def launch(self) -> int:
"""Execute the :class:`Mutate <model.mutate.Mutate>` object."""
# Setup Biobb
if self.check_restart(): return 0
self.stage_files()
# Create command line
self.cmd = [self.check_structure_path,
'-i', self.stage_io_dict["in"]["input_pdb_path"],
'-o', self.stage_io_dict["out"]["output_pdb_path"],
'mutateside', '--mut', self.mutation_list]
if self.use_modeller:
if modeller_installed(self.out_log, self.global_log):
self.cmd.append('--rebuild')
else:
fu.log(f"Modeller is not installed --rebuild option can not be used proceeding without using it",
self.out_log, self.global_log)
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
# Remove temporal files
self.tmp_files.append(self.stage_io_dict.get("unique_dir"))
self.remove_tmp_files()
return self.return_code
def check_in_path(path, out_log, classname):
""" Checks input instructions file """
if not Path(path).exists():
fu.log(classname + ': Unexisting input instructions file, exiting',
out_log)
raise SystemExit(classname + ': Unexisting input instructions file')
# check syntax for instructions file
syntax_instructions = True
err_instructions = ''
if not 'parm ' in open(path).read():
syntax_instructions = False
err_instructions += 'No topology provided'
if not 'trajin ' in open(path).read():
syntax_instructions = False
err_instructions += ' No input trajectory provided'
if not syntax_instructions:
fu.log(
classname +
': Incorrect syntax for instructions file: %s, exiting' %
err_instructions, out_log)
raise SystemExit(
classname +
': Incorrect syntax for instructions file: %s, exiting' %
err_instructions)
def get_end(properties, out_log, classname):
""" Gets end """
end = properties.get('end', get_default_value('end'))
if not is_valid_int(end):
fu.log(classname + ': Incorrect end provided, exiting', out_log)
raise SystemExit(classname + ': Incorrect end provided')
return str(end)
def launch(self):
"""Launches the execution of the Open Babel module."""
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# check input/output paths and parameters
self.check_data_params(out_log, err_log)
# Check the properties
fu.check_properties(self, self.properties)
if self.restart:
output_file_list = [self.output_path_par, self.output_path_inp, self.output_path_top]
if fu.check_complete_files(output_file_list):
fu.log('Restart is enabled, this step: %s will the skipped' % self.step, out_log, self.global_log)
return 0
# create unique name for temporary folder (created by acpype)
self.unique_name = create_unique_name(6)
# create command line instruction
cmd = self.create_cmd(out_log, err_log)
# execute cmd
fu.log('Running %s, this execution can take a while' % self.acpype_path, out_log)
returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log, self.global_log).launch()
# move files to output_path and removes temporary folder
process_output(self.unique_name, self.basename + "." + self.unique_name + ".acpype", self.remove_tmp, self.basename, get_default_value(self.__class__.__name__), self.output_files, out_log)
return returncode
def get_parameters(properties, type, classname, out_log):
""" Gets in_parameters and out_parameters """
if not properties.get(type, dict()):
fu.log('No %s parameters provided' % type, out_log)
return get_default_value(classname)[type]
return {k: v for k, v in properties.get(type, dict()).items()}
def get_fit(properties, out_log, classname):
""" Gets fit """
fit = properties.get('fit', get_default_value('fit'))
if not is_valid_fit(fit):
fu.log(classname + ': Incorrect fit provided, exiting', out_log)
raise SystemExit(classname + ': Incorrect fit provided')
return fit
def get_start(properties, out_log, classname):
""" Gets start """
start = properties.get('start', get_default_value('start'))
if not is_valid_int(start):
fu.log(classname + ': Incorrect start provided, exiting', out_log)
raise SystemExit(classname + ': Incorrect start provided')
return str(start)
def get_center(properties, out_log, classname):
""" Gets center """
center = properties.get('center', get_default_value('center'))
if not is_valid_boolean(center):
fu.log(classname + ': Incorrect center provided, exiting', out_log)
raise SystemExit(classname + ': Incorrect center provided')
return center
def get_ur(properties, out_log, classname):
""" Gets ur """
ur = properties.get('ur', get_default_value('ur'))
if not is_valid_ur(ur):
