"""
   process_predicted_model: tools to update B-values used in some
    model predictions as an error estimate indicator and to split up model
    into domains that contain the more confident predictions
"""
from __future__ import division, print_function
import sys

################################################################################
#################### TOOLS FOR PROCESSING A PREDICTED MODEL ####################
################################################################################


from scitbx.array_family import flex
from libtbx.utils import Sorry
from scitbx.matrix import col
from libtbx import group_args
from cctbx.maptbx.segment_and_split_map import get_co
import iotbx.phil

################################################################################
####################   process_predicted_model  ################################
################################################################################


master_phil_str = """
  process_predicted_model{

    remove_low_confidence_residues = True
      .type = bool
      .help = Remove low-confidence residues (based on minimum plddt or \
             maximum_rmsd, whichever is specified)
      .short_caption = Remove low-confidence residues
      .expert_level = 3

    continuous_chain = False
      .type = bool
      .help = When removing low-confidence residues, only trim from ends
      .short_caption = Maintain continuous chain
      .expert_level = 3

    split_model_by_compact_regions = True
      .type = bool
      .help = Split model into compact regions after removing \
           low-confidence residues.
      .short_caption = Split model into compact regions
      .expert_level = 3

    maximum_domains = 3
      .type = int
      .help = Maximum domains to obtain.  You can use this to merge \
                the closest domains at the end of splitting the model. Make\
                it bigger (and optionally make domain_size smaller) to \
                get more domains.  If model is processed in chunks, \
                maximum_domains will apply to each chunk.
      .short_caption = Maximum domains

    domain_size = 15
      .type = float
      .help = Approximate size of domains to be found (A units).  This is the \
               resolution that \
              will be used to make a domain map.  If you are getting too many \
              domains, try making domain_size bigger (maximum is 70 A).
      .short_caption = Domain size (A)

    adjust_domain_size = True
      .type = bool
      .help = If more that maximum_domains are initially found, increase \
               domain_size in increments of 5 A and take the value that \
               gives the smallest number of domains, but at \
               least maximum_domains.
      .short_caption = Adjust domain size

    minimum_domain_length = None
      .type = float
      .help = Minimum length of a domain to keep (reject at end if smaller).\
              Default is 10 if no pae matrix or alt_pae_params=False and \
                20 for pae_matrix with alt_pae_params=True
      .short_caption = Minimum domain length (residues)

    maximum_fraction_close = 0.3
      .type = float
      .help = Maximum fraction of CA in one domain close to one in another \
              before merging them
      .short_caption = Maximum fraction close

    minimum_sequential_residues = None
      .type = int
      .help = Minimum length of a short segment to keep (reject at end ). \
              Default is 5 if no pae matrix or alt_pae_params=False and \
                4 for pae_matrix with alt_pae_params=True
      .short_caption = Minimum sequential_residues

    minimum_remainder_sequence_length = 15
      .type = int
      .help = used to choose whether the sequence of a removed \
               segment is written to the remainder sequence file.
      .short_caption = Minimum remainder sequence length

    b_value_field_is = *plddt rmsd b_value
      .type = choice
      .help = The B-factor field in predicted models can be pLDDT \
             (confidence, 0-1 or 0-100) or rmsd (A) or a B-factor
      .short_caption = Contents of B-value field for input models
      .expert_level = 3

    input_plddt_is_fractional = None
      .type = bool
      .help = You can specify if the input plddt values (in B-factor field) \
                are fractional (0-1) or not (0-100). By default if all  \
               values are between 0 and 1 it is fractional.
      .short_caption = Input plddt is fractional

    minimum_plddt = None
      .type = float
      .help = If low-confidence residues are removed, the cutoff is defined by \
          minimum_plddt or maximum_rmsd, whichever is defined (you cannot \
          define both).  A minimum plddt of 0.70 corresponds to a maximum rmsd \
          of 1.5.  Minimum plddt values are fractional or not depending on \
          the value of input_plddt_is_fractional.
      .short_caption = Minimum plddt


    maximum_rmsd = 1.5
      .type = float
      .help = If low-confidence residues are removed, the cutoff is defined by \
          minimum_plddt or maximum_rmsd, whichever is defined (you cannot \
          define both).  A minimum plddt of 0.70 corresponds to a maximum rmsd \
          of 1.5.  Minimum plddt values are fractional or not depending on \
          the value of input_plddt_is_fractional.
      .short_caption = Maximum rmsd

    default_maximum_rmsd = 1.5
      .type = float
      .help = Default value of maximum_rmsd, used if maximum_rmsd is not set
      .short_caption = default_maximum_rmsd

    subtract_minimum_b = False
      .type = bool
      .help = If set, subtract the lowest B-value from all B-values \
          just before writing \
          out the final files.  Does not affect the cutoff for removing low-\
           confidence residues.

     pae_power = None
       .type = float
       .help = If PAE matrix (predicted alignment error matrix) is supplied,\
            each edge in the graph will be weighted proportional to \
              (1/pae**pae_power). Use this to try and get the number of domains\
              that you want (try 1, 0.5, 1.5, 2). \
             Default is 1 alt_pae_params=False and 2 for alt_pae_params=True
       .short_caption = PAE power (if PAE matrix supplied)

     pae_cutoff = None
       .type = float
       .help = If PAE matrix (predicted alignment error matrix) is supplied,\
            graph edges will only be created for residue pairs with \
            pae<pae_cutoff. \
          Default is 5 alt_pae_params=False and 4 for alt_pae_params=True
       .short_caption = PAE cutoff (if PAE matrix supplied)

     pae_graph_resolution = None
       .type = float
       .help = If PAE matrix (predicted alignment error matrix) is supplied,\
            pae_graph_resolution regulates how aggressively the clustering \
            algorithm is. Smaller values lead to larger clusters. Value \
            should be larger than zero, and values larger than 5 are \
            unlikely to be useful, \
          Default is 0.5 alt_pae_params=False and 4 for alt_pae_params=True
       .short_caption = PAE graph resolution (if PAE matrix supplied)

     alt_pae_params = False
       .type = bool
       .help = If PAE matrix is supplied, use alternative set of defaults \
           (minimum_domain_length=20 minimum_sequential_residues=10 \
            pae_power=2 pae_cutoff=4 pae_graph_resolution=4). \
           Standard parameters (alt_pae_params=False) are: \
           (minimum_domain_length=10 minimum_sequential_residues=5 \
            pae_power=1 pae_cutoff=5 pae_graph_resolution=0.5).
       .short_caption = Use PAE defaults for pae_power=2

     weight_by_ca_ca_distance = False
       .type = bool
       .help = Adjust the edge weighting for each residue pair according  \
             to the distance between CA residues. If this is True, \
             then distance_model can be provided, otherwise supplied model \
             will be used. See also distance_power
       .short_caption = Weight by CA-CA distance

     distance_power = 1
       .type = float
       .help = If weight_by_ca_ca_distance is True, then edge weights will \
          be multiplied by 1/distance**distance_power.
       .short_caption = Distance power (for weighting by CA-CA distance)

     stop_if_no_residues_obtained = True
      .type = bool
      .help = Raise Sorry and stop if processing yields no residues
      .short_caption = Stop if no result

     keep_all_if_no_residues_obtained = False
      .type = bool
      .help = Keep everything if processing yields no residues
      .short_caption = Keep all if no result

     vrms_from_rmsd_intercept = 0.25
       .type = float
       .help = Estimate of vrms (error in model) from pLDDT will be based on\
           vrms_from_rmsd_intercept + vrms_from_rmsd_slope * pLDDT \
           where mean pLDDT of non-low_confidence_residues is used.
       .short_caption = vRMS intercept

     vrms_from_rmsd_slope = 1.0
       .type = float
       .help = Estimate of vrms (error in model) from pLDDT will be based on\
           vrms_from_rmsd_intercept + vrms_from_rmsd_slope * pLDDT \
           where mean pLDDT of non-low_confidence_residues is used.
       .short_caption = vRMS slope

     break_into_chunks_if_length_is = 1500
       .type = int
       .help = If a sequence is at least \
                break_into_chunks_if_length_is, break it into chunks \
                of length chunk_size with overlap of overlap_size for \
                domain identification using split_model_by_compact_regions \
                without a pae matrix
       .short_caption = Threshold for domain identification in chunks

     chunk_size = 600
       .type = int
       .help = If a sequence is at least \
                break_into_chunks_if_length_is, break it into chunks \
                of length chunk_size with overlap of overlap_size for \
                domain identification using split_model_by_compact_regions \
                without a pae_matrix
       .short_caption = Chunk size

     overlap_size = 200
       .type = int
       .help = If a sequence is at least \
                break_into_chunks_if_length_is, break it into chunks \
                of length chunk_size with overlap of overlap_size for \
                domain identification using split_model_by_compact_regions \
                without a pae_matrix
       .short_caption = Overlap length



    }

    """


def process_predicted_model(
    model,
    params,
    pae_matrix = None,
    distance_model = None,
    mark_atoms_to_keep_with_occ_one = False,
    log = sys.stdout):


  """
  process_predicted_model:
  Purpose:  Convert values in B-value field to pseudo-B-values, remove
    low_confidence residues, optionally split into compact regions.
  Rationale: predicted models may have regions of low and high confidence.
    This routine uses values in the B-value field to identify confidence,
    removes low-confidence regions, and then examines the remaining model to
    find regions that are compact (residues have high contact with neighbors)
    and that are separate from other regions (low contact with neigbors).

