def _run_script_on_coder(self, base_values):
self.output_dataset_coder_path = self.output_dataset_path + '/' + self.coder_dictionary['o_folder']
create_folder(self.output_dataset_coder_path)
coder_name = self.coder_dictionary['name']
if coder_name == 'CoderBase':
base_values = self._run_script_on_base_coder(base_values)
else:
self._run_script_of_other_coders(base_values)
return base_values
def _run_script_on_dataset(self, dataset_dictionary):
self.input_path = self.DATASETS_PATH + dataset_dictionary['folder']
logger_name = dataset_dictionary['name'].lower() + '.log'
logger_filename = self.output_path + logger_name
self.logger = setup_logger(logger_name, logger_filename)
self.output_dataset_path = self.output_path + dataset_dictionary['o_folder']
create_folder(self.output_dataset_path)
dataset_name = dataset_dictionary['name']
for file_index, self.input_filename in enumerate(ExperimentsUtils.dataset_csv_filenames(dataset_name)):
self.row = [dataset_name] if file_index == 0 else [None]
self._run_script_on_file(file_index)
def separate_ligands(file_path, folder):
"""
Separate .mae file into entries.
:param str file_path: .mae file to separate
:param str folder: workspace folder to save separated files
:var str intro: required intro part to write into each new .mae file
:var list parts: sections of the file
:return int error_code:
1: No input provided
2: File doesn't exist
:return list or None titles_file: returns files paths in the same order as in the input (file_path)
"""
try:
file = open(file_path).read()
except TypeError:
print("No input file!")
return 1, None
except FileNotFoundError:
print("No such file: %s" % file_path)
return 2, None
create_folder(folder) # utils.py
parts = file.split(' } \n} \n') # Splits .mae file into separate sections
intro = parts[0].split(
"} \n\n"
)[0] # First section will also contain intro part, here we also separate it.
intro = "".join([intro, "} \n"])
parts[0] = parts[0].split("} \n\n")[1]
titles_file = []
for i in range(len(parts) - 1):
title0 = parts[i].split(" :::")[1].split('\n')[1].strip(
) # Suitable descriptor for file name can be found here.
title1 = title0.split(":")[-1]
titles_file.append(title1)
out = open("%s/%s.mae" % (folder, title1),
'w') # Saving single section with intro.
out.write(intro)
out.write(parts[i])
out.write(" } \n} \n")
out.close()
return 0, titles_file
def main():
"""
Main function. Creates Maestro script.
"""
# Storing paths to files and normalizing them
GLOBAL_VARIABLES = CONFIGURE(args.update) # utils.py
workspace_folder = os.path.abspath("./workspace")
docking_folder = os.path.abspath("./docking")
docking_file = os.path.abspath(args.docking)
ligands_folder = os.path.abspath("./ligands")
create_folder(workspace_folder, True) # utils.py
unzipped = unzip(docking_file, workspace_folder) # SMARTS_extract.py
SMARTS = SMARTS_extract(required, unzipped, docking_folder,
workspace_folder) # SMARTS_extract.py
os.system("%s %s/run pv_convert.py -mode merge %s" %
(GLOBAL_VARIABLES[1], GLOBAL_VARIABLES[0], unzipped))
input_file = ""
for i in os.listdir(workspace_folder):
if unzipped.rstrip(
"_pv.mae"
) in i and "out_complex" in i and "maegz" not in i:
input_file = "/".join([workspace_folder, i])
break
titles_file = []
if input_file:
error_code, titles_file = separate_ligands(
input_file, ligands_folder) # file_separate.py
if error_code != 0:
parser.print_help()
exit(error_code)
else:
print("File not found - complex.")
exit()
maestro_writer(args.output, args.crystal, input_file, titles_file,
SMARTS) # utils.py
if args.remove:
paths = [ligands_folder, docking_folder,
workspace_folder] # Folders to clean.
