def main():
args = parse_args()
try:
os.makedirs(args.directory)
except OSError:
pass
structure = Structure.fromfile(args.structure).reorder()
for residue in structure.extract('record',"ATOM").extract(
'resn', "HOH","!=").residue_groups:
altlocs = sorted(list(set(residue.altloc)))
resi = residue.resi[0]
chainid = residue.chain[0]
tot_rmsd = 0.0
numlocs = 0
if len(altlocs) > 1:
try:
altlocs.remove('')
except ValueError:
pass
for altloc in altlocs:
conf1 = residue.extract('altloc',altloc)
for altloc2 in altlocs:
if altloc != altloc2:
conf2 = residue.extract('altloc',altloc2)
rmsd = conf1.rmsd(conf2)
tot_rmsd += rmsd
numlocs += 1
if numlocs > 0:
print(resi,chainid,round(tot_rmsd/numlocs,2),len(altlocs))
else:
print(resi,chainid,0.0,len(altlocs))
def main():
args = parse_args()
try:
structure = Structure.fromfile(args.structure)
except Exception as e:
raise type(
e)('qFit requires a valid structure file, but could not find one'
) from e
ligands = structure.extract('record', 'HETATM')
max_lig = 0
lig_name = None
for chain in np.unique(ligands.chain):
ligand2 = ligands.extract('chain', chain, '==')
for ligand_name in list(set(ligand2.resn)):
if ligand_name not in known_ligands:
ligand = ligand2.extract('resn', ligand_name, '==')
mask = ligand.e != 'H'
if len(mask) >= 10:
if len(ligand.name[mask]) > max_lig:
max_lig = len(ligand.name[mask])
lig_name = ligand_name
if lig_name:
with open('args.pdb' + '_ligand_name.txt', 'w') as file:
file.write(lig_name)
def main():
args = parse_args()
structure = Structure.fromfile(args.structure)
structure_resi = structure.extract('resn', args.lig_name)
chain = np.unique(structure_resi.chain)
resi = np.unique(structure_resi.resi)
chain2 = ' '.join(map(str, chain))
resi2 = ' '.join(map(str, resi))
with open(args.lig_name + '_chain_resi.txt', 'w') as file:
file.write(chain2 + ',' + resi2)
def main():
args = parse_args()
print(args)
try:
os.mkdir(args.directory)
except OSError:
pass
# Load structure and prepare it
apo_structure = Structure.fromfile(
args.apo_structure).reorder() #put H20 on the bottom
print(apo_structure)
apo_structure = apo_structure.extract('e', 'H', '!=')
holo_structure = Structure.fromfile(
args.holo_structure).reorder() #put H20 on the bottom
holo_structure = holo_structure.extract('e', 'H', '!=')
options_multi = QFitMultiResOptions()
options_multi.apply_command_args(args)
time0 = time.time()
sub_structure = QFitMultiResidue(holo_structure, apo_structure,
options_multi)
substructure = sub_structure.run()
print(f"Total time: {time.time() - time0}s")
def _main():
# Collect and act on arguments
# (When args==None, argparse will default to sys.argv[1:])
argparser = _build_argparser()
cmdline_args = argparser.parse_args(args=None)
try:
os.mkdir(cmdline_args.directory)
except OSError:
pass
# Run main script
get_metrics(Structure.fromfile(cmdline_args.structure).reorder())
def get_metrics(structure: Structure) -> None:
"""Calculate RMSF by residue and altloc.
Iterate through altlocs of each residue,
reporting mean heavy-atom RMSD from all other altlocs of the residue."""
# Print a column header
print("resi", "chain", "residue_altloc_rmsd", "n_altlocs")
for residue in (
structure.extract('record', "ATOM") # Don't analyse metals/ligands
.extract('resn', "HOH", "!=") # Don't analyse waters
.extract(
'name', "H", "!="
) # Sometimes backbone N-H atoms are present in some altlocs, not all. Avoid analysing them.
.extract(
'e', "H", "!="
) # Sometimes His protonation states differ between altlocs. Avoid analysing all H.
).residue_groups:
altlocs = sorted(list(set(residue.altloc)))
resi = residue.resi[0]
chainid = residue.chain[0]
# Guard: if there's only 1 altloc at this residue...
if len(altlocs) == 1:
print(resi, chainid, 0., len(altlocs))
continue
try:
altlocs.remove(
'') # Remove the 'common backbone' from analysis, if present
except ValueError:
pass
for altloc1, remaining_altlocs in pivot_and_remainder(altlocs):
conf1 = residue.extract('altloc', altloc1)
tot_rmsd: float = 0.
numlocs: int = 0
for altloc2 in remaining_altlocs:
conf2 = residue.extract('altloc', altloc2)
tot_rmsd += conf1.rmsd(conf2)
numlocs += 1
try:
avg_rmsd: float = tot_rmsd / numlocs
except ZeroDivisionError:
avg_rmsd = 0.
print(resi, chainid, round(avg_rmsd, 2), len(altlocs))
p.add_argument("-d", "--directory", help="Directory where results are stored.")
p.add_argument("-p",
"--nprocessors",
type=int,
default=1,
help="Number of processors to run.")
p.add_argument(
'-bb',
'--backbone',
action='store_true',
help="Sample backbone locally using inverse kinematics null space sampling."
)
args = p.parse_args()
s = Structure.fromfile(args.structure)
run_dirs = []
selections = []
for chain in s.chains:
chainid = chain.chain[0]
conformer = chain.conformers[0]
for residue in conformer.residues:
resseq, icode = residue.id
sel = f'{chainid},{resseq}'
if icode:
sel += f':{icode}'
run_dir = os.path.join(args.directory, f'{chainid}_{resseq}{icode}')
run_dirs.append(run_dir)
selections.append(sel)