def main():
dataset_name = sys.argv[1]
homedir = shell('echo $HOME')
if homedir == '/home/sry':
print('---On server ibm')
maximumlst = [11, 12, 13, 14, 15]
elif homedir == '/public/home/sry':
print('---On server hp')
maximumlst = [5, 6, 7, 8, 9, 10]
else:
print('[ERROR] Failed to select server!')
exit(1)
class_numlst = [2, 8]
centerlst = ['CA', 'geometric']
minimum = 0.1
# maximumlst = [5,6,7,8,9,10,11,12,13,14,15]
steplst = [0.5, 1, 1.5, 2]
# class_numlst = [2,8]# @@++
# centerlst = ['CA','geometric']# @@++
# minimum = 0.5# @@++
# maximumlst = [5]# @@++
# steplst = [1.5]# @@++
QR = QsubRunner(homedir, dataset_name, class_numlst, centerlst, minimum,
maximumlst, steplst)
QR.mCSM_runner()
def main():
dataset_name = sys.argv[1]
HOMEdir = shell('echo $HOME')
Calculator = CalculateMSA(dataset_name, HOMEdir)
Calculator.pdb2seq()
Calculator.run_psiblast()
Calculator.blast2msa()
def main():
dataset_name = 'TR'
homedir = shell('echo $HOME')
appdir = '%s/bin/stride' % homedir
pdb_wild_dir = '%s/mCNN/dataset/%s/pdb_chain' % (homedir, dataset_name
) #wild_pdb_dir
pdb_TR_dir = '%s/mCNN/dataset/%s/output' % (homedir, dataset_name)
outdir_wild = '%s/mCNN/dataset/%s/feature/stride/wild' % (homedir,
dataset_name)
outdir_TR = '%s/mCNN/dataset/%s/feature/stride/TR' % (homedir,
dataset_name)
calSA(appdir, outdir_wild, outdir_TR, pdb_wild_dir, pdb_TR_dir)
def main():
homedir = shell('echo $HOME')
featurelst = ' '.join([
'depth', 'rsa', 'thermo', 'onehot', 'pharm', 'hp', 'mass', 'deltar',
'pharm_deltar', 'hp_deltar', 'msa', 'energy', 'ddg'
])
# ------------------------------------------------------------------------------------------------------------------
## parse argument
parser = argparse.ArgumentParser()
parser.add_argument('dataset_name', type=str, help='dataset name')
parser.add_argument(
'--flag',
type=str,
choices=['first', 'all'],
default='all',
help=
'"first" calc df_feature only, "all" calc df_neighbor and df_feature, default is "all".'
)
parser.add_argument('-k',
'--k_neighbor',
type=int,
required=True,
nargs='+',
help='The k_neighbor list.')
parser.add_argument('-C',
'--center',
type=str,
required=True,
nargs='+',
choices=['CA', 'geometric'],
help='The MT site center type.')
parser.add_argument('-T',
'--pca',
type=str,
default='False',
choices=['False', 'True'],
help='If consider pca transform, the default is False')
args = parser.parse_args()
dataset_name = args.dataset_name
flag = args.flag
k_neighborlst = args.k_neighbor
centerlst = args.center
pca = str2bool(args.pca)
QR = CoordRunner(homedir, dataset_name, flag, k_neighborlst, centerlst,
featurelst)
QR.coord_runner()
if flag == 'first':
## first means only calc df_feature (ALL the ATOMS), do not run the latter part in this main function
exit(0)
def main():
dataset_name = sys.argv[1]
homedir = shell('echo $HOME')
appdir = '%s/mCNN/src/Stride/stride' % homedir
pdb_ref_path = '%s/mCNN/dataset/%s/feature/rosetta/ref_output' % (
homedir, dataset_name)
pdb_mut_path = '%s/mCNN/dataset/%s/feature/rosetta/mut_output' % (
homedir, dataset_name)
outdir_mutant = '%s/mCNN/dataset/%s/feature/stride/mutant' % (homedir,
dataset_name)
outdir_wild = '%s/mCNN/dataset/%s/feature/stride/wild' % (homedir,
dataset_name)
calSA(appdir, outdir_mutant, outdir_wild, pdb_ref_path, pdb_mut_path)
def main():
dataset_name, flag = sys.argv[1:]
HOMEdir = shell('echo $HOME')
ROS = RosettaEnergy(dataset_name, HOMEdir)
if flag == 'first':
ROS.get_mdl0(
) # mdl0 are needed by others, split two steps for this parallel computing.
elif flag == 'second':
ROS.run_ref()
ROS.mapping_pos()
ROS.rewrite_mtcsv()
ROS.run_mut()
ROS.check_result()
ROS.get_energy()
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys, os
from mCNN.processing import shell
dataset_name = sys.argv[1]
homedir = shell('echo $HOME')
def check_mCNN(homedir,dataset_name):
wild_qsublog_dir = '%s/mCNN/dataset/%s/feature/mCNN/wild/qsublog'%(homedir,dataset_name)
mutant_qsublog_dir = '%s/mCNN/dataset/%s/feature/mCNN/mutant/qsublog'%(homedir,dataset_name)
wild_qsubtag_dir_lst = [wild_qsublog_dir+'/'+x for x in os.listdir(wild_qsublog_dir)]
mutant_qsubtag_dir_lst = [mutant_qsublog_dir+'/'+x for x in os.listdir(mutant_qsublog_dir)]
for wild_qsubtag_dir in wild_qsubtag_dir_lst:
errdirlst = [wild_qsubtag_dir+'/'+x+'/err' for x in os.listdir(wild_qsubtag_dir)]
for errdir in errdirlst:
if not os.path.exists(errdir):
print('DO Not Exist',errdir)
continue
if int(os.path.getsize(errdir)) > 0:
# print(os.path.getsize(errdir))
# print(type(os.path.getsize(errdir)))
print(errdir)
for mutant_qsubtag_dir in mutant_qsubtag_dir_lst:
errdirlst = [mutant_qsubtag_dir+'/'+x+'/err' for x in os.listdir(mutant_qsubtag_dir)]
for errdir in errdirlst:
if not os.path.exists(errdir):
print('DO Not Exist',errdir)