def exercise_get_atom_selections (verbose=False) :
pdb_in = """\
CRYST1 15.000 15.000 15.000 90.00 90.00 90.00 P 212121
HETATM 115 O HOH A 18 3.000 5.000 5.000 1.00 10.00 O
HETATM 115 O HOH A 19 5.000 5.000 8.000 1.00 10.00 O
HETATM 115 O HOH A 20 5.000 5.000 8.000 1.00 10.00 O
END"""
log = null_out()
if (verbose) :
log = sys.stdout
processed_pdb_files_srv = utils.process_pdb_file_srv(log=log)
processed_pdb_file, pdb_inp = processed_pdb_files_srv.process_pdb_files(
raw_records=pdb_in.splitlines())
selections1 = utils.get_atom_selections(
all_chain_proxies=processed_pdb_file.all_chain_proxies,
xray_structure=processed_pdb_file.xray_structure(),
selection_strings=["resseq 18", "resseq 19", "resseq 20"],
parameter_name="refine.occupancy")
try :
selections2 = utils.get_atom_selections(
all_chain_proxies=processed_pdb_file.all_chain_proxies,
xray_structure=processed_pdb_file.xray_structure(),
selection_strings=["resseq 18:19", "resseq 19:20"],
parameter_name="refine.occupancy")
except Sorry, s :
assert (str(s) == """\
One or more overlapping selections for refine.occupancy:
resseq 18:19
resseq 19:20""")
def exercise_get_atom_selections(verbose=False):
pdb_in = """\
CRYST1 15.000 15.000 15.000 90.00 90.00 90.00 P 212121
HETATM 115 O HOH A 18 3.000 5.000 5.000 1.00 10.00 O
HETATM 115 O HOH A 19 5.000 5.000 8.000 1.00 10.00 O
HETATM 115 O HOH A 20 5.000 5.000 8.000 1.00 10.00 O
END"""
log = null_out()
if (verbose):
log = sys.stdout
model = mmtbx.model.manager(
model_input = iotbx.pdb.input(lines=pdb_in.splitlines(), source_info=None),
process_input = True)
processed_pdb_files_srv = utils.process_pdb_file_srv(log=log)
processed_pdb_file, pdb_inp = processed_pdb_files_srv.process_pdb_files(
raw_records=pdb_in.splitlines())
selections1 = utils.get_atom_selections(
model = model,
selection_strings=["resseq 18", "resseq 19", "resseq 20"],
parameter_name="refine.occupancy")
try :
selections2 = utils.get_atom_selections(
model = model,
selection_strings=["resseq 18:19", "resseq 19:20"],
parameter_name="refine.occupancy")
except Sorry, s :
assert (str(s) == """\
One or more overlapping selections for refine.occupancy:
resseq 18:19
resseq 19:20""")
def __init__(self,
start_pdb,
target_I,
ntotal,
nmodes,
max_rmsd,
backbone_scale,
prefix,
weight='i',
method='rtb',
log='tmp.log'):
self.counter = 0
self.nmode_init = ntotal
self.method = method
self.nmodes = nmodes
self.topn = 10
self.Niter = 0
self.modes = flex.int(range(self.nmode_init)) + 7
self.cutoff = 8
self.weighted = True
self.log = open(log, 'w')
self.chi = open(prefix + '.chi', 'w')
pdb_inp = pdb.input(file_name=start_pdb)
crystal_symmetry = pdb_inp.xray_structure_simple().\
cubic_unit_cell_around_centered_scatterers(
buffer_size = 10).crystal_symmetry()
self.pdb_processor = process_pdb_file_srv(
crystal_symmetry=crystal_symmetry)
self.expt = saxs_read_write.read_standard_ascii_qis(target_I)
self.q = self.expt.q
self.expt_I = self.expt.i
self.expt_s = self.expt.s
if (self.q.size() > 100):
self.q = self.interpolation(self.q, n_pts=30)
self.expt_I = flex.linear_interpolation(self.expt.q, self.expt.i,
self.q)
self.expt_s = flex.linear_interpolation(self.expt.q, self.expt.s,
self.q)
#if( weight=='i'):
self.expt_s = self.expt_I
for aa, bb, cc in zip(self.q, self.expt_I, self.expt_s):
print aa, bb, cc
start_name = start_pdb
self.pdb = PDB(start_name, method=self.method)
self.she_engine = she.she(start_name, self.q)
self.natom = self.pdb.natm
self.scale_factor = backbone_scale
self.pdb.Hessian(self.cutoff, self.nmode_init, self.scale_factor)
self.root = prefix
self.scale = 0
self.drmsd = max_rmsd
if (self.method == 'rtb'):
self.drmsd = self.drmsd * 2
self.Rmax2 = self.natom * (self.drmsd)**2.0
self.step_size = sqrt(self.Rmax2 / self.nmodes) * 6.0
self.new_indx = flex.int(range(self.natom))
self.stop = False
self.minscore = 1e20
self.minDev = 0 #minimum deviations of refined structures, compared to refined structure from the previous step
self.optNum = 1 #number of iterations between geometry optimization
