Python temp_change_dir Examples

Example #1

File: 4.generate_rst7_parm7_files.py Project: hainm/amber_rosetta_methods

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)

Example #2

File: mpi_generate_rst7_parm7_files.py Project: hainm/rosseta_amber

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:

Example #3

File: move.py Project: hainm/rosseta_amber

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

Example #4

File: move.py Project: hainm/rosseta_amber

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

Example #5

File: mpi_generate_rst7_parm7_files.py Project: hainm/rosseta_amber

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
                ]]