modeller/__init__.py

# This file was automatically generated by SWIG (https://www.swig.org).
# Version 4.2.1
#
# Do not make changes to this file unless you know what you are doing - modify
# the SWIG interface file instead.


# This wrapper is part of IMP,
# Copyright 2007-2024 IMP Inventors. All rights reserved.

from __future__ import print_function, division, absolute_import



from sys import version_info as _swig_python_version_info
import _IMP_modeller

try:
    import builtins as __builtin__
except ImportError:
    import __builtin__

def _swig_repr(self):
    try:
        strthis = "proxy of " + self.this.__repr__()
    except __builtin__.Exception:
        strthis = ""
    return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)


def _swig_setattr_nondynamic_instance_variable(set):
    def set_instance_attr(self, name, value):
        if name == "this":
            set(self, name, value)
        elif name == "thisown":
            self.this.own(value)
        elif hasattr(self, name) and isinstance(getattr(type(self), name), property):
            set(self, name, value)
        else:
            raise AttributeError("You cannot add instance attributes to %s" % self)
    return set_instance_attr


def _swig_setattr_nondynamic_class_variable(set):
    def set_class_attr(cls, name, value):
        if hasattr(cls, name) and not isinstance(getattr(cls, name), property):
            set(cls, name, value)
        else:
            raise AttributeError("You cannot add class attributes to %s" % cls)
    return set_class_attr


def _swig_add_metaclass(metaclass):
    """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
    def wrapper(cls):
        return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
    return wrapper


class _SwigNonDynamicMeta(type):
    """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
    __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)


import weakref

class IMP_MODELLER_SwigPyIterator(object):
    r"""Proxy of C++ swig::IMP_MODELLER_SwigPyIterator class."""

    thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")

    def __init__(self, *args, **kwargs):
        raise AttributeError("No constructor defined - class is abstract")
    __repr__ = _swig_repr
    __swig_destroy__ = _IMP_modeller.delete_IMP_MODELLER_SwigPyIterator

    def value(self):
        r"""value(IMP_MODELLER_SwigPyIterator self) -> PyObject *"""
        return _IMP_modeller.IMP_MODELLER_SwigPyIterator_value(self)

    def incr(self, n=1):
        r"""incr(IMP_MODELLER_SwigPyIterator self, size_t n=1) -> IMP_MODELLER_SwigPyIterator"""
        return _IMP_modeller.IMP_MODELLER_SwigPyIterator_incr(self, n)

    def decr(self, n=1):
        r"""decr(IMP_MODELLER_SwigPyIterator self, size_t n=1) -> IMP_MODELLER_SwigPyIterator"""
        return _IMP_modeller.IMP_MODELLER_SwigPyIterator_decr(self, n)

    def distance(self, x):
        r"""distance(IMP_MODELLER_SwigPyIterator self, IMP_MODELLER_SwigPyIterator x) -> ptrdiff_t"""
        return _IMP_modeller.IMP_MODELLER_SwigPyIterator_distance(self, x)

    def equal(self, x):
        r"""equal(IMP_MODELLER_SwigPyIterator self, IMP_MODELLER_SwigPyIterator x) -> bool"""
        return _IMP_modeller.IMP_MODELLER_SwigPyIterator_equal(self, x)

    def copy(self):
        r"""copy(IMP_MODELLER_SwigPyIterator self) -> IMP_MODELLER_SwigPyIterator"""
        return _IMP_modeller.IMP_MODELLER_SwigPyIterator_copy(self)

    def next(self):
        r"""next(IMP_MODELLER_SwigPyIterator self) -> PyObject *"""
        return _IMP_modeller.IMP_MODELLER_SwigPyIterator_next(self)

    def __next__(self):
        r"""__next__(IMP_MODELLER_SwigPyIterator self) -> PyObject *"""
        return _IMP_modeller.IMP_MODELLER_SwigPyIterator___next__(self)

    def previous(self):
        r"""previous(IMP_MODELLER_SwigPyIterator self) -> PyObject *"""
        return _IMP_modeller.IMP_MODELLER_SwigPyIterator_previous(self)

