def screen_molecules(screener, mols_to_screen, activity, conformers_dir,
output_name):
"""Run the ligand screener and write out the screened conformations.
Return sorted list of ranked scores.
:param screener:
:param mols_to_screen: Screening set
:param activity: 1 if the molecule is active, 0 if it's a decoy
:param nconformers: Number of conformers to screen for each molecule in screening set
:param nthreads: Number of threads on which to run the conformer generation
:param output_name: File name for the result molecules
:return: sorted list of ranked scores
"""
screen_set = [m for m in MoleculeReader(mols_to_screen)
] ### Read the molecules to screen
scores = []
molwriter = MoleculeWriter(output_name)
for mol in screen_set:
mol_id = mol.identifier
list_of_conformers_files = read_mol2_file(conformers_dir)
for conformers_file in list_of_conformers_files:
if conformers_file.startswith(mol_id):
print(conformers_file)
conformers_file_path = os.path.join(conformers_dir,
conformers_file)
print(conformers_file_path)
conformers = [[
x for x in MoleculeReader(conformers_file_path)
]]
print(type(conformers))
print("yeah!!!!!! start screening")
res = screener.screen(conformers) # Screening step
scores.extend([(r.score, activity, r.identifier) for r in res])
# Write results
for r in res:
molwriter.write(r.molecule)
molwriter.close()
return sorted(scores)
def screen_molecules(screener, mols_to_screen, activity, nconformers,
output_name):
"""Run the ligand screener and write out the screened conformations.
Return sorted list of ranked scores.
:param screener:
:param mols_to_screen: Screening set
:param activity: 1 if the molecule is active, 0 if it's a decoy
:param nconformers: Number of conformers to screen for each molecule in screening set
:param nthreads: Number of threads on which to run the conformer generation
:param output_name: File name for the result molecules
:return: sorted list of ranked scores
"""
screen_set = [m for m in MoleculeReader(mols_to_screen)
] ### Read the molecules to screen
scores = []
molwriter = MoleculeWriter(output_name)
for mol in screen_set:
# If nconformers=0 the input conformation is used, otherwise the CSD-driven conformer
# generator is called and a number of conformations equal to nconformers is generated.
if nconformers == 0:
confs = [[standardise(mol)]]
else:
try:
confs = generate_confs(mol, nconformers, nthreads)
except:
confs = [[standardise(mol)]]
res = screener.screen(confs) # Screening step
scores.extend([(r.score, activity, r.identifier) for r in res])
# Write results
for r in res:
molwriter.write(r.molecule)
molwriter.close()
return sorted(scores)