def atoms(xray_structure, short_sfac):
if (short_sfac):
celcon = calculate_cell_content(xray_structure).keys()
lines = []
l = lines.append
i = 0
for scatterer in xray_structure.scatterers():
i += 1
lbl = scatterer.scattering_type + str(i)
if (short_sfac):
sfac = celcon.index(scatterer.scattering_type) + 1
else:
sfac = i
coor = []
for x in scatterer.site:
coor.append(NOFIX(x))
coor = dot6fdot_list(coor)
sof = NOFIX(scatterer.weight())
if (not scatterer.flags.use_u_aniso()):
l("%-4s %d %s %s %s" % (lbl, sfac, coor, dot6gdot(sof),
dot6gdot(NOFIX(scatterer.u_iso))))
else:
u = adptbx.u_star_as_u_cif(xray_structure.unit_cell(),
scatterer.u_star)
u_fix = []
for c in u:
u_fix.append(NOFIX(c))
u = u_fix
l("%-4s %d %s %s %s =" %
(lbl, sfac, coor, dot6gdot(sof), dot6gdot_list(u[:2])))
l(" %s" % dot6gdot_list((u[2], u[5], u[4], u[3])))
return lines
def atoms(xray_structure, short_sfac):
if (short_sfac):
celcon = calculate_cell_content(xray_structure).keys()
lines = []
l = lines.append
i = 0
for scatterer in xray_structure.scatterers():
i += 1
lbl = scatterer.scattering_type + str(i)
if (short_sfac):
sfac = celcon.index(scatterer.scattering_type) + 1
else:
sfac = i
coor = []
for x in scatterer.site: coor.append(NOFIX(x))
coor = dot6fdot_list(coor)
sof = NOFIX(scatterer.weight())
if (not scatterer.flags.use_u_aniso()):
l("%-4s %d %s %s %s" % (lbl, sfac, coor, dot6gdot(sof),
dot6gdot(NOFIX(scatterer.u_iso))))
else:
u = adptbx.u_star_as_u_cif(xray_structure.unit_cell(), scatterer.u_star)
u_fix = []
for c in u: u_fix.append(NOFIX(c))
u = u_fix
l("%-4s %d %s %s %s =" % (lbl, sfac, coor, dot6gdot(sof),
dot6gdot_list(u[:2])))
l(" %s" % dot6gdot_list((u[2], u[5], u[4], u[3])))
return lines
def atoms(lapp, sfac_indices, xray_structure, encoded_sites):
spis = xray_structure.special_position_indices()
if (encoded_sites is None):
enc_dict = {}
else:
assert len(encoded_sites) == spis.size()
enc_dict = dict(zip(spis, encoded_sites))
ss = xray_structure.space_group_info().structure_seminvariants()
if (ss.number_of_continuous_allowed_origin_shifts() == 0):
caosh_flags = None
caosh_i_sc = None
else:
assert ss.continuous_shifts_are_principal()
caosh_flags = ss.principal_continuous_shift_flags()
reg = xray_structure.scattering_type_registry()
w_max = None
for i_sc,sc in enumerate(xray_structure.scatterers()):
gaussian = reg.gaussian(sc.scattering_type)
w = abs(sc.weight() * gaussian.at_stol(0))
if (w_max is None or w_max < w):
w_max = w
caosh_i_sc = i_sc
assert w_max is not None
for i_sc,sc in enumerate(xray_structure.scatterers()):
st = sc.scattering_type
lbl = "%s%02d" % (st, i_sc+1)
sfac = sfac_indices[st]
enc_site = enc_dict.get(i_sc)
coor = []
if (caosh_i_sc is None or i_sc != caosh_i_sc):
if (enc_site is None):
for x in sc.site: coor.append(NOFIX(x))
else:
coor = enc_site
else:
if (enc_site is None):
for x,f in zip(sc.site, caosh_flags):
if (f): fix = FIX
else: fix = NOFIX
coor.append(fix(x))
else:
for x,f in zip(enc_site, caosh_flags):
if (f):
coor.append(FIX(x))
else:
coor.append(x)
coor = dot6fdot_list(coor)
sof = FIX(sc.weight())
if (not sc.flags.use_u_aniso()):
lapp("%-4s %d %s %s %s" % (lbl, sfac, coor, dot6gdot(sof),
dot6gdot(NOFIX(sc.u_iso))))
else:
u = adptbx.u_star_as_u_cif(xray_structure.unit_cell(), sc.u_star)
u_fix = []
for c in u: u_fix.append(NOFIX(c))
u = u_fix
lapp("%-4s %d %s %s %s =" % (lbl, sfac, coor, dot6gdot(sof),
dot6gdot_list(u[:2])))
lapp(" %s" % dot6gdot_list((u[2], u[5], u[4], u[3])))
def write_shelx76_ls(
f_obs,
xray_structure,
titl=None,
l_s_parameters="0",
