def main():
parser = argparse.ArgumentParser(description='Perform chunking in preparation for dynamic undocking')
parser.add_argument('-p', '--protein', help='Apoprotein in PDB format')
parser.add_argument('-l', '--ligand', help='Ligand in mol format')
# parser.add_argument('-o', '--output', help="PDB output")
parser.add_argument('-c', '--cutoff', type=float, help='Cutoff for chunk calculation')
parser.add_argument('-b', '--ignore-buffers', action='store_true', help='Do not remove buffers (solvent, ions etc.)')
parser.add_argument('-i', '--interaction', help='Protein atom to use for ligand interaction.')
args = parser.parse_args()
# A couple of file name
orig_file = prot_file = args.protein
chunk_protein = "protein_out.pdb"
chunk_protein_prot = "protein_out_prot.pdb"
# Do the removal of buffer mols and alt locs
if not args.ignore_buffers:
prot_file = remove_prot_buffers_alt_locs(prot_file)
# Do the chunking and the protonation
chunk_with_amber(
args.ligand, prot_file, args.interaction, chunk_protein, args.cutoff, orig_file
)
# Protonate
disulfides = find_disulfides(chunk_protein)
do_tleap(chunk_protein, chunk_protein_prot, disulfides)
def run(self):
proasis_hit = ProasisHits.objects.get(crystal_name_id=self.crystal_id, refinement_id=self.refinement_id)
tmp_file = remove_prot_buffers_alt_locs(self.input().path)
shutil.move(os.path.join(os.getcwd(), tmp_file), self.output().path)
proasis_out = ProasisOut.objects.filter(proasis=proasis_hit, ligid=ligid)
for o in proasis_out:
o.stripped = self.output().path.split('/')[-1]
o.save()
def main(prot_file, mol_file, interaction, cutoff):
# A couple of file name
orig_file = prot_file
chunk_protein = "protein_out.pdb"
chunk_protein_prot = "protein_out_prot.pdb"
# Do the removal of buffer mols and alt locs
prot_file = remove_prot_buffers_alt_locs(prot_file)
# Do the chunking and the protonation
# Chunk
chunk_with_amber(mol_file, prot_file, interaction, chunk_protein, cutoff,
orig_file)
# Protontate
disulfides = find_disulfides(chunk_protein)
do_tleap(chunk_protein, chunk_protein_prot, disulfides)
def run(self):
proasis_hit = ProasisHits.objects.get(crystal_name_id=self.crystal_id,
refinement_id=self.refinement_id,
altconf=self.altconf)
proasis_out = ProasisOut.objects.get(proasis=proasis_hit,
crystal=proasis_hit.crystal_name,
ligand=self.ligand,
ligid=self.ligid)
# remove altconfs and buffers from input and save to a temporary path defined by the function
tmp_file = remove_prot_buffers_alt_locs(self.input().path)
# move the tmp file to the output path
shutil.move(os.path.join(os.getcwd(), tmp_file), self.output().path)
# save the output file to proasis_out model
proasis_out.stripped = self.output().path.split('/')[-1]
proasis_out.save()
def test_prep(mol_file, prot_file):
chunk_protein = "protein_out.pdb"
chunk_protein_prot = "protein_out_prot.pdb"
# Now it does the magic
# Chunk
removed = remove_prot_buffers_alt_locs(prot_file)
chunk_with_amber(mol_file, removed, chunk_protein, 12)
# Protontate
do_tleap(chunk_protein, chunk_protein_prot)
protein = parmed.load_file(chunk_protein_prot)
protein.write_pdb("fixed.pdb")
protein = parmed.load_file("fixed.pdb")["!(:HOH,NA,CL,SO4,EDO)"]
forcefield_str = 'amber99sb.xml'
forcefield = app.ForceField(forcefield_str)
protein_system = forcefield.createSystem(protein.topology)
protein_pmd = parmed.openmm.load_topology(protein.topology, protein_system,
protein.positions)
def clean_up_prot(pdb_file):
remove_prot_buffers_alt_locs(pdb_file)
def run_simulation(
prot_file,
mol_file,
prot_code,
prot_int,
cutoff,
init_velocity,
num_smd_cycles,
gpu_id,
md_len,
params,
):
if not os.path.isfile("equil.chk"):
# A couple of file name
orig_file = prot_file
chunk_protein = "protein_out.pdb"
chunk_protein_prot = "protein_out_prot.pdb"
# Do the removal of buffer mols and alt locs
if params.get("remove_buffers", True):
prot_file = remove_prot_buffers_alt_locs(prot_file)
# Do the chunking and the protonation
if params.get("prep_chunk", True):
# Chunk
chunk_with_amber(mol_file, prot_file, prot_int, chunk_protein,
cutoff, orig_file)
# Protontate
disulfides = find_disulfides(chunk_protein)
do_tleap(chunk_protein, chunk_protein_prot, disulfides)
else:
chunk_protein_prot = prot_file
# Paramaterize the ligand
mol2_file = params.get("mol2_file_prepped", None)
if not mol2_file:
results = prep_lig(mol_file, prot_code)
mol2_file = results[0]
prepare_system(mol2_file, chunk_protein_prot)
# Now find the interaction and save to a file
results = find_interaction(prot_int, orig_file)
startdist = params.get("distance", results[2])
# Now do the equlibration
do_equlibrate(gpu_id=gpu_id)
else:
# Now find the interaction and save to a file
results = find_interaction(prot_int, prot_file)
startdist = params.get("distance", results[2])
# Open the file and check that the potential is stable and negative
if not check_if_equlibrated("density.csv", 1):
print("SYSTEM NOT EQUILIBRATED")
sys.exit()
if params.get("just_equilib", False):
print("SYSTEM FENISHED EQULIBRATING")
return
# Now do the MD
for i in range(num_smd_cycles):
if i == 0:
md_start = "equil.chk"
else:
md_start = "md_" + str(i - 1) + ".chk"
log_file = "md_" + str(i) + ".csv"
perform_md(
md_start,
"md_" + str(i) + ".chk",
log_file,
"md_" + str(i) + ".pdb",
md_len=md_len,
gpu_id=gpu_id,
)
# Open the file and check that the potential is stable and negative
if not check_if_equlibrated(log_file, 3):
print("SYSTEM NOT EQUILIBRATED")
sys.exit()
# Now find the interaction and save to a file
run_steered_md(
300,
"md_" + str(i) + ".chk",
"smd_" + str(i) + "_300.csv",
"smd_" + str(i) + "_300.dat",
"smd_" + str(i) + "_300.pdb",
"smd_" + str(i) + "_300.dcd",
startdist,
init_velocity=init_velocity,
gpu_id=gpu_id,
)
run_steered_md(
325,
"md_" + str(i) + ".chk",
"smd_" + str(i) + "_325.csv",
"smd_" + str(i) + "_325.dat",
"smd_" + str(i) + "_325.pdb",
"smd_" + str(i) + "_325.dcd",
startdist,
init_velocity=init_velocity,
gpu_id=gpu_id,
)