
from __future__ import absolute_import, division, print_function
import os
from mmtbx.command_line import geometry_minimization
from libtbx.utils import Usage
from six.moves import cStringIO as StringIO

def parse_user_mods(filename):
  flipped_residues = []
  f = open(filename, 'rb')
  for line in f.readlines():
    if line.startswith("USER  MOD"):
      if "FLIP" in line:
        temp = line.strip().split(':')
        flipped_residues.append(temp[1].rstrip())
  f.close()
  return flipped_residues

def finalize_coords(filename, outfile, updated_coords):
  f = open(filename, 'rb')
  out_f = open(outfile, 'w')
  for line in f.readlines():
    if line.startswith("ATOM  "):
      key = line[12:26]
      if key in updated_coords:
        new_line = line[:30]+updated_coords[key]+line[54:]
        print(new_line.strip(), file=out_f)
      else:
        print(line.strip(), file=out_f)

    else:
      print(line.strip(), file=out_f)
  f.close()
  out_f.close()

def run(args):
  #log = StringIO()
  if len(args) != 3:
    raise Usage(
      "mmtbx.nqh_minimize input.pdb output.pdb temp_dir_path")
  filename = args[0]
  outfile = args[1]
  temp_dir = args[2]
  basename = os.path.basename(filename)
  flipped_residues = parse_user_mods(filename=filename)
  selection = "selection = (not (name ' CA ' or name ' N  ' or name ' C  ' " +\
              "or name ' O  ' or name ' HA ' or name ' H  ' " +\
              "or name ' OXT')) and ("
  restrain = "pdb_interpretation.reference_coordinate_restraints.selection = " +\
             "(not (name ' CA ' or name ' N  ' or name ' C  ' " +\
             "or name ' O  ' or name ' HA ' or name ' H  ' " +\
             "or name ' OXT')) and ("
  is_first = True
  for flip in flipped_residues:
    if not is_first:
      selection += " or"
      restrain += " or"
    else:
      is_first = False
    chain_id = flip[0:2]
    if (len(flip) == 10): #not an altloc
      if chain_id == '  ':
        selection += " (resseq %s and resname %s)" % \
          (flip[2:6].strip(), flip[7:])
        restrain += " (resseq %s and resname %s)" % \
          (flip[2:6].strip(), flip[7:])
      else:
        selection += " (chain '%s' and resseq %s and resname %s)" % \
          (flip[0:2], flip[2:6].strip(), flip[7:])
        restrain += " (chain '%s' and resseq %s and resname %s)" % \
          (flip[0:2], flip[2:6].strip(), flip[7:])
    else: #is an alternate
      if chain_id == '  ':
        selection += \
          " (resseq %s and resname %s and altid '%s')" % \
          (flip[2:6].strip(), flip[7:10], flip[-1:])
        restrain += \
          " (resseq %s and resname %s and altid '%s')" % \
          (flip[2:6].strip(), flip[7:10], flip[-1:])
      else:
        selection += \
          " (chain '%s' and resseq %s and resname %s and altid '%s')" % \
          (flip[0:2], flip[2:6].strip(), flip[7:10], flip[-1:])
        restrain += \
          " (chain '%s' and resseq %s and resname %s and altid '%s')" % \
          (flip[0:2], flip[2:6].strip(), flip[7:10], flip[-1:])
  selection += " )"
  restrain += " )"
  sigma = "pdb_interpretation.reference_coordinate_restraints.sigma=0.05"
  directory = "directory="+temp_dir
  params = os.path.join(temp_dir, "nqh.params")
  p = open(params, 'w')
  print(selection, file=p)
  print(restrain, file=p)
  print(sigma, file=p)
  print("pdb_interpretation.reference_coordinate_restraints.enabled=True", file=p)
  print(directory, file=p)
  print("stop_for_unknowns=False", file=p)
  print("pdb_interpretation.clash_guard.nonbonded_distance_threshold=None", file=p)
  p.close()
  temp_pdb = os.path.join(temp_dir, "nqh_flips.pdb")
  out = open(temp_pdb, 'w')
  f = open(filename, 'rb')
  for line in f.readlines():
    if line.startswith("ATOM  "):
      id_str = line[16:26]
      key = id_str[4:6]+id_str[6:]+' '+id_str[1:4]
      if id_str[0] != ' ':
        key = key+"    %s" % id_str[0]
      if key in flipped_residues:
        print(line.strip(), file=out)
  out.close()
  f.close()
  min_args = []
  min_args.append(filename)
  min_args.append(params)

  log_file = os.path.join(temp_dir, "nqh.log")
  log = open(log_file, 'w')

  o = geometry_minimization.run(min_args, log=log)

  updated_coords = {}
  ind = max(0,basename.rfind("."))
  ofn = \
    basename+"_minimized.pdb" if ind==0 else basename[:ind]+"_minimized.pdb"
  min_file = open(os.path.join(temp_dir, ofn), 'rb')
  for line in min_file.readlines():
    if line.startswith("ATOM  "):
      id_str = line[16:26]
      check_key = id_str[4:6]+id_str[6:]+' '+id_str[1:4]
      if id_str[0] != ' ':
        check_key = check_key+"    %s" % id_str[0]
      if check_key in flipped_residues:
        key = line[12:26]
        coords = line[30:54]
        updated_coords[key] = coords
  min_file.close()
  finalize_coords(
    filename=filename,
    outfile=outfile,
    updated_coords=updated_coords)