fu.log(classname + ': Incorrect ur provided, exiting', out_log)
raise SystemExit(classname + ': Incorrect ur provided')
return ur
def process_output_gmx(unique_name, files_folder, remove_tmp, basename,
class_params, output_files, out_log):
""" Moves and removes temporal files generated by the wrapper """
path = files_folder
suffix = class_params['suffix']
src_files = glob.glob(path + '/' + basename + '.' + unique_name + suffix +
'*')
# copy files for the requested topology to the output_path
for file_name in src_files:
# replace random name by original name in all files
with fileinput.FileInput(file_name, inplace=True) as file:
for line in file:
print(line.replace(basename + '.' + unique_name, basename),
end='')
if (Path(file_name).is_file()):
file_extension = PurePath(file_name).suffix
# in top files for gromacs, replace file.itp by name given by user
if (file_extension[1:] == 'top'):
with open(file_name) as f:
newText = f.read().replace(
basename + '_GMX.itp',
PurePath(output_files['itp']).name)
with open(file_name, "w") as f:
f.write(newText)
shutil.copy(file_name, output_files[file_extension[1:]])
fu.log(
'File %s succesfully created' %
output_files[file_extension[1:]], out_log)
if remove_tmp:
# remove temporary folder
fu.rm(files_folder)
fu.log('Removed temporary folder: %s' % files_folder, out_log)
def get_pbc(properties, out_log, classname):
""" Gets pbc """
pbc = properties.get('pbc', get_default_value('pbc'))
if not is_valid_pbc(pbc):
fu.log(classname + ': Incorrect pbc provided, exiting', out_log)
raise SystemExit(classname + ': Incorrect pbc provided')
return pbc
def process_output(unique_name, files_folder, remove_tmp, basename,
class_params, output_files, out_log):
""" Moves and removes temporal files generated by the wrapper """
path = files_folder
suffix = class_params['suffix']
src_files = glob.glob(path + '/' + basename + '.' + unique_name + suffix +
'*')
# copy files for the requested topology to the output_path
for file_name in src_files:
# replace random name by original name in all files
with fileinput.FileInput(file_name, inplace=True) as file:
for line in file:
print(line.replace(basename + '.' + unique_name, basename),
end='')
if (Path(file_name).is_file()):
file_extension = PurePath(file_name).suffix
shutil.copy(file_name, output_files[file_extension[1:]])
fu.log(
'File %s succesfully created' %
output_files[file_extension[1:]], out_log)
if remove_tmp:
# remove temporary folder
fu.rm(files_folder)
fu.log('Removed temporary folder: %s' % files_folder, out_log)
def check_mandatory_property(property, name, out_log, classname):
""" Checks mandatory properties """
if not property:
fu.log(classname + ': Unexisting %s property, exiting' % name, out_log)
raise SystemExit(classname + ': Unexisting %s property' % name)
return property
def get_memprotmd_sim_search(collection_name,
keyword,
out_log=None,
global_log=None):
""" Performs advanced searches in the MemProtMD DB using its REST API and a given keyword """
fu.log(
'Getting search results from the MemProtMD REST API. Collection name: %s, keyword: %s'
% (collection_name, keyword), out_log, global_log)
url = "http://memprotmd.bioch.ox.ac.uk/api/search/advanced"
json_query = {
"collectionName": collection_name,
"query": {
"keywords": keyword
},
"projection": {
"simulations": 1
},
"options": {}
}
json_obj = requests.post(url, json=json_query).json()
json_string = json.dumps(json_obj, indent=4)
# get total number of simulation
list_kw = []
for sim_list in json_obj:
for sim in sim_list['simulations']:
list_kw.append(sim)
fu.log('Total number of simulations: %d' % (len(list_kw)), out_log,
global_log)
return json_string
def get_dt(properties, out_log, classname):
""" Gets dt """
dt = properties.get('dt', get_default_value('dt'))
if not is_valid_int(dt):
fu.log(classname + ': Incorrect dt provided, exiting', out_log)
raise SystemExit(classname + ': Incorrect dt provided')
return str(dt)
def get_xvg(properties, out_log, classname):
""" Gets xvg """
xvg = properties.get('xvg', get_default_value('xvg'))
if not is_valid_xvg_param(xvg):
fu.log(classname + ': Incorrect xvg provided, exiting', out_log)
raise SystemExit(classname + ': Incorrect xvg provided')
return xvg
def launch(self) -> int:
"""Execute the :class:`PdbClusterZip <api.pdb_cluster_zip.PdbClusterZip>` api.pdb_cluster_zip.PdbClusterZip object."""
