def execute_gypsum_dl(contnrs, params):
"""A function for doing all of the manipulations to each molecule.
:param contnrs: A list of all molecules.
:type contnrs: list
:param params: A dictionary containing all of the parameters.
:type params: dict
"""
# Start creating the models.
# Prepare the smiles. Desalt, consider alternate ionization, tautometeric,
# stereoisomeric forms, etc.
prepare_smiles(contnrs, params)
# Convert the processed SMILES strings to 3D.
prepare_3d(contnrs, params)
# Add in name and unique id to each molecule.
add_mol_id_props(contnrs)
# Output the current SMILES.
Utils.print_current_smiles(contnrs)
# Write any mols that fail entirely to a file.
deal_with_failed_molecules(contnrs, params)
# Process the output.
proccess_output(contnrs, params)
def prepare_smiles(contnrs, params):
"""Runs the appropriate steps for processing the SMILES strings.
:param contnrs: A list of containers (MolContainer.MolContainer).
:type contnrs: list
:param params: The user parameters.
:type params: dict
"""
# Unpack some of the parameter values.
min_ph = params["min_ph"]
max_ph = params["max_ph"]
std_dev = params["pka_precision"]
max_variants_per_compound = params["max_variants_per_compound"]
thoroughness = params["thoroughness"]
num_procs = params["num_processors"]
job_manager = params["job_manager"]
let_tautomers_change_chirality = params["let_tautomers_change_chirality"]
parallelizer_obj = params["Parallelizer"]
debug = True
# Desalt the molecules. Note that the program always desalts (can't turn it
# off).
# Utils.log("Begin Desaltings")
desalt_orig_smi(contnrs, num_procs, job_manager, parallelizer_obj)
# Utils.log("Done with Desalting")
# Filter the containers to remove ones that have bad substrings (metal,
# etc.) in the desalted smiles, assuming durrant lab filter turned on. Note
# that some compounds aren't filtered until later.
if params["use_durrant_lab_filters"] == True:
contnrs = [
c for c in contnrs if not durrant_lab_contains_bad_substr(c.orig_smi_deslt)
]
if debug:
Utils.print_current_smiles(contnrs)
# Add hydrogens for user-specified pH, if requested.
if not params["skip_adding_hydrogen"]:
# Utils.log("Ionizing Molecules")
add_hydrogens(
contnrs,
min_ph,
max_ph,
std_dev,
max_variants_per_compound,
thoroughness,
num_procs,
job_manager,
parallelizer_obj,
)
# Utils.log("Done with Ionization")
else:
Utils.log("Skipping ionization")
wrap_molecules(contnrs)
if debug:
Utils.print_current_smiles(contnrs)
# Make alternate tautomeric forms, if requested.
if not params["skip_making_tautomers"]:
# Utils.log("Tautomerizing Molecules")
make_tauts(
contnrs,
max_variants_per_compound,
thoroughness,
num_procs,
job_manager,
let_tautomers_change_chirality,
parallelizer_obj,
)
# Utils.log("Done with Tautomerization")
else:
Utils.log("Skipping tautomerization")
if debug:
Utils.print_current_smiles(contnrs)
# Apply Durrant-lab filters if requested
if params["use_durrant_lab_filters"]:
# Utils.log("Applying Durrant-Lab Filters")
durrant_lab_filters(contnrs, num_procs, job_manager, parallelizer_obj)
# Utils.log("Done Applying Durrant-Lab Filters")
else:
Utils.log("Not applying Durrant-lab filters")
if debug:
Utils.print_current_smiles(contnrs)
# Make alternate chiral forms, if requested.
if not params["skip_enumerate_chiral_mol"]:
# Utils.log("Enumerating Chirality")
enumerate_chiral_molecules(
contnrs,
max_variants_per_compound,
thoroughness,
num_procs,
job_manager,
parallelizer_obj,
)
# Utils.log("Done with Chirality Enumeration")
else:
Utils.log("Skipping chirality enumeration")
if debug:
Utils.print_current_smiles(contnrs)
# Make alternate double-bond isomers, if requested.
if not params["skip_enumerate_double_bonds"]:
# Utils.log("Enumerating Double Bonds")
enumerate_double_bonds(
contnrs,
max_variants_per_compound,
thoroughness,
num_procs,
job_manager,
parallelizer_obj,
)
# Utils.log("Done with Double Bond Enumeration")
else:
Utils.log("Skipping double bond enumeration")
if debug:
Utils.print_current_smiles(contnrs)