cleanup(paths) # utils.py
def update_pkg(pkg_name,
target_folder,
src_folder=None,
create_bkup=False,
compile=True):
"""install or update a packagein a specific folder
expect to download and extract a wheel file e.g. "yt_dlp-2020.10.24.post6-py2.py3-none-any.whl", which in fact
is a zip file
Args:
pkg_name (str): package name
url (str): download url (for a wheel file)
target_folder (str): target installation folder for the package
src_folder (str): if specified, will skip downloading from pypi and use it instead
"""
# paths
temp_folder = os.path.join(target_folder, f'temp_{pkg_name}')
extract_folder = os.path.join(temp_folder, 'extracted')
z_fn = f'{pkg_name}.zip'
z_fp = os.path.join(temp_folder, z_fn)
old_pkg_path = os.path.join(target_folder, pkg_name)
new_pkg_path = os.path.join(extract_folder, pkg_name)
# make temp folder structure
delete_folder(temp_folder)
create_folder(extract_folder)
# start processing -------------------------------------------------------
print(f'start updating {pkg_name} please wait ...')
if create_bkup:
print(f'backup {pkg_name}')
bkup(old_pkg_path)
if not src_folder:
# get download url
latest_version, url = get_pkg_latest_version(pkg_name)
if url:
print(f'Found {pkg_name} version: {latest_version}')
else:
print('Failed to get url for:', pkg_name)
return
# download from pypi
print(f'step 1 of 4: downloading {pkg_name} files')
data = download(url, fp=z_fp)
if not data:
print(f'failed to download {pkg_name}, abort update')
return
# extract zip file
print(f'step 2 of 4: extracting {z_fn}')
extract(z_fp, extract_folder)
else:
# copy pkg folder to temp folder
shutil.copytree(src_folder, new_pkg_path)
# compile files from py to pyc
print('step 3 of 4: compiling files, please wait')
if compile:
compile_pkg(new_pkg_path)
# delete old package and replace it with new one
print(f'step 4 of 4: overwrite old {pkg_name} files')
delete_folder(old_pkg_path)
shutil.move(new_pkg_path, target_folder)
print('new package copied to:', old_pkg_path)
# .dist-info folder, eg: FireDM-2021.2.9.dist-info
r = re.compile(f'{pkg_name}.*dist-info', re.IGNORECASE)
# delete old dist-info folder if found
match = list(filter(r.match, os.listdir(target_folder)))
if match:
old_dist_info_folder = os.path.join(target_folder, match[0])
delete_folder(old_dist_info_folder)
print('delete old dist-info folder:', old_dist_info_folder)
# copy new dist-info folder to destination folder
match = list(filter(r.match, os.listdir(extract_folder)))
if match:
new_dist_info_folder = os.path.join(extract_folder, match[0])
shutil.move(new_dist_info_folder, target_folder)
print('install new dist-info folder:', new_dist_info_folder)
# clean old files
print('delete temp folder')
delete_folder(temp_folder)
print(f'{pkg_name} ..... done updating')
return True
def main():
"""
Main function. Creates Maestro script.
"""
GLOBAL_VARIABLES = CONFIGURE(args.update) # configuration_scripts.py
ligand_main_directory = os.path.abspath("./workspace/ligands")
ligand_mae_path = os.path.abspath("./workspace/ligand_mae")
combined_ligand_filename = os.path.abspath("./workspace/ligands/ligs.mae")
preprocessed_ligand_path = os.path.abspath("./workspace/ligands/preprocessed_ligands")
# ligand_protein_filename = os.path.abspath("./workspace/all.mae")
protein_original_path = os.path.abspath("./workspace/proteins")
# protein_filename = os.path.abspath("bialko.mae")
# complex_input_filename = os.path.abspath("./workspace/complex/all-out_complex.mae")
complex_original_path = os.path.abspath("./workspace/complex/original")
complex_deleted_path = os.path.abspath("./workspace/complex/deleted")
SMARTS_filename = os.path.abspath("./workspace/SMARTS.txt")
create_folder(os.path.abspath("./workspace"), True)
create_folder(os.path.abspath(ligand_main_directory), False)
create_folder(os.path.abspath(ligand_mae_path), False)
create_folder(os.path.abspath(preprocessed_ligand_path), False)
create_folder(os.path.abspath(protein_original_path), False)
create_folder(os.path.abspath(complex_deleted_path), False)
create_folder(os.path.abspath(complex_original_path), False)
"""
workspace
| SMARTS.txt
ligands
| ligs.mae
ligand_mae
| *.mae (from pdb)
preprocessed_lignads
| preprocessed_ligands.pdb
proteins
| protein_input.mae
| protein_deleted.mae
complex
original # not-modified
| *.pv (maestro)
| *.out_complex
deleted
| *.pv (maestro)
| *.out_complex
"""
ligand_files = []
try:
ligand_files = os.listdir(args.ligand)
except FileNotFoundError:
print("Folder not found %s" % args.ligand)
parser.print_help()
exit()