  Inputs (supplied as model and a params object):
    model:  iotbx.model.model object containing model information.
           Normally contains a single chain.   If multiple chains, process
           each separately.

    b_value_field_is:  'plddt' or 'rmsd' or 'b_value'.  For AlphaFold models
                        the b-value field is a value of pLDDT (confidence)
                        on scale of 0-1 or 0-100
                        For RoseTTAFold, the B-value field is rmsd (A)
                        If b_value... it is left as is.

    input_plddt_is_fractional:  if True, input plddt is scale of 0 to 1,
        otherwise 0 - 100
       If None, set to True if all plddt are from 0 to 1
    remove_low_confidence_residues: remove residues with low confidence
        (plddt or rmsd as set below)
    continuous_chain: if removing low-confidence residues, trim ends only. Note
         that if this is set, only the pae_matrix method of finding domains
         will work; the standard method will give a single domain.
    minimum_plddt: minimum plddt to keep residues (on same scale as b_value_field,
      if not set, calculated from maximum_rmsd).
    maximum_rmsd: alternative specification of minimum confidence based on rmsd.
        If not set, calculated from minimum_plddt.
    default_maximum_rmsd:  used as default if nothing specified for
         maximum_rmsd or minimum_plddt .Default is 1.5 A,
    split_model_by_compact_regions: split resulting model into compact regions
      and return a list of models in the group_arg return object
    pae_matrix:  matrix of predicted aligned errors (e.g., from AlphaFold2), NxN
      matrix of RMSD values, N = number of residues in model.
      Alternative to splitting by compact regions. Split to minimize predicted
          aligned errors in each grouping.
        pae_power (default=1): each edge in the graph will be weighted
           proportional to (1/pae**pae_power)
        pae_cutoff (optional, default=5): graph edges will only be created for
         residue pairs with pae<pae_cutoff
    weight_by_ca_ca_distance: (optional, default=False): adjust the edge
        weighting for each residue pair according to the distance between
        CA residues. If this is True, then distance_model must be provided.
    distance_power (optional, default=1): If weight_by_ca_ca_distance` is True,
         then edge weights will be multiplied by 1/distance**distance_power.
    distance_model ((optional, default=None): A model corresponding to the
        PAE matrix. Only needed if weight_by_ca_ca_distances is True.

    domain_size: typical size of domains (resolution used for filtering is
       the domain size)
    adjust_domain_size: increase domain_size if more than maximum domains found
    minimum_domain_length: minimum length (residues) of a domain to keep
    maximum_fraction_close: Merge domains with more than this fraction of close
                           CA atoms
    maximum_domains: if more than this many domains, merge close ones to reduce
       number
    chain_id: if model contains more than one chain, split this chain only.
              NOTE: only one chain can be processed at a time.
    if subtract_minimum_b is set, subtract minimum(B values) from all B values
       after applying any B value cutoffs

    If mark_atoms_to_keep_with_occ_one is set, return list of models, each
      of which is complete, but in which occupancy = 1 marks atoms to include
      and occupancy=0 marks those to exclude

    If stop_if_no_residues_obtained (default), stop with Sorry if no residues
      are obtained after processing, except if
        keep_all_if_no_residues_obtained (not default), then take everything.

    break_into_chunks_if_length_is, chunk_size, overlap_size:
       If a sequence is at least break_into_chunks_if_length_is, break
         it into chunks of length chunk_size with overlap of overlap_size for
         domain identification using split_model_by_compact_regions without
         pae_matrix

    alt_pae_params: Use alternative set of defaults for pae params if pae_matrix
        is present. Two possibilities are:
          Alternative if pae_matrix:
           (minimum_domain_length=20 minimum_sequential_residues=10 \
            pae_power=2 pae_cutoff=4 pae_graph_resolution=4).
           Standard parameters (alt_pae_params=False or no pae_matrix) are:
           (minimum_domain_length=10 minimum_sequential_residues=5
            pae_power=1 pae_cutoff=5 pae_graph_resolution=0.5).


  Output:
    processed_model_info: group_args object containing:
      processed_model:  single model with regions identified in chainid field
      model_list:  list of models representing domains
      plddt_list: one plddt on scale of 0 to 1 for each residue in input model.
      vrms_list: one vrms estimate (rms model error in A for each model)

  How to get the parameters object set up:

    You can set up a parameters object like this (see example at end of this
    file as well:

    master_phil = iotbx.phil.parse(master_phil_str)
    params = master_phil.extract()
    from mmtbx.process_predicted_model import set_defaults
    set_defaults(params, pae_matrix = pae_matrix)

    The default values are set in the master_phil_str string above.
    You can then set values of params:

    params.process_predicted_model.split_model_by_compact_regions = True


  """

  # Make sure we have what we expect:
  import mmtbx.model
  assert isinstance(model, mmtbx.model.manager)

  # Make sure we have just 1 chain or a chain ID supplied
  chain_ids = model.chain_ids()
  if len(chain_ids) != 1:
    chain_id = model.first_chain_id()
    model.add_crystal_symmetry_if_necessary()
    model = model.apply_selection_string('chain %s' %(chain_id))

  # Decide what to do
  p = params.process_predicted_model
  set_defaults(p, pae_matrix = pae_matrix)

  # initialize variable
  selection_for_b_factor_filtering_no_chain_id = None

  # Determine if input plddt is fractional and get b values

  b_value_field = model.get_hierarchy().atoms().extract_b()
  if p.b_value_field_is == 'plddt':
    if p.input_plddt_is_fractional is None:
      sel = (b_value_field < 0) | (b_value_field > 1)
      p.input_plddt_is_fractional = (sel.count(True) == 0)

    b_values = get_b_values_from_plddt(b_value_field,
       input_plddt_is_fractional = p.input_plddt_is_fractional)

    if p.input_plddt_is_fractional:
      print("B-value field interpreted as pLDDT %s" %("(0 - 1)"), file = log)
    else:
      print("B-value field interpreted as pLDDT %s" %("(0 - 100)"), file = log)

  elif p.b_value_field_is == 'rmsd':
    b_values = get_b_values_rmsd(b_value_field)
    print("B-value field interpreted as rmsd %s" %("(0 - 1)"), file = log)

  elif p.b_value_field_is == 'b_value':
    b_values = b_value_field
    print("B-value field interpreted as b_values", file = log)
  else:
    raise Sorry("Please set b_value_field_is to b_value, plddt or rmsd")

  if (not p.input_plddt_is_fractional):
    if p.minimum_plddt is not None: # convert to fractional
      p.minimum_plddt = p.minimum_plddt * 0.01
      print("Minimum pLDDT converted to %.2f" %(p.minimum_plddt), file = log)

  # From here on we work only with fractional plddt

  # Get confidence cutoff if needed
  if p.remove_low_confidence_residues:
    maximum_b_value = get_cutoff_b_value(
      p.maximum_rmsd,
      p.minimum_plddt,
      default_maximum_rmsd = p.default_maximum_rmsd,
      log = log)
  else:
    maximum_b_value = None


  # Offset b-values and cutoff if requested
  if p.subtract_minimum_b:
    minimum_b = b_values.min_max_mean().min
    b_values -= minimum_b
    assert b_values.min_max_mean().min == 0
    if maximum_b_value is not None:
      maximum_b_value -= minimum_b  # offset this too
    print("Subtracting minimum B of " +
      "%.2f from values and from cutoff (now %s)" %(
      minimum_b, " %.2f" %maximum_b_value if maximum_b_value is not None else "None"), file = log)

  # Make a new model with new B-values

  ph  = model.get_hierarchy().deep_copy()
  ph.atoms().set_b(b_values)
  full_model_with_new_b_values = \
     model.as_map_model_manager().model_from_hierarchy(
     ph, return_as_model = True)

  # Remove low_confidence regions if desired
  if p.remove_low_confidence_residues:
    n_before = ph.overall_counts().n_residues
    selection_string = " (bfactor < %s)" %maximum_b_value

    # Get selection based on CA/P atoms
    asc1 = ph.atom_selection_cache()
    sel1 = asc1.selection('(name ca or name P) and (%s) ' %selection_string)
    if p.continuous_chain:  # trim ends only
       restore_true_except_at_ends(sel1)
    ca_ph = ph.select(sel1)
    selection_string_2 = get_selection_for_short_segments(ca_ph,None)

    # Apply this selection to full hierarchy
    asc1 = ph.atom_selection_cache()
    sel = asc1.selection(selection_string_2)
    working_ph = ph.select(sel).deep_copy() # XXX for double selection

    if p.minimum_sequential_residues:  #
      # Remove any very short segments
      asc1 = working_ph.atom_selection_cache()
      sel1 = asc1.selection('name ca or name P')
      ca_ph = working_ph.select(sel1)
      selection_to_remove = get_selection_for_short_segments(ca_ph,
         p.minimum_sequential_residues)
      if selection_to_remove:
        print("Removing short segments: %s" %(selection_to_remove), file = log)
        asc1 = ph.atom_selection_cache() # original ph
        sel2 = asc1.selection(selection_to_remove)
        sel = ~ (~sel | sel2)

    new_ph = ph.select(sel).deep_copy()
    n_after = new_ph.overall_counts().n_residues
    print("Total of %s of %s residues kept after B-factor filtering" %(
       n_after, n_before), file = log)
    from mmtbx.secondary_structure.find_ss_from_ca import \
     get_selection_string_from_model
    selection_for_b_factor_filtering = get_selection_string_from_model(
      hierarchy = new_ph)
    if mark_atoms_to_keep_with_occ_one:
      selection_for_b_factor_filtering_no_chain_id = \
        get_selection_string_from_model(
      hierarchy = new_ph, skip_chain_id = True)
    print("\nSelection string for B-factor filtering: %s" %(
      selection_for_b_factor_filtering), file = log)
    keep_all = False
    remainder_sequence_str = None
    if n_after == 0:
      if p.stop_if_no_residues_obtained:
        raise Sorry("No residues remaining after filtering...please check if "+
         "B-value field is really '%s'. Adjust maximum_rmsd if necessary." %(
           p.b_value_field_is))
      elif p.keep_all_if_no_residues_obtained:
        keep_all = True
        print("Keeping everything as no residues obtained after filtering",
           file = log)
      else:
        return group_args(
         group_args_type = 'processed predicted model',
         model = None,
         model_list = [],
         chainid_list = [],
         remainder_sequence_str = "",
         b_values = [],
         )

    if not keep_all:
      removed_ph = ph.select(~sel).deep_copy()
      from mmtbx.secondary_structure.find_ss_from_ca import model_info, \
         split_model
      remainder_sequence_str = ""
      for m in split_model(model_info(removed_ph)):
        seq = m.hierarchy.as_sequence(as_string = True)
        if len(seq) >= p.minimum_remainder_sequence_length:
          remainder_sequence_str += "\n> fragment sequence "
          remainder_sequence_str += "\n%s\n" %(
            m.hierarchy.as_sequence(as_string = True))
      ph = new_ph
  else:
    remainder_sequence_str = None
  # Get a new model
  new_model = model.as_map_model_manager().model_from_hierarchy(
     ph, return_as_model = True)