    def advance(self, n):
        r"""advance(IMP_MODELLER_SwigPyIterator self, ptrdiff_t n) -> IMP_MODELLER_SwigPyIterator"""
        return _IMP_modeller.IMP_MODELLER_SwigPyIterator_advance(self, n)

    def __eq__(self, x):
        r"""__eq__(IMP_MODELLER_SwigPyIterator self, IMP_MODELLER_SwigPyIterator x) -> bool"""
        return _IMP_modeller.IMP_MODELLER_SwigPyIterator___eq__(self, x)

    def __ne__(self, x):
        r"""__ne__(IMP_MODELLER_SwigPyIterator self, IMP_MODELLER_SwigPyIterator x) -> bool"""
        return _IMP_modeller.IMP_MODELLER_SwigPyIterator___ne__(self, x)

    def __iadd__(self, n):
        r"""__iadd__(IMP_MODELLER_SwigPyIterator self, ptrdiff_t n) -> IMP_MODELLER_SwigPyIterator"""
        return _IMP_modeller.IMP_MODELLER_SwigPyIterator___iadd__(self, n)

    def __isub__(self, n):
        r"""__isub__(IMP_MODELLER_SwigPyIterator self, ptrdiff_t n) -> IMP_MODELLER_SwigPyIterator"""
        return _IMP_modeller.IMP_MODELLER_SwigPyIterator___isub__(self, n)

    def __add__(self, n):
        r"""__add__(IMP_MODELLER_SwigPyIterator self, ptrdiff_t n) -> IMP_MODELLER_SwigPyIterator"""
        return _IMP_modeller.IMP_MODELLER_SwigPyIterator___add__(self, n)

    def __sub__(self, *args):
        r"""
        __sub__(IMP_MODELLER_SwigPyIterator self, ptrdiff_t n) -> IMP_MODELLER_SwigPyIterator
        __sub__(IMP_MODELLER_SwigPyIterator self, IMP_MODELLER_SwigPyIterator x) -> ptrdiff_t
        """
        return _IMP_modeller.IMP_MODELLER_SwigPyIterator___sub__(self, *args)
    def __iter__(self):
        return self

# Register IMP_MODELLER_SwigPyIterator in _IMP_modeller:
_IMP_modeller.IMP_MODELLER_SwigPyIterator_swigregister(IMP_MODELLER_SwigPyIterator)

_value_types=[]
_object_types=[]
_raii_types=[]
_plural_types=[]

IMP_DEBUG = _IMP_modeller.IMP_DEBUG

IMP_RELEASE = _IMP_modeller.IMP_RELEASE

IMP_SILENT = _IMP_modeller.IMP_SILENT

IMP_PROGRESS = _IMP_modeller.IMP_PROGRESS

IMP_TERSE = _IMP_modeller.IMP_TERSE

IMP_VERBOSE = _IMP_modeller.IMP_VERBOSE

IMP_MEMORY = _IMP_modeller.IMP_MEMORY

IMP_NONE = _IMP_modeller.IMP_NONE

IMP_USAGE = _IMP_modeller.IMP_USAGE

IMP_INTERNAL = _IMP_modeller.IMP_INTERNAL

IMP_KERNEL_HAS_LOG4CXX = _IMP_modeller.IMP_KERNEL_HAS_LOG4CXX

IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_modeller.IMP_COMPILER_HAS_CEREAL_RAW_POINTER

IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_modeller.IMP_COMPILER_HAS_DEBUG_VECTOR

IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_modeller.IMP_COMPILER_HAS_RANDOM_SHUFFLE

IMP_COMPILER_HAS_THREE_WAY = _IMP_modeller.IMP_COMPILER_HAS_THREE_WAY

IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_modeller.IMP_KERNEL_HAS_BOOST_RANDOM

IMP_KERNEL_HAS_NUMPY = _IMP_modeller.IMP_KERNEL_HAS_NUMPY

IMP_KERNEL_HAS_GPERFTOOLS = _IMP_modeller.IMP_KERNEL_HAS_GPERFTOOLS

IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_modeller.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER

IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_modeller.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER

IMPKERNEL_SHOW_WARNINGS = _IMP_modeller.IMPKERNEL_SHOW_WARNINGS


import sys
class _DirectorObjects(object):
    """@internal Simple class to keep references to director objects
       to prevent premature deletion."""
    def __init__(self):
        self._objects = []
    def register(self, obj):
        """Take a reference to a director object; will only work for
           refcounted C++ classes"""
        if hasattr(obj, 'get_ref_count'):
            self._objects.append(obj)
    def cleanup(self):
        """Only drop our reference and allow cleanup by Python if no other
           Python references exist (we hold 3 references: one in self._objects,
           one in x, and one in the argument list for getrefcount) *and* no
           other C++ references exist (the Python object always holds one)"""
        objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
                                         or x.get_ref_count() > 1]
# Do in two steps so the references are kept until the end of the
# function (deleting references may trigger a fresh call to this method)
        self._objects = objs
    def get_object_count(self):
        """Get number of director objects (useful for testing only)"""
        return len(self._objects)
_director_objects = _DirectorObjects()

class _ostream(object):
    r"""Proxy of C++ std::ostream class."""

    thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")

    def __init__(self, *args, **kwargs):
        raise AttributeError("No constructor defined")
    __repr__ = _swig_repr

    def write(self, osa_buf):
        r"""write(_ostream self, char const * osa_buf)"""
        return _IMP_modeller._ostream_write(self, osa_buf)

# Register _ostream in _IMP_modeller:
_IMP_modeller._ostream_swigregister(_ostream)
IMP_C_OPEN_BINARY = _IMP_modeller.IMP_C_OPEN_BINARY

import IMP
IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_modeller.IMP_CGAL_HAS_BOOST_FILESYSTEM

IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_modeller.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS

IMP_CGAL_HAS_BOOST_RANDOM = _IMP_modeller.IMP_CGAL_HAS_BOOST_RANDOM

IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_modeller.IMP_CGAL_HAS_BOOST_SYSTEM

IMP_CGAL_HAS_NUMPY = _IMP_modeller.IMP_CGAL_HAS_NUMPY

IMPCGAL_SHOW_WARNINGS = _IMP_modeller.IMPCGAL_SHOW_WARNINGS

import IMP.cgal
IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_modeller.IMP_ALGEBRA_HAS_IMP_CGAL

IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_modeller.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM

IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_modeller.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS

IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_modeller.IMP_ALGEBRA_HAS_BOOST_RANDOM

IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_modeller.IMP_ALGEBRA_HAS_BOOST_SYSTEM

IMP_ALGEBRA_HAS_CGAL = _IMP_modeller.IMP_ALGEBRA_HAS_CGAL

IMP_ALGEBRA_HAS_NUMPY = _IMP_modeller.IMP_ALGEBRA_HAS_NUMPY

IMP_ALGEBRA_HAS_ANN = _IMP_modeller.IMP_ALGEBRA_HAS_ANN

IMPALGEBRA_SHOW_WARNINGS = _IMP_modeller.IMPALGEBRA_SHOW_WARNINGS

import IMP.algebra
IMP_DISPLAY_HAS_IMP_CGAL = _IMP_modeller.IMP_DISPLAY_HAS_IMP_CGAL

IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_modeller.IMP_DISPLAY_HAS_BOOST_FILESYSTEM

IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_modeller.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS

IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_modeller.IMP_DISPLAY_HAS_BOOST_RANDOM

IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_modeller.IMP_DISPLAY_HAS_BOOST_SYSTEM

IMP_DISPLAY_HAS_CGAL = _IMP_modeller.IMP_DISPLAY_HAS_CGAL

IMP_DISPLAY_HAS_NUMPY = _IMP_modeller.IMP_DISPLAY_HAS_NUMPY

IMPDISPLAY_SHOW_WARNINGS = _IMP_modeller.IMPDISPLAY_SHOW_WARNINGS

import IMP.display
IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_modeller.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL

IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_modeller.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM

IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_modeller.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS

IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_modeller.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM

IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_modeller.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM

IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_modeller.IMP_SCORE_FUNCTOR_HAS_CGAL

IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_modeller.IMP_SCORE_FUNCTOR_HAS_HDF5

IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_modeller.IMP_SCORE_FUNCTOR_HAS_NUMPY

IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_modeller.IMPSCOREFUNCTOR_SHOW_WARNINGS

import IMP.score_functor
IMP_CORE_HAS_IMP_CGAL = _IMP_modeller.IMP_CORE_HAS_IMP_CGAL