# check input/output paths and parameters
self.check_data_params(self.out_log, self.err_log)
# Setup Biobb
if self.check_restart(): return 0
self.stage_files()
check_mandatory_property(self.pdb_code, 'pdb_code', self.out_log, self.__class__.__name__)
self.pdb_code = self.pdb_code.strip().lower()
file_list = []
#Downloading PDB_files
pdb_code_list = get_cluster_pdb_codes(pdb_code=self.pdb_code, cluster=self.cluster, out_log=self.out_log, global_log=self.global_log)
unique_dir = fu.create_unique_dir()
for pdb_code in pdb_code_list:
pdb_file = os.path.join(unique_dir, pdb_code+".pdb")
pdb_string = download_pdb(pdb_code=pdb_code, api_id=self.api_id, out_log=self.out_log, global_log=self.global_log)
write_pdb(pdb_string, pdb_file, self.filter, self.out_log, self.global_log)
file_list.append(os.path.abspath(pdb_file))
#Zipping files
fu.log("Zipping the pdb files to: %s" % self.output_pdb_zip_path)
fu.zip_list(self.output_pdb_zip_path, file_list, out_log=self.out_log)
if self.remove_tmp:
# remove temporary folder
fu.rm(unique_dir)
fu.log('Removed temporary folder: %s' % unique_dir, self.out_log)
return 0
def launch(self) -> int:
"""Execute the :class:`ApiBindingSite <api.api_binding_site.ApiBindingSite>` api.api_binding_site.ApiBindingSite object."""
# check input/output paths and parameters
self.check_data_params(self.out_log, self.err_log)
# Setup Biobb
if self.check_restart(): return 0
self.stage_files()
check_mandatory_property(self.pdb_code, 'pdb_code', self.out_log,
self.__class__.__name__)
self.pdb_code = self.pdb_code.strip().lower()
url = "https://www.ebi.ac.uk/pdbe/api/pdb/entry/binding_sites/%s"
# get JSON object
json_string = download_binding_site(self.pdb_code, url, self.out_log,
self.global_log)
# get number of binding sites
fu.log(
'%d binding sites found' %
(len(json.loads(json_string)[self.pdb_code])), self.out_log,
self.global_log)
# write JSON file
write_json(json_string, self.output_json_path, self.out_log,
self.global_log)
return 0
def get_cutoff(properties, out_log, classname):
""" Gets cutoff """
cutoff = properties.get('cutoff', get_default_value('cutoff'))
if not is_valid_float(cutoff):
fu.log(classname + ': Incorrect cutoff provided, exiting', out_log)
raise SystemExit(classname + ': Incorrect cutoff provided')
return str(cutoff)
def process_output_fpocket_filter(search_list, tmp_folder, input_pockets_zip,
output_filter_pockets_zip, remove_tmp,
out_log):
""" Creates the output_filter_pockets_zip """
# decompress the input_pockets_zip file to tmp_folder
cluster_list = fu.unzip_list(zip_file=input_pockets_zip,
dest_dir=tmp_folder,
out_log=out_log)
# list all files of tmp_folder
pockets_list = [str(i) for i in Path(tmp_folder).iterdir()]
# select search_list items from pockets_list
sel_pockets_list = [
p for p in pockets_list for s in search_list if s + '_' in p
]
fu.log('Creating %s output file' % output_filter_pockets_zip, out_log)
# compress output to output_filter_pockets_zip
fu.zip_list(zip_file=output_filter_pockets_zip,
file_list=sel_pockets_list,
out_log=out_log)
if remove_tmp:
# remove temporary folder
fu.rm(tmp_folder)
fu.log('Removed temporary folder: %s' % tmp_folder, out_log)
def get_method(properties, out_log, classname):
""" Gets method """
method = properties.get('method', get_default_value('method'))
if not is_valid_method_param(method):
fu.log(classname + ': Incorrect method provided, exiting', out_log)
raise SystemExit(classname + ': Incorrect method provided')
return method
def get_dista(properties, out_log, classname):
""" Gets dista """
dista = properties.get('dista', get_default_value('dista'))
if not is_valid_boolean(dista):
fu.log(classname + ': Incorrect dista provided, exiting', out_log)
raise SystemExit(classname + ': Incorrect dista provided')
return dista
def launch(self) -> int:
"""Execute the :class:`Gmxselect <gromacs.gmxselect.Gmxselect>` object."""
