Exemplos de generate_magnessium_inputs em Python

Exemplo n.º 1

Arquivo: tst_pick_mg.py Projeto: zhuligs/cctbx_project

def exercise():
    from mmtbx.regression.make_fake_anomalous_data import generate_magnessium_inputs
    base = "tst_pick_mg"
    mtz_file, pdb_file = generate_magnessium_inputs(file_base=base,
                                                    anonymize=True)
    time.sleep(2)
    args = [
        "\"%s\"" % pdb_file,
        "\"%s\"" % mtz_file, "nproc=1", "use_phaser=False", "elements=MG"
    ]
    result = easy_run.fully_buffered("mmtbx.water_screen %s" %
                                     " ".join(args)).raise_if_errors()
    n_mg = 0
    for line in result.stdout_lines:
        if ("Probable cation: MG+2" in line):
            n_mg += 1
    if n_mg != 2:
        print "\n".join(result.stdout_lines)
        raise RuntimeError("Expected 2 MG+2, found %d" % n_mg)
    os.remove(pdb_file)
    os.remove(mtz_file)
    # "zn_frag_hoh.pdb" => "zn_frag_fmodel.eff"
    os.remove(os.path.splitext(pdb_file)[0][:-4] + ".pdb")
    os.remove(os.path.splitext(pdb_file)[0][:-4] + "_fmodel.eff")
    print "OK"

Exemplo n.º 2

Arquivo: tst_validate_mg.py Projeto: cctbx/cctbx-playground

def exercise () :
  from mmtbx.regression.make_fake_anomalous_data import generate_magnessium_inputs
  base = "tst_validate_mg"
  mtz_file, pdb_file = generate_magnessium_inputs(file_base=base, anonymize=False)
  time.sleep(2)
  args = ["\"%s\"" % pdb_file, "\"%s\"" % mtz_file, "nproc=1"]
  result = easy_run.fully_buffered("mmtbx.validate_ions %s" % " ".join(args)
    ).raise_if_errors()
  n_mg, n_bad = 0, 0
  for line in result.stdout_lines :
    if "| MG" in line:
      n_mg += 1
    if "!!!" in line:
      n_bad += 1
  assert n_mg == 2 and n_bad == 0
  for ext in [".pdb", ".mtz", "_fmodel.eff"]:
    os.remove(base + ext)
  print "OK"

Exemplo n.º 3

Arquivo: tst_validate_mg.py Projeto: yayahjb/cctbx_project

def exercise():
  from mmtbx.regression.make_fake_anomalous_data import generate_magnessium_inputs
  base = "tst_validate_mg"
  mtz_file, pdb_file = generate_magnessium_inputs(file_base=base, anonymize=False)
  time.sleep(2)
  args = ["\"%s\"" % pdb_file, "\"%s\"" % mtz_file, "nproc=1"]
  result = easy_run.fully_buffered("mmtbx.validate_ions %s" % " ".join(args)
    ).raise_if_errors()
  n_mg, n_bad = 0, 0
  for line in result.stdout_lines :
    if "| MG" in line:
      n_mg += 1
    if "!!!" in line:
      n_bad += 1
  assert n_mg == 2 and n_bad == 0
  for ext in [".pdb", ".mtz", "_fmodel.eff"]:
    os.remove(base + ext)
  print("OK")

Exemplo n.º 4

Arquivo: tst_pick_mg.py Projeto: cctbx/cctbx-playground

def exercise () :
  from mmtbx.regression.make_fake_anomalous_data import generate_magnessium_inputs
  base = "tst_pick_mg"
  mtz_file, pdb_file = generate_magnessium_inputs(file_base=base, anonymize=True)
  time.sleep(2)
  args = [ "\"%s\"" % pdb_file, "\"%s\"" % mtz_file, "nproc=1",
           "use_phaser=False", "elements=MG" ]
  result = easy_run.fully_buffered("mmtbx.water_screen %s" % " ".join(args)
    ).raise_if_errors()
  n_mg = 0
  for line in result.stdout_lines :
    if ("Probable cation: MG+2" in line) :
      n_mg += 1
  if n_mg != 2:
    print "\n".join(result.stdout_lines)
    raise RuntimeError("Expected 2 MG+2, found %d" % n_mg)
  os.remove(pdb_file)
  os.remove(mtz_file)
  # "zn_frag_hoh.pdb" => "zn_frag_fmodel.eff"
  os.remove(os.path.splitext(pdb_file)[0][:-4] + ".pdb")
  os.remove(os.path.splitext(pdb_file)[0][:-4] + "_fmodel.eff")
  print "OK"