterrfile))
nma_inp = path.join(scratchfolder, 'nma.inp')
nma_inp_back = path.join(nadir, 'charmm_inp', f'nma_{cutoff:.2f}.inp')
copyfile(nma_inp, nma_inp_back)
nma_dat = path.join(scratchfolder, 'nma.dat')
nma_dat_back = path.join(nadir, 'charmm_dat', f'nma_{cutoff:.2f}.dat')
copyfile(nma_dat, nma_dat_back)
def check_result_zipfolder(self, ziproot):
zip_host_folder = path.join(ziproot, self.host)
zip_na_folder = path.join(zip_host_folder, self.type_na)
zip_time_folder = path.join(zip_na_folder, self.time_label)
for folder in [zip_host_folder, zip_na_folder, zip_time_folder]:
check_dir_exist_and_make(folder)
def initialize_scratch_folders(self):
for folder in [self.scr_host, self.scr_na, self.scratchfolder]:
check_dir_exist_and_make(folder)
def unarchive_folder(self):
check_dir_exist_and_make(self.host_folder)
with zipfile.ZipFile(self.f_zip, 'r') as zip_ref:
zip_ref.extractall(self.host_folder)
info = f'Unzip {self.f_zip} into {self.host_folder}'
print(info)
