from __future__ import absolute_import, division, print_function
# LIBTBX_SET_DISPATCHER_NAME mmtbx.fix_rotamer_outliers

import sys
import iotbx.pdb
import iotbx.phil
import iotbx.pdb
import mmtbx.model
import scitbx.math
import mmtbx.idealized_aa_residues.rotamer_manager
import mmtbx.refinement.real_space.fit_residues

master_phil_str = """
show_all_params = False
  .type = bool
  .style = hidden
radius = 5.
  .type = float
  .help = radius for determining surrounding atoms around the residue
  .style = hidden
output_prefix = rotamer_fixed
  .type = str
file_name = None
  .type = path
  .optional = True
  .style = hidden
"""

master_phil = iotbx.phil.parse(master_phil_str, process_includes=True)

def show_usage():
  help_msg = """\
phenix.fix_rotamer_outliers: tool for fixing rotamer outliers.
    For every rotamer outlier it will choose the rotamer with minimum
    clashes with surrounding atoms.

Usage examples:
  mmtbx.fix_rotamer_outliers model.pdb
  mmtbx.fix_rotamer_outliers model.pdb
  mmtbx.fix_rotamer_outliers model.pdb ligands.cif output_prefix=rot_fixed

Full scope of parameters:
  """
  print(help_msg)
  master_phil.show()

def run(args, params=None, out=sys.stdout, model=None):
  if model is None:
    if ( ((len(args) == 0) and (params is None)) or
         ((len(args) > 0) and ((args[0] == "-h") or (args[0] == "--help"))) ):
      show_usage()
      return

    if (params is None):
      pcl = iotbx.phil.process_command_line_with_files(
        args=args,
        master_phil_string=master_phil_str,
        pdb_file_def="file_name")
      work_params = pcl.work.extract()
    # or use parameters defined by GUI
    else:
      work_params = params
    pdb_inp = iotbx.pdb.input(file_name=work_params.file_name)

    pdb_int_params = mmtbx.model.manager.get_default_pdb_interpretation_params()
    pdb_int_params.pdb_interpretation.clash_guard.nonbonded_distance_threshold=None
    model = mmtbx.model.manager(model_input = pdb_inp)
    model.process(pdb_interpretation_params=pdb_int_params,
      make_restraints=True)
  else:
    work_params = params
    if params is None:
      work_params = master_phil.extract()

  result = mmtbx.refinement.real_space.fit_residues.run(
      pdb_hierarchy     = model.get_hierarchy(),
      crystal_symmetry  = model.crystal_symmetry(),
      map_data          = None,
      rotamer_manager   = mmtbx.idealized_aa_residues.rotamer_manager.load(
        rotamers="favored_allowed"),
      sin_cos_table     = scitbx.math.sin_cos_table(n=10000),
      backbone_sample   = False,
      rotatable_hd      = model.rotatable_hd_selection(iselection=False),
      mon_lib_srv       = model.get_mon_lib_srv(),
      log               = out)
  model.set_sites_cart(
      sites_cart = result.pdb_hierarchy.atoms().extract_xyz())
  res_pdb_str = model.model_as_pdb()
  with open("%s.pdb" % work_params.output_prefix, "w") as f:
    f.write(res_pdb_str)
  return model

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