  # Get high-confidence regions as domains if desired:
  if p.split_model_by_compact_regions:

    if pae_matrix is not None: # use pae matrix method
      info = split_model_with_pae(model, new_model, pae_matrix,
        maximum_domains = p.maximum_domains,
        pae_power = p.pae_power,
        pae_cutoff = p.pae_cutoff,
        pae_graph_resolution = p.pae_graph_resolution,
        minimum_domain_length = p.minimum_domain_length,
        weight_by_ca_ca_distance = p.weight_by_ca_ca_distance,
        distance_power = p.distance_power,
        distance_model = distance_model,
        log = log)
    else: # usual
      info = split_model_into_compact_units(new_model,
        d_min = p.domain_size,
        adjust_domain_size = p.adjust_domain_size,
        maximum_domains = p.maximum_domains,
        minimum_domain_length = p.minimum_domain_length,
        maximum_fraction_close = p.maximum_fraction_close,
        break_into_chunks_if_length_is = p.break_into_chunks_if_length_is,
        chunk_size = p.chunk_size,
        overlap_size = p.overlap_size,
        log = log)
    if info is None:
      print("No compact regions identified", file = log)
      chainid_list = []
      model_list = []
    else:
      new_model = info.model
      chainid_list = info.chainid_list
      print("Total of %s regions identified" %(
        len(chainid_list)), file = log)
      model_list = split_model_by_chainid(new_model, chainid_list,
        mark_atoms_to_keep_with_occ_one = mark_atoms_to_keep_with_occ_one,
        full_model = full_model_with_new_b_values,
        selection_for_b_factor_filtering_no_chain_id =
          selection_for_b_factor_filtering_no_chain_id
       )
  else:
    model_list = []
    chainid_list = []

  # Estimate vrms (model error) for each domain
  vrms_list = get_vrms_list(p, model_list, log = log)
  return group_args(
    group_args_type = 'processed predicted model',
    model = new_model,
    model_list = model_list,
    chainid_list = chainid_list,
    remainder_sequence_str = remainder_sequence_str,
    b_values = b_values,
    vrms_list = vrms_list,
    )

def set_defaults(p, pae_matrix = None, log = sys.stdout):
  # Set defaults for some parameters that depend on inputs
  if p.minimum_domain_length is None:
    if (pae_matrix is not None) and p.alt_pae_params:
      p.minimum_domain_length = 20
    else:
      p.minimum_domain_length = 10
    print("Minimum_domain_length=%s" %(p.minimum_domain_length), file = log)
  if p.minimum_sequential_residues is None:
    if (pae_matrix is not None) and p.alt_pae_params:
      p.minimum_sequential_residues = 10
    else:
      p.minimum_sequential_residues = 5
    print("Minimum_sequential_residues=%s" %(p.minimum_sequential_residues),
      file = log)
  if p.pae_power is None:
    if (pae_matrix is not None) and p.alt_pae_params:
      p.pae_power = 2
    else:
      p.pae_power = 1
    print("pae_power=%s" %(p.pae_power), file = log)
  if p.pae_cutoff is None:
    if (pae_matrix is not None) and p.alt_pae_params:
      p.pae_cutoff = 4
    else:
      p.pae_cutoff = 5
    print("pae_cutoff=%s" %(p.pae_cutoff), file = log)
  if p.pae_graph_resolution is None:
    if (pae_matrix is not None) and p.alt_pae_params:
      p.pae_graph_resolution = 4
    else:
      p.pae_graph_resolution = 0.5
    print("pae_graph_resolution=%s" %(p.pae_graph_resolution), file = log)

def convert_model_from_plddt_to_b(m, input_plddt_is_fractional = None):
  '''Convert values in B-value field from pLDDT to B values'''
  plddt_values = m.get_b_iso()
  b_values = get_b_values_from_plddt(plddt_values)
  m.set_b_iso(b_values)
  m.reset_after_changing_hierarchy()

def convert_model_from_b_to_plddt(m, input_plddt_is_fractional = True):
  ''' Convert values in B-value field from  B values to pLDDT values.
   If input_plddt_is_fractional is False, multiply by 100 at end'''
  b_values = m.get_b_iso()
  plddt_values = get_plddt_from_b(b_values)
  if (not input_plddt_is_fractional):
     plddt_values = plddt_values * 100
  m.set_b_iso(plddt_values)
  m.reset_after_changing_hierarchy()

def restore_true_except_at_ends(sel1):
  ''' Set all values that are not at ends of sel1 to False (any number
    at ends may be False)'''

  values = list(sel1)
  if not True in values:
    return  # nothing to do
  first_true = values.index(True)
  values.reverse()
  last_true_from_end = values.index(True)
  last_true = len(values) - last_true_from_end
  for i in range(first_true,last_true):
    sel1[i] = True

def get_vrms_list(p, model_list, log = sys.stdout):
  vrms_list = []
  for m in model_list:
    s = m.as_sequence(as_string = True)
    b_values = m.apply_selection_string(
       '(name ca or name P) and not element ca').get_b_iso()

    plddt_values = get_plddt_from_b(b_values)
    rmsd = get_rmsd_from_plddt(plddt_values).min_max_mean().mean
    rmsd2 = get_rmsd_from_plddt(get_plddt_from_b(b_values)).min_max_mean().mean
    assert rmsd == rmsd2

    mean_b = b_values.min_max_mean().mean
    mean_plddt = plddt_values.min_max_mean().mean



    vrms = rmsd * p.vrms_from_rmsd_slope + p.vrms_from_rmsd_intercept
    print("VRMS calculation for '%s':" %(m.info().file_name) +
      "\nMean B: %.1f  pLDDT (0-100) : %.2f RMSD: %.1f A  VRMS: %.1f A" %(
      mean_b, 100*mean_plddt, rmsd, vrms), file = log)
    vrms_list.append(vrms)
  return vrms_list

def get_selection_for_short_segments(ph, minimum_sequential_residues):
  chain_dict = {}
  for model in ph.models():
    for chain in model.chains():
      residue_list = []
      for rg in chain.residue_groups():
        resseq_int = rg.resseq_as_int()
        residue_list.append(resseq_int)
      residue_list = sorted(residue_list)
      chain_dict[chain.id] = residue_list
  selections = []
  for chain_id in chain_dict.keys():
    residue_list = chain_dict[chain_id]
    for r in get_indices_as_ranges(residue_list):
      if (minimum_sequential_residues is None) or (
          r.end - r.start + 1 < minimum_sequential_residues):
        selections.append("(chain '%s' and resseq %s:%s)" %(
          chain_id, r.start, r.end))
  selection_string = " or ".join(selections)
  return selection_string




def split_model_by_chainid(m, chainid_list,
    mark_atoms_to_keep_with_occ_one = False, full_model = None,
    selection_for_b_factor_filtering_no_chain_id = None):

  """
   Split a model into pieces based on chainid
   Optionally write out everything for each model, using
      occupancy=0 to mark everything that is not select3ed
  """
  split_model_list = []
  for chainid in chainid_list:
    selection_string = "chain %s" %(chainid)
    ph = m.get_hierarchy()
    asc1 = ph.atom_selection_cache()
    sel = asc1.selection(selection_string)
    if (not mark_atoms_to_keep_with_occ_one): # usual
      m1 = m.select(sel)
    else:  # for Voyager, mark unused with zero occupancies
      # Start with full model
      m1a = m.select(sel)
      from mmtbx.secondary_structure.find_ss_from_ca import \
         get_selection_string_from_model
      selection_for_working = get_selection_string_from_model(model = m1a,
        skip_chain_id = True)
      full_selection = "(%s) and (%s)" %(
        selection_for_b_factor_filtering_no_chain_id,
         selection_for_working)

      m1 = full_model.deep_copy()
      ph1 = m1.get_hierarchy()
      asc1 = ph1.atom_selection_cache()
      sel1 = asc1.selection(full_selection)

      atoms = ph1.atoms()
      occupancies = atoms.extract_occ()
      occupancies.set_selected(sel1, 1)
      occupancies.set_selected(~sel1, 0)
      atoms.set_occ(occupancies)
    split_model_list.append(m1)
  return split_model_list

def get_cutoff_b_value(
    maximum_rmsd,
    minimum_plddt,
    default_maximum_rmsd = None,
    log = sys.stdout):

  # Get B-value cutoff

  if maximum_rmsd is None and minimum_plddt is None:
    maximum_rmsd = default_maximum_rmsd
    assert maximum_rmsd is not None

  if maximum_rmsd is not None:
    print("Maximum rmsd of %.2f A used" %(maximum_rmsd), file = log)
  elif minimum_plddt:
    print("Minimum confidence level is %.2f" %(
      minimum_plddt), file = log)
    if minimum_plddt< 0 or \
      minimum_plddt> 1:
      raise Sorry("minimum_plddt must "+
         "be between 0 and 1")
    maximum_rmsd = get_rmsd_from_plddt(
           flex.double(1,minimum_plddt),
           is_fractional = True)[0]
    print("Maximum rmsd set to %.2f A based on confidence cutoff of %.2f" %(
       maximum_rmsd, minimum_plddt), file = log)
  else:
     raise Sorry( "Need to set either maximum_rmsd or " +
          "minimum_plddt")

  maximum_b_value = get_b_values_rmsd(
     flex.double(1,maximum_rmsd))[0]

  print("Maximum B-value to be included: %.2f A**2" %(maximum_b_value),
    file = log)
  return maximum_b_value




