pmi/topology/__init__.py

"""@namespace IMP.pmi.topology
 Set of Python classes to create a multi-state, multi-resolution IMP hierarchy.
* Start by creating a System with
  `model = IMP.Model(); s = IMP.pmi.topology.System(model)`. The System
  will store all the states.
* Then call System.create_state(). You can easily create a multistate system
  by calling this function multiple times.
* For each State, call State.create_molecule() to add a Molecule (a uniquely
  named polymer). This function returns the Molecule object which can be
  passed to various PMI functions.
* Some useful functions to help you set up your Molecules:
 * Access the sequence residues with slicing (Molecule[a:b]) or functions
   like Molecule.get_atomic_residues() and Molecule.get_non_atomic_residues().
   These functions all return Python sets for easy set arithmetic using
   & (and), | (or), - (difference)
 * Molecule.add_structure() to add structural information from a PDB file.
 * Molecule.add_representation() to create a representation unit - here you
   can choose bead resolutions as well as alternate representations like
   densities or ideal helices.
 * Molecule.create_clone() lets you set up a molecule with identical
   representations, just a different chain ID. Use Molecule.create_copy()
   if you want a molecule with the same sequence but that allows custom
   representations.
* Once data has been added and representations chosen, call System.build()
  to create a canonical IMP hierarchy.
* Following hierarchy construction, setup rigid bodies, flexible beads, etc
  in IMP::pmi::dof.
* Check your representation with a nice printout:
  IMP::atom::show_with_representation()

See a [comprehensive example](https://integrativemodeling.org/nightly/doc/ref/pmi_2multiscale_8py-example.html) for using these classes.

Alternatively one can construct the entire topology and degrees of freedom
via formatted text file with TopologyReader and
IMP::pmi::macros::BuildSystem(). This is used in the
[PMI tutorial](@ref rnapolii_stalk). Note that this only allows a limited
set of the full options available to PMI users
(rigid bodies only, fixed resolutions).
"""  # noqa: E501

from __future__ import print_function
import IMP
import IMP.atom
import IMP.algebra
import IMP.pmi
import IMP.pmi.tools
import IMP.pmi.alphabets
import os
import re
from collections import defaultdict, namedtuple
from . import system_tools
from bisect import bisect_left
from math import pi, cos, sin
from operator import itemgetter
import weakref
import warnings


def _build_ideal_helix(model, residues, coord_finder):
    """Creates an ideal helix from the specified residue range
    Residues MUST be contiguous.
    This function actually adds them to the TempResidue hierarchy
    """
    created_hiers = []

    # this function creates a CAlpha helix structure (which can be used
    # for coarsening)
    prev_idx = -9999
    for n, tempres in enumerate(residues):
        if tempres.get_has_structure():
            raise ValueError("You tried to build ideal_helix for a residue "
                             "that already has structure: %s" % tempres)
        if n > 0 and tempres.get_index() != prev_idx + 1:
            raise ValueError(
                "Passed non-contiguous segment to "
                "build_ideal_helix for %s" % tempres.get_molecule())

        # New residue particle will replace the TempResidue's existing
        # (empty) hierarchy
        rp = IMP.Particle(model)
        rp.set_name("Residue_%i" % tempres.get_index())

        # Copy the original residue type and index
        this_res = IMP.atom.Residue.setup_particle(rp, tempres.get_hierarchy())

        # Create the CAlpha
        ap = IMP.Particle(model)
        d = IMP.core.XYZR.setup_particle(ap)
        x = 2.3 * cos(n * 2 * pi / 3.6)
        y = 2.3 * sin(n * 2 * pi / 3.6)
        z = 6.2 / 3.6 / 2 * n * 2 * pi / 3.6
        d.set_coordinates(IMP.algebra.Vector3D(x, y, z))
        d.set_radius(1.0)
        # Decorating as Atom also decorates as Mass
        a = IMP.atom.Atom.setup_particle(ap, IMP.atom.AT_CA)
        IMP.atom.Mass(ap).set_mass(110.0)
        this_res.add_child(a)

        # Add this structure to the TempResidue
        tempres.set_structure(this_res)
        created_hiers.append(this_res)
        prev_idx = tempres.get_index()
    # the coord finder is for placing beads (later)
    coord_finder.add_residues(created_hiers)


class _SystemBase(object):
    """The base class for System, State and Molecule
    classes. It contains shared functions in common to these classes
    """

    def __init__(self, model=None):
        if model is None:
            self.model = IMP.Model()
        else:
            self.model = model

    def _create_hierarchy(self):
        """create a new hierarchy"""
        tmp_part = IMP.Particle(self.model)
        return IMP.atom.Hierarchy.setup_particle(tmp_part)

    def _create_child(self, parent_hierarchy):
        """create a new hierarchy, set it as child of the input
        one, and return it"""
        child_hierarchy = self._create_hierarchy()
        parent_hierarchy.add_child(child_hierarchy)
        return child_hierarchy

    def build(self):
        """Build the coordinates of the system.
        Loop through stored(?) hierarchies and set up coordinates!"""
        pass


class System(_SystemBase):
    """Represent the root node of the global IMP.atom.Hierarchy."""

    _all_systems = set()

    def __init__(self, model=None, name="System"):
        """Constructor.

           @param model The IMP::Model in which to construct this system.
           @param name  The name of the top-level hierarchy node.
        """
        _SystemBase.__init__(self, model)
        self._number_of_states = 0
        self._protocol_output = []
        self.states = []
        self.built = False

        System._all_systems.add(weakref.ref(self))

        # the root hierarchy node
        self.hier = self._create_hierarchy()
        self.hier.set_name(name)
        self.hier._pmi2_system = weakref.ref(self)

    def __del__(self):
        System._all_systems = set(x for x in System._all_systems
                                  if x() not in (None, self))

    def get_states(self):
        """Get a list of all State objects in this system"""
        return self.states

    def create_state(self):
        """Makes and returns a new IMP.pmi.topology.State in this system"""
        self._number_of_states += 1
        state = State(self, self._number_of_states-1)
        self.states.append(state)
        return state

    def __repr__(self):
        return self.hier.get_name()

    def get_number_of_states(self):
        """Returns the total number of states generated"""
        return self._number_of_states

    def get_hierarchy(self):
        """Return the top-level IMP.atom.Hierarchy node for this system"""
        return self.hier

    def build(self, **kwargs):
        """Build all states"""
        if not self.built:
            for state in self.states:
                state.build(**kwargs)
            self.built = True
        return self.hier

    def add_protocol_output(self, p):
        """Capture details of the modeling protocol.
           @param p an instance of IMP.pmi.output.ProtocolOutput or a subclass.
        """
        self._protocol_output.append(p)
#       p._each_metadata.append(self._metadata)
#       p._file_datasets.append(self._file_dataset)
        for state in self.states:
            state._add_protocol_output(p, self)


class State(_SystemBase):
    """Stores a list of Molecules all with the same State index.
    Also stores number of copies of each Molecule for easy selection.
    """
    def __init__(self, system, state_index):
        """Define a new state
        @param system        the PMI System
        @param state_index   the index of the new state
        @note It's expected that you will not use this constructor directly,
        but rather create it with System.create_state()
        """
        self.model = system.get_hierarchy().get_model()
        self.system = system
        self.hier = self._create_child(system.get_hierarchy())
        self.short_name = self.long_name = "State_" + str(state_index)
        self.hier.set_name(self.short_name)
        # key is molecule name. value are the molecule copies!
        self.molecules = IMP.pmi.tools.OrderedDict()
        IMP.atom.State.setup_particle(self.hier, state_index)
        self.built = False
        self._protocol_output = []
        for p in system._protocol_output:
            self._add_protocol_output(p, system)

    def __repr__(self):
        return self.system.__repr__()+'.'+self.hier.get_name()

    def _add_protocol_output(self, p, system):
        state = p._add_state(self)
        self._protocol_output.append((p, state))
        state.model = system.model
        state.prot = self.hier

    def get_molecules(self):
        """Return a dictionary where key is molecule name and value
        is a list of all copies of that molecule in setup order"""
        return self.molecules

    def get_molecule(self, name, copy_num=0):
        """Access a molecule by name and copy number
        @param name The molecule name used during setup
        @param copy_num The copy number based on input order.
        Default: 0. Set to 'all' to get all copies
        """
        if name not in self.molecules:
            raise KeyError("Could not find molname %s" % name)
        if copy_num == 'all':
            return self.molecules[name]
        else:
            return self.molecules[name][copy_num]

    def create_molecule(self, name, sequence='', chain_id='',
                        alphabet=IMP.pmi.alphabets.amino_acid):
        """Create a new Molecule within this State
        @param name                the name of the molecule (string);
                                   it must not be already used
        @param sequence            sequence (string)
        @param chain_id            Chain ID to assign to this molecule
        @param alphabet            Mapping from FASTA codes to residue types
        """
        # check whether the molecule name is already assigned
        if name in self.molecules:
            raise ValueError('Cannot use a molecule name already used')