IMP_CORE_HAS_IMP_KERNEL = _IMP_modeller.IMP_CORE_HAS_IMP_KERNEL

IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_modeller.IMP_CORE_HAS_BOOST_FILESYSTEM

IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_modeller.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS

IMP_CORE_HAS_BOOST_RANDOM = _IMP_modeller.IMP_CORE_HAS_BOOST_RANDOM

IMP_CORE_HAS_BOOST_SYSTEM = _IMP_modeller.IMP_CORE_HAS_BOOST_SYSTEM

IMP_CORE_HAS_CGAL = _IMP_modeller.IMP_CORE_HAS_CGAL

IMP_CORE_HAS_HDF5 = _IMP_modeller.IMP_CORE_HAS_HDF5

IMP_CORE_HAS_NUMPY = _IMP_modeller.IMP_CORE_HAS_NUMPY

IMPCORE_SHOW_WARNINGS = _IMP_modeller.IMPCORE_SHOW_WARNINGS

import IMP.core
IMP_MODELLER_HAS_IMP_ALGEBRA = _IMP_modeller.IMP_MODELLER_HAS_IMP_ALGEBRA

IMP_MODELLER_HAS_IMP_CGAL = _IMP_modeller.IMP_MODELLER_HAS_IMP_CGAL

IMP_MODELLER_HAS_IMP_DISPLAY = _IMP_modeller.IMP_MODELLER_HAS_IMP_DISPLAY

IMP_MODELLER_HAS_IMP_KERNEL = _IMP_modeller.IMP_MODELLER_HAS_IMP_KERNEL

IMP_MODELLER_HAS_IMP_SCORE_FUNCTOR = _IMP_modeller.IMP_MODELLER_HAS_IMP_SCORE_FUNCTOR

IMP_MODELLER_HAS_BOOST_FILESYSTEM = _IMP_modeller.IMP_MODELLER_HAS_BOOST_FILESYSTEM

IMP_MODELLER_HAS_BOOST_PROGRAMOPTIONS = _IMP_modeller.IMP_MODELLER_HAS_BOOST_PROGRAMOPTIONS

IMP_MODELLER_HAS_BOOST_RANDOM = _IMP_modeller.IMP_MODELLER_HAS_BOOST_RANDOM

IMP_MODELLER_HAS_BOOST_SYSTEM = _IMP_modeller.IMP_MODELLER_HAS_BOOST_SYSTEM

IMP_MODELLER_HAS_CGAL = _IMP_modeller.IMP_MODELLER_HAS_CGAL

IMP_MODELLER_HAS_HDF5 = _IMP_modeller.IMP_MODELLER_HAS_HDF5

IMP_MODELLER_HAS_NUMPY = _IMP_modeller.IMP_MODELLER_HAS_NUMPY

IMP_MODELLER_HAS_PYTHON_IHM = _IMP_modeller.IMP_MODELLER_HAS_PYTHON_IHM

IMPMODELLER_SHOW_WARNINGS = _IMP_modeller.IMPMODELLER_SHOW_WARNINGS



import os
import tempfile
import shutil
import IMP.atom
import IMP.container
import modeller.scripts
import modeller.optimizers


# Use Modeller 10 class names
if not hasattr(modeller.terms, 'EnergyTerm'):
    modeller.terms.EnergyTerm = modeller.terms.energy_term
    modeller.Selection = modeller.selection


class _TempDir(object):
    """Make a temporary directory that is deleted when the object is."""

    def __init__(self):
        self.tmpdir = tempfile.mkdtemp()

    def __del__(self):
        shutil.rmtree(self.tmpdir, ignore_errors=True)


class IMPRestraints(modeller.terms.EnergyTerm):
    """A Modeller restraint which evaluates an IMP scoring function.
       This can be used to incorporate IMP Restraints into an existing
       comparative modeling pipeline, or to use Modeller optimizers or
       protocols.
    """