################################################################################
####################   get_b_values_from_plddt  ################################
################################################################################

def get_b_values_from_plddt(plddt_values,
    input_plddt_is_fractional = True):
  """
  get_b_values_from_plddt:
  Purpose:  AlphaFold models are supplied with values of pLDDT (predicted
   local-distance difference test) in the B-value field.  This routine
   uses the formula from:

     Hiranuma, N., Park, H., Baek, M. et al. Improved protein structure
       refinement guided by deep learning based accuracy estimation.
       Nat Commun 12, 1340 (2021).
       https://doi.org/10.1038/s41467-021-21511-x

   to convert these values to error estimates,
   and then uses the relation between B-values and coordinate rms to
   generate pseudo-B-factors

  NOTE: formulas taken from phaser_voyager implementation by
  Claudia Millan and Massimo Sammito at
  phaser_voyager/src/Voyager/MDSLibraries/pdb_structure.py


  Inputs:
    plddt_values: flex array of plddt values
    input_plddt_is_fractional: if False, convert by multiplying * 0.01
  Outputs:
    flex array of B-values
  """

  if input_plddt_is_fractional:
    rmsd = get_rmsd_from_plddt(plddt_values) # usual
  else:
    rmsd = get_rmsd_from_plddt(0.01 * plddt_values)
  b_values = get_b_values_rmsd(rmsd)

  return b_values

################################################################################
####################   get_plddt_from_b          ################################
################################################################################

def get_plddt_from_b(b_values, input_plddt_is_fractional = True):
  """  Inverse of get_b_values_from_plddt
  Inputs:
    flex array of B-values
    input_plddt_is_fractional: if False, convert by multiplying * 100 at end
  Outputs:
    plddt_values: flex array of plddt values
  """
  if not b_values:
    return None

  # b_values = flex.pow2(rmsd) * ((8 * (3.14159 ** 2)) / 3.0)
  if b_values.min_max_mean().min < 0:
    b_values = b_values.deep_copy()
    b_values.set_selected(b_values < 0, 0)
  rmsd = flex.sqrt( b_values/ ((8 * (3.14159 ** 2)) / 3.0))

  # rmsd  = 1.5 * flex.exp(4*(0.7-plddt))
  plddt = 0.7 - 0.25 * flex.log(rmsd/1.5)
  if plddt.min_max_mean().min < 0 or plddt.min_max_mean().max > 1:
    plddt.set_selected(plddt < 0, 0)
    plddt.set_selected(plddt > 1, 1)

  if not input_plddt_is_fractional:
    plddt = plddt * 100

  return plddt


################################################################################
####################   get_rmsd_from_plddt  ################################
################################################################################

def get_rmsd_from_plddt(plddt_values, is_fractional = None):
  """
  get_rmsd_from_plddt:
  Purpose:  AlphaFold models come with predicted pLDDT values in the B-value
   field to indicate confidence.  This routine uses a formula provided in the
   supplementary material of the RoseTTAFold paper to convert these values
   to error estimates.
  NOTE: plddt_values can be fractional (0 to 1) or percentage (0 to 100)
  If is_fractional is not set, assume fractional if all between 0 and 1
  rmsd_est = 1.5 * flex.exp(4*(0.7-fractional_values))

  NOTE: formulas taken from phaser_voyager implementation by
  Claudia Millan and Massimo Sammito at
  phaser_voyager/src/Voyager/MDSLibraries/pdb_structure.py


  Inputs:
    plddt_values: flex array of plddt values
  Outputs:
    flex array of error estimates (A)
  """
  if is_fractional is None:
    is_fractional = ( plddt_values.min_max_mean().min >= 0  and
      plddt_values.min_max_mean().max <= 1 )

  if is_fractional:
    fractional_values = plddt_values.deep_copy()
  else:
    fractional_values = plddt_values * 0.01

  fractional_values.set_selected((fractional_values < 0), 0)
  fractional_values.set_selected((fractional_values > 1), 1)

  rmsd_est = 1.5 * flex.exp(4*(0.7-fractional_values))
  return rmsd_est

################################################################################
####################   get_b_values_rmsd #######################
################################################################################

def get_b_values_rmsd(rmsd):
  """
  get_b_values_rmsd:
  Purpose:  TTAFold models are supplied with values of rmsd (A)
   in the B-value field.  This routine converts error estimates into
   b-values

  NOTE: formulas taken from phaser_voyager implementation by
  Claudia Millan and Massimo Sammito at
  phaser_voyager/src/Voyager/MDSLibraries/pdb_structure.py


  Inputs:
    rmsd: flex array of error estimates (A)
  Outputs:
    flex array of B-values (A**2)
  """

  rmsd = rmsd.deep_copy() # do not change original

  # Make sure error estimates are in reasonable range
  rmsd.set_selected((rmsd < 0), 0)
  rmsd.set_selected((rmsd > 20), 20)

  b_values = flex.pow2(rmsd) * ((8 * (3.14159 ** 2)) / 3.0)
  return b_values

################################################################################
####################   split_model_with_pae  ###################################
################################################################################

def split_model_with_pae(
     model,
     m,
     pae_matrix,
     maximum_domains = None,
     pae_power = 1.,
     pae_cutoff = 5.,
     pae_graph_resolution = 0.5,
     minimum_domain_length = 10,
     weight_by_ca_ca_distance = False,
     distance_power = 1,
     distance_model = None,
     log = sys.stdout):

  """
   Function to identify groups of atoms in a model that form compact units
   using a predicted alignment error matrix (pae_matrix).
   Normally used after trimming low-confidence regions in
   predicted models to isolate domains that are likely to have indeterminate
   relationships.

   m:  cctbx.model.model object containing information about the input model
     after trimming
   model: model before trimming
   pae_matrix:  matrix of predicted aligned errors (e.g., from AlphaFold2), NxN
       matrix of RMSD values, N = number of residues in model.
   maximum_domains:  If more than this many domains, merge closest ones until
     reaching this number
   pae_power (default=1): each edge in the graph will be weighted
       proportional to (1/pae**pae_power)
   pae_cutoff (optional, default=5): graph edges will only be created for
       residue pairs with pae<pae_cutoff
   pae_graph_resolution (optional, default = 0.5): regulates how aggressively
       the clustering algorithm is. Smaller values lead to larger clusters.
       Value should be larger than zero, and values larger than 5 are
        unlikely to be useful
   weight_by_ca_ca_distance: (optional, default=False): adjust the edge
        weighting for each residue pair according to the distance between
        CA residues. If this is True, then distance_model must be provided.
   distance_power (optional, default=1): If weight_by_ca_ca_distance` is True,
         then edge weights will be multiplied by 1/distance**distance_power.
   distance_model ((optional, default=None): A model corresponding to the
        PAE matrix. Only needed if weight_by_ca_ca_distances is True.
   minimum_domain_length:  if a region is smaller than this, skip completely

   Output:
   group_args object with members:
    m:  new model with chainid values from 0 to N where there are N domains
      chainid 1 to N are the N domains, roughly in order along the chain.
    chainid_list:  list of all the chainid values

   On failure:  returns None
  """

  print("\nSelecting domains with predicted alignment uncertainty estimates",
     file = log)
  # Select CA and P atoms with B-values in range
  selection_string = '(name ca or name p)'
  m_ca_or_p = m.apply_selection_string(selection_string)
  n = model.apply_selection_string(selection_string
       ).get_hierarchy().overall_counts().n_residues

  # Make sure matrix matches
  if tuple(pae_matrix.shape) != (n, n):
     raise Sorry("The pae matrix has a size of (%s,%s) " %(
      tuple(pae_matrix.shape)) +
      "but the number of residues in the model is %s" %(n))
  first_resno = model.first_resseq_as_int()

  #  Assign all CA in model to a region
  from mmtbx.domains_from_pae import get_domain_selections_from_pae_matrix
  selection_list = get_domain_selections_from_pae_matrix(
    pae_matrix = pae_matrix,
     pae_power = pae_power,
     pae_cutoff = pae_cutoff,
     graph_resolution = pae_graph_resolution,
     first_resno = first_resno,
     weight_by_ca_ca_distance = weight_by_ca_ca_distance,
     distance_power = distance_power,
     distance_model = distance_model,
    )

  # And apply to full model

  unique_regions = list(range(len(selection_list)))

  keep_list = []
  good_selections = []
  ph = m.get_hierarchy()
  ca_or_p_string =  '(name ca or name p)'

  for selection_string, region_number in zip(selection_list,unique_regions):
    asc1 = ph.atom_selection_cache()
    sel = asc1.selection("(%s) and %s" %(selection_string,ca_or_p_string))
    if sel.count(True) >= minimum_domain_length:
      keep_list.append(True)
      good_selections.append(selection_string)
    else:
      keep_list.append(False)
  if keep_list.count(False) > 0:
    print("Skipping %s regions that contain fewer than %s residues" %(
         keep_list.count(False), minimum_domain_length),
        file = log)

  region_name_dict, chainid_list = get_region_name_dict(m, unique_regions,
    keep_list = keep_list)
  print("\nSelection list based on PAE values:", file =log)

