# LIBTBX_SET_DISPATCHER_NAME phenix.clashscore

from __future__ import division
import mmtbx.validation.clashscore
import iotbx.phil
from libtbx.utils import Usage
import sys

def get_master_phil () :
  return iotbx.phil.parse("""
model = None
  .type = path

verbose = True
  .type = bool

keep_hydrogens = True
  .type = bool
  .help = '''Keep hydrogens in input file'''

nuclear = False
  .type = bool
  .help = '''Use nuclear hydrogen positions'''

time_limit = 120
  .type = int
  .help = '''Time limit (sec) for Reduce optimization'''

b_factor_cutoff = None
  .type = int
  .help = '''B factor cutoff for use with MolProbity'''
""")

usage_string = """\
phenix.clashscore file.pdb [params.eff] [options ...]

Options:

  model=input_file      input PDB file
  keep_hydrogens=True   keep input hydrogen files (otherwise regenerate)
  nuclear=False         use nuclear x-H distances and vdW radii
  verbose=True          verbose text output
  b_factor_cutoff=40    B factor cutoff for clash analysis

Example:

  phenix.clashscore model=1ubq.pdb keep_hydrogens=True

"""

def run (args, out=sys.stdout, quiet=None) :
  cmdline = iotbx.phil.process_command_line_with_files(
    args=args,
    master_phil=get_master_phil(),
    pdb_file_def="model",
    usage_string=usage_string)
  params = cmdline.work.extract()
  if (params.model is None) :
    raise Usage(usage_string)
  pdb_in = cmdline.get_file(params.model, force_type="pdb")
  hierarchy = pdb_in.file_object.hierarchy
  result = mmtbx.validation.clashscore.clashscore(
    pdb_hierarchy=hierarchy,
    keep_hydrogens=params.keep_hydrogens,
    nuclear=params.nuclear,
    out=out,
    verbose=params.verbose and not quiet,
    b_factor_cutoff=params.b_factor_cutoff)
  if params.verbose:
    result.show_old_output(out=out)

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