        # check for something that looks like a copy number
        if re.search(r'\.\d+$', name):
            warnings.warn(
                "It is recommended not to end the molecule name with "
                ".(number) as it may be confused with the copy number "
                "(the copy number for new molecules is always 0, so to "
                "select this molecule, use '%s.0'). Use create_clone() or "
                "create_copy() instead if a copy of an existing molecule "
                "is desired." % name, IMP.pmi.ParameterWarning)

        mol = Molecule(self, name, sequence, chain_id, copy_num=0,
                       alphabet=alphabet)
        self.molecules[name] = [mol]
        return mol

    def get_hierarchy(self):
        """Get the IMP.atom.Hierarchy node for this state"""
        return self.hier

    def get_number_of_copies(self, molname):
        """Get the number of copies of the given molecule (by name)

           @param molname  The name of the molecule
        """
        return len(self.molecules[molname])

    def _register_copy(self, molecule):
        molname = molecule.get_hierarchy().get_name()
        self.molecules[molname].append(molecule)

    def build(self, **kwargs):
        """Build all molecules (automatically makes clones)"""
        if not self.built:
            for molname in self.molecules:
                for mol in reversed(self.molecules[molname]):
                    mol.build(**kwargs)
            self.built = True
        return self.hier


# Track residues read from PDB files
_PDBElement = namedtuple('PDBElement', ['offset', 'filename', 'chain_id'])


class _RepresentationHandler(object):
    """Handle PMI representation and use it to populate that of any attached
       ProtocolOutput objects"""
    def __init__(self, name, pos, pdb_elements):
        self.name = name
        self.pos = pos
        self.last_index = None
        self.last_pdb_index = None
        self.pdb_for_residue = {}
        for residues, pdb in pdb_elements:
            for r in residues:
                self.pdb_for_residue[r.get_index()] = pdb

    def _get_pdb(self, h):
        """Return a PDBElement if the given hierarchy was read from a
           PDB file"""
        if IMP.atom.Residue.get_is_setup(h):
            rind = IMP.atom.Residue(h).get_index()
            return self.pdb_for_residue.get(rind, None)

    def __call__(self, res):
        """Handle a single residue"""
        if len(self.pos) == 0:
            return
        h = res.hier
        pi = h.get_particle_index()
        # Do nothing if we already saw this hierarchy
        if self.last_index is None or pi != self.last_index:
            pdb = self._get_pdb(h)
            self.last_index = pi
            if pdb:
                assert IMP.atom.Fragment.get_is_setup(h.get_parent())
                frag = IMP.atom.Fragment(h.get_parent())
                fragi = frag.get_particle_index()
                # Do nothing if we already saw this PDB fragment
                if self.last_pdb_index is not None \
                   and self.last_pdb_index == fragi:
                    return
                self.last_pdb_index = fragi
                indices = frag.get_residue_indexes()
                for p, state in self.pos:
                    p.add_pdb_element(state, self.name,
                                      indices[0], indices[-1], pdb.offset,
                                      pdb.filename, pdb.chain_id, frag)
            elif IMP.atom.Fragment.get_is_setup(h):
                frag = IMP.atom.Fragment(h)
                indices = frag.get_residue_indexes()
                for p, state in self.pos:
                    p.add_bead_element(state, self.name,
                                       indices[0], indices[-1], 1, h)
            elif IMP.atom.Residue.get_is_setup(h):
                resind = IMP.atom.Residue(h).get_index()
                for p, state in self.pos:
                    p.add_bead_element(state, self.name, resind, resind, 1, h)
            else:
                raise TypeError("Unhandled hierarchy %s" % str(h))


class Molecule(_SystemBase):
    """Stores a named protein chain.
    This class is constructed from within the State class.
    It wraps an IMP.atom.Molecule and IMP.atom.Copy.
    Structure is read using this class.
    Resolutions and copies can be registered, but are only created
    when build() is called.

    A Molecule acts like a simple Python list of residues, and can be indexed
    by integer (starting at zero) or by string (starting at 1).
    """

    def __init__(self, state, name, sequence, chain_id, copy_num,
                 mol_to_clone=None, alphabet=IMP.pmi.alphabets.amino_acid):
        """The user should not call this directly; instead call
           State.create_molecule()

        @param state           The parent PMI State
        @param name            The name of the molecule (string)
        @param sequence        Sequence (string)
        @param chain_id        The chain of this molecule
        @param copy_num        Store the copy number
        @param mol_to_clone    The original molecule (for cloning ONLY)
        @note It's expected that you will not use this constructor directly,
        but rather create a Molecule with State.create_molecule()
        """
        # internal data storage
        self.model = state.get_hierarchy().get_model()
        self.state = state
        self.sequence = sequence
        self.built = False
        self.mol_to_clone = mol_to_clone
        self.alphabet = alphabet
        self.representations = []  # list of stuff to build
        self._pdb_elements = []
        # residues with representation
        self._represented = IMP.pmi.tools.OrderedSet()
        # helps you place beads by storing structure
        self.coord_finder = _FindCloseStructure()
        # list of OrderedSets of tempresidues set to ideal helix
        self._ideal_helices = []

        # create root node and set it as child to passed parent hierarchy
        self.hier = self._create_child(self.state.get_hierarchy())
        self.hier.set_name(name)
        IMP.atom.Copy.setup_particle(self.hier, copy_num)
        self._name_with_copy = "%s.%d" % (name, copy_num)
        # store the sequence
        self.chain = IMP.atom.Chain.setup_particle(self.hier, chain_id)
        self.chain.set_sequence(self.sequence)
        # create TempResidues from the sequence (if passed)
        self.residues = []
        for ns, s in enumerate(sequence):
            r = TempResidue(self, s, ns+1, ns, alphabet)
            self.residues.append(r)

    def __repr__(self):
        return self.state.__repr__() + '.' + self.get_name() + '.' + \
               str(IMP.atom.Copy(self.hier).get_copy_index())

    def __getitem__(self, val):
        if isinstance(val, int):
            return self.residues[val]
        elif isinstance(val, str):
            return self.residues[int(val)-1]
        elif isinstance(val, slice):
            return IMP.pmi.tools.OrderedSet(self.residues[val])
        else:
            raise TypeError("Indexes must be int or str")

    def get_hierarchy(self):
        """Return the IMP Hierarchy corresponding to this Molecule"""
        return self.hier

    def get_name(self):
        """Return this Molecule name"""
        return self.hier.get_name()

    def get_state(self):
        """Return the State containing this Molecule"""
        return self.state

    def get_ideal_helices(self):
        """Returns list of OrderedSets with requested ideal helices"""
        return self._ideal_helices

    def residue_range(self, a, b, stride=1):
        """Get residue range from a to b, inclusive.
        Use integers to get 0-indexing, or strings to get PDB-indexing"""
        if isinstance(a, int) and isinstance(b, int) \
                and isinstance(stride, int):
            return IMP.pmi.tools.OrderedSet(self.residues[a:b+1:stride])
        elif isinstance(a, str) and isinstance(b, str) \
                and isinstance(stride, int):
            return IMP.pmi.tools.OrderedSet(
                self.residues[int(a)-1:int(b):stride])
        else:
            raise TypeError("Range ends must be int or str. "
                            "Stride must be int.")

    def get_residues(self):
        """Return all modeled TempResidues as a set"""
        all_res = IMP.pmi.tools.OrderedSet(self.residues)
        return all_res

    def get_represented(self):
        """Return set of TempResidues that have representation"""
        return self._represented

    def get_atomic_residues(self):
        """Return a set of TempResidues that have associated structure
           coordinates"""
        atomic_res = IMP.pmi.tools.OrderedSet()
        for res in self.residues:
            if res.get_has_structure():
                atomic_res.add(res)
        return atomic_res

    def get_non_atomic_residues(self):
        """Return a set of TempResidues that don't have associated
           structure coordinates"""
        non_atomic_res = IMP.pmi.tools.OrderedSet()
        for res in self.residues:
            if not res.get_has_structure():
                non_atomic_res.add(res)
        return non_atomic_res

    def create_copy(self, chain_id):
        """Create a new Molecule with the same name and sequence but a
        higher copy number. Returns the Molecule. No structure or
        representation will be copied!