  # Now create new model with chains based on region list
  full_new_model = None
  for keep, selection_string, region_number in zip(
     keep_list, selection_list,unique_regions):
    if not keep: continue
    new_m = m.apply_selection_string(selection_string)
    print("%s (%s residues)  "%(selection_string,
      new_m.get_hierarchy().overall_counts().n_residues), file = log)
    # Now put all of new_m in a chain with chain.id = str(region_number)
    for model in new_m.get_hierarchy().models()[:1]: # only one model
      for chain in model.chains()[:1]: # only allowing one chain
        chain.id = region_name_dict[region_number]
    new_m._update_atom_selection_cache() # changed chain IDs...
    if full_new_model:
      full_new_model = add_model(full_new_model, new_m)
    else:
      full_new_model = new_m
  m = full_new_model

  from mmtbx.secondary_structure.find_ss_from_ca import \
     get_selection_string_from_model
  if m:
    selection_for_full_model = get_selection_string_from_model(model = m)
    print("\nSelection string for final model: %s" %(selection_for_full_model),
      file = log)
    print("Total residues in final model: %s" %(
     m.overall_counts().n_residues), file = log)
  else:
    print("No model obtained...", file = log)


  # All done
  return group_args(
    group_args_type = 'model_info',
    model = m,
    chainid_list = chainid_list)

################################################################################
####################   split_model_into_compact_units_by_chunks   ##############
################################################################################

def split_model_into_compact_units_by_chunks(
     m,
     d_min = 15,
     grid_resolution = 6,
     close_distance = 15,
     minimum_domain_length = 10,
     maximum_fraction_close = 0.3,
     maximum_domains = None,
     adjust_domain_size = None,
     break_into_chunks_if_length_is = None,
     chunk_size = None,
     overlap_size = None,
     log = sys.stdout):

  """
   Function to sequentially run split_model_into_compact_units on
    chunks of a large model, breaking into overlapping chunks of size
    chunk_size, get domains from each, putting them together.
   The value of maximum_domains will apply only within a chunk.
   See split_model_into_compact_units for details

  """
  first_resno = m.first_resseq_as_int()
  last_resno = m.last_resseq_as_int()
  # Select CA and P atoms with B-values in range
  selection_string = '(name ca or name p)'
  m_ca_or_p = m.apply_selection_string(selection_string)
  print("Residue range: (%s - %s) " %(first_resno,last_resno), file = log)
  chunks = get_residue_ranges_for_chunks(model = m,
     first_resno = first_resno,
     last_resno = last_resno,
     chunk_size = chunk_size, overlap_size = overlap_size)
  print("Residue ranges for chunks:", file = log)
  for c in chunks:
    print(c, file = log)

  info_list = []
  for c in chunks:
    selection_text = "resseq %s:%s" %(c[0], c[1])
    working_m = m.apply_selection_string(selection_text)
    print("\nGetting compact domains in residue range %s" %(selection_text),
      file = log)
    info = split_model_into_compact_units(
     working_m,
     d_min = d_min,
     grid_resolution = grid_resolution,
     close_distance = close_distance,
     minimum_domain_length = minimum_domain_length,
     maximum_fraction_close = maximum_fraction_close,
     maximum_domains = maximum_domains,
     adjust_domain_size = adjust_domain_size,
     break_into_chunks_if_length_is = working_m.overall_counts().n_residues + 1,
     log = log)
    info.first_resno = c[0]
    info.last_resno = c[1]
    info.residues_present = get_residues_present_list(working_m)
    info_list.append(info)

  # Find crossover points between each block that minimizes
  #   crossing over between parts of a domain
  crossover_points_list = find_crossover_points(info_list)

  # Assemble into full list. Crossover is residue number of last residue
  new_regions_list = []
  numbers_list = []
  for info, start_crossover, end_crossover in zip(
     info_list, [None] + crossover_points_list , crossover_points_list +[None]):
    if start_crossover in info.residues_present:
      working_start_crossover = info.residues_present.index(start_crossover)
    else:
      working_start_crossover = None
    if end_crossover in info.residues_present:
      working_end_crossover = info.residues_present.index(end_crossover)
    else:
      working_end_crossover = None
    r1 = list(info.residues_present)
    if (working_start_crossover is not None) and (
       working_end_crossover is not None):
      section = info.regions_list[
           working_start_crossover:working_end_crossover]
      numbers_section = r1[working_start_crossover:working_end_crossover]
    elif working_start_crossover is not None:
      section = info.regions_list[working_start_crossover:]
      numbers_section = r1[working_start_crossover:]
    else:
      numbers_section = r1[:working_end_crossover]
      section = info.regions_list[:working_end_crossover]
    unique_numbers = get_unique_values(section)
    used_numbers = get_unique_values(new_regions_list)
    new_numbers = get_new_numbers(unique_numbers, used_numbers)
    new_section = replace_numbers(section, unique_numbers, new_numbers)
    new_regions_list += new_section


  new_regions_list = flex.int(new_regions_list)
  # Update region list
  new_regions_list = recalculate_regions_list(new_regions_list,
     minimum_domain_length = minimum_domain_length,
     model = m_ca_or_p, close_distance = close_distance,
     maximum_domains = maximum_domains * len(chunks) if \
       maximum_domains is not None else None,
     maximum_fraction_close = maximum_fraction_close,
     log = log)

  # Get unique domain ids for each chunk and make globally unique
  info = set_chain_id_by_region(m, m_ca_or_p, new_regions_list, log = log)

  return info

def get_residues_present_list(m):
  hierarchy = m.get_hierarchy()
  residue_list = []
  for model in hierarchy.models()[:1]:
    for chain in model.chains()[:1]:
       for rg in chain.residue_groups():
          residue_list.append(rg.resseq_as_int())
  return residue_list

def replace_numbers(section, unique_numbers, new_numbers):
  s = flex.int(section)
  for old,new in zip(unique_numbers, new_numbers):
    sel = (s == old)
    s.set_selected(sel, new)
  return list(s)

def get_new_numbers(unique_numbers, used_numbers, keep_zeros = True):
  if used_numbers:
    max_n = max(used_numbers)
  else:
    max_n = 0
  new_numbers = []
  for i in unique_numbers:
    if keep_zeros and i == 0:
      if not 0 in used_numbers:
        used_numbers.append(i)
      new_numbers.append(i)
    if not i in used_numbers:
      used_numbers.append(i)
      new_numbers.append(i)
    else:
      max_n = max_n + 1
      used_numbers.append(max_n)
      new_numbers.append(max_n)
  return new_numbers

def find_crossover_points(info_list):
  # Try to find crossover points between each block that minimizes
  #   crossing over between parts of a domain
  crossover_points_list = []
  for info_1, info_2 in zip(info_list, info_list[1:]):
    crossover_points_list.append(find_one_crossover_point(info_1, info_2))
  return crossover_points_list

def find_one_crossover_point(info_1, info_2):
  # Try to find crossover points between blocks info_1 and info_2 that
  #  minimizes crossing over between parts of a domain at least on one of
  # the two chains
  unique_regions_1 = get_unique_values(info_1.regions_list)
  unique_regions_2 = get_unique_values(info_2.regions_list)
  # Find places in overlap where all values in info_1 after overlap are
  #   different from all values before, and same for info_2
  first_crossover = info_2.first_resno
  last_crossover = info_1.last_resno
  best_crossover = None
  best_crossover_score = None
  for crossover in range(first_crossover, last_crossover + 1):
    crossover_info = get_crossover_info(info_1, info_2, crossover)
    if not crossover_info:
      continue
    unique_regions_1a = crossover_info.unique_regions_1a
    unique_regions_1b = crossover_info.unique_regions_1b
    unique_regions_2a = crossover_info.unique_regions_2a
    unique_regions_2b = crossover_info.unique_regions_2b
    values_distinct_1 = not values_overlap(unique_regions_1a, unique_regions_1b)
    if values_distinct_1:
      overlap_1 = 0
    else:
      overlap_1 = count_overlap(unique_regions_1a, unique_regions_1b)
    values_distinct_2 = not values_overlap(unique_regions_2a, unique_regions_2b)
    if values_distinct_2:
      overlap_2 = 0
    else:
      overlap_2 = count_overlap(unique_regions_2a, unique_regions_2b)

    if values_distinct_1 and values_distinct_2: # perfect
      if (best_crossover_score is None) or (best_crossover_score < 3):
        best_crossover_score = 3
        best_crossover = crossover
    elif unique_regions_1a and unique_regions_1b and values_distinct_1:
      if (best_crossover_score is None) or (best_crossover_score < 2):
        best_crossover_score = 2
        best_crossover = crossover
    elif unique_regions_2a and unique_regions_2b and values_distinct_2:
      if (best_crossover_score is None) or (best_crossover_score < 2):
        best_crossover_score = 2
        best_crossover = crossover
    else:
      score = -1 * min(overlap_1, overlap_2)
      if (best_crossover_score is None) or (best_crossover_score < score):
        best_crossover_score = score
        best_crossover = crossover

  # Here everything is distinct
  print("Found overlap at %s" %(best_crossover))
  print("Found overlap at %s" %(best_crossover - info_1.first_resno ))
  crossover_info = get_crossover_info(info_1, info_2, best_crossover)
  unique_regions_1a = crossover_info.unique_regions_1a
  unique_regions_1b = crossover_info.unique_regions_1b
  unique_regions_2a = crossover_info.unique_regions_2a
  unique_regions_2b = crossover_info.unique_regions_2b

  print("Unique values in info 1: (%s), (%s)  info 2: (%s), (%s)" %(
    str(unique_regions_1a),str(unique_regions_1b),
    str(unique_regions_2a),str(unique_regions_2b),))
  return best_crossover

def get_crossover_info(info_1, info_2, crossover):
    # crossover is residue number to cross over. crossover_1 and _2 are
    #   indices in the full_regions_list that correspond to this residue
    #   number
    if info_1.residues_present and (not crossover in info_1.residues_present):
      return None
    if info_2.residues_present and (not crossover in info_2.residues_present):
      return None
    crossover_1 = info_1.residues_present.index(crossover)
    crossover_2 = info_2.residues_present.index(crossover)
    unique_regions_1a = get_unique_values(
        info_1.regions_list[:crossover_1])
    unique_regions_1b = get_unique_values(
        info_1.regions_list[crossover_1:])
    unique_regions_2a = get_unique_values(
        info_2.regions_list[:crossover_2])
    unique_regions_2b = get_unique_values(
        info_2.regions_list[crossover_2:])
    return group_args(group_args_type = 'overlap info',
      unique_regions_1a = unique_regions_1a,
      unique_regions_1b = unique_regions_1b,
      unique_regions_2a = unique_regions_2a,
      unique_regions_2b = unique_regions_2b,
      )
def count_overlap(v1,v2):
  count = 0
  for v in v1:
    if v in v2:
      count += 1
  return count

def values_overlap(v1,v2):
  for v in v1:
    if v in v2:
      return True
  return False

def get_residue_ranges_for_chunks(model = None,
     first_resno = None, last_resno = None,
     chunk_size = None, overlap_size = None):
  resno_list = list(range(first_resno, last_resno+1))

  chunks = []
  while resno_list:
    if len(resno_list) < 2*chunk_size and len(resno_list) > chunk_size:
      c = resno_list[:chunk_size]
      resno_list = resno_list[-chunk_size:] # take last chunk_size
      print(len(resno_list))
    else: # usual
      c = resno_list[:chunk_size]
      resno_list = resno_list[chunk_size-overlap_size:]
      if len(resno_list) < chunk_size: # we are done
        resno_list = ""
      print(len(resno_list))
    chunks.append([c[0], c[-1]])
  return chunks