# for file in ligand_files:
# base = os.path.basename(file)
# nazwa = "%s/%s.mae" % (ligand_path, os.path.splitext(base)[0])
# os.system("%s %s/run structconvert.py -ipdb %s %s" % (GLOBAL_VARIABLES[1], GLOBAL_VARIABLES[0], file, nazwa))
# # TODO wyciągnąć nazwy z : jak w file_separate.py
# titles_file = []
# for i in os.listdir(ligand_path):
# temp = open("%s/%s" % (ligand_path, i)).read()
# title0 = temp.split(" :::")[2].split('\n')[1].strip() # Suitable descriptor for file name can be found here.
# title1 = title0.split(":")[-1]
# titles_file.append(title1)
titles_file = []
for file in ligand_files:
temp, base_lig = pdb_to_mae(file, ligand_mae_path, GLOBAL_VARIABLES[0], GLOBAL_VARIABLES[1])
titles_file.append(base_lig)
# TODO #####
os.system("SCHRODINGER/utilities/structcat %s -omae ./workspace/ligand_mae/ligs.mae" % " ".join("/".join([" ./workspace/ligand_mae/", os.listdir("./workspace/ligand_mae")])))
# TODO #####
os.system("%s %s/run gen_smarts.py %s/%s %s" % (GLOBAL_VARIABLES[1], GLOBAL_VARIABLES[0], ligand_mae_path, combined_ligand_filename, SMARTS_filename))
SMARTS = open(SMARTS_filename).readlines()
SMARTS = [i.rstrip() for i in SMARTS]
# os.system("%s %s/run structconvert.py -ipdb %s %s" % (GLOBAL_VARIABLES[1], GLOBAL_VARIABLES[0], args.protein, protein_filename))
###
protein_path, protein_base = pdb_to_mae(args.protein, protein_original_path, GLOBAL_VARIABLES[0], GLOBAL_VARIABLES[1])
###
### łączenie białka z ligandami i usuwanie albo i nie
# pose_viewer file and complex file for name_prot
os.system("%s %s/utilities/structcat -imae %s -imae %s -omae %s_pv.mae" % (GLOBAL_VARIABLES[1], GLOBAL_VARIABLES[0], protein_path, combined_ligand_filename, os.path.abspath(complex_original_path + "/" + protein_base)))
os.system("%s %s/run pv_convert.py -mode merge %s_pv.mae" % (GLOBAL_VARIABLES[1], GLOBAL_VARIABLES[0], os.path.abspath(complex_original_path + "/" + protein_base))) # TODO ścieżki
input_file = os.path.abspath(complex_original_path + "/" + protein_base) + "-out_complex.mae"
# pose_viewer file and complex file for name_prot2
if args.toaa != 0:
protein_base_deleted = protein_base + "_deleted"
protein_path_deleted = os.path.abspath("workspace/" + protein_base_deleted + ".mae")
os.system("%s %s/run delete_atoms.py -asl \"res.num %s-%s\" %s %s" % (GLOBAL_VARIABLES[1], GLOBAL_VARIABLES[0], args.fromaa, args.toaa, protein_path, protein_path_deleted))
os.system("%s %s/utilities/structcat -imae %s -imae %s -omae %s_pv.mae" % (GLOBAL_VARIABLES[1], GLOBAL_VARIABLES[0], protein_path_deleted, combined_ligand_filename, os.path.abspath(complex_deleted_path + "/" + protein_base_deleted)))
os.system("%s %s/run pv_convert.py -mode merge %s_pv.mae" % (GLOBAL_VARIABLES[1], GLOBAL_VARIABLES[0], os.path.abspath(complex_deleted_path + "/" + protein_base_deleted)))
input_file = os.path.abspath(complex_deleted_path + "/" + protein_base_deleted + "-out_complex.mae")
maestro_writer(args.output, args.crystal, input_file, titles_file, SMARTS) # utils.py
if args.remove:
paths = [os.path.abspath("./workspace")] # Folders to clean.
