def plants_docking(self, request, claims):
"""
Perform a PLANTS (Protein-Ligand ANT System) molecular docking.
For a detail description of the input see the file:
schemas/endpoints/docking-request.v1.json
"""
# Validate input path_file object for protein and ligand file
protein_file = mol_validate_file_object(request['protein_file'])
ligand_file = mol_validate_file_object(request['ligand_file'])
# Run docking
base_dir = os.environ.get('BASE_WORK_DIR', request.get('base_work_dir'))
for drop_key in ('protein_file', 'ligand_file', 'base_work_dir'):
if drop_key in request:
del request[drop_key]
docking = PlantsDocking(log=self.log, base_work_dir=base_dir, **request)
if docking.run(protein_file['content'], ligand_file['content']):
return {'status': 'completed', 'result': docking.get_results()}
self.log.error('PLANTS docking failed')
return {'status': 'failed'}
def smartcyp_prediction(self, request, claims):
"""
Run a SMARTCyp prediction for a molecule
:param request:
:param claims:
:return:
"""
# Validate input path_file object for mol
ligand_file = mol_validate_file_object(request['ligand_file'])
# Run smartcyp
base_dir = os.environ.get('BASE_WORK_DIR', request.get('base_work_dir'))
smartcyp = SmartCypRunner(log=self.log, base_work_dir=base_dir)
result_dict = smartcyp.run(ligand_file['content'],
is_smiles=ligand_file['extension'] == 'smi',
output_format=request['output_format'],
noempcorr=request['noempcorr'])
# Remove temporary working directory
smartcyp.delete()
result_dict['status'] = 'completed' if result_dict['result'] is not None else 'failed'
return result_dict
def smartcyp_prediction(ligand_file=None,
smiles=None,
output_format='json',
noempcorr=False,
output_png=False):
"""
Run a REST based SMARTCyp prediction for a molecule
:param ligand_file: molecule to make prediction for
:type ligand_file: :py:str
:param smiles: molecule as SMILES or InChI string
:type smiles: :py:str
:param output_format: output format as CSV, JSON or HTML
:type output_format: :py:str
:param noempcorr: do not use the empirical N-oxidation correction
(smartcyp >= v2.3)
:type noempcorr: :py:bool
:param output_png: export PNG image files for the prediction
:return: SMARTCyp results as JSON, CSV or HTML
:rtype: :py:str
"""
# Input molecule is either a SMILES/InChI string or file object
path_file_object = {
'content': smiles,
'extension': 'smi' if smiles else None,
'path': None
}
if isinstance(ligand_file, FileStorage):
path_file_object['content'] = ligand_file.read().decode('utf-8')
if '.' in os.path.basename(ligand_file.filename):
path_file_object['extension'] = ligand_file.filename.split('.')[-1]
path_file_object['path'] = ligand_file.filename
if path_file_object['content'] is None:
return "Ligand input from file 'mol' or as 'smiles' string required", 401
# Validate path_file_object: valid SMILES or InChI strings
path_file_object = mol_validate_file_object(path_file_object)
# Run SMARTCyp
smartcyp = SmartCypRunner()
try:
result_dict = smartcyp.run(
path_file_object['content'],
is_smiles=path_file_object['extension'] == 'smi',
input_format=path_file_object.get('extension', 'mol2'),
output_format=output_format,
noempcorr=noempcorr,
output_png=output_png)
except Exception as e:
return str(e), 500
finally:
smartcyp.delete()
return result_dict
def som_prediction(self, request, claims):
"""
Run a REST based SOM prediction run
"""
# Validate input path_file object for protein and ligand file
ligand_file = mol_validate_file_object(request['ligand_file'])
# Run combined structure/reactivity prediction
base_dir = os.environ.get('BASE_WORK_DIR', request.get('base_work_dir'))
sompred = CombinedPrediction(base_work_dir=base_dir, **request)
prediction = sompred.run(ligand_file, filter_clusters=request['filter_clusters'])
if prediction:
return {'status': 'completed', 'output': prediction}
self.log.error('SOM prediction failed')
return {'status': 'failed'}
def spores_run(self, request, claims):
"""
Perform a SPORES (Structure PrOtonation and REcognition System) structure preparation.
For a detail description of the input see the file:
schemas/endpoints/spores-request.v1.json
"""
# Validate input path_file object for mol
mol = mol_validate_file_object(request['mol'])
spores = SporesRunner(log=self.log, base_work_dir=os.environ.get('BASE_WORK_DIR', request.get('base_work_dir')))
try:
result_dict = spores.run(mol['content'], mode=request['spores_mode'], input_format=request['input_format'])
except Exception as e:
self.log.error(str(e))
return {'status': 'failed'}
finally:
spores.delete()
return {'status': 'completed', 'result': result_dict}