################################################################################
####################   split_model_into_compact_units   ########################
################################################################################

def split_model_into_compact_units(
     m,
     d_min = 15,
     grid_resolution = 6,
     close_distance = 15,
     minimum_domain_length = 10,
     maximum_fraction_close = 0.3,
     maximum_domains = None,
     adjust_domain_size = None,
     break_into_chunks_if_length_is = None,
     chunk_size = None,
     overlap_size = None,
     log = sys.stdout):

  """
   Function to identify groups of atoms in a model that form compact units
   (domains).  Normally used after trimming low-confidence regions in
   predicted models to isolate domains that are likely to have indeterminate
   relationships.

   Method: calculate a low-resolution map based on the input model; identify
    large blobs corresponding to domains.  Assign all atoms in structure to
    a domain.  Then regroup in order to have few cases where small parts of
    model are part of one domain but neighboring parts are part of another.

   For very long chains (longer than break_into_chunks_if_length_is), break
   into overlapping chunks of size chunk_size, get domains from each, put
   them together.

   Inputs:
   m:  cctbx.model.model object containing information about the input model
   d_min:  resolution used for low-res map.  Corresponds roughly to domain size.
   adjust_domain_size: Vary d_min to try and obtain maximum_domains in initial
                       domain identification
   grid_resolution:  resolution of map used to define the gridding
   close_distance:  distance between two CA (or P) atoms considered close
                    NOTE: may be useful to double default for P compared to CA
   minimum_domain_length: typical size (CA or P) of smallest segments to keep
   minimum_remainder_sequence_length: minimum length of a removed sequence
      segment to write out to a new sequence file
   bfactor_min: smallest bfactor for atoms to include in calculations
   bfactor_max: largest bfactor for atoms to include in calculations
   maximum_domains:  If more than this many domains, merge closest ones until
     reaching this number
   break_into_chunks_if_length_is, chunk_size, overlap_size:
       If a sequence is at least break_into_chunks_if_length_is, break
         it into chunks of length chunk_size with overlap of overlap_size.
         Run on each chunk, then apply results to whole.
   Output:
   group_args object with members:
    m:  new model with chainid values from 0 to N where there are N domains
      chainid 1 to N are the N domains, roughly in order along the chain.
    chainid_list:  list of all the chainid values

   On failure:  returns None
  """
  if break_into_chunks_if_length_is is not None and \
       m.overall_counts().n_residues >= break_into_chunks_if_length_is:
    return split_model_into_compact_units_by_chunks(
     m,
     d_min = d_min,
     grid_resolution = grid_resolution,
     close_distance = close_distance,
     minimum_domain_length = minimum_domain_length,
     maximum_fraction_close = maximum_fraction_close,
     maximum_domains = maximum_domains,
     adjust_domain_size = adjust_domain_size,
     break_into_chunks_if_length_is = break_into_chunks_if_length_is,
     chunk_size = chunk_size,
     overlap_size = overlap_size,
     log = log)


  print("\nSelecting domains as compact chains",
     file = log)
  d_min = min(50, d_min) # limitation in fmodel

  # Make sure the model has P1 crystal_symmetry.  Put a box around it that is
  #  big (do not use original crystal symmetry because it might  be too big
  #  or too small)

  m = m.deep_copy()  # don't modify original

  box_cushion = 0.5 * d_min  # big box
  original_crystal_symmetry = m.crystal_symmetry()
  original_uc_crystal_symmetry = m.unit_cell_crystal_symmetry()
  m.add_crystal_symmetry_if_necessary(box_cushion = box_cushion, force = True)
  m.set_shift_cart(None)
  m.set_unit_cell_crystal_symmetry(m.crystal_symmetry())

  # Select CA and P atoms with B-values in range
  selection_string = '(name ca or name p)'
  m_ca_or_p = m.apply_selection_string(selection_string)


  # Put the model inside a box and get a map_model_manager
  put_model_inside_cell(m_ca_or_p, grid_resolution)

  # Generate map at medium_res for this model and use it to get domains
  info = get_map_and_d_min(
    m_ca_or_p, d_min = d_min, target_regions = maximum_domains,
    adjust_domain_size = adjust_domain_size,
    grid_resolution = grid_resolution, log = log)
  if not info:
    print("Failed to find domains", file = log)
    return # Nothing to do
  map_data = info.map_data
  co_info = info.co_info


  # Assign all points in box to a grouping
  co_info = assign_all_points(co_info, map_data, log = log)

  #  Assign all CA in model to a region
  regions_list = assign_ca_to_region(co_info, m_ca_or_p, minimum_domain_length,
     close_distance,
     maximum_domains = maximum_domains,
     maximum_fraction_close = maximum_fraction_close,
     log = log)

  info = set_chain_id_by_region(m, m_ca_or_p, regions_list, log = log)
  if original_crystal_symmetry and info and info.model:
    info.model.set_crystal_symmetry(original_crystal_symmetry)
  return info

def get_map_and_d_min(m_ca_or_p, d_min = None,
      adjust_domain_size = None, target_regions = None,
      grid_resolution = None,
      log = sys.stdout):
  # Choose d_min that give about target_regions clusters
  best_co_info = None
  best_map_data = None
  best_n = None
  best_d_min = None
  if adjust_domain_size:
     n_offset = 10
  else:
     n_offset = 1
  for offset in range(n_offset):
    mmm = m_ca_or_p.as_map_model_manager()
    d_min_use = d_min + 5 * offset
    if d_min_use > 70:
      continue # max is about 70
    mmm.set_resolution(d_min_use)
    try:
      mmm.generate_map(d_min_use,
        resolution_factor = 0.25 * grid_resolution/d_min )
    except Exception as e: # too low resolution
      continue

    # Box the map and set SD to 1 mean to 0
    box_mmm = mmm.extract_all_maps_around_model()
    box_mmm.map_manager().set_mean_zero_sd_one()

    # Now get regions where there is model
    map_data = box_mmm.map_manager().map_data()

    #  Get a connectivity analysis of this map data
    co_info = get_best_co(map_data)
    if not co_info:
      continue
    n = len(co_info.sorted_by_volume)
    if (best_n is None) or (target_regions is None) or (
        (n >= target_regions) and (n < best_n)):
      best_n = n
      best_co_info = co_info
      best_map_data = map_data
      best_d_min = d_min_use
  if co_info is None:
    return # Nothing to do
  n = best_n
  d_min = best_d_min
  co_info = best_co_info
  map_data = best_map_data
  print("Best resolution for domains is %.1f A giving %s regions" %(
        d_min, n), file = log)
  return group_args(group_args_type = 'co_info and map_data',
    d_min = d_min,
    co_info = co_info,
    map_data = map_data,)


def get_region_name_dict(m, unique_regions, keep_list = None):
  region_name_dict = {}
  chainid_list = []
  chainid = m.first_chain_id().strip()
  if not keep_list:
    keep_list = len(unique_regions) * [True]
  assert len(keep_list) == len(unique_regions)

  i = 0
  for region_number, keep in zip(unique_regions, keep_list):
      if not keep: continue
      i += 1
      if len(chainid) == 1 and i < 10:
          region_name = "%s%s" %(chainid,i)
      else:
          region_name = str(i)
      region_name_dict[region_number] = region_name
      chainid_list.append(region_name)
  return region_name_dict, chainid_list

def set_chain_id_by_region(m, m_ca_or_p, regions_list, log = sys.stdout):
  # Set chainid based on regions_list

  atoms = m_ca_or_p.get_hierarchy().atoms()  # new
  unique_regions = get_unique_values(regions_list)

  region_name_dict, chainid_list = get_region_name_dict(m, unique_regions)

  region_dict = {}
  for at, region_number in zip(atoms, regions_list):
    resseq_int = at.parent().parent().resseq_as_int()
    region_dict[resseq_int] = region_number

  # And apply to full model
  full_regions_list = flex.int()
  for at in m.get_hierarchy().atoms():
    resseq_int = at.parent().parent().resseq_as_int()
    region = region_dict.get(resseq_int,0)
    full_regions_list.append(region)

  # Now create new model with chains based on region list
  full_new_model = None
  print("\nSelection list based on domains:", file =log)
  for region_number in unique_regions:
    sel = (full_regions_list == region_number)
    new_m = m.select(sel)
    selection_string = selection_string_from_model(
       new_m.apply_selection_string("name ca or name P"))

    print("%s (%s residues)  "%(selection_string,
      new_m.get_hierarchy().overall_counts().n_residues), file = log)
    # Now put all of new_m in a chain with chain.id = str(region_number)
    for model in new_m.get_hierarchy().models()[:1]: # only one model
      for chain in model.chains()[:1]: # only allowing one chain
        chain.id = region_name_dict[region_number]
    if full_new_model:
      full_new_model = add_model(full_new_model, new_m)
    else:
      full_new_model = new_m
  full_new_model.reset_after_changing_hierarchy()
  m = full_new_model

