Esempi in Python per ISPyBXmlHandler.add_xcrystal

Esempio n. 1

def ispyb_object():
    assert os.path.exists("xia2.json")
    assert os.path.exists("xia2.txt")
    command_line = ""
    for record in open("xia2.txt"):
        if record.startswith("Command line:"):
            command_line = record.replace("Command line:", "").strip()
    xinfo = XProject.from_json(filename="xia2.json")
    crystals = xinfo.get_crystals()
    assert len(crystals) == 1
    crystal = next(iter(crystals.values()))
    ispyb_hdl = ISPyBXmlHandler(xinfo)
    ispyb_hdl.add_xcrystal(crystal)
    return ispyb_hdl.json_object(command_line=command_line)

Esempio n. 2

def ispyb_object():
    from xia2.Interfaces.ISPyB.ISPyBXmlHandler import ISPyBXmlHandler

    assert os.path.exists("xia2.json")
    assert os.path.exists("xia2.txt")
    command_line = ""
    for record in open("xia2.txt"):
        if record.startswith("Command line:"):
            command_line = record.replace("Command line:", "").strip()
    xinfo = XProject.from_json(filename="xia2.json")
    crystals = xinfo.get_crystals()
    assert len(crystals) == 1
    crystal = next(crystals.itervalues())
    ISPyBXmlHandler.add_xcrystal(crystal)
    return ISPyBXmlHandler.json_object(command_line=command_line)

Esempio n. 3

File: ispyb_xml.py Progetto: xia2/xia2

def ispyb_xml(xml_out):
  from xia2.Interfaces.ISPyB.ISPyBXmlHandler import ISPyBXmlHandler
  import os
  assert os.path.exists('xia2.json')
  assert os.path.exists('xia2.txt')
  command_line = ''
  for record in open('xia2.txt'):
    if record.startswith('Command line:'):
      command_line = record.replace('Command line:', '').strip()
  from xia2.Schema.XProject import XProject
  xinfo = XProject.from_json(filename='xia2.json')
  crystals = xinfo.get_crystals()
  assert len(crystals) == 1
  crystal = next(crystals.itervalues())
  ISPyBXmlHandler.add_xcrystal(crystal)
  ISPyBXmlHandler.write_xml(xml_out, command_line)

Esempio n. 4

File: ispyb_xml.py Progetto: ndevenish/xia2

def ispyb_xml(xml_out):
  from xia2.Interfaces.ISPyB.ISPyBXmlHandler import ISPyBXmlHandler
  import os
  assert os.path.exists('xia2.json')
  assert os.path.exists('xia2.txt')
  command_line = ''
  for record in open('xia2.txt'):
    if record.startswith('Command line:'):
      command_line = record.replace('Command line:', '').strip()
  from xia2.Schema.XProject import XProject
  xinfo = XProject.from_json(filename='xia2.json')
  crystals = xinfo.get_crystals()
  assert len(crystals) == 1
  crystal = next(crystals.itervalues())
  ISPyBXmlHandler.add_xcrystal(crystal)
  ISPyBXmlHandler.write_xml(xml_out, command_line)

Esempio n. 5

File: ispyb_xml.py Progetto: BlenderCN-Org/dials-dev20190819

def ispyb_xml(xml_out):
    assert os.path.exists("xia2.json")
    assert os.path.exists("xia2.txt")
    assert os.path.exists("xia2-working.phil")
    command_line = ""
    for record in open("xia2.txt"):
        if record.startswith("Command line:"):
            command_line = record.replace("Command line:", "").strip()
    with open("xia2-working.phil", "rb") as f:
        working_phil = iotbx.phil.parse(f.read())
    xinfo = XProject.from_json(filename="xia2.json")
    crystals = xinfo.get_crystals()
    assert len(crystals) == 1
    crystal = next(crystals.itervalues())
    ISPyBXmlHandler.add_xcrystal(crystal)
    ISPyBXmlHandler.write_xml(xml_out, command_line, working_phil=working_phil)