from __future__ import absolute_import, division, print_function
from libtbx.str_utils import make_sub_header
from libtbx.utils import null_out
import os.path
import sys

extend_master_phil = """
include scope mmtbx.building.extend_sidechains.master_params
output_model = None
  .type = path
output_map_coeffs = None
  .type = path
"""

def get_master_phil():
  from mmtbx.command_line import generate_master_phil_with_inputs
  return generate_master_phil_with_inputs(phil_string=extend_master_phil,
    enable_automatic_twin_detection=True)

def run(args, out=sys.stdout, verbose=True):
  import mmtbx.building.extend_sidechains
  import mmtbx.command_line
  input_out = out
  if (not verbose):
    input_out = null_out()
  cmdline = mmtbx.command_line.load_model_and_data(
    args=args,
    master_phil=get_master_phil(),
    process_pdb_file=False,
    out=input_out,
    usage_string="""\
mmtbx.extend_sidechains model.pdb data.mtz [restraints.cif] [options]

Rebuild sidechains with missing non-hydrogen atoms.  Includes real-space
refinement (but needs work).""")
  params = cmdline.params
  prefix = os.path.splitext(os.path.basename(params.input.pdb.file_name[0]))[0]
  pdb_hierarchy = cmdline.pdb_hierarchy
  xray_structure = cmdline.xray_structure
  if (cmdline.params.input.sequence is not None):
    from iotbx.bioinformatics import any_sequence_format
    sequences, nc = any_sequence_format(cmdline.params.input.sequence)
    make_sub_header("Correcting model sequence", out=out)
    n_changed = mmtbx.building.extend_sidechains.correct_sequence(
      pdb_hierarchy=pdb_hierarchy,
      sequences=sequences,
      out=out)
    if (n_changed == 0):
      print("  No modifications required.", file=out)
    else :
      xray_structure = pdb_hierarchy.extract_xray_structure(
        crystal_symmetry=xray_structure.crystal_symmetry())
      cmdline.fmodel.update_xray_structure(xray_structure,
        update_f_calc=True)
  return mmtbx.building.extend_sidechains.extend_and_refine(
    pdb_hierarchy=pdb_hierarchy,
    xray_structure=xray_structure,
    fmodel=cmdline.fmodel,
    params=params,
    prefix=prefix,
    cif_objects=[ co for fn, co in cmdline.cif_objects ],
    out=out,
    verbose=verbose,
    output_model=params.output_model,
    output_map_coeffs=params.output_map_coeffs)

if (__name__ == "__main__"):
  run(sys.argv[1:])