  # All done
  return group_args(
    group_args_type = 'model_info',
    model = m,
    chainid_list = chainid_list,
    regions_list = regions_list,
    full_regions_list = full_regions_list)

def selection_string_from_model(model):
    resno_list = get_residue_numbers_in_model(model)
    from mmtbx.domains_from_pae import cluster_as_selection
    selection_string = cluster_as_selection(resno_list)
    return selection_string


def assign_ca_to_region(co_info,
    m,
    minimum_domain_length,
    close_distance,
    maximum_domains = None,
    maximum_fraction_close = None,
    log = sys.stdout):
  region_id_map = co_info.region_id_map
  id_list = co_info.id_list
  regions_list = flex.int()
  sites_frac = m.crystal_symmetry().unit_cell().fractionalize(m.get_sites_cart())
  for sf in sites_frac:
    regions_list.append(int(region_id_map.value_at_closest_grid_point(sf)))
  # Now remove occasional ones out of place

  regions_list = recalculate_regions_list(regions_list,
     minimum_domain_length = minimum_domain_length,
     model = m, close_distance = close_distance,
     maximum_domains = maximum_domains,
     maximum_fraction_close = maximum_fraction_close,
     log = log)

  return regions_list

def recalculate_regions_list(regions_list,
     minimum_domain_length = None,
     model = None,
     close_distance = None,
     maximum_domains = None,
     maximum_fraction_close = None,
     n_cycles = 10,
     log = sys.stdout):

  for cycle in range(n_cycles):
    regions_list = replace_lone_sites(regions_list)
    regions_list = replace_short_segments(regions_list, minimum_domain_length)
    for i in range(len(get_unique_values(regions_list))):
      new_regions_list = swap_close_regions(
        model.get_sites_cart(),
       regions_list, minimum_domain_length, close_distance)
      if new_regions_list:
         regions_list = new_regions_list
      else:
       break
  # Merge close regions if there are too many
  for k in range(len(get_unique_values(regions_list))):
    if maximum_domains and \
         len((get_unique_values(regions_list))) > maximum_domains:
      regions_list = merge_closest_regions(model.get_sites_cart(), regions_list,
        close_distance, log = log)
    else:
      break

  # Merge close regions if they are really close
  for k in range(len(get_unique_values(regions_list))):
    regions_list = merge_very_close_regions(model.get_sites_cart(),
        regions_list,
        close_distance,
        minimum_domain_length =  minimum_domain_length,
        maximum_fraction_close = maximum_fraction_close,
        log = log)

  # Finally check for any short fragments not attached to neighbors
  regions_list = remove_short_fragments_obscured_by_gap(regions_list,
    model, minimum_domain_length)
  return regions_list

def remove_short_fragments_obscured_by_gap(regions_list,
    m, minimum_domain_length):
  # Find any regions that are very short (<minimum_domain_length) and merge
  # with adjacent sequence if available
  # This catches cases where there was a gap in sequence.

  region_dict = {}
  for at, region_number in zip(m.get_hierarchy().atoms(), regions_list):
    resseq_int = at.parent().parent().resseq_as_int()
    region_dict[resseq_int] = region_number

  # Find all cases where regions go like:
  #  1 1 1 2 2 (gap)   -> 1 1 1 1 1 (gap)
  #  1 1 1 2 2 3 3 3 3  -> 1 1 1 1 1 3 3 3 3 or 1 1 1 3 3 3 3 3 3
  #  (gap) 2 2 3 3 3 3 -> (gap) 3 3 3 3 3 3
  # First split up resseq_int into ranges..
  residues_as_groups = get_indices_as_ranges(list(region_dict.keys()))
  for r in residues_as_groups:
    # Find all the places where region_number changes
    working_regions = []
    working_region = None
    for i in range(r.start, r.end+1):
      region_number = region_dict[i]
      if not working_region or region_number !=working_region.region_number:
        working_region = group_args(
          group_args_type = 'working region',
          region_number = region_number,
          start = i,
          end = i,
          )
        working_regions.append(working_region)
      else:
        working_region.end = i
    for previous_region,working_region,next_region in zip(
      [None]+working_regions[:-1], working_regions, working_regions[1:]+[None]):
      if (working_region.end - working_region.start + 1) < \
           minimum_domain_length:
        if previous_region:
          working_region.region_number = previous_region.region_number
        elif next_region:
          working_region.region_number = next_region.region_number
        else:  # skip as nothing to do
          pass
    # And update dictionary
    for working_region in working_regions:
      for i in range(working_region.start, working_region.end+1):
        region_dict[i] = working_region.region_number
  # And use dictionary to update regions_list

  new_regions_list = regions_list.deep_copy()
  i = -1
  for at in m.get_hierarchy().atoms():
    i += 1
    resseq_int = at.parent().parent().resseq_as_int()
    new_regions_list[i] = region_dict[resseq_int]

  return new_regions_list

def merge_very_close_regions(sites_cart, regions_list, close_distance,
     minimum_domain_length= None,
     maximum_fraction_close = None,
     log = sys.stdout):
  unique_values = get_unique_values(regions_list)
  n = len(unique_values)
  close_to_other_info  = get_close_to_other_list(sites_cart, regions_list,
     close_distance)
  if close_to_other_info.n_close_list:  # there are close pairs
    # Get best pair
    n_close_list = sorted(close_to_other_info.n_close_list,
      key = lambda c: c.n_close, reverse = True)
    best_pair = n_close_list[0]
    n_close = best_pair.n_close
    n_possible = best_pair.n_possible
    if n_possible >=  minimum_domain_length and \
        n_close >= n_possible * maximum_fraction_close and \
        best_pair.i is not None:
      best_i = best_pair.i
      best_j = best_pair.j
      print("Merging groups with %s sets of close residues" %(
        best_pair.n_close), file = log)

      sel = (regions_list == best_j)
      regions_list.set_selected(sel, best_i)
      update_regions_list(regions_list)

  return regions_list
def merge_closest_regions(sites_cart, regions_list, close_distance,
     log = sys.stdout):
  unique_values = get_unique_values(regions_list)
  n = len(unique_values)
  close_to_other_info  = get_close_to_other_list(sites_cart, regions_list,
     close_distance)
  if close_to_other_info.n_close_list:  # there are close pairs
    # Get best pair
    n_close_list = sorted(close_to_other_info.n_close_list,
      key = lambda c: c.n_close, reverse = True)
    best_pair = n_close_list[0]
    best_i = best_pair.i
    best_j = best_pair.j
    if best_i is not None:
      print("Merging groups with %s sets of close residues" %(
        best_pair.n_close), file = log)
  else:  # just take the pair that comes closest
    best_i = None
    best_j = None
    best_dist = None
    for k in range(len(unique_values)):
      i = unique_values[k]
      sc1 = sites_cart.select(regions_list == i)
      for l in range(k+1, len(unique_values)):
        j = unique_values[l]
        sc2 = sites_cart.select(regions_list == j)
        dist, i1, i2 = sc1.min_distance_between_any_pair_with_id(sc2)
        if dist and (best_dist is None or (dist < best_dist)):
          best_i = i
          best_j = j
          best_dist = dist
    if best_i is not None:
      print("Merging groups with distance of %.2f A" %(best_dist), file = log)

  if best_i is not None:
    sel = (regions_list == best_j)
    regions_list.set_selected(sel, best_i)
    update_regions_list(regions_list)

  return regions_list

def get_unique_values(regions_list):
  unique_values = []
  for x in regions_list:
    if not x in unique_values:
      unique_values.append(x)
  return unique_values

def swap_close_regions(sites_cart, regions_list, minimum_domain_length,
    close_distance = None):

  # Count number of residues in each pair that are close to the other
  # Split a group if some residues are close to other and not to self

  close_to_other_info  = get_close_to_other_list(sites_cart, regions_list,
     close_distance)
  close_to_other_list = close_to_other_info.close_to_other_list

  closer_to_other_swaps = get_closer_to_other(close_to_other_list,
      minimum_domain_length)
  found_something = False
  # Apply close swaps
  for s in closer_to_other_swaps:
    c = s.k_list[0]
    for k in range(c.start, c.end+1):
      regions_list[k] = s.j
      found_something = True

  update_regions_list(regions_list)

  if found_something:
    return regions_list

def get_close_to_other_list(sites_cart, regions_list, close_distance):

  sites_dict = {}
  index_dict = {}
  id_list = get_unique_values(regions_list)

  for co_id in id_list:
    sel = (regions_list == co_id)
    sites_dict[co_id] = sites_cart.select(sel)
    index_dict[co_id] = sel.iselection()

  n_close_list = []
  typical_n_close = 0
  typical_n_close_n = 0
  close_to_other_list = []
  for i in id_list:
    for j in id_list:
      if i==j: continue
      n_close = 0 # number in i close to j
      n_possible = 0

      for k in range(sites_dict[i].size()):
         index = index_dict[i][k]
         distances = (sites_dict[j] - col(sites_dict[i][k])).norms()
         local_n_close = (distances < close_distance).count(True)
         if local_n_close > 0:
           n_close += 1
         n_possible += 1
         distances_self = (sites_dict[i] - col(sites_dict[i][k])).norms()
         self_local_n_close = (distances_self < close_distance).count(True) - 1
         if local_n_close > self_local_n_close:
           close_to_other_list.append(
             group_args(group_args_type = 'closer to other',
             excess = local_n_close - self_local_n_close,
             index = index,
             i = i,
             k = k,
             j = j))


      n_close_list.append(group_args(  # how many in i close to j
        group_args_type = 'n close',
        n_close = n_close,
        n_possible = n_possible,
        i = i,
        j = j,))
  return group_args(
    group_args_type = 'close to other and close list',
      n_close_list = n_close_list,
      close_to_other_list = close_to_other_list)