        @param chain_id  Chain ID of the new molecule
        """
        mol = Molecule(
            self.state, self.get_name(), self.sequence, chain_id,
            copy_num=self.state.get_number_of_copies(self.get_name()))
        self.state._register_copy(mol)
        return mol

    def create_clone(self, chain_id):
        """Create a Molecule clone (automatically builds same structure
        and representation)

        @param chain_id If you want to set the chain ID of the copy
               to something
        @note You cannot add structure or representations to a clone!
        """
        mol = Molecule(
            self.state, self.get_name(), self.sequence, chain_id,
            copy_num=self.state.get_number_of_copies(self.get_name()),
            mol_to_clone=self)
        self.state._register_copy(mol)
        return mol

    def add_structure(self, pdb_fn, chain_id, res_range=[],
                      offset=0, model_num=None, ca_only=False,
                      soft_check=False):
        """Read a structure and store the coordinates.
        @return the atomic residues (as a set)
        @param pdb_fn     The file to read
        @param chain_id   Chain ID to read
        @param res_range  Add only a specific set of residues from the PDB
                          file. res_range[0] is the starting and res_range[1]
                          is the ending residue index.
        @param offset     Apply an offset to the residue indexes of the PDB
                          file. This number is added to the PDB sequence.
        @param model_num  Read multi-model PDB and return that model
        @param ca_only    Only read the CA positions from the PDB file
        @param soft_check If True, it only warns if there are sequence
                          mismatches between the PDB and the Molecule (FASTA)
                          sequence, and uses the sequence from the PDB.
                          If False (Default), it raises an error when there
                          are sequence mismatches.
        @note If you are adding structure without a FASTA file, set soft_check
              to True.
        """
        if self.mol_to_clone is not None:
            raise ValueError('You cannot call add_structure() for a clone')

        self.pdb_fn = pdb_fn

        # get IMP.atom.Residues from the pdb file
        rhs = system_tools.get_structure(self.model, pdb_fn, chain_id,
                                         res_range, offset,
                                         ca_only=ca_only)
        self.coord_finder.add_residues(rhs)

        if len(self.residues) == 0:
            warnings.warn(
                "Substituting PDB residue type with FASTA residue type. "
                "Potentially dangerous.", IMP.pmi.StructureWarning)

        # Store info for ProtocolOutput usage later
        self._pdb_elements.append(
            (rhs, _PDBElement(offset=offset, filename=pdb_fn,
                              chain_id=chain_id)))

        # load those into TempResidue object
        # collect integer indexes of atomic residues to return
        atomic_res = IMP.pmi.tools.OrderedSet()
        for nrh, rh in enumerate(rhs):
            pdb_idx = rh.get_index()
            raw_idx = pdb_idx - 1

            # add ALA to fill in gaps
            while len(self.residues) < pdb_idx:
                r = TempResidue(self, 'A', len(self.residues)+1,
                                len(self.residues),
                                IMP.pmi.alphabets.amino_acid)
                self.residues.append(r)
                self.sequence += 'A'

            internal_res = self.residues[raw_idx]
            if len(self.sequence) < raw_idx:
                self.sequence += IMP.atom.get_one_letter_code(
                    rh.get_residue_type())
            internal_res.set_structure(rh, soft_check)
            atomic_res.add(internal_res)

        self.chain.set_sequence(self.sequence)
        return atomic_res

    def add_representation(self,
                           residues=None,
                           resolutions=[],
                           bead_extra_breaks=[],
                           bead_ca_centers=True,
                           bead_default_coord=[0, 0, 0],
                           density_residues_per_component=None,
                           density_prefix=None,
                           density_force_compute=False,
                           density_voxel_size=1.0,
                           setup_particles_as_densities=False,
                           ideal_helix=False,
                           color=None):
        """Set the representation for some residues. Some options
        (beads, ideal helix) operate along the backbone. Others (density
        options) are volumetric.
        Some of these you can combine e.g., beads+densities or helix+densities
        See @ref pmi_resolution
        @param residues Set of PMI TempResidues for adding the representation.
               Can use Molecule slicing to get these, e.g. mol[a:b]+mol[c:d]
               If None, will select all residues for this Molecule.
        @param resolutions Resolutions for beads representations.
               If structured, will average along backbone, breaking at
               sequence breaks. If unstructured, will just create beads.
               Pass an integer or list of integers
        @param bead_extra_breaks Additional breakpoints for splitting beads.
               The value can be the 0-ordered position, after which it'll
               insert the break.
               Alternatively pass PDB-style (1-ordered) indices as a string.
               I.e., bead_extra_breaks=[5,25] is the same as ['6','26']
        @param bead_ca_centers Set to True if you want the resolution=1 beads
               to be at CA centers (otherwise will average atoms to get
               center). Defaults to True.
        @param bead_default_coord Advanced feature. Normally beads are placed
               at the nearest structure. If no structure provided (like an
               all bead molecule), the beads go here.
        @param density_residues_per_component Create density (Gaussian
               Mixture Model) for these residues. Must also supply
               density_prefix
        @param density_prefix Prefix (assuming '.txt') to read components
               from or write to.
               If exists, will read unless you set density_force_compute=True.
               Will also write map (prefix+'.mrc').
               Must also supply density_residues_per_component.
        @param density_force_compute Set true to force overwrite density file.
        @param density_voxel_size Advanced feature. Set larger if densities
               taking too long to rasterize.
               Set to 0 if you don't want to create the MRC file
        @param setup_particles_as_densities Set to True if you want each
               particle to be its own density.
               Useful for all-atom models or flexible beads.
               Mutually exclusive with density_ options
        @param ideal_helix Create idealized helix structures for these
               residues at resolution 1.
               Any other resolutions passed will be coarsened from there.
               Resolution 0 will not work; you may have to use MODELLER
               to do that (for now).
        @param color the color applied to the hierarchies generated.
               Format options: tuple (r,g,b) with values 0 to 1;
               float (from 0 to 1, a map from Blue to Green to Red);
               a [Chimera name](https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortables.html);
               a hex RGB string (e.g. "#ff0000");
               an IMP.display.Color object
        @note You cannot call add_representation multiple times for the
              same residues.
        """  # noqa: E501

        # can't customize clones
        if self.mol_to_clone is not None:
            raise ValueError(
                'You cannot call add_representation() for a clone.'
                ' Maybe use a copy instead.')

