def prep_for_fitting(self, molecule: Ligand) -> List[str]:
"""
For the given ligand prep the input files ready for torsion profile fitting.
Args:
molecule: The molecule object that we need to prep for fitting, this should have qm reference data stored in molecule.qm_scans.
Note:
We assume we are already in the targets folder.
Returns:
A list of target folder names made by this target.
Raises:
MissingReferenceData: If the molecule does not have any torsion drive reference data saved in molecule.qm_scans.
"""
# make sure we have data
if not molecule.qm_scans:
raise MissingReferenceData(
f"Can not prepare a forcebalance fitting target for {molecule.name} as the reference data is missing!"
)
# write out the qdata and other input files for each scan
target_folders = []
# keep track of where we start
base_folder = os.getcwd()
# loop over each scanned bond and make a target folder
for scan in molecule.qm_scans:
task_name = (
f"{self.target_name}_{scan.central_bond[0]}_{scan.central_bond[1]}"
)
target_folders.append(task_name)
make_and_change_into(name=task_name)
# make the pdb topology file
if molecule.has_ub_terms():
molecule._to_ub_pdb(file_name="molecule")
else:
molecule.to_file(file_name="molecule.pdb")
# write the qdata file
export_torsiondrive_data(molecule=molecule, tdrive_data=scan)
# make the metadata
self.make_metadata(torsiondrive_data=scan)
# now move back to the base
os.chdir(base_folder)
return target_folders
def _get_prmtop(self, molecule: Ligand) -> str:
"""Method to run Antechamber, parmchk2 and tleap."""
# file paths when moving in and out of temp locations
cwd = os.getcwd()
mol2 = os.path.abspath(f"{molecule.name}.mol2")
frcmod_file = os.path.abspath(f"{molecule.name}.frcmod")
prmtop_file = os.path.abspath(f"{molecule.name}.prmtop")
inpcrd_file = os.path.abspath(f"{molecule.name}.inpcrd")
ant_log = os.path.abspath("Antechamber.log")
# Call Antechamber
# Do this in a temp directory as it produces a lot of files
with TemporaryDirectory() as temp:
os.chdir(temp)
molecule.to_file(file_name="in.sdf")
# Call Antechamber
cmd = f"antechamber -i in.sdf -fi sdf -o out.mol2 -fo mol2 -s 2 -m {molecule.multiplicity} -c bcc -nc {molecule.charge} -pf yes"
with open("ante_log.txt", "w+") as log:
sp.run(cmd, shell=True, stdout=log, stderr=log)
# Ensure command worked
try:
# Copy the gaff mol2 and antechamber file back
shutil.copy("ante_log.txt", cwd)
shutil.copy("out.mol2", mol2)
except FileNotFoundError:
os.chdir(cwd)
raise FileNotFoundError(
"Antechamber could not convert this file type; is it a valid pdb?"
)
os.chdir(cwd)
# Work in temp directory due to the amount of files made by antechamber
with TemporaryDirectory() as temp:
os.chdir(temp)
shutil.copy(mol2, "out.mol2")
# Run parmchk
with open("Antechamber.log", "a") as log:
sp.run(
f"parmchk2 -i out.mol2 -f mol2 -o out.frcmod -s {self.force_field}",
shell=True,
stdout=log,
stderr=log,
)
# Ensure command worked
if not os.path.exists("out.frcmod"):
raise FileNotFoundError(
"out.frcmod not found parmchk2 failed!")
# Now get the files back from the temp folder
shutil.copy("out.mol2", mol2)
shutil.copy("out.frcmod", frcmod_file)
shutil.copy("Antechamber.log", ant_log)
# Now we need to run tleap to get the prmtop and inpcrd files
with TemporaryDirectory() as temp:
os.chdir(temp)
shutil.copy(mol2, "in.mol2")
shutil.copy(frcmod_file, "in.frcmod")
shutil.copy(ant_log, "Antechamber.log")
# make tleap command file
with open("tleap_commands", "w+") as tleap:
tleap.write("""source oldff/leaprc.ff99SB
source leaprc.gaff
LIG = loadmol2 in.mol2
check LIG
loadamberparams in.frcmod
saveamberparm LIG out.prmtop out.inpcrd
quit""")
# Now run tleap
with open("Antechamber.log", "a") as log:
sp.run("tleap -f tleap_commands",
shell=True,
stdout=log,
stderr=log)
# Check results present
if not os.path.exists("out.prmtop") or not os.path.exists(
"out.inpcrd"):
raise FileNotFoundError(
"Neither out.prmtop nor out.inpcrd found; tleap failed!")
shutil.copy("Antechamber.log", ant_log)
shutil.copy("out.prmtop", prmtop_file)
shutil.copy("out.inpcrd", inpcrd_file)
os.chdir(cwd)
# Now give the file names to parametrisation method
prmtop = f"{molecule.name}.prmtop"
return prmtop