def get_closer_to_other(close_to_other_list, minimum_domain_length):
  close_dict = {}
  for c in close_to_other_list:
    i,j = c.i,c.j
    if not i in close_dict.keys():
       close_dict[i] = {}
    if not j in close_dict[i].keys():
      close_dict[i][j] = 0
    close_dict[i][j] += 1
  for i in close_dict.keys():
    for j in close_dict[i].keys():
      if close_dict[i][j] >= 0: # minimum_domain_length//2:
        pass
      else:
        del close_dict[i][j]
        if not close_dict[i]:
          del close_dict[i]
  all_k_list = []
  for i in close_dict.keys():
    for j in close_dict[i].keys():
      k_list = get_k_list(i,j,close_to_other_list)
      k_list = merge_k_list(k_list, minimum_domain_length)
      if not k_list:continue
      all_k_list.append(group_args(
        group_args_type = 'k list',
        i = i,
        j = j,
        k_list = k_list,
       ))
  return all_k_list


def merge_k_list(k_list, minimum_domain_length):
  n = len(k_list)
  for i in range(n):
    last_n = len(k_list)
    k_list = merge_k_list_once(k_list)
    if len(k_list) == last_n:
      break

  new_k_list = []
  for k1 in k_list:
    n1 = k1.end - k1.start + 1
    if n1 >= minimum_domain_length//3:
      new_k_list.append(k1)
  return new_k_list

def merge_k_list_once(k_list):
  new_k_list = []
  for k1,k2 in zip(k_list,k_list[1:]):
    n1 = k1.end - k1.start + 1
    n2 = k2.end - k2.start + 1
    n_between = k2.start - k1.end - 1
    if n_between < min(n1,n2):
      k1.end = k2.end
      k2.start  = None
      k2.end = None
      break
  for k1 in k_list:
    if k1.start is not None:
      new_k_list.append(k1)
  return new_k_list


def get_k_list(i,j,close_to_other_list):
  k_list = []
  for c in close_to_other_list:
    if c.i==i and c.j==j:
      k_list.append(c.index)
  k_list.sort()
  k_list_as_groups = get_indices_as_ranges(k_list)
  return k_list_as_groups

def replace_short_segments(regions_list, minimum_domain_length):
  id_list = get_unique_values(regions_list)
  new_regions_list = regions_list.deep_copy()
  for co_id in id_list:
    indices = (regions_list == co_id).iselection()
    indices_as_ranges = get_indices_as_ranges(indices)
    for r in indices_as_ranges:
      if r.end - r.start + 1 < minimum_domain_length:
        value = regions_list[r.start - 1] if r.start > 0 else \
           regions_list[min(regions_list.size() - 1, r.end + 1)]
        for i in range(r.start,r.end+1):
          new_regions_list[i] = value

  regions_list = new_regions_list
  update_regions_list(regions_list)
  return regions_list

def update_regions_list(regions_list):
  id_list = get_unique_values(regions_list)
  new_id_dict = {}
  i = 0
  for id_value in id_list:
    i += 1
    new_id_dict[id_value] = i
  new_id_list = list(new_id_dict.keys())

  for i in range(regions_list.size()):
    regions_list[i] = new_id_dict[regions_list[i]]

def get_indices_as_ranges(indices):
  indices = sorted(indices)
  ranges = []
  grouping = None
  for index in indices:
    if not grouping or index != grouping.end + 1: # new grouping
      grouping = group_args(
        group_args_type = 'grouping',
        start = index,
        end = index)
      ranges.append(grouping)
    else:
      grouping.end = index
  return ranges

def replace_lone_sites(regions_list):
  regions_list[0] = regions_list[1]
  regions_list[-1] = regions_list[-2]
  o0 = regions_list[:-2]
  o1 = regions_list[1:-1]
  o2 = regions_list[2:]
  # find o1 is different than 0 or 2 and 0 and 2 are the same
  same_02 = (o2 == o0)
  different_01 = (o1 != 00)
  lone = (same_02 & different_01)
  for i in lone.iselection():
    index = i + 1
    regions_list[i + 1] =  regions_list[i]
  update_regions_list(regions_list)
  return regions_list

def put_model_inside_cell(m, grid_resolution):
  # Put model inside cell
  sc = m.get_sites_cart()
  sc -= col(sc.min())
  sc += col((grid_resolution,grid_resolution,grid_resolution))  # inside box
  m.set_sites_cart(sc)
  return m

def assign_all_points(co_info, map_data, log = sys.stdout):
  # add shells around all co until everything is covered
  co = co_info.co
  id_list = []
  for i in range(1,len(co_info.sorted_by_volume)):
    id_list.append(co_info.sorted_by_volume[i][1])


  # Set starting points
  region_id_map = co.result()

  done = False
  for i in range(1,map_data.all()[0]):  # max possible
    if done: continue
    for co_id in id_list:
      if done: continue
      available = (region_id_map == 0)
      if available.count(True) == 0:
        done = True
        break

      bool_region_mask = co.expand_mask(
        id_to_expand = co_id, expand_size = i)
      new = (bool_region_mask & available)
      region_id_map.set_selected(new, co_id)

  co_info.region_id_map = region_id_map
  co_info.id_list = id_list
  return co_info

def get_best_co(map_data, min_cutoff = 0.5):
  max_value = map_data.as_1d().min_max_mean().max
  avg_value = map_data.as_1d().min_max_mean().mean

  # Find max number of clusters in range of 0.5 to 1.0 * max
  n = 100
  max_clusters = None
  cutoff= None
  for t in range(int(min_cutoff*n),n+1):
    threshold = avg_value + t * (max_value-avg_value)/n
    co, sorted_by_volume, min_b, max_b  = get_co(
      map_data, threshold = threshold, wrapping = False)
    if ((not max_clusters) or (len(sorted_by_volume) > max_clusters)) and (
        len(sorted_by_volume) > 1 ):
     max_clusters = len(sorted_by_volume)
     cutoff = threshold
  if max_clusters is None:
    return None
  print("Clusters: %s   Threshold: %.2f " %(max_clusters, cutoff))
  co, sorted_by_volume, min_b, max_b  = get_co(
      map_data, threshold = cutoff , wrapping = False)
  return group_args(
    group_args_type = 'co info',
    co = co,
    sorted_by_volume = sorted_by_volume)

################################################################################
####################   end of split_model_into_compact_units   #################
################################################################################

################################################################################
####################   Convenience functions          ##########################
################################################################################
def set_high_pae_for_missing(pae_matrix, pae_cutoff,
      residues_remaining):
   n,n = tuple(pae_matrix.shape)
   pae_1d = pae_matrix.flatten().tolist()
   skip_this_one = []
   for i in range(n):
     if i in residues_remaining:
        skip_this_one.append(False)
     else:
        skip_this_one.append(True)
   n_skipped = 0
   ii = -1
   for i in range(n):
     for j in range(n):
       ii += 1
       if skip_this_one[i] or skip_this_one[j]:
         pae_1d[ii] = pae_cutoff + 10
         n_skipped += 1
   import numpy

   matrix = numpy.empty((n, n))

   matrix.ravel()[:] = pae_1d
   return matrix


def get_residue_numbers_in_model(m_ca_or_p, remove_offset_of = None):
  residue_numbers = []
  for at in m_ca_or_p.get_hierarchy().atoms():
    resseq_int = at.parent().parent().resseq_as_int()
    if remove_offset_of is not None:
      resseq_int = resseq_int - remove_offset_of
    residue_numbers.append(resseq_int)
  return residue_numbers

def add_model(s1, s2):
  ''' add chains from s2 to existing s1'''
  s1 = s1.deep_copy()
  s1_ph = s1.get_hierarchy() # working hierarchy
  existing_chain_ids = s1_ph.chain_ids()
  for model_mm_2 in s2.get_hierarchy().models()[:1]:
    for chain in model_mm_2.chains():
      assert chain.id not in existing_chain_ids # duplicate chains in add_model
      new_chain = chain.detached_copy()
      for model_mm in s1_ph.models()[:1]:
        model_mm.append_chain(new_chain)

  s1.reset_after_changing_hierarchy()
  return s1
################################################################################
####################   END Convenience functions          ######################
################################################################################

if __name__ == "__main__":
  # run a simple version by default to demo usage
  args = sys.argv[1:]

  master_phil = iotbx.phil.parse(master_phil_str)
  params = master_phil.extract()
  master_phil.format(python_object=params).show(out=sys.stdout)
  p = params.process_predicted_model

  if len(args) < 2:
    print("libtbx.python process_predicted_model.py input.pdb output.pdb")
  else:
    input_file_name = args[0]
    output_file_name = args[1]
    if len(args) > 2:
       p.b_value_field_is = args[2]
    else:
       p.b_value_field_is = 'plddt'
    if len(args) > 3:
       p.domain_size = float(args[3])
    else:
       p.domain_size = 15
    from iotbx.data_manager import DataManager
    dm = DataManager()
    dm.set_overwrite(True)
    m = dm.get_model(input_file_name)

    p.remove_low_confidence_residues = True
    p.maximum_rmsd = 1.5
    p.split_model_by_compact_regions = True

    print("\nProcessing and splitting model into domains")
    model_info = process_predicted_model(m,  params)

    chainid_list = model_info.chainid_list
    print("Segments found: %s" %(" ".join(chainid_list)))

    mmm = model_info.model.as_map_model_manager()
    mmm.write_model(output_file_name)
    for chainid in chainid_list:
      selection_string = "chain %s" %(chainid)
      ph = model_info.model.get_hierarchy()
      asc1 = ph.atom_selection_cache()
      sel = asc1.selection(selection_string)
      m1 = model_info.model.select(sel)
      dm.write_model_file(m1, '%s_%s.pdb' %(output_file_name[:-4],chainid))