        # format input
        if residues is None:
            res = IMP.pmi.tools.OrderedSet(self.residues)
        elif residues == self:
            res = IMP.pmi.tools.OrderedSet(self.residues)
        elif type(residues) is IMP.pmi.topology.TempResidue:
            res = IMP.pmi.tools.OrderedSet([residues])
        elif hasattr(residues, '__iter__'):
            if len(residues) == 0:
                raise Exception(
                    'You passed an empty set to add_representation')
            if type(residues) is IMP.pmi.tools.OrderedSet \
               and type(next(iter(residues))) is TempResidue:
                res = residues
            elif (type(residues) is set
                  and type(next(iter(residues))) is TempResidue):
                res = IMP.pmi.tools.OrderedSet(residues)
            elif type(residues) is list and type(residues[0]) is TempResidue:
                res = IMP.pmi.tools.OrderedSet(residues)
            else:
                raise Exception("You passed an iterable of something other "
                                "than TempResidue", res)
        else:
            raise Exception("add_representation: you must pass a set of "
                            "residues or nothing(=all residues)")

        # check that each residue has not been represented yet
        ov = res & self._represented
        if ov:
            raise Exception('You have already added representation for ' +
                            self.get_hierarchy().get_name() + ': ' +
                            ov.__repr__())
        self._represented |= res

        # check you aren't creating multiple resolutions without structure
        if not hasattr(resolutions, '__iter__'):
            if type(resolutions) is int:
                resolutions = [resolutions]
            else:
                raise Exception("you tried to pass resolutions that are not "
                                "int or list-of-int")
        if len(resolutions) > 1 and not ideal_helix:
            for r in res:
                if not r.get_has_structure():
                    raise Exception(
                        'You are creating multiple resolutions for '
                        'unstructured regions. This will have unexpected '
                        'results.')

        # check density info is consistent
        if density_residues_per_component or density_prefix:
            if not density_residues_per_component and density_prefix:
                raise Exception(
                    'If requesting density, must provide '
                    'density_residues_per_component AND density_prefix')
        if density_residues_per_component and setup_particles_as_densities:
            raise Exception(
                'Cannot create both volumetric density '
                '(density_residues_per_component) AND '
                'individual densities (setup_particles_as_densities) '
                'in the same representation')
        if len(resolutions) > 1 and setup_particles_as_densities:
            raise Exception(
                'You have multiple bead resolutions but are attempting to '
                'set them all up as individual Densities. '
                'This could have unexpected results.')

        # check helix not accompanied by other resolutions
        # (densities OK though!)
        if ideal_helix:
            if 0 in resolutions:
                raise Exception(
                    "For ideal helices, cannot build resolution 0: "
                    "you have to do that in MODELLER")
            if 1 not in resolutions:
                resolutions = [1] + list(resolutions)
            self._ideal_helices.append(res)

        # check residues are all part of this molecule:
        for r in res:
            if r.get_molecule() != self:
                raise Exception(
                    'You are adding residues from a different molecule to',
                    self.__repr__())

        # unify formatting for extra breaks
        breaks = []
        for b in bead_extra_breaks:
            if type(b) == str:
                breaks.append(int(b)-1)
            else:
                breaks.append(b)
        # store the representation group
        self.representations.append(_Representation(
            res, resolutions, breaks, bead_ca_centers, bead_default_coord,
            density_residues_per_component, density_prefix,
            density_force_compute, density_voxel_size,
            setup_particles_as_densities, ideal_helix, color))

    def _all_protocol_output(self):
        return self.state._protocol_output

    def build(self):
        """Create all parts of the IMP hierarchy
        including Atoms, Residues, and Fragments/Representations and,
        finally, Copies.
        Will only build requested representations.
        @note Any residues assigned a resolution must have an IMP.atom.Residue
              hierarchy containing at least a CAlpha. For missing residues,
              these can be constructed from the PDB file.
        """
        if not self.built:
            # Add molecule name and sequence to any ProtocolOutput objects
            name = self.hier.get_name()
            for po, state in self._all_protocol_output():
                po.create_component(state, name, True,
                                    asym_name=self._name_with_copy)
                po.add_component_sequence(state, name, self.sequence,
                                          asym_name=self._name_with_copy,
                                          alphabet=self.alphabet)
            # if requested, clone structure and representations
            # BEFORE building original
            if self.mol_to_clone is not None:
                for nr, r in enumerate(self.mol_to_clone.residues):
                    if r.get_has_structure():
                        clone = IMP.atom.create_clone(r.get_hierarchy())
                        self.residues[nr].set_structure(
                            IMP.atom.Residue(clone), soft_check=True)
                for old_rep in self.mol_to_clone.representations:
                    new_res = IMP.pmi.tools.OrderedSet()
                    for r in old_rep.residues:
                        new_res.add(self.residues[r.get_internal_index()])
                        self._represented.add(
                            self.residues[r.get_internal_index()])
                    new_rep = _Representation(
                        new_res, old_rep.bead_resolutions,
                        old_rep.bead_extra_breaks, old_rep.bead_ca_centers,
                        old_rep.bead_default_coord,
                        old_rep.density_residues_per_component,
                        old_rep.density_prefix, False,
                        old_rep.density_voxel_size,
                        old_rep.setup_particles_as_densities,
                        old_rep.ideal_helix, old_rep.color)
                    self.representations.append(new_rep)
                self.coord_finder = self.mol_to_clone.coord_finder

            # give a warning for all residues that don't have representation
            no_rep = [r for r in self.residues if r not in self._represented]
            if len(no_rep) > 0:
                warnings.warn(
                    'Residues without representation in molecule %s: %s'
                    % (self.get_name(), system_tools.resnums2str(no_rep)),
                    IMP.pmi.StructureWarning)

            # first build any ideal helices (fills in structure for
            # the TempResidues)
            for rep in self.representations:
                if rep.ideal_helix:
                    _build_ideal_helix(self.model, rep.residues,
                                       self.coord_finder)

            # build all the representations
            built_reps = []

            rephandler = _RepresentationHandler(
                self._name_with_copy, list(self._all_protocol_output()),
                self._pdb_elements)

            for rep in self.representations:
                built_reps += system_tools.build_representation(
                    self, rep, self.coord_finder, rephandler)

            # sort them before adding as children
            built_reps.sort(
                key=lambda r: IMP.atom.Fragment(r).get_residue_indexes()[0])
            for br in built_reps:
                self.hier.add_child(br)
                br.update_parents()
            self.built = True

            for res in self.residues:
                # first off, store the highest resolution available
                # in residue.hier
                new_ps = IMP.atom.Selection(
                    self.hier,
                    residue_index=res.get_index(),
                    resolution=1).get_selected_particles()
                if len(new_ps) > 0:
                    new_p = new_ps[0]
                    if IMP.atom.Atom.get_is_setup(new_p):
                        # if only found atomic, store the residue
                        new_hier = IMP.atom.get_residue(IMP.atom.Atom(new_p))
                    else:
                        # otherwise just store what you found
                        new_hier = IMP.atom.Hierarchy(new_p)
                    res.hier = new_hier
                    rephandler(res)
                else:
                    res.hier = None
            self._represented = IMP.pmi.tools.OrderedSet(
                [a for a in self._represented])
        print('done building', self.get_hierarchy())
        return self.hier

    def get_particles_at_all_resolutions(self, residue_indexes=None):
        """Helpful utility for getting particles at all resolutions from
           this molecule. Can optionally pass a set of residue indexes"""
        if not self.built:
            raise Exception(
                "Cannot get all resolutions until you build the Molecule")
        if residue_indexes is None:
            residue_indexes = [r.get_index() for r in self.get_residues()]
        ps = IMP.pmi.tools.select_at_all_resolutions(
            self.get_hierarchy(), residue_indexes=residue_indexes)
        return ps


class _Representation(object):
    """Private class just to store a representation request"""
    def __init__(self,
                 residues,
                 bead_resolutions,
                 bead_extra_breaks,
                 bead_ca_centers,
                 bead_default_coord,
                 density_residues_per_component,
                 density_prefix,
                 density_force_compute,
                 density_voxel_size,
                 setup_particles_as_densities,
                 ideal_helix,
                 color):
        self.residues = residues
        self.bead_resolutions = bead_resolutions
        self.bead_extra_breaks = bead_extra_breaks
        self.bead_ca_centers = bead_ca_centers
        self.bead_default_coord = bead_default_coord
        self.density_residues_per_component = density_residues_per_component
        self.density_prefix = density_prefix
        self.density_force_compute = density_force_compute
        self.density_voxel_size = density_voxel_size
        self.setup_particles_as_densities = setup_particles_as_densities
        self.ideal_helix = ideal_helix
        self.color = color


