def main():
for code in PDBLIST:
with temp_change_dir(code):
try:
pdbfiles = glob(PDB_PATTERN)
for pdbfile in pdbfiles:
parm = pmd.load_file(pdbfile)
pdbfile_root = pdbfile.replace('.pdb', '')
fn = 'NoH_' + pdbfile
new_parm = parm[[index for index, atom in enumerate(
parm.atoms) if atom.atomic_number != 1]]
new_parm.save(fn, overwrite=True)
run_tleap(code, pdbfile_root, tleap_template)
except TypeError:
print('type error: ', code)
except IndexError:
print('index error: ', code)
quit
'''
pdb_pattern = 'empty*.pdb'
def run_tleap(code, pdbfile_root, tleap_template):
leap_fn = 'tleap.{}.in'.format(pdbfile_root)
with open(leap_fn, 'w') as fh:
cm = tleap_template.format(pdbfile_root=pdbfile_root)
fh.write(cm)
os.system('tleap -f {}'.format(leap_fn))
os.remove(leap_fn)
os.remove('log.{}'.format(pdbfile_root))
for code in PDBLIST:
with temp_change_dir(code):
try:
# os.system('rm *.parm7')
# os.system('cp {} ./{}.parm7'.format(parmfile, code))
# parmfile = glob('*.parm7')[0]
# os.system('cp {parmfile} {code}.parm7'.format(parmfile=parmfile, code=code))
pdbfiles = glob(pdb_pattern)
my_pdbfiles = get_commands_for_my_rank(pdbfiles, rank=rank)
for pdbfile in my_pdbfiles:
parm = pmd.load_file(pdbfile)
pdbfile_root = pdbfile.replace('.pdb', '')
fn = 'NoH_' + pdbfile
new_parm = parm[[index for index, atom in enumerate(parm.atoms) if atom.atomic_number != 1]]
new_parm.save(fn, overwrite=True)
run_tleap(code, pdbfile_root, tleap_template)
except TypeError:
from glob import iglob, glob
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.rank
sys.path.append(
'/project1/dacase-001/haichit/rosseta_amber/DecoyDiscrimination/scripts/elf1/'
)
from submit_elf1 import temp_change_dir
from run_min import get_total_commands, get_commands_for_my_rank, run_each_core
script = "/project1/dacase-001/haichit/rosseta_amber/DecoyDiscrimination/scripts/elf1/move_unqualified_rst7_files.py"
for fn in get_commands_for_my_rank(glob('./*'), rank):
if not os.path.isfile(fn):
# folder
try:
with temp_change_dir(fn):
print(fn)
os.system('python {}'.format(script))
no_restraint_fn = fn + '/no_restraint/'
if os.path.exists(no_restraint_fn):
with temp_change_dir(no_restraint_fn):
print(no_restraint_fn)
os.system('python {}'.format(script))
except IndexError:
pass
import os, sys
from glob import iglob, glob
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.rank
sys.path.append('/project1/dacase-001/haichit/rosseta_amber/DecoyDiscrimination/scripts/elf1/')
from submit_elf1 import temp_change_dir
from run_min import get_total_commands, get_commands_for_my_rank, run_each_core
script = "/project1/dacase-001/haichit/rosseta_amber/DecoyDiscrimination/scripts/elf1/move_unqualified_rst7_files.py"
for fn in get_commands_for_my_rank(glob('./*'), rank):
if not os.path.isfile(fn):
# folder
try:
with temp_change_dir(fn):
print(fn)
os.system('python {}'.format(script))
no_restraint_fn = fn + '/no_restraint/'
if os.path.exists(no_restraint_fn):
with temp_change_dir(no_restraint_fn):
print(no_restraint_fn)
os.system('python {}'.format(script))
except IndexError:
pass
pdb_pattern = 'empty*.pdb'
def run_tleap(code, pdbfile_root, tleap_template):
leap_fn = 'tleap.{}.in'.format(pdbfile_root)
with open(leap_fn, 'w') as fh:
cm = tleap_template.format(pdbfile_root=pdbfile_root)
fh.write(cm)
os.system('tleap -f {}'.format(leap_fn))
os.remove(leap_fn)
os.remove('log.{}'.format(pdbfile_root))
for code in PDBLIST:
with temp_change_dir(code):
try:
# os.system('rm *.parm7')
# os.system('cp {} ./{}.parm7'.format(parmfile, code))
# parmfile = glob('*.parm7')[0]
# os.system('cp {parmfile} {code}.parm7'.format(parmfile=parmfile, code=code))
pdbfiles = glob(pdb_pattern)
my_pdbfiles = get_commands_for_my_rank(pdbfiles, rank=rank)
for pdbfile in my_pdbfiles:
parm = pmd.load_file(pdbfile)
pdbfile_root = pdbfile.replace('.pdb', '')
fn = 'NoH_' + pdbfile
new_parm = parm[[
index for index, atom in enumerate(parm.atoms)
if atom.atomic_number != 1
]]