def create_DRY_cvs(normalize=True):
active_traj = utils.load_pdb("3p0g")
inactive_traj = utils.load_pdb("2rh1")
q = "chainid 0 and protein and (resSeq 130 to 132)"
active_DRY_rmsd = RmsdCV("rmsd-active-DRY", active_traj, q)
inactive_DRY_rmsd = RmsdCV("rmsd-inactive-DRY", inactive_traj, q)
if normalize:
active_DRY_rmsd.normalize(trajs=[active_traj, inactive_traj])
inactive_DRY_rmsd.normalize(trajs=[active_traj, inactive_traj])
return active_DRY_rmsd, inactive_DRY_rmsd
def create_loose_coupling_cvs(normalize=True):
active_traj = utils.load_pdb("3p0g")
inactive_traj = utils.load_pdb("2rh1")
ligand_cv = LigandBindingCV(active_traj)
connector_cv = ConnectorRegionCV(active_traj, inactive_traj)
gprotein_cv = CADistanceCv("helix_63_dist(CA)", 131, 272)
if normalize:
ligand_cv.normalize(trajs=[active_traj, inactive_traj])
connector_cv.normalize(trajs=[active_traj, inactive_traj])
gprotein_cv.normalize(trajs=[active_traj, inactive_traj])
return ligand_cv, connector_cv, gprotein_cv
def create_5cvs(normalize=True, pbc=True):
cvs = np.array([
CADistanceCv("ALA76-CYS327", 76, 327, pbc),
CADistanceCv("GLU268-LYS147", 268, 147, pbc),
CADistanceCv("CYS327-LYS147", 327, 147, pbc),
CADistanceCv("LEU115-LEU275", 115, 275, pbc),
CADistanceCv("LYS267-PHE223", 267, 223, pbc)
])
if normalize:
active_traj = utils.load_pdb("3p0g")
inactive_traj = utils.load_pdb("2rh1")
# Note that the original CVs were normalized by a FreeMD trajectory and not just the reference structures.
for cv in cvs:
cv.normalize(trajs=[active_traj, inactive_traj])
return cvs
def runSingle(self, x):
prot = x[1] # x[2] is None
prot_name = CleanName(prot[:-4])
utils.load_pdb(prot, prot_name)
rec_name = prot_name + '_R'
lig_name = prot_name + '_L'
eprint('cmd.select %s, %s & chain %s' % (
rec_name, prot_name, '+'.join(self._test_rec_chains)))
eprint('cmd.select %s, %s & chain %s' % (
lig_name, prot_name, '+'.join(self._test_lig_chains)))
cmd.select(rec_name, '%s & chain %s' %(
prot_name, '+'.join(self._test_rec_chains)))
cmd.select(lig_name, '%s & chain %s' %(
prot_name, '+'.join(self._test_lig_chains)))
rms = x[0].RMSDSep(rec_name, lig_name)
return (prot_name, rms)
def runSingle(self, x):
lig = x[1]
lig_name = CleanName(lig[:-4]) # Remove the '.pdb'
utils.load_pdb(lig, lig_name)
# One case where these come together (SwarmDock).
if x[2] == _REC_TOGETHER:
return (lig_name, x[0].RMSDTog(lig_name))
# Normal, separate function.
rec = x[2]
rec_name = CleanName(rec[:-4])
if rec_name != 'pRp':
utils.load_pdb(rec, rec_name)
rms = x[0].RMSDSep(rec_name, lig_name)
#print 'Finished, rms is %f' % rms
return (lig_name, rms)
def __init__(self, args):
utils.load_pdb(args.gold_p, 'goldp')
utils.load_pdb(args.test_p, 'testp')
eprint('goldp & chain %s' % '+'.join(args.gold_rec_chains))
cmd.create('pR', 'goldp & chain %s' % '+'.join(args.gold_rec_chains))
cmd.create('pL', 'goldp & chain %s' % '+'.join(args.gold_lig_chains))
cmd.create('pRp', 'testp & chain %s' % '+'.join(args.test_rec_chains))
cmd.create('pLp', 'testp & chain %s' % '+'.join(args.test_lig_chains))
eassert(cmd.count_atoms('pR') > 0, 'no atoms in gold:R')
eassert(cmd.count_atoms('pL') > 0, 'no atoms in gold:L')
eassert(cmd.count_atoms('pRp') > 0, 'no atoms in test:R')
eassert(cmd.count_atoms('pLp') > 0, 'no atoms in test:L')
for obj in cmd.get_names():
eprint('obj is %s' % obj)
self._gold_rec_chains = args.gold_rec_chains
self._gold_lig_chains = args.gold_lig_chains
self._test_rec_chains = args.test_rec_chains
self._test_lig_chains = args.test_lig_chains
self._test_confs = getRegexFiles(args.test_confs, args.input_fn)
def RunSingleR(obj):
rec = obj[1]
rec_name = CleanName(rec[:-4]) # Remove the '.pdb'
utils.load_pdb(rec, rec_name)
if obj[3]: # both
bound_rms = obj[0].RMSDSep(rec_name,
'pLp',
also_separate=True,
fail_on_error=False)
unbound_rms = obj[0].RMSDSepSelf(rec_name,
'pLp',
also_separate=True,
fail_on_error=False)
return [
bound_rms or [None, float('nan'), float('nan')], unbound_rms
or [None, float('nan'), float('nan')]
]
return obj[0].RMSDSep(rec_name,
obj[2],
also_separate=True,
fail_on_error=False)
def RunSingleL(obj):
lig = obj[2]
lig_name = CleanName(lig[:-4]) # Remove the '.pdb'
utils.load_pdb(lig, lig_name)
if obj[3]: # both
bound_rms = obj[0].RMSDSep('pRp',
lig_name,
also_separate=True,
fail_on_error=False)
unbound_rms = obj[0].RMSDSepSelf('pRp',
lig_name,
also_separate=True,
fail_on_error=False)
return [
bound_rms or [None, float('nan'), float('nan')], unbound_rms
or [None, float('nan'), float('nan')]
]
return obj[0].RMSDSep(obj[1],
lig_name,
also_separate=True,
fail_on_error=False)
def __init__(self, args):