class _FindCloseStructure(object):
    """Utility to get the nearest observed coordinate"""
    def __init__(self):
        self.coords = []

    def add_residues(self, residues):
        for r in residues:
            idx = IMP.atom.Residue(r).get_index()
            catypes = [IMP.atom.AT_CA, system_tools._AT_HET_CA]
            ca = IMP.atom.Selection(
                r, atom_types=catypes).get_selected_particles()
            p = IMP.atom.Selection(
                r, atom_type=IMP.atom.AtomType("P")).get_selected_particles()
            if len(ca) == 1:
                xyz = IMP.core.XYZ(ca[0]).get_coordinates()
                self.coords.append([idx, xyz])
            elif len(p) == 1:
                xyz = IMP.core.XYZ(p[0]).get_coordinates()
                self.coords.append([idx, xyz])
            else:
                raise ValueError("_FindCloseStructure: wrong selection")

        self.coords.sort(key=itemgetter(0))

    def find_nearest_coord(self, query):
        if self.coords == []:
            return None
        keys = [r[0] for r in self.coords]
        pos = bisect_left(keys, query)
        if pos == 0:
            ret = self.coords[0]
        elif pos == len(self.coords):
            ret = self.coords[-1]
        else:
            before = self.coords[pos - 1]
            after = self.coords[pos]
            if after[0] - query < query - before[0]:
                ret = after
            else:
                ret = before
        return ret[1]


class Sequences(object):
    """A dictionary-like wrapper for reading and storing sequence data.
       Keys are FASTA sequence names, and each value a string of one-letter
       codes."""
    def __init__(self, fasta_fn, name_map=None):
        """Read a FASTA file and extract all the requested sequences
        @param fasta_fn sequence file
        @param name_map dictionary mapping the FASTA name to final stored name
        """
        self.sequences = IMP.pmi.tools.OrderedDict()
        self.read_sequences(fasta_fn, name_map)

    def __len__(self):
        return len(self.sequences)

    def __contains__(self, x):
        return x in self.sequences

    def __getitem__(self, key):
        if type(key) is int:
            allseqs = list(self.sequences.keys())
            try:
                return self.sequences[allseqs[key]]
            except IndexError:
                raise IndexError("You tried to access sequence number %d "
                                 "but there's only %d" % (key, len(allseqs)))
        else:
            return self.sequences[key]

    def __iter__(self):
        return self.sequences.__iter__()

    def __repr__(self):
        ret = ''
        for s in self.sequences:
            ret += '%s\t%s\n' % (s, self.sequences[s])
        return ret

    def read_sequences(self, fasta_fn, name_map=None):
        code = None
        seq = None
        with open(fasta_fn, 'r') as fh:
            for (num, line) in enumerate(fh):
                if line.startswith('>'):
                    if seq is not None:
                        self.sequences[code] = seq.strip('*')
                    code = line.rstrip()[1:]
                    if name_map is not None:
                        try:
                            code = name_map[code]
                        except KeyError:
                            pass
                    seq = ''
                else:
                    line = line.rstrip()
                    if line:  # Skip blank lines
                        if seq is None:
                            raise Exception(
                                "Found FASTA sequence before first header "
                                "at line %d: %s" % (num + 1, line))
                        seq += line
        if seq is not None:
            self.sequences[code] = seq.strip('*')


class PDBSequences(object):
    """Data structure for reading and storing sequence data from PDBs.

       @see fasta_pdb_alignments."""
    def __init__(self, model, pdb_fn, name_map=None):
        """Read a PDB file and return all sequences for each contiguous
           fragment
        @param pdb_fn  file
        @param name_map dictionary mapping the pdb chain id to final
               stored name
        """
        self.model = model
        # self.sequences data-structure: (two-key dictionary)
        # it contains all contiguous fragments:
        # chain_id, tuples indicating first and last residue, sequence
        # example:
        # key1, key2, value
        # A (77, 149) VENPSLDLEQYAASYSGLMR....
        # A (160, 505) PALDTAWVEATRKKALLKLEKLDTDLKNYKGNSIK.....
        # B (30, 180) VDLENQYYNSKALKEDDPKAALSSFQKVLELEGEKGEWGF...
        # B (192, 443) TQLLEIYALEIQMYTAQKNNKKLKALYEQSLHIKSAIPHPL
        self.sequences = IMP.pmi.tools.OrderedDict()
        self.read_sequences(pdb_fn, name_map)

    def read_sequences(self, pdb_fn, name_map):
        read_file = IMP.atom.read_pdb
        if pdb_fn.endswith('.cif'):
            read_file = IMP.atom.read_mmcif
        t = read_file(pdb_fn, self.model, IMP.atom.ATOMPDBSelector())
        cs = IMP.atom.get_by_type(t, IMP.atom.CHAIN_TYPE)
        for c in cs:
            id = IMP.atom.Chain(c).get_id()
            print(id)
            if name_map:
                try:
                    id = name_map[id]
                except KeyError:
                    print("Chain ID %s not in name_map, skipping" % id)
                    continue
            rs = IMP.atom.get_by_type(c, IMP.atom.RESIDUE_TYPE)
            rids = []
            rids_olc_dict = {}
            for r in rs:
                dr = IMP.atom.Residue(r)
                rid = dr.get_index()

                isprotein = dr.get_is_protein()
                isrna = dr.get_is_rna()
                isdna = dr.get_is_dna()
                if isprotein:
                    olc = IMP.atom.get_one_letter_code(dr.get_residue_type())
                    rids.append(rid)
                    rids_olc_dict[rid] = olc
                elif isdna:
                    if dr.get_residue_type() == IMP.atom.DADE:
                        olc = "A"
                    if dr.get_residue_type() == IMP.atom.DURA:
                        olc = "U"
                    if dr.get_residue_type() == IMP.atom.DCYT:
                        olc = "C"
                    if dr.get_residue_type() == IMP.atom.DGUA:
                        olc = "G"
                    if dr.get_residue_type() == IMP.atom.DTHY:
                        olc = "T"
                    rids.append(rid)
                    rids_olc_dict[rid] = olc
                elif isrna:
                    if dr.get_residue_type() == IMP.atom.ADE:
                        olc = "A"
                    if dr.get_residue_type() == IMP.atom.URA:
                        olc = "U"
                    if dr.get_residue_type() == IMP.atom.CYT:
                        olc = "C"
                    if dr.get_residue_type() == IMP.atom.GUA:
                        olc = "G"
                    if dr.get_residue_type() == IMP.atom.THY:
                        olc = "T"
                    rids.append(rid)
                    rids_olc_dict[rid] = olc
            group_rids = self.group_indexes(rids)
            contiguous_sequences = IMP.pmi.tools.OrderedDict()
            for group in group_rids:
                sequence_fragment = ""
                for i in range(group[0], group[1]+1):
                    sequence_fragment += rids_olc_dict[i]
                contiguous_sequences[group] = sequence_fragment
            self.sequences[id] = contiguous_sequences

    def group_indexes(self, indexes):
        from itertools import groupby
        ranges = []
        for k, g in groupby(enumerate(indexes), lambda x: x[0]-x[1]):
            group = [x[1] for x in g]
            ranges.append((group[0], group[-1]))
        return ranges