from __future__ import absolute_import, division, print_function
import os
from mmtbx.command_line import geometry_minimization
from libtbx.utils import Usage
from six.moves import cStringIO as StringIO

def parse_user_mods(filename):
  flipped_residues = []
  f = open(filename, 'rb')
  for line in f.readlines():
    if line.startswith("USER  MOD"):
      if "FLIP" in line:
        temp = line.strip().split(':')
        flipped_residues.append(temp[1].rstrip())
  f.close()
  return flipped_residues

def finalize_coords(filename, outfile, updated_coords):
  f = open(filename, 'rb')
  out_f = open(outfile, 'w')
  for line in f.readlines():
    if line.startswith("ATOM  "):
      key = line[12:26]
      if key in updated_coords:
        new_line = line[:30]+updated_coords[key]+line[54:]
        print(new_line.strip(), file=out_f)
      else:
        print(line.strip(), file=out_f)

    else:
      print(line.strip(), file=out_f)
  f.close()
  out_f.close()

def run(args):
  #log = StringIO()
  if len(args) != 3:
    raise Usage(
      "mmtbx.nqh_minimize input.pdb output.pdb temp_dir_path")
  filename = args[0]
  outfile = args[1]
  temp_dir = args[2]
  basename = os.path.basename(filename)
  flipped_residues = parse_user_mods(filename=filename)
  selection = "selection = (not (name ' CA ' or name ' N  ' or name ' C  ' " +\
              "or name ' O  ' or name ' HA ' or name ' H  ' " +\
              "or name ' OXT')) and ("
  restrain = "pdb_interpretation.reference_coordinate_restraints.selection = " +\
             "(not (name ' CA ' or name ' N  ' or name ' C  ' " +\
             "or name ' O  ' or name ' HA ' or name ' H  ' " +\
             "or name ' OXT')) and ("
  is_first = True
  for flip in flipped_residues:
    if not is_first:
      selection += " or"
      restrain += " or"
    else:
      is_first = False
    chain_id = flip[0:2]
    if (len(flip) == 10): #not an altloc
      if chain_id == '  ':
        selection += " (resseq %s and resname %s)" % \
          (flip[2:6].strip(), flip[7:])
        restrain += " (resseq %s and resname %s)" % \
          (flip[2:6].strip(), flip[7:])
      else:
        selection += " (chain '%s' and resseq %s and resname %s)" % \
          (flip[0:2], flip[2:6].strip(), flip[7:])
        restrain += " (chain '%s' and resseq %s and resname %s)" % \
          (flip[0:2], flip[2:6].strip(), flip[7:])
    else: #is an alternate
      if chain_id == '  ':
        selection += \
          " (resseq %s and resname %s and altid '%s')" % \
          (flip[2:6].strip(), flip[7:10], flip[-1:])
        restrain += \
          " (resseq %s and resname %s and altid '%s')" % \
          (flip[2:6].strip(), flip[7:10], flip[-1:])
      else:
        selection += \
          " (chain '%s' and resseq %s and resname %s and altid '%s')" % \
          (flip[0:2], flip[2:6].strip(), flip[7:10], flip[-1:])
        restrain += \
          " (chain '%s' and resseq %s and resname %s and altid '%s')" % \
          (flip[0:2], flip[2:6].strip(), flip[7:10], flip[-1:])
  selection += " )"
  restrain += " )"
  sigma = "pdb_interpretation.reference_coordinate_restraints.sigma=0.05"
  directory = "directory="+temp_dir
  params = os.path.join(temp_dir, "nqh.params")
  p = open(params, 'w')
  print(selection, file=p)
  print(restrain, file=p)
  print(sigma, file=p)
  print("pdb_interpretation.reference_coordinate_restraints.enabled=True", file=p)
  print(directory, file=p)
  print("stop_for_unknowns=False", file=p)
  print("pdb_interpretation.clash_guard.nonbonded_distance_threshold=None", file=p)
  p.close()
  temp_pdb = os.path.join(temp_dir, "nqh_flips.pdb")
  out = open(temp_pdb, 'w')
  f = open(filename, 'rb')
  for line in f.readlines():
    if line.startswith("ATOM  "):
      id_str = line[16:26]
      key = id_str[4:6]+id_str[6:]+' '+id_str[1:4]
      if id_str[0] != ' ':
        key = key+"    %s" % id_str[0]
      if key in flipped_residues:
        print(line.strip(), file=out)
  out.close()
  f.close()
  min_args = []
  min_args.append(filename)
  min_args.append(params)

  log_file = os.path.join(temp_dir, "nqh.log")
  log = open(log_file, 'w')

  o = geometry_minimization.run(min_args, log=log)

  updated_coords = {}
  ind = max(0,basename.rfind("."))
  ofn = \
    basename+"_minimized.pdb" if ind==0 else basename[:ind]+"_minimized.pdb"
  min_file = open(os.path.join(temp_dir, ofn), 'rb')
  for line in min_file.readlines():
    if line.startswith("ATOM  "):
      id_str = line[16:26]
      check_key = id_str[4:6]+id_str[6:]+' '+id_str[1:4]
      if id_str[0] != ' ':
        check_key = check_key+"    %s" % id_str[0]
      if check_key in flipped_residues:
        key = line[12:26]
        coords = line[30:54]
        updated_coords[key] = coords
  min_file.close()
  finalize_coords(
    filename=filename,
    outfile=outfile,
    updated_coords=updated_coords)

#log = StringIO() #not an altloc #is an alternate