fvars=None,
encoded_sites=None):
assert xray_structure.scatterers().size() > 0
assert (fvars is None) == (encoded_sites is None)
lines = []
lapp = lines.append
if (titl is None):
titl = str(xray_structure.space_group_info())
lapp("TITL " + titl)
lapp("CELL 0.7 " + dot6gdot_list(xray_structure.unit_cell().parameters()))
s = StringIO()
LATT_SYMM(s, xray_structure.space_group(), decimal=True)
lapp(s.getvalue()[:-1])
sfac_indices = sfac_unit(lapp, xray_structure)
if (fvars is None):
lapp("FVAR 1.0")
else:
for fv in fvars:
lapp("FVAR %.6f" % fv)
lapp("L.S. %s" % l_s_parameters)
atoms(lapp, sfac_indices, xray_structure, encoded_sites)
HKLF(lapp, f_obs, skip_zeros=True)
lapp("END")
print >> open("tmp.ins", "w"), "\n".join(lines)
def run_shelx(shelx_titl, structure_factors, short_sfac=False, verbose=0):
run_shelx.counter += 1
xray_structure = structure_factors.xray_structure()
assert xray_structure.scatterers().size() > 0
pre_check(xray_structure)
f_calc = structure_factors.f_calc()
lines = []
l = lines.append
l("TITL " + shelx_titl)
l("CELL 1.0 " + dot6gdot_list(xray_structure.unit_cell().parameters()))
l("ZERR 1 0.01 0.01 0.01 0 0 0")
s = StringIO()
LATT_SYMM(s, xray_structure.space_group())
l(s.getvalue()[:-1])
lines += SFAC_DISP_UNIT(xray_structure, short_sfac)
l("FVAR 1.")
l("L.S. 1")
l("BLOC 0")
l("SPEC -0.1")
l("WPDB 2")
lines += atoms(xray_structure, short_sfac)
HKLF(l, f_calc)
with open("tmp%02d.ins" % run_shelx.counter, "w") as f:
for l in lines:
if (0 or verbose): print l
f.write(l + "\n")
sys.stdout.flush()
sys.stderr.flush()
try:
os.unlink("tmp%02d.lst" % run_shelx.counter)
except KeyboardInterrupt:
raise
except Exception:
pass
shelxl_out = easy_run.fully_buffered(command="shelxl tmp%02d" % run_shelx.counter) \
.raise_if_errors() \
.stdout_lines
if (0 or verbose):
for l in shelxl_out:
print l
sys.stderr.flush()
with open("tmp%02d.lst" % run_shelx.counter, "r") as f:
shelx_lst = f.readlines()
with open("tmp%02d.pdb" % run_shelx.counter, "r") as f:
shelx_pdb = f.readlines()
if (0 or verbose):
for l in shelx_lst:
print l[:-1]
sys.stdout.flush()
check_r1(f_calc, shelx_lst, verbose)
check_anisou(shelx_titl, xray_structure, shelx_pdb, verbose)
def run_shelx(shelx_titl, structure_factors, short_sfac=False, verbose=0):
xray_structure = structure_factors.xray_structure()
assert xray_structure.scatterers().size() > 0
pre_check(xray_structure)
f_calc = structure_factors.f_calc()
lines = []
l = lines.append
l("TITL " + shelx_titl)
l("CELL 1.0 " + dot6gdot_list(xray_structure.unit_cell().parameters()))
l("ZERR 1 0.01 0.01 0.01 0 0 0")
s = StringIO()
LATT_SYMM(s, xray_structure.space_group())
l(s.getvalue()[:-1])
lines += SFAC_DISP_UNIT(xray_structure, short_sfac)
l("FVAR 1.")
l("L.S. 1")
l("BLOC 0")
l("SPEC -0.1")
l("WPDB 2")
lines += atoms(xray_structure, short_sfac)
HKLF(l, f_calc)
f = open("tmp.ins", "w")
for l in lines:
if (0 or verbose): print l
f.write(l + "\n")
f.close()
sys.stdout.flush()
sys.stderr.flush()
try: os.unlink("tmp.lst")
except KeyboardInterrupt: raise
except Exception: pass
shelxl_out = easy_run.fully_buffered(command="shelxl tmp") \
.raise_if_errors() \
.stdout_lines
if (0 or verbose):
for l in shelxl_out: print l
f = open("tmp.lst", "r")
shelx_lst = f.readlines()
f.close()
sys.stderr.flush()
f = open("tmp.pdb", "r")
shelx_pdb = f.readlines()
f.close()
sys.stderr.flush()
if (0 or verbose):
for l in shelx_lst: print l[:-1]
sys.stdout.flush()
check_r1(f_calc, shelx_lst, verbose)
check_anisou(shelx_titl, xray_structure, shelx_pdb, verbose)