def fasta_pdb_alignments(fasta_sequences, pdb_sequences, show=False):
    '''This function computes and prints the alignment between the
    fasta file and the pdb sequence, computes the offsets for each contiguous
    fragment in the PDB.
    @param fasta_sequences  IMP.pmi.topology.Sequences object
    @param pdb_sequences IMP.pmi.topology.PDBSequences object
    @param show boolean default False, if True prints the alignments.
    The input objects should be generated using map_name dictionaries
    such that fasta_id
    and pdb_chain_id are mapping to the same protein name. It needs BioPython.
    Returns a dictionary of offsets, organized by peptide range (group):
    example: offsets={"ProtA":{(1,10):1,(20,30):10}}'''
    from Bio import pairwise2
    from Bio.pairwise2 import format_alignment
    if type(fasta_sequences) is not IMP.pmi.topology.Sequences:
        raise Exception("Fasta sequences not type IMP.pmi.topology.Sequences")
    if type(pdb_sequences) is not IMP.pmi.topology.PDBSequences:
        raise Exception("pdb sequences not type IMP.pmi.topology.PDBSequences")
    offsets = IMP.pmi.tools.OrderedDict()
    for name in fasta_sequences.sequences:
        print(name)
        seq_fasta = fasta_sequences.sequences[name]
        if name not in pdb_sequences.sequences:
            print("Fasta id %s not in pdb names, aligning against every "
                  "pdb chain" % name)
            pdbnames = pdb_sequences.sequences.keys()
        else:
            pdbnames = [name]
        for pdbname in pdbnames:
            for group in pdb_sequences.sequences[pdbname]:
                if group[1] - group[0] + 1 < 7:
                    continue
                seq_frag_pdb = pdb_sequences.sequences[pdbname][group]
                if show:
                    print("########################")
                    print(" ")
                    print("protein name", pdbname)
                    print("fasta id", name)
                    print("pdb fragment", group)
                align = pairwise2.align.localms(seq_fasta, seq_frag_pdb,
                                                2, -1, -.5, -.1)[0]
                for a in [align]:
                    offset = a[3] + 1 - group[0]
                    if show:
                        print("alignment sequence start-end",
                              (a[3] + 1, a[4] + 1))
                        print("offset from pdb to fasta index", offset)
                        print(format_alignment(*a))
                    if name not in offsets:
                        offsets[pdbname] = {}
                        if group not in offsets[pdbname]:
                            offsets[pdbname][group] = offset
                    else:
                        if group not in offsets[pdbname]:
                            offsets[pdbname][group] = offset
    return offsets


class TempResidue(object):
    "Temporarily stores residue information, even without structure available."
    # Consider implementing __hash__ so you can select.
    def __init__(self, molecule, code, index, internal_index, alphabet):
        """setup a TempResidue
        @param molecule PMI Molecule to which this residue belongs
        @param code     one-letter residue type code
        @param index    PDB index
        @param internal_index The number in the sequence
        """
        # these attributes should be immutable
        self.molecule = molecule
        self.rtype = alphabet.get_residue_type_from_one_letter_code(code)
        self.pdb_index = index
        self.internal_index = internal_index
        self.copy_index = IMP.atom.Copy(self.molecule.hier).get_copy_index()
        self.state_index = \
            IMP.atom.State(self.molecule.state.hier).get_state_index()
        # these are expected to change
        self._structured = False
        self.hier = IMP.atom.Residue.setup_particle(
            IMP.Particle(molecule.model), self.rtype, index)

    def __str__(self):
        return str(self.state_index) + "_" + self.molecule.get_name() + "_" \
               + str(self.copy_index) + "_" + self.get_code() \
               + str(self.get_index())

    def __repr__(self):
        return self.__str__()

    def __key(self):
        # this returns the immutable attributes only
        return (self.state_index, self.molecule, self.copy_index, self.rtype,
                self.pdb_index, self.internal_index)

    def __eq__(self, other):
        return type(other) == type(self) and self.__key() == other.__key()

    def __hash__(self):
        return hash(self.__key())

    def get_index(self):
        return self.pdb_index

    def get_internal_index(self):
        return self.internal_index

    def get_code(self):
        return IMP.atom.get_one_letter_code(self.get_residue_type())

    def get_residue_type(self):
        return self.rtype

    def get_hierarchy(self):
        return self.hier

    def get_molecule(self):
        return self.molecule

    def get_has_structure(self):
        return self._structured

    def set_structure(self, res, soft_check=False):
        if res.get_residue_type() != self.get_residue_type():
            if (res.get_residue_type() == IMP.atom.MSE
                    and self.get_residue_type() == IMP.atom.MET):
                # MSE in the PDB file is OK to match with MET in the FASTA
                # sequence
                pass
            elif soft_check:
                # note from commit a2c13eaa1 we give priority to the
                # FASTA and not the PDB
                warnings.warn(
                    'Inconsistency between FASTA sequence and PDB sequence. '
                    'FASTA type %s %s and PDB type %s'
                    % (self.get_index(), self.hier.get_residue_type(),
                       res.get_residue_type()),
                    IMP.pmi.StructureWarning)
                self.hier.set_residue_type((self.get_residue_type()))
                self.rtype = self.get_residue_type()
            else:
                raise Exception(
                    'ERROR: PDB residue index', self.get_index(), 'is',
                    IMP.atom.get_one_letter_code(res.get_residue_type()),
                    'and sequence residue is', self.get_code())

        for a in res.get_children():
            self.hier.add_child(a)
            atype = IMP.atom.Atom(a).get_atom_type()
            a.get_particle().set_name(
                'Atom %s of residue %i' % (atype.__str__().strip('"'),
                                           self.hier.get_index()))
        self._structured = True


class TopologyReader(object):
    """Automatically setup Sytem and Degrees of Freedom with a formatted
       text file.
    The file is read in and each part of the topology is stored as a
    ComponentTopology object for input into IMP::pmi::macros::BuildSystem.
    The topology file should be in a simple pipe-delimited format:
    @code{.txt}
|molecule_name|color|fasta_fn|fasta_id|pdb_fn|chain|residue_range|pdb_offset|bead_size|em_residues_per_gaussian|rigid_body|super_rigid_body|chain_of_super_rigid_bodies|flags|
|Rpb1   |blue   |1WCM.fasta|1WCM:A|1WCM.pdb|A|1,1140   |0|10|0|1|1,3|1||
|Rpb1   |blue   |1WCM.fasta|1WCM:A|1WCM.pdb|A|1141,1274|0|10|0|2|1,3|1||
|Rpb1   |blue   |1WCM.fasta|1WCM:A|1WCM.pdb|A|1275,END |0|10|0|3|1,3|1||
|Rpb2   |red    |1WCM.fasta|1WCM:B|1WCM.pdb|B|all      |0|10|0|4|2,3|2||
|Rpb2.1 |green  |1WCM.fasta|1WCM:B|1WCM.pdb|B|all      |0|10|0|4|2,3|2||

    @endcode

    These are the fields you can enter:
    - `molecule_name`: Name of the molecule (chain). Serves as the parent
      hierarchy for this structure. Multiple copies of the same molecule
      can be created by appending a copy number after a period; if none is
      specified, a copy number of 0 is assumed (e.g. Rpb2.1 is the second copy
      of Rpb2 or Rpb2.0).
    - `color`: The color used in the output RMF file. Uses
      [Chimera names](https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortables.html),
      (e.g. "red"), or R,G,B values as three comma-separated floating point
      numbers from 0 to 1 (e.g. "1.0, 0.0, 0.0") or a 6-digit hex string
      starting with '#' (e.g. #ff0000).
    - `fasta_fn`: Name of FASTA file containing this component.
    - `fasta_id`: String found in FASTA sequence header line. The sequence read
      from the file is assumed to be a protein sequence. If it should instead
      be treated as RNA or DNA, add an ',RNA' or ',DNA' suffix. For example,
      a `fasta_id` of 'myseq,RNA' will read the sequence 'myseq' from the
      FASTA file and treat it as RNA.
    - `pdb_fn`: Name of PDB or mmCIF file with coordinates (if available).
       If left empty, will set up as BEADS (you can also specify "BEADS")
       Can also write "IDEAL_HELIX".
    - `chain`: Chain ID of this domain in the PDB file.
    - `residue_range`: Comma delimited pair defining range.
       Can leave empty or use 'all' for entire sequence from PDB file.
       The second item in the pair can be END to select the last residue in the
       PDB chain.
    - `pdb_offset`: Offset to sync PDB residue numbering with FASTA numbering.
      For example, an offset of -10 would match the first residue in the
      FASTA file (which is always numbered sequentially starting from 1) with
      residue 11 in the PDB file.
    - `bead_size`: The size (in residues) of beads used to model areas not
      covered by PDB coordinates. These will be built automatically.
    - `em_residues`: The number of Gaussians used to model the electron
      density of this domain. Set to zero if no EM fitting will be done.
      The GMM files will be written to <gmm_dir>/<component_name>_<em_res>.txt
      (and .mrc)
    - `rigid_body`: Leave empty if this object is not in a rigid body.
       Otherwise, this is a number corresponding to the rigid body containing
       this object. The number itself is just used for grouping things.
    - `super_rigid_body`: Add a mover that periodically moves several related
      domains as if they were a single large rigid body. In between such moves,
      the domains move independently. This can improve sampling.
    - `chain_of_super_rigid_bodies`: Do super-rigid-body moves (as above)
      for all adjacent pairs of domains in the chain.
    - `flags` additional flags for advanced options
    @note All filenames are relative to the paths specified in the constructor.