### set running env for pulchra ###
import libtbx.env_config
env = libtbx.env_config.unpickle()
self.pulchra = env.build_path + '/pulchra/exe/pulchra'
self.iterate()
self.log.close()
self.chi.close()
def __init__(self,
start_pdb,
target_I,
max_rmsd,
backbone_scale,
prefix,
nstep_per_cycle=100,
method='ca',
weight='i',
log='tmp.log'):
self.counter = 0
self.topn = 3
self.Niter = 0
self.method = method
self.cutoff = 12
self.log = open(log, 'w')
self.nstep_per_cycle = nstep_per_cycle
self.pdb_obj = PDB(start_pdb, method=self.method)
crystal_symmetry = self.pdb_obj.pdbi.xray_structure_simple().\
cubic_unit_cell_around_centered_scatterers(
buffer_size = 10).crystal_symmetry()
self.pdb_processor = process_pdb_file_srv(
crystal_symmetry=crystal_symmetry)
self.expt = saxs_read_write.read_standard_ascii_qis(target_I)
self.q = self.expt.q
self.expt_I = self.expt.i
self.expt_s = self.expt.s
if (self.q.size() > 20):
self.q = self.interpolation(self.q, n_pts=20)
self.expt_I = flex.linear_interpolation(self.expt.q, self.expt.i,
self.q)
self.expt_s = flex.linear_interpolation(self.expt.q, self.expt.s,
self.q)
if (weight == 'i'):
self.expt_s = flex.sqrt(self.expt_I)
self.time_nm = 0
self.time_she = 0
self.she_engine = she.she(start_pdb, self.q)
self.natom = self.pdb_obj.natm
self.nbeads = self.pdb_obj.n_block
self.scale_factor = backbone_scale
time1 = time.time()
self.time_nm += (time.time() - time1)
self.root = prefix
self.drmsd = max_rmsd
self.step_size = self.drmsd * 3
self.threshold = self.drmsd**2.0
self.new_indx = flex.int(range(self.natom))
self.stop = False
self.minscore = 1e20
self.minDev = 0 #minimum deviations of refined structures, compared to refined structure from the previous step
self.optNum = 10 #number of iterations between geometry optimization
#self.estimate_init_weight()
#self.restraint_weight *= 8 ## contribute 8x of chi initially
self.iterate()
self.log.close()
print "time used for NM : %d" % self.time_nm
print "time used for she: %d" % self.time_she
def __init__(self,
start_pdb,
target_I,
ntotal,
nmodes,
max_rmsd,
backbone_scale,
prefix,
weight='i',
method='rtb',
log='tmp.log'):
self.counter = 0
self.nmode_init = ntotal
self.nmodes = 3 #nmodes
self.method = method
self.topn = 3
self.Niter = 0
self.modes = flex.int(range(self.nmode_init)) + 7
self.cutoff = 12
self.weighted = True
self.log = open(log, 'w')
pdb_inp = pdb.input(file_name=start_pdb)
crystal_symmetry = pdb_inp.xray_structure_simple().\
cubic_unit_cell_around_centered_scatterers(
buffer_size = 10).crystal_symmetry()
# uc=cctbx.uctbx.unit_cell("300,300,300,90,90,90")
# crystal_symmetry=cctbx.crystal.symmetry(uc, 'P1')
self.pdb_processor = process_pdb_file_srv(
crystal_symmetry=crystal_symmetry)
self.expt = saxs_read_write.read_standard_ascii_qis(target_I)
self.q = self.expt.q
self.expt_I = self.expt.i
self.expt_s = self.expt.s
if (self.q.size() > 50):
self.q = self.interpolation(self.q, n_pts=50)
self.expt_I = flex.linear_interpolation(self.expt.q, self.expt.i,
self.q)
self.expt_s = flex.linear_interpolation(self.expt.q, self.expt.s,
self.q)
if (weight == 'i'):
self.expt_s = self.expt_I
self.time_nm = 0
self.time_she = 0
start_name = start_pdb
self.pdb = PDB(start_name, method=self.method)
self.she_engine = she.she(start_name, self.q)
self.natom = self.pdb.natm
self.scale_factor = backbone_scale
time1 = time.time()
self.nmode = self.pdb.Hessian(self.cutoff, self.nmode_init,
self.scale_factor)
self.time_nm += (time.time() - time1)
self.root = prefix
self.drmsd = max_rmsd
self.Rmax2 = self.natom * (self.drmsd)**2.0
self.step_size = sqrt(self.Rmax2 / self.nmodes) * 5.0
self.new_indx = flex.int(range(self.natom))
self.stop = False
self.minscore = 1e20
self.minDev = 0 #minimum deviations of refined structures, compared to refined structure from the previous step
self.optNum = 10 #number of iterations between geometry optimization
self.iterate()
self.log.close()
print "time used for NM : %d" % self.time_nm
print "time used for she: %d" % self.time_she