# Load the proteins.
utils.load_pdb(args.gold_r, 'pR')
utils.load_pdb(args.test_r, 'pRp')
utils.load_pdb(args.gold_l, 'pL')
utils.load_pdb(args.test_l, 'pLp')
if args.prot_confs:
self._lig_confs = getRegexFiles(args.prot_confs, args.input_fn)
self._rec_confs = [_REC_TOGETHER] * len(self._lig_confs)
else:
self._lig_confs = getRegexFiles(args.lig_confs, args.input_fn)
if args.rec_confs:
self._rec_confs = getRegexFiles(args.rec_confs, args.input_fn)
else:
self._rec_confs = ['pRp.pdb'] * len(self._lig_confs)
def create_COM_distance_cv(id_prefix,
res1,
res2,
res1_atom,
res2_atom,
normalize=True):
active_traj = utils.load_pdb("3p0g")
inactive_traj = utils.load_pdb("2rh1")
if res1_atom == "CA" and res2_atom == "CA":
# Optimization
cv = CADistanceCv(id_prefix + "(CA-CA)", res1, res2)
elif res1_atom == None and res2_atom == None:
cv = COMDistanceCv(id_prefix + "(COM)",
"protein and resSeq " + str(res1),
"protein and resSeq " + str(res2))
else:
cv = COMDistanceCv(
id_prefix + "({}-{})".format(res1_atom, res2_atom),
"protein and resSeq {} and name {}".format(res1, res1_atom),
"protein and resSeq {} and name {}".format(res2, res2_atom))
if normalize:
cv.normalize(trajs=[active_traj, inactive_traj])
return cv
def get_nodes_ordering(graph, options):
if options.pdb:
res = []
pdb = load_pdb(options.pdb)
graph_nodes = set(graph.nodes())
for c in pdb.get_chains():
for r in c:
node_id = c.id + str(r.get_id()[1]) + r.get_id()[2].strip()
if node_id in graph_nodes:
res.append(node_id)
return res
else:
def nodes_ordering(x):
m = re.match("^(.)([0-9]+)(.*)$", x)
if m:
return (m.group(1), int(m.group(2)), m.group(3))
else:
return (x[0], x[1:], "")
return sorted(graph.nodes(), key=nodes_ordering)
default=False,
help='Print quite a bit of output',
action='store_true')
return parser
def main():
try:
args = get_parser().parse_args()
except SystemExit, ext:
return
# Print the output from this.
utils._VERBOSE = 1
utils.load_pdb(args.gold_r, 'pR')
utils.load_pdb(args.test_r, 'pRp')
utils.load_pdb(args.gold_l, 'pL')
utils.load_pdb(args.test_l, 'pLp')
if args.verbose:
print('Using verbose output')
utils._VERBOSE = 1
else:
utils._VERBOSE = 0
alnr = PyMolAligner('pR', 'pRp', 'pL', 'pLp', args.dist)
print(alnr)
pLList = get_test_structures(args.test_l, args.test_l_files)
if len(pRList) != 0:
pRp = pRList[0]
if len(pLList) != 0:
pLp = pLList[0]
# We want to do something a bit different if --both is specified.
if args.both:
pRp = args.test_r
pLp = args.test_l
pRList = get_test_structures(None, args.test_r_files)
pLList = get_test_structures(None, args.test_l_files)
if utils._VERBOSE:
print('pRList is %d, pLList is %d' % (len(pRList), len(pLList)))
utils.load_pdb(pR, 'pR')
utils.load_pdb(pRp, 'pRp')
utils.load_pdb(pL, 'pL')
utils.load_pdb(pLp, 'pLp')
alnr = PyMolAligner('pR', 'pRp', 'pL', 'pLp', args.dist)