    """  # noqa: E501
    def __init__(self, topology_file, pdb_dir='./', fasta_dir='./',
                 gmm_dir='./'):
        """Constructor.
        @param topology_file Pipe-delimited file specifying the topology
        @param pdb_dir Relative path to the pdb directory
        @param fasta_dir Relative path to the fasta directory
        @param gmm_dir Relative path to the GMM directory
        """
        self.topology_file = topology_file
        # key=molname, value=TempMolecule
        self.molecules = IMP.pmi.tools.OrderedDict()
        self.pdb_dir = pdb_dir
        self.fasta_dir = fasta_dir
        self.gmm_dir = gmm_dir
        self._components = self.read(topology_file)

    def write_topology_file(self, outfile):
        with open(outfile, "w") as f:
            f.write("|molecule_name|color|fasta_fn|fasta_id|pdb_fn|chain|"
                    "residue_range|pdb_offset|bead_size|"
                    "em_residues_per_gaussian|rigid_body|super_rigid_body|"
                    "chain_of_super_rigid_bodies|\n")
            for c in self._components:
                output = c.get_str()+'\n'
                f.write(output)
        return outfile

    def get_components(self, topology_list="all"):
        """ Return list of ComponentTopologies for selected components
        @param topology_list List of indices to return"""
        if topology_list == "all":
            topologies = self._components
        else:
            topologies = []
            for i in topology_list:
                topologies.append(self._components[i])
        return topologies

    def get_molecules(self):
        return self.molecules

    def read(self, topology_file, append=False):
        """Read system components from topology file. append=False will erase
        current topology and overwrite with new
        """
        is_topology = False
        is_directories = False
        linenum = 1
        if not append:
            self._components = []

        with open(topology_file) as infile:
            for line in infile:
                if line.lstrip() == "" or line[0] == "#":
                    continue
                elif line.split('|')[1].strip() in ("molecule_name"):
                    is_topology = True
                    is_directories = False
                    old_format = False
                    continue
                elif line.split('|')[1] == "component_name":
                    is_topology = True
                    IMP.handle_use_deprecated(
                          "Old-style topology format (using "
                          "|component_name|) is deprecated. Please switch to "
                          "the new-style format (using |molecule_name|)\n")
                    old_format = True
                    is_directories = False
                    continue
                elif line.split('|')[1] == "directories":
                    IMP.handle_use_deprecated(
                          "Setting directories in the topology file "
                          "is deprecated. Please do so through the "
                          "TopologyReader constructor. Note that new-style "
                          "paths are relative to the current working "
                          "directory, not the topology file.\n")
                    is_directories = True
                elif is_directories:
                    fields = line.split('|')
                    setattr(self, fields[1],
                            IMP.get_relative_path(topology_file, fields[2]))
                if is_topology:
                    new_component = self._parse_line(line, linenum, old_format)
                    self._components.append(new_component)
                    linenum += 1
        return self._components

    def _parse_line(self, component_line, linenum, old_format):
        """Parse a line of topology values and matches them to their key.
        Checks each value for correct syntax
        Returns a list of Component objects
        fields:
        """
        c = _Component()
        values = [s.strip() for s in component_line.split('|')]
        errors = []

        # Required fields
        if old_format:
            c.molname = values[1]
            c.copyname = ''
            c._domain_name = values[2]
            c.color = 'blue'
        else:
            names = values[1].split('.')
            if len(names) == 1:
                c.molname = names[0]
                c.copyname = ''
            elif len(names) == 2:
                c.molname = names[0]
                c.copyname = names[1]
            else:
                c.molname = names[0]
                c.copyname = names[1]
                errors.append("Molecule name should be <molecule.copyID>")
                errors.append("For component %s line %d "
                              % (c.molname, linenum))
            c._domain_name = c.molname + '.' + c.copyname
            colorfields = values[2].split(',')
            if len(colorfields) == 3:
                c.color = [float(x) for x in colorfields]
                if any([x > 1 for x in c.color]):
                    c.color = [x/255 for x in c.color]
            else:
                c.color = values[2]
        c._orig_fasta_file = values[3]
        c.fasta_file = values[3]
        fasta_field = values[4].split(",")
        c.fasta_id = fasta_field[0]
        c.fasta_flag = None
        if len(fasta_field) > 1:
            c.fasta_flag = fasta_field[1]
        c._orig_pdb_input = values[5]
        pdb_input = values[5]
        tmp_chain = values[6]
        rr = values[7]
        offset = values[8]
        bead_size = values[9]
        emg = values[10]
        if old_format:
            rbs = srbs = csrbs = ''
        else:
            rbs = values[11]
            srbs = values[12]
            csrbs = values[13]

        if c.molname not in self.molecules:
            self.molecules[c.molname] = _TempMolecule(c)
        else:
            # COPY OR DOMAIN
            c._orig_fasta_file = \
                self.molecules[c.molname].orig_component._orig_fasta_file
            c.fasta_id = self.molecules[c.molname].orig_component.fasta_id
            self.molecules[c.molname].add_component(c, c.copyname)

        # now cleanup input
        c.fasta_file = os.path.join(self.fasta_dir, c._orig_fasta_file)
        if pdb_input == "":
            errors.append("PDB must have BEADS, IDEAL_HELIX, or filename")
            errors.append("For component %s line %d is not correct"
                          "|%s| was given." % (c.molname, linenum, pdb_input))
        elif pdb_input in ("IDEAL_HELIX", "BEADS"):
            c.pdb_file = pdb_input
        else:
            c.pdb_file = os.path.join(self.pdb_dir, pdb_input)

            # PDB chain must be one or two characters
            if len(tmp_chain) == 1 or len(tmp_chain) == 2:
                c.chain = tmp_chain
            else:
                errors.append(
                    "PDB Chain identifier must be one or two characters.")
                errors.append("For component %s line %d is not correct"
                              "|%s| was given."
                              % (c.molname, linenum, tmp_chain))

        # Optional fields
        # Residue Range
        if rr.strip() == 'all' or str(rr) == "":
            c.residue_range = None
        elif (len(rr.split(',')) == 2 and self._is_int(rr.split(',')[0]) and
              (self._is_int(rr.split(',')[1]) or rr.split(',')[1] == 'END')):
            # Make sure that is residue range is given, there are only
            # two values and they are integers
            c.residue_range = (int(rr.split(',')[0]), rr.split(',')[1])
            if c.residue_range[1] != 'END':
                c.residue_range = (c.residue_range[0], int(c.residue_range[1]))
            # Old format used -1 for the last residue
            if old_format and c.residue_range[1] == -1:
                c.residue_range = (c.residue_range[0], 'END')
        else:
            errors.append("Residue Range format for component %s line %d is "
                          "not correct" % (c.molname, linenum))
            errors.append(
                "Correct syntax is two comma separated integers:  "
                "|start_res, end_res|. end_res can also be END to select the "
                "last residue in the chain. |%s| was given." % rr)
            errors.append("To select all residues, indicate |\"all\"|")

        # PDB Offset
        if self._is_int(offset):
            c.pdb_offset = int(offset)
        elif len(offset) == 0:
            c.pdb_offset = 0
        else:
            errors.append("PDB Offset format for component %s line %d is "
                          "not correct" % (c.molname, linenum))
            errors.append("The value must be a single integer. |%s| was given."
                          % offset)