cleanup(paths) # utils.py
project_folder = os.path.dirname(os.path.dirname(current_folder))
build_folder = current_folder
app_folder = os.path.join(build_folder, APP_NAME)
icon_path = os.path.join(
project_folder, 'icons',
'48_32_16.ico') # best use size 48, and must be an "ico" format
version_fp = os.path.join(project_folder, 'firedm', 'version.py')
requirements_fp = os.path.join(project_folder, 'requirements.txt')
main_script_path = os.path.join(project_folder, 'firedm.py')
sys.path.insert(0, project_folder) # for imports to work
from scripts.utils import download, delete_folder, create_folder
# create build folder
create_folder(build_folder)
# get version
version_module = {}
with open(version_fp) as f:
exec(
f.read(),
version_module) # then we can use it as: version_module['__version__']
version = version_module['__version__']
# get required packages
with open(requirements_fp) as f:
packages = [
line.strip().split(' ')[0] for line in f.readlines() if line.strip()
] + ['firedm']
packages.remove('Pillow')
def update_pkg(pkg_name,
target_folder,
src_folder=None,
create_bkup=False,
compile=True):
"""install or update a packagein a specific folder
expect to download and extract a wheel file e.g. "yt_dlp-2020.10.24.post6-py2.py3-none-any.whl", which in fact
is a zip file
Args:
pkg_name (str): package name
url (str): download url (for a wheel file)
target_folder (str): target installation folder for the package
src_folder (str): if specified, will skip downloading from pypi and use it instead
"""
# paths
temp_folder = os.path.join(target_folder, f'temp_{pkg_name}')
extract_folder = os.path.join(temp_folder, 'extracted')
z_fn = f'{pkg_name}.zip'
z_fp = os.path.join(temp_folder, z_fn)
old_pkg_path = os.path.join(target_folder, pkg_name)
new_pkg_path = os.path.join(extract_folder, pkg_name)
delete_folder(temp_folder)
# start processing -------------------------------------------------------
print(f'start updating {pkg_name} please wait ...')
if create_bkup:
print(f'backup {pkg_name}')
bkup(old_pkg_path)
if src_folder:
# copy pkg folder to temp folder
shutil.copytree(src_folder, new_pkg_path, dirs_exist_ok=True)
else:
# get download url
latest_version, url = get_pkg_latest_version(pkg_name)
current_version = get_pkg_version(old_pkg_path)
print(
f'{pkg_name}, current: {current_version} - latest: {latest_version}'
)
if parse_version(latest_version) <= parse_version(current_version):
print(f'{pkg_name} is up-to-date')
return
if url:
print(f'Found {pkg_name} version: {latest_version}')
else:
print('Failed to get url for:', pkg_name)
return
# download from pypi
print(f'downloading {pkg_name} files')
data = download(url, fp=z_fp)
if not data:
print(f'failed to download {pkg_name}, abort update')
return
# make temp folder structure
create_folder(extract_folder)
# extract zip file
print(f'extracting {z_fn}')
extract(z_fp, extract_folder)
# # compile files from py to pyc
# if compile:
# print('compiling files, please wait')
# compile_pkg(new_pkg_path)
# # delete old package and replace it with new one
# print(f'overwrite old {pkg_name} files')
# delete_folder(old_pkg_path)
# shutil.move(new_pkg_path, target_folder)
# print('new package copied to:', old_pkg_path)
# .dist-info folder, eg: FireDM-2021.2.9.dist-info
r = re.compile(f'{pkg_name}.*dist-info', re.IGNORECASE)
# delete old dist-info folder if found
match = list(filter(r.match, os.listdir(target_folder)))
if match:
old_dist_info_folder = os.path.join(target_folder, match[0])
delete_folder(old_dist_info_folder)
print('delete old dist-info folder:', old_dist_info_folder)
# # copy new dist-info folder to destination folder
# match = list(filter(r.match, os.listdir(extract_folder)))
# if match:
# new_dist_info_folder = os.path.join(extract_folder, match[0])
# shutil.move(new_dist_info_folder, target_folder)
# print('install new dist-info folder:', new_dist_info_folder)
# move folders under extracted folder to target folder (e.g: sitepackages)
src, dest = extract_folder, target_folder
folders = [
f for f in os.listdir(src) if os.path.isdir(os.path.join(src, f))
]
# execlude .data folders
folders = [f for f in folders if not f.endswith('.data')]
src_folders = [os.path.join(src, f) for f in folders]
dest_folders = [os.path.join(dest, f) for f in folders]
# delete dest folders
for folder in dest_folders:
delete_folder(folder)
for folder in src_folders:
shutil.move(folder, dest)
# clean old files
delete_folder(temp_folder, verbose=True)
print(f'{pkg_name} ..... done updating \n')
return True