def coord_runner(self):
df_mt = read_csv(self.mt_csv_dir)
df_mt[['POSITION']] = df_mt[['POSITION']].astype(str)
for rosetta_mut_tag in os.listdir(self.mut_pdb_dir):
pdbid, wtaa, chain, pos, _, mtaa = rosetta_mut_tag.split('_')
mutant_tag = '_'.join([pdbid, wtaa, chain, pos, mtaa])
try:
ph, T, ddg = df_mt.loc[
(df_mt.PDB == pdbid) & (df_mt.WILD_TYPE == wtaa) &
(df_mt.CHAIN == chain) & (df_mt.POSITION == pos) &
(df_mt.MUTANT == mtaa),
['PH', 'TEMPERATURE', 'DDG']].values[0, :]
thermo = str(ph) + ' ' + str(T)
except:
print('[ERROR] mutation %s index failed in %s' %
(mutant_tag, self.mt_csv_dir))
sys.exit(1)
for k_neighbor in self.k_neighborlst:
for center in self.centerlst:
self.run_cal_wild(mutant_tag, k_neighbor, center, thermo,
ddg)
self.run_cal_mutant(rosetta_mut_tag, mutant_tag,
k_neighbor, center, thermo, ddg)
check_qsub(tag='coord_%s' % self.dataset_name,
sleep_time=self.sleep_time)
def run_ref(self):
'''refine mdl0 file'''
ref_tag = 'rosetta_ref_%s' % self.dataset_name
qsub_ref(self.homedir, self.refdir, self.outpath_pdb_mdl0,
self.outpath_ref, ref_tag)
check_qsub(tag=ref_tag, sleep_time=self.sleep_time)
self.ref_tagdirlst = [
self.outpath_ref + '/' + x for x in os.listdir(self.outpath_ref)
]
def mCSM_runner(self):
for class_num in self.class_numlst:
for center in self.centerlst:
for maximum in self.maximumlst:
for step in self.steplst:
self.run_wild_mCSM(class_num, center, maximum, step)
self.run_mutant_mCSM(class_num, center, maximum, step)
check_qsub(tag='mCSM_%s' % self.dataset_name,
sleep_time=self.sleep_time)
def run_mut(self):
mt_csv_dir_rewrite = '%s/%s.csv' % (
self.outpath_global, self.dataset_name) ## the rewrite mt_csv
mut_tag = 'rosetta_mut_%s' % self.dataset_name
qsub_mut(self.homedir, self.mutdir, self.outpath_ref, self.outpath_mut,
mt_csv_dir_rewrite, mut_tag)
check_qsub(tag=mut_tag, sleep_time=self.sleep_time)
self.mut_tagdirlst = [
self.outpath_mut + '/' + x for x in os.listdir(self.outpath_mut)
]
def run_psiblast(self):
wild_tag = 'psiblast_%s_wt' % self.dataset_name
mutant_tag = 'psiblast_%s_mt' % self.dataset_name
blast_tag = 'psiblast_%s' % self.dataset_name
qsub_wild(app=self.appdir,
libdir=self.libdir,
seq_path=self.wild_seq_path,
qsubid_prefix=wild_tag)
qsub_mutant(app=self.appdir,
libdir=self.libdir,
seq_path=self.mutant_seq_path,
qsubid_prefix=mutant_tag)
check_qsub(tag=blast_tag, sleep_time=self.sleep_time)