# Setup Biobb
if self.check_restart(): return 0
self.stage_files()
self.cmd = [
self.gmx_path, 'select', '-s',
self.stage_io_dict["in"]["input_structure_path"], '-on',
self.stage_io_dict["out"]["output_ndx_path"]
]
if self.stage_io_dict["in"].get("input_ndx_path") and Path(
self.stage_io_dict["in"].get("input_ndx_path")).exists():
self.cmd.append('-n')
self.cmd.append(self.stage_io_dict["in"].get("input_ndx_path"))
self.cmd.append('-select')
self.cmd.append("\'" + self.selection + "\'")
if self.gmx_lib:
self.environment = os.environ.copy()
self.environment['GMXLIB'] = self.gmx_lib
# Check GROMACS version
if not self.container_path:
if self.gmx_version < 512:
raise GromacsVersionError(
"Gromacs version should be 5.1.2 or newer %d detected" %
self.gmx_version)
fu.log(
"GROMACS %s %d version detected" %
(self.__class__.__name__, self.gmx_version), self.out_log)
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
if self.io_dict["in"].get("input_ndx_path"):
if self.append:
fu.log(
f"Appending {self.io_dict['in'].get('input_ndx_path')} to {self.io_dict['out']['output_ndx_path']}",
self.out_log, self.global_log)
with open(self.io_dict["out"]["output_ndx_path"],
'a') as out_ndx_file:
out_ndx_file.write('\n')
with open(self.io_dict["in"].get(
"input_ndx_path")) as in_ndx_file:
for line in in_ndx_file:
out_ndx_file.write(line)
# Remove temporal files
self.tmp_files.append(self.stage_io_dict.get("unique_dir"))
self.remove_tmp_files()
return self.return_code
def write_mmcif(mmcif_string,
output_mmcif_path,
out_log=None,
global_log=None):
""" Writes a mmcif """
fu.log("Writting mmcif to: %s" % (output_mmcif_path), out_log, global_log)
with open(output_mmcif_path, 'w') as output_mmcif_file:
output_mmcif_file.write(mmcif_string)
def getWeight(weight, data, out_log, classname):
if 'index' in weight:
return data.iloc[:, weight['index']]
elif 'column' in weight:
return data[weight['column']]
else:
fu.log(classname + ': Incorrect weight format', out_log)
raise SystemExit(classname + ': Incorrect weight format')
def getTarget(target, data, out_log, classname):
if 'index' in target:
return data.iloc[:, target['index']]
elif 'column' in target:
return data[target['column']]
else:
fu.log(classname + ': Incorrect target format', out_log)
raise SystemExit(classname + ': Incorrect target format')
def checkResamplingType(type_, out_log, classname):
""" Gets resampling type """
if not type_:
fu.log(classname + ': Missed mandatory type property', out_log)
raise SystemExit(classname + ': Missed mandatory type property')
if type_ != 'regression' and type_ != 'classification':
fu.log(classname + ': Unknown %s type property' % type_, out_log)
raise SystemExit(classname + ': Unknown %s type property' % type_)
def get_ph(p, out_log):
""" Checks if provided coordinates value is correct """
ph = str(p)
if p and not isinstance(p, float) and not isinstance(p, int):
ph = ''
fu.log('Incorrect format for pH, no value assigned', out_log)
return ph
def get_coordinates(coordinates, out_log):
""" Checks if provided coordinates value is correct """
crd = str(coordinates)
if crd != '3' and crd != '2':
fu.log('Value %s is not compatible as a coordinates value' % crd, out_log)
crd = ''
return crd
def write_fasta(fasta_string,
output_fasta_path,
out_log=None,
global_log=None):
""" Writes a FASTA """
fu.log("Writting FASTA to: %s" % (output_fasta_path), out_log, global_log)
with open(output_fasta_path, 'w') as output_fasta_file:
output_fasta_file.write(fasta_string)