        # Bead Size
        if self._is_int(bead_size):
            c.bead_size = int(bead_size)
        elif len(bead_size) == 0:
            c.bead_size = 0
        else:
            errors.append("Bead Size format for component %s line %d is "
                          "not correct" % (c.molname, linenum))
            errors.append("The value must be a single integer. |%s| was given."
                          % bead_size)

        # EM Residues Per Gaussian
        if self._is_int(emg):
            if int(emg) > 0:
                c.density_prefix = os.path.join(self.gmm_dir,
                                                c.get_unique_name())
                c.gmm_file = c.density_prefix + '.txt'
                c.mrc_file = c.density_prefix + '.gmm'

                c.em_residues_per_gaussian = int(emg)
            else:
                c.em_residues_per_gaussian = 0
        elif len(emg) == 0:
            c.em_residues_per_gaussian = 0
        else:
            errors.append("em_residues_per_gaussian format for component "
                          "%s line %d is not correct" % (c.molname, linenum))
            errors.append("The value must be a single integer. |%s| was given."
                          % emg)

        # rigid bodies
        if len(rbs) > 0:
            if not self._is_int(rbs):
                errors.append(
                    "rigid bodies format for component "
                    "%s line %d is not correct" % (c.molname, linenum))
                errors.append("Each RB must be a single integer, or empty. "
                              "|%s| was given." % rbs)
            c.rigid_body = int(rbs)

        # super rigid bodies
        if len(srbs) > 0:
            srbs = srbs.split(',')
            for i in srbs:
                if not self._is_int(i):
                    errors.append(
                        "super rigid bodies format for component "
                        "%s line %d is not correct" % (c.molname, linenum))
                    errors.append(
                        "Each SRB must be a single integer. |%s| was given."
                        % srbs)
            c.super_rigid_bodies = srbs

        # chain of super rigid bodies
        if len(csrbs) > 0:
            if not self._is_int(csrbs):
                errors.append(
                    "em_residues_per_gaussian format for component "
                    "%s line %d is not correct" % (c.molname, linenum))
                errors.append(
                    "Each CSRB must be a single integer. |%s| was given."
                    % csrbs)
            c.chain_of_super_rigid_bodies = csrbs

        # done
        if errors:
            raise ValueError("Fix Topology File syntax errors and rerun: "
                             + "\n".join(errors))
        else:
            return c

    def set_gmm_dir(self, gmm_dir):
        """Change the GMM dir"""
        self.gmm_dir = gmm_dir
        for c in self._components:
            c.gmm_file = os.path.join(self.gmm_dir,
                                      c.get_unique_name() + ".txt")
            c.mrc_file = os.path.join(self.gmm_dir,
                                      c.get_unique_name() + ".mrc")
            print('new gmm', c.gmm_file)

    def set_pdb_dir(self, pdb_dir):
        """Change the PDB dir"""
        self.pdb_dir = pdb_dir
        for c in self._components:
            if c._orig_pdb_input not in ("", "None", "IDEAL_HELIX", "BEADS"):
                c.pdb_file = os.path.join(self.pdb_dir, c._orig_pdb_input)

    def set_fasta_dir(self, fasta_dir):
        """Change the FASTA dir"""
        self.fasta_dir = fasta_dir
        for c in self._components:
            c.fasta_file = os.path.join(self.fasta_dir, c._orig_fasta_file)

    def _is_int(self, s):
        # is this string an integer?
        try:
            float(s)
            return float(s).is_integer()
        except ValueError:
            return False

    def get_rigid_bodies(self):
        """Return list of lists of rigid bodies (as domain name)"""
        rbl = defaultdict(list)
        for c in self._components:
            if c.rigid_body:
                rbl[c.rigid_body].append(c.get_unique_name())
        return rbl.values()

    def get_super_rigid_bodies(self):
        """Return list of lists of super rigid bodies (as domain name)"""
        rbl = defaultdict(list)
        for c in self._components:
            for rbnum in c.super_rigid_bodies:
                rbl[rbnum].append(c.get_unique_name())
        return rbl.values()

    def get_chains_of_super_rigid_bodies(self):
        "Return list of lists of chains of super rigid bodies (as domain name)"
        rbl = defaultdict(list)
        for c in self._components:
            for rbnum in c.chain_of_super_rigid_bodies:
                rbl[rbnum].append(c.get_unique_name())
        return rbl.values()


class _TempMolecule(object):
    """Store the Components and any requests for copies"""
    def __init__(self, init_c):
        self.molname = init_c.molname
        self.domains = IMP.pmi.tools.OrderedDefaultDict(list)
        self.add_component(init_c, init_c.copyname)
        self.orig_copyname = init_c.copyname
        self.orig_component = self.domains[init_c.copyname][0]

    def add_component(self, component, copy_id):
        self.domains[copy_id].append(component)
        component.domainnum = len(self.domains[copy_id])-1

    def __repr__(self):
        return ','.join('%s:%i'
                        % (k, len(self.domains[k])) for k in self.domains)


class _Component(object):
    """Stores the components required to build a standard IMP hierarchy
    using IMP.pmi.BuildModel()
    """
    def __init__(self):
        self.molname = None
        self.copyname = None
        self.domainnum = 0
        self.fasta_file = None
        self._orig_fasta_file = None
        self.fasta_id = None
        self.fasta_flag = None
        self.pdb_file = None
        self._orig_pdb_input = None
        self.chain = None
        self.residue_range = None
        self.pdb_offset = 0
        self.bead_size = 10
        self.em_residues_per_gaussian = 0
        self.gmm_file = ''
        self.mrc_file = ''
        self.density_prefix = ''
        self.color = 0.1
        self.rigid_body = None
        self.super_rigid_bodies = []
        self.chain_of_super_rigid_bodies = []

    def _l2s(self, rng):
        return ",".join("%s" % x for x in rng)

    def __repr__(self):
        return self.get_str()

    def get_unique_name(self):
        return "%s.%s.%i" % (self.molname, self.copyname, self.domainnum)

    def get_str(self):
        res_range = self.residue_range
        if self.residue_range is None:
            res_range = []
        name = self.molname
        if self.copyname != '':
            name += '.' + self.copyname
        if self.chain is None:
            chain = ' '
        else:
            chain = self.chain
        color = self.color
        if isinstance(color, list):
            color = ','.join([str(x) for x in color])
        fastaid = self.fasta_id
        if self.fasta_flag:
            fastaid += "," + self.fasta_flag
        a = '|' + '|'.join([name, color, self._orig_fasta_file, fastaid,
                            self._orig_pdb_input, chain,
                            self._l2s(list(res_range)),
                            str(self.pdb_offset),
                            str(self.bead_size),
                            str(self.em_residues_per_gaussian),
                            str(self.rigid_body) if self.rigid_body else '',
                            self._l2s(self.super_rigid_bodies),
                            self._l2s(self.chain_of_super_rigid_bodies)]) + '|'
        return a


class PMIMoleculeHierarchy(IMP.atom.Molecule):
    '''Extends the functionality of IMP.atom.Molecule'''

    def __init__(self, hierarchy):
        IMP.atom.Molecule.__init__(self, hierarchy)

    def get_state_index(self):
        state = self.get_parent()
        return IMP.atom.State(state).get_state_index()

    def get_copy_index(self):
        return IMP.atom.Copy(self).get_copy_index()

    def get_extended_name(self):
        return self.get_name() + "." + \
               str(self.get_copy_index()) + \
               "." + str(self.get_state_index())

    def get_sequence(self):
        return IMP.atom.Chain(self).get_sequence()

    def get_residue_indexes(self):
        return IMP.pmi.tools.get_residue_indexes(self)

    def get_residue_segments(self):
        return IMP.pmi.tools.Segments(self.get_residue_indexes())

    def get_chain_id(self):
        return IMP.atom.Chain(self).get_id()

    def __repr__(self):
        s = 'PMIMoleculeHierarchy '
        s += self.get_name()
        s += " " + "Copy  " + str(IMP.atom.Copy(self).get_copy_index())
        s += " " + "State " + str(self.get_state_index())
        s += " " + "N residues " + str(len(self.get_sequence()))
        return s