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How to use get_cc method in autotest

Best Python code snippet using autotest_python

tst_composite_omit_map_2.py

Source:tst_composite_omit_map_2.py

...31ATOM     18  CA  PHE A   2       8.874  10.605   8.831  1.00 10.00           C32TER33END34"""35def get_cc(mc1, mc2, xrs):36  crystal_gridding = mc1.crystal_gridding(37    d_min             = mc1.d_min(),38    symmetry_flags    = maptbx.use_space_group_symmetry,39    resolution_factor = 0.25)40  fft_map = miller.fft_map(41    crystal_gridding     = crystal_gridding,42    fourier_coefficients = mc1)43  fft_map.apply_sigma_scaling()44  m1 = fft_map.real_map_unpadded()45  fft_map = miller.fft_map(46    crystal_gridding     = crystal_gridding,47    fourier_coefficients = mc2)48  fft_map.apply_sigma_scaling()49  m2 = fft_map.real_map_unpadded()50  assert m1.focus()==m2.focus()51  assert m1.all()==m2.all()52  sel = maptbx.grid_indices_around_sites(53    unit_cell  = mc1.unit_cell(),54    fft_n_real = m1.focus(),55    fft_m_real = m1.all(),56    sites_cart = flex.vec3_double(xrs.sites_cart()),57    site_radii = flex.double([1.5]*xrs.scatterers().size()))58  cc = flex.linear_correlation(x=m1.select(sel), y=m2.select(sel)).coefficient()59  def md(m, xrs):60    r = flex.double()61    for sf in xrs.sites_frac():62      r.append(m.eight_point_interpolation(sf))63    return flex.mean(r)64  return cc, md(m=m1, xrs=xrs), md(m=m2, xrs=xrs)65def run(args):66  pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str)67  ph = pdb_inp.construct_hierarchy()68  ph.write_pdb_file(file_name="m.pdb")69  xrs = pdb_inp.xray_structure_simple()70  sel = ph.atom_selection_cache().selection("resseq 1")71  xrs1 = xrs.select( sel)72  xrs2 = xrs.select(~sel)73  #74  F  =  xrs.structure_factors(d_min=1.5).f_calc()75  FB = xrs1.structure_factors(d_min=1.5).f_calc()76  FC =   FB.phase_transfer(phase_source=F)77  #78  mtz_dataset = abs(FB).as_mtz_dataset(column_root_label="F-obs")79  mtz_dataset.add_miller_array(miller_array=FB.generate_r_free_flags(),80    column_root_label="R-free-flags")81  mtz_object = mtz_dataset.mtz_object()82  mtz_object.write(file_name = "data.mtz")83  #84  mtz_dataset = F.as_mtz_dataset(column_root_label="f")85  mtz_dataset.add_miller_array(miller_array=FB, column_root_label="FB")86  mtz_dataset.add_miller_array(miller_array=FC, column_root_label="FC")87  mtz_dataset.add_miller_array(miller_array=abs(FB), column_root_label="FOBS")88  #89  fmodel = mmtbx.f_model.manager(f_obs = abs(FB), xray_structure = xrs)90  # mc is model biased: one should not see any density for resseq 291  mc = fmodel.electron_density_map().map_coefficients(92    map_type     = "Fo",93    isotropize   = False,94    fill_missing = False)95  #96  print(get_cc(mc1=mc, mc2=F,  xrs=xrs1), get_cc(mc1=mc, mc2=F,  xrs=xrs2))97  print(get_cc(mc1=mc, mc2=FB, xrs=xrs1), get_cc(mc1=mc, mc2=FB, xrs=xrs2))98  print(get_cc(mc1=mc, mc2=FC, xrs=xrs1), get_cc(mc1=mc, mc2=FC, xrs=xrs2))99  print()100  #101  crystal_gridding = fmodel.f_obs().crystal_gridding(102    d_min             = fmodel.f_obs().d_min(),103    symmetry_flags    = maptbx.use_space_group_symmetry,104    resolution_factor = 0.25)105  #106  oo = mmtbx.maps.composite_omit_map.run(107    crystal_gridding     = crystal_gridding,108    full_resolution_map  = False,109    fmodel               = fmodel.deep_copy(),110    box_size_as_fraction = 0.2)111  mco = oo.map_coefficients(filter_noise=False)112  print(get_cc(mc1=mco, mc2=F, xrs=xrs1), get_cc(mc1=mco, mc2=F, xrs=xrs2))113  #114  mtz_dataset.add_miller_array(miller_array=mco, column_root_label="O")115  mtz_dataset.add_miller_array(miller_array=mc, column_root_label="mc")116  #117  mtz_object = mtz_dataset.mtz_object()118  mtz_object.write(file_name = "m.mtz")119if (__name__ == "__main__"):...

drink.py

Source:drink.py

...10d = None11character().create_cc_nx(cc, 0, constitution*6, 'long', reset_to="0")12#return f'''embed -title "Test" -desc "{character().resistances}" '''13if help:14	return f'''embed -title "{name} considers getting another drink" -desc "What's one more, right?\n\n**Intoxication**\n{character().get_cc(cc)}/{character().get_cc_max(cc)}\n\n**Stage**\n{floor(character().get_cc(cc)/constitution)}/6"'''15else:16	for x in drinks:17		if args[0].lower() in x.lower():18			au += drinks[x]19			d = x20	if not d:21		return f'''embed -title "{name} drinks...something we don't sell here" -desc "Check your spelling of the drink!" '''22	au = int(au/2) if "poison" in str(character().resistances.resist) else au23	#return f'''embed -title "Test" -desc "{au}" '''24	au = int(au*2) if get('size','Medium') == "Small" or get('size','Medium') == "Tiny" else au25	#return f'''embed -title "Test" -desc "{au}" '''26	character().mod_cc(cc, au)27	cs = floor(character().get_cc(cc)/constitution)28	drunk = statlist[cs]29	if d == "Phoenix Fire":30		beakRoll = roll("1d4")31		beakd = this["Beak"][str(beakRoll)]32		if beakRoll == 1:33			dmg = vroll("1d4[fire]")34			totaldmg = dmg.total35			character().modify_hp(-totaldmg)36			return f'''embed -title "{name} drinks {d} and is {drunk}!" -desc "{status[drunk]}\n\n**Talon of the Phoenix**\nYou take {dmg} fire damage as the drink burns your stomach internally\n\n**Intoxication**\n{character().get_cc(cc)}/{character().get_cc_max(cc)}\n\n**Stage**\n{cs}/6\n\n**{name}**\n{character().hp_str()}" '''37		return f'''embed -title "{name} drinks {d} and is {drunk}!" -desc "{status[drunk]}\n\n**Talon of the Phoenix**\n{beakd}\n\n**Intoxication**\n{character().get_cc(cc)}/{character().get_cc_max(cc)}\n\n**Stage**\n{cs}/6" '''38	return f'''embed -title "{name} drinks {d} and is {drunk}!" -desc "{status[drunk]}\n\n**Intoxication**\n{character().get_cc(cc)}/{character().get_cc_max(cc)}\n\n**Stage**\n{cs}/6" '''39</drac2>40-thumb "<image>"...

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