コード例 #1
0
def thorough_exercise():
    """
  This exercises all currently available options, so makes 64 requests.
  Took 20 minutes, therefore disabled from the general testing.
  """
    lysozyme = """KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL"""
    n_good = 0
    for po in [True, False]:
        for do in [True, False]:
            for sbr in [True, False]:
                for xro in [True, False]:
                    for d_max in [None, 3.0]:
                        for d_min in [None, 1.0]:
                            print("ARGUMENTS:", po, do, sbr, xro, d_max, d_min)
                            homologs = rcsb_web_services.sequence_search(
                                lysozyme,
                                xray_only=xro,
                                d_max=d_max,
                                d_min=d_min,
                                protein_only=po,
                                data_only=do,
                                sort_by_resolution=sbr)
                            if len(homologs) > 200:
                                n_good += 1
                                print("GOOD:", n_good)
    print(n_good)
    assert n_good == 64
コード例 #2
0
def exercise():
    lysozyme = """KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL"""
    homologs = rcsb_web_services.sequence_search(lysozyme, d_max=2.0)
    assert (len(homologs) > 500)
    atp_binding = rcsb_web_services.chemical_id_search("ATP",
                                                       protein_only=True)
    assert (len(atp_binding) > 650)
    report = rcsb_web_services.get_high_resolution_for_structures(atp_binding)
    assert (len(report) == len(atp_binding)) and (len(report[0]) == 2)
    # print (report)
    report = rcsb_web_services.get_high_resolution_and_residue_count_for_structures(
        atp_binding)
    assert (len(report) == len(atp_binding)) and (len(report[0]) == 3)
    # print (report)
    ligand_info = rcsb_web_services.get_ligand_info_for_structures(['1mru'])
    # print (ligand_info)
    assert ligand_info == [
        ['1MRU', 'A', 'MG', 24.305, 'Mg', 'MAGNESIUM ION', '[Mg++]'],
        ['1MRU', 'B', 'MG', 24.305, 'Mg', 'MAGNESIUM ION', '[Mg++]'],
        [
            '1MRU', 'A', 'AGS', 523.247, 'C10 H16 N5 O12 P3 S',
            'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER',
            'Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O'
        ],
        [
            '1MRU', 'B', 'AGS', 523.247, 'C10 H16 N5 O12 P3 S',
            'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER',
            'Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O'
        ]
    ]
コード例 #3
0
def exercise () :
  from mmtbx.wwpdb import rcsb_web_services
  lysozyme = """KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL"""
  homologs = rcsb_web_services.sequence_search(lysozyme, d_max=2.0)
  assert (len(homologs) > 500)
  atp_binding = rcsb_web_services.chemical_id_search("ATP", protein_only=True)
  assert (len(atp_binding) > 650)
  report = rcsb_web_services.get_high_resolution_for_structures(atp_binding)
  assert (len(report) == len(atp_binding)) and (len(report[0]) == 2)
  ligand_info = rcsb_web_services.get_ligand_info_for_structures(['1mru'])
  assert (len(ligand_info) == 4)
  print "OK"
コード例 #4
0
def exercise () :
  from mmtbx.wwpdb import rcsb_web_services
  lysozyme = """KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL"""
  homologs = rcsb_web_services.sequence_search(lysozyme, d_max=2.0)
  assert (len(homologs) > 500)
  atp_binding = rcsb_web_services.chemical_id_search("ATP", protein_only=True)
  assert (len(atp_binding) > 650)
  report = rcsb_web_services.get_high_resolution_for_structures(atp_binding)
  assert (len(report) == len(atp_binding)) and (len(report[0]) == 2)
  ligand_info = rcsb_web_services.get_ligand_info_for_structures(['1mru'])
  assert (len(ligand_info) == 4)
  assert (ligand_info[1][-1] == u'[Mg+2]')
  print "OK"
コード例 #5
0
ファイル: make_library.py プロジェクト: yayahjb/cctbx_project
def fetch_similar_pdb_ids(
    sequence,
    min_identity=0.95,
    min_resolution=3.0,
    xray_only=True,
    data_only=False,
    expect=0.0000001,
    sort_by_resolution=True,
    ligands=None,
    log=None):
  """
  Finds closely related structures in the RCSB database, optionally limited to
  structures with specific ligands.
  """
  if (log is None) : log = null_out()
  from mmtbx.wwpdb import rcsb_web_services
  allowed_set = None
  if (ligands is not None) and (len(ligands) > 0):
    for lig_str in ligands :
      resnames = lig_str.replace(" ", ",").split(",")
      for resname in resnames :
        ids = rcsb_web_services.chemical_id_search(
          resname=resname,
          d_max=min_resolution,
          xray_only=xray_only,
          data_only=data_only)
        if (allowed_set is None) : allowed_set = set([])
        allowed_set.update([ pdb_id.lower() for pdb_id in ids ])
  matching_ids = rcsb_web_services.sequence_search(
    sequence=sequence,
    min_identity=min_identity,
    expect=expect,
    xray_only=xray_only,
    data_only=data_only,
    d_max=min_resolution,
    sort_by_resolution=sort_by_resolution,
    log=log)
  filtered = []
  for pdb_id in matching_ids :
    pdb_id = pdb_id.lower()
    if (allowed_set is not None) and (not pdb_id in allowed_set):
      continue
    filtered.append(pdb_id)
  return filtered
コード例 #6
0
def fetch_similar_pdb_ids (
    sequence,
    min_identity=0.95,
    min_resolution=3.0,
    xray_only=True,
    data_only=False,
    expect=0.0000001,
    sort_by_resolution=True,
    ligands=None,
    log=None) :
  """
  Finds closely related structures in the RCSB database, optionally limited to
  structures with specific ligands.
  """
  if (log is None) : log = null_out()
  from mmtbx.wwpdb import rcsb_web_services
  allowed_set = None
  if (ligands is not None) and (len(ligands) > 0) :
    for lig_str in ligands :
      resnames = lig_str.replace(" ", ",").split(",")
      for resname in resnames :
        ids = rcsb_web_services.chemical_id_search(
          resname=resname,
          d_max=min_resolution,
          xray_only=xray_only,
          data_only=data_only)
        if (allowed_set is None) : allowed_set = set([])
        allowed_set.update([ pdb_id.lower() for pdb_id in ids ])
  matching_ids = rcsb_web_services.sequence_search(
    sequence=sequence,
    min_identity=min_identity,
    expect=expect,
    xray_only=xray_only,
    data_only=data_only,
    d_max=min_resolution,
    sort_by_resolution=sort_by_resolution,
    log=log)
  filtered = []
  for pdb_id in matching_ids :
    pdb_id = pdb_id.lower()
    if (allowed_set is not None) and (not pdb_id in allowed_set) :
      continue
    filtered.append(pdb_id)
  return filtered