# Test with a single one because Pool hides traceback.
if utils._VERBOSE:
if len(pRList) != 0:
rms = RunSingleR((alnr, pRList[0], 'pLp', args.both))
prot = pRList[0]
else:
rms = RunSingleL((alnr, 'pRp', pLList[0], args.both))
prot = pLList[0]
if rms:
def convert_parameters(
source_directory="original/",
source_crd="full.crds",
source_top="full.topo",
destination_directory="generated/",
destination_crd="smirnoff.inpcrd",
destination_top="smirnoff.prmtop",
host_resname="MGO",
guest_resname="BAM",
atom_mapping=None,
residue_mapping=None,
):
create_pdb_with_conect(
solvated_pdb=source_directory + source_crd,
amber_prmtop=source_directory + source_top,
output_pdb=destination_directory + "full.pdb",
)
prune_conect(input_pdb="full.pdb",
output_pdb="full_conect.pdb",
path=destination_directory)
components = split_topology(file_name=destination_directory + "full.pdb")
hg_topology = create_host_guest_topology(components,
host_resname=host_resname,
guest_resname=guest_resname)
create_host_mol2(
solvated_pdb=destination_directory + "full.pdb",
amber_prmtop=source_directory + source_top,
mask=host_resname,
output_mol2=destination_directory + host_resname + ".mol2",
)
convert_mol2_to_sybyl_antechamber(
input_mol2=destination_directory + host_resname + ".mol2",
output_mol2=destination_directory + host_resname + "-sybyl.mol2",
ac_doctor=True,
)
host = load_mol2(
filename=destination_directory + host_resname + "-sybyl.mol2",
name=host_resname,
add_tripos=True,
)
guest = load_mol2(
filename=source_directory + guest_resname.lower() + ".mol2",
name=guest_resname,
add_tripos=False,
)
check_unique_atom_names(host)
check_unique_atom_names(guest)
molecules = [host, guest]
ff = ForceField("forcefield/smirnoff99Frosst.ffxml")
system = ff.createSystem(
hg_topology.topology,
molecules,
nonbondedCutoff=1.1 * unit.nanometer,
ewaldErrorTolerance=1e-4,
)
hg_structure = pmd.openmm.topsystem.load_topology(hg_topology.topology,
system,
hg_topology.positions)
check_bond_lengths(hg_structure, threshold=4)
try:
hg_structure.save(destination_directory + "hg.prmtop")
except OSError:
logging.warning(
"Check if the host-guest parameter file already exists...")
try:
hg_structure.save(destination_directory + "hg.inpcrd")
except OSError:
logging.warning(
"Check if the host-guest coordinate file already exists...")
extract_water_and_ions(
amber_prmtop=source_directory + source_top,
amber_inpcrd=source_directory + source_crd,
host_residue=":" + host_resname,
guest_residue=":" + guest_resname,
dummy=None,
output_pdb=destination_directory + "water_ions.pdb",
)
create_water_and_ions_parameters(
input_pdb="water_ions.pdb",
output_prmtop="water_ions.prmtop",
output_inpcrd="water_ions.inpcrd",
dummy_atoms=True,
path=destination_directory,
)
water_and_ions = pmd.amber.AmberParm(
destination_directory + "water_ions.prmtop",
xyz=destination_directory + "water_ions.inpcrd",
)
merged = mergeStructure(hg_structure, water_and_ions)
try:
merged.save(destination_directory + destination_top)
except:
logging.warning("Check if solvated parameter file already exists...")
try:
merged.save(destination_directory + destination_crd)
except:
logging.warning("Check if solvated coordinate file already exists...")
reference = pmd.load_file(source_directory + source_top,
source_directory + source_crd)
try:
reference.save(destination_directory + "reference.pdb")
reference.save(destination_directory + "reference.mol2")
except OSError:
logging.warning("Check if file exists...")
target = pmd.load_file(destination_directory + destination_top,
destination_directory + destination_crd)
try:
target.save(destination_directory + "target.pdb")
target.save(destination_directory + "target.mol2")
except OSError:
logging.warning("Check if file exists...")
if not atom_mapping:
reference_mol = load_mol2(destination_directory + "reference.mol2")
target_mol = load_mol2(destination_directory + "target.mol2")
atom_mapping = map_atoms(reference_mol, target_mol)
if not residue_mapping:
reference_mol = load_pdb(destination_directory + "reference.pdb")
target_mol = load_pdb(destination_directory + "target.pdb")
residue_mapping = map_residues(atom_mapping, reference_mol, target_mol)
# for file in ["mini.in", "therm1.in", "therm2.in", "eqnpt.in", "mdin"]:
# rewrite_amber_input_file(
# reference_input=source_directory + file,
# target_input=destination_directory + file,
# reference_to_target_mapping=residue_mapping,
# dt_override=False,
# target_prmtop=merged,
# )
# rewrite_restraints_file(
# reference_restraints=source_directory + "disang.rest",
# target_restraints=destination_directory + "disang.rest",
# reference_to_target_mapping=atom_mapping,
# )
# For some reason, this must come last, otherwise it gets removed again
merged.box = reference.box
try:
os.remove(destination_directory + destination_top)
os.remove(destination_directory + destination_crd)
except OSError:
pass
merged.save(destination_directory + destination_crd)
merged.save(destination_directory + destination_top)
return atom_mapping, residue_mapping