def testWriteRmsd(self):
directory_name = None
try:
directory_name = tempfile.mkdtemp()
rfname = os.path.join(directory_name, EVEN_KEY)
write_rmsd(EVEN_DATA, rfname)
self.assertAlmostEqual(EVEN_DATA, read_rmsd(rfname))
finally:
shutil.rmtree(directory_name)
def testWriteRmsd(self):
directory_name = None
try:
directory_name = tempfile.mkdtemp()
rfname = os.path.join(directory_name, EVEN_KEY)
write_rmsd(EVEN_DATA, rfname)
self.assertAlmostEqual(EVEN_DATA, read_rmsd(rfname))
finally:
shutil.rmtree(directory_name)
def write_avg_rmsd(tgt_dir, rmsd, overwrite=False):
"""
Writes out all of the described RMSD files into the given target directory.
:param tgt_dir: The data where the files will go.
:param rmsd: A dict of an array of floats keyed by file name.
:param overwrite: Whether to overwrite existing files.
"""
for rmsd_fname, data in rmsd.items():
f_name = os.path.join(tgt_dir, rmsd_fname)
if allow_write(f_name, overwrite=overwrite):
write_rmsd(data, f_name)
def write_avg_rmsd(tgt_dir, rmsd, overwrite=False):
"""
Writes out all of the described RMSD files into the given target directory.
:param tgt_dir: The data where the files will go.
:param rmsd: A dict of an array of floats keyed by file name.
:param overwrite: Whether to overwrite existing files.
"""
for rmsd_fname, data in rmsd.items():
f_name = os.path.join(tgt_dir, rmsd_fname)
if allow_write(f_name, overwrite=overwrite):
write_rmsd(data, f_name)
def rmsd_split(meta_file,
steps,
tpl_dir=DEF_TPL_DIR,
overwrite=False,
base_dir=None):
"""
Reads the given meta file, fetches the RMSD files in the inventory, and creates a succession
of directories that split the original RMSD files into a larger number of chunks for each step
such that step 1 will create a split of 2 in 01_01 and 01_02, etc.
:param meta_file: The initial meta file.
:param steps: The number of averaging steps to perform.
:param tpl_dir: The directory that contains the submit templates.
:param overwrite: Whether to overwrite existing files.
:param base_dir: The base directory to write to (defaults to the meta file's dir)
"""
meta = read_meta(meta_file)
rmsd = read_meta_rmsd(meta)
sub_tpl_base = read_tpl(os.path.join(tpl_dir, DEF_BASE_SUBMIT_TPL))
sub_tpl_line = read_tpl(os.path.join(tpl_dir, DEF_PART_LINE_SUBMIT_TPL))
if not base_dir:
base_dir = meta[DIR_KEY]
for step in range(1, steps + 1):
for rmsd_fname, data in rmsd.items():
data_len = len(data)
chunk_num = step + 1
chunk_size = math.floor(data_len / chunk_num)
logger.debug(STEP_DBG_MSG, step, data_len, rmsd_fname, chunk_num,
chunk_size)
rmsd_chunks = [ch for ch in chunk(data, chunk_size, list)]
for step_part in range(1, chunk_num + 1):
rmsd_tgt_dir = os.path.join(
base_dir, SPLIT_DIR_FMT.format(step, step_part))
if not os.path.exists(rmsd_tgt_dir):
os.makedirs(rmsd_tgt_dir)
f_name = os.path.join(rmsd_tgt_dir, rmsd_fname)
if allow_write(f_name, overwrite=overwrite):
write_rmsd(rmsd_chunks[step_part - 1], f_name)
write_meta(base_dir, meta, step, overwrite)
write_submit(base_dir, sub_tpl_base, sub_tpl_line, step, overwrite)
def rmsd_split(meta_file, steps, tpl_dir=DEF_TPL_DIR, overwrite=False, base_dir=None):
"""
Reads the given meta file, fetches the RMSD files in the inventory, and creates a succession
of directories that split the original RMSD files into a larger number of chunks for each step
such that step 1 will create a split of 2 in 01_01 and 01_02, etc.
:param meta_file: The initial meta file.
:param steps: The number of averaging steps to perform.
:param tpl_dir: The directory that contains the submit templates.
:param overwrite: Whether to overwrite existing files.
:param base_dir: The base directory to write to (defaults to the meta file's dir)
"""
meta = read_meta(meta_file)
rmsd = read_meta_rmsd(meta)
sub_tpl_base = read_tpl(os.path.join(tpl_dir, DEF_BASE_SUBMIT_TPL))
sub_tpl_line = read_tpl(os.path.join(tpl_dir, DEF_PART_LINE_SUBMIT_TPL))
if not base_dir:
base_dir = meta[DIR_KEY]
for step in range(1, steps + 1):
for rmsd_fname, data in rmsd.items():
data_len = len(data)
chunk_num = step + 1
chunk_size = math.floor(data_len / chunk_num)
logger.debug(STEP_DBG_MSG, step, data_len, rmsd_fname, chunk_num, chunk_size)
rmsd_chunks = [ch for ch in chunk(data, chunk_size, list)]
for step_part in range(1, chunk_num + 1):
rmsd_tgt_dir = os.path.join(base_dir, SPLIT_DIR_FMT.
format(step, step_part))
if not os.path.exists(rmsd_tgt_dir):
os.makedirs(rmsd_tgt_dir)
f_name = os.path.join(rmsd_tgt_dir, rmsd_fname)
if allow_write(f_name, overwrite=overwrite):
write_rmsd(rmsd_chunks[step_part - 1], f_name)
write_meta(base_dir, meta, step, overwrite)
write_submit(base_dir, sub_tpl_base, sub_tpl_line, step, overwrite)