    _physical_type = modeller.physical.absposition

    def __init__(self, particles, scoring_function=None):
        """Constructor.
           @param particles A list of the IMP atoms (as Particle objects),
                            same order as the Modeller atoms.
           @param scoring_function An IMP::ScoringFunction object that will
                            be incorporated into the Modeller score (molpdf).
           @note since Modeller, unlike IMP, is sensitive to the ordering
                 of atoms, it usually makes sense to create the model in
                 Modeller and then use ModelLoader to load it into IMP,
                 since that will preserve the Modeller atom ordering in IMP.
        """
        modeller.terms.EnergyTerm.__init__(self)
        self._particles = particles
        if scoring_function:
            self._sf = scoring_function
        else:
            self._sf = particles[0].get_model()

    def eval(self, mdl, deriv, indats):
        atoms = self.indices_to_atoms(mdl, indats)
        _copy_modeller_coords_to_imp(atoms, self._particles)
        if len(self._particles) == 0:
            score = 0.
        else:
            score = self._sf.evaluate(deriv)
        if deriv:
            dvx = [0.] * len(indats)
            dvy = [0.] * len(indats)
            dvz = [0.] * len(indats)
            _get_imp_derivs(self._particles, dvx, dvy, dvz)
            return (score, dvx, dvy, dvz)
        else:
            return score


class ModellerRestraints(IMP.Restraint):
    """An IMP restraint using all defined Modeller restraints.
       This is useful if you want to use Modeller restraints with an IMP
       optimizer, or in combination with IMP restraints.

       @note Currently only the coordinates of the atoms are translated
             between Modeller and IMP; thus, a Modeller restraint which
             uses any other attribute (e.g. charge) will not react if
             this attribute is changed by IMP.
    """

    def __init__(self, model, modeller_model, particles):
        """Constructor.
           @param model The IMP Model object.
           @param modeller_model The Modeller model object.
           @param particles A list of the IMP atoms (as Particle objects),
                            in the same order as the Modeller atoms.
           @note since Modeller, unlike IMP, is sensitive to the ordering
                 of atoms, it usually makes sense to create the model in
                 Modeller and then use ModelLoader to load it into IMP,
                 since that will preserve the Modeller atom ordering in IMP.
        """
        def get_particle(x):
            if hasattr(x, 'get_particle'):
                return x.get_particle()
            else:
                return x
        IMP.Restraint.__init__(self, model, "ModellerRestraints %1%")
        self._modeller_model = modeller_model
        self._particles = [get_particle(x) for x in particles]

    def unprotected_evaluate(self, accum):
        atoms = self._modeller_model.atoms
        sel = modeller.Selection(self._modeller_model)
        _copy_imp_coords_to_modeller(self._particles, atoms)
        energies = sel.energy()
        if accum:
            _add_modeller_derivs_to_imp(atoms, self._particles, accum)

        return energies[0]

    def get_version_info(self):
        return IMP.VersionInfo("IMP developers", "0.1")
    def do_show(self, fh):
        fh.write("ModellerRestraints")
    def do_get_inputs(self):
        return self._particles


def _copy_imp_coords_to_modeller(particles, atoms):
    """Copy atom coordinates from IMP to Modeller"""
    xkey = IMP.FloatKey("x")
    ykey = IMP.FloatKey("y")
    zkey = IMP.FloatKey("z")
    for (num, at) in enumerate(atoms):
        at.x = particles[num].get_value(xkey)
        at.y = particles[num].get_value(ykey)
        at.z = particles[num].get_value(zkey)


def _copy_modeller_coords_to_imp(atoms, particles):
    """Copy atom coordinates from Modeller to IMP"""
    xkey = IMP.FloatKey("x")
    ykey = IMP.FloatKey("y")
    zkey = IMP.FloatKey("z")
    for (num, at) in enumerate(atoms):
        particles[num].set_value(xkey, at.x)
        particles[num].set_value(ykey, at.y)
        particles[num].set_value(zkey, at.z)


def _add_modeller_derivs_to_imp(atoms, particles, accum):
    """Add atom derivatives from Modeller to IMP"""
    for (num, at) in enumerate(atoms):
        xyz = IMP.core.XYZ(particles[num])
        xyz.add_to_derivative(0, at.dvx, accum)
        xyz.add_to_derivative(1, at.dvy, accum)
        xyz.add_to_derivative(2, at.dvz, accum)


def _get_imp_derivs(particles, dvx, dvy, dvz):
    """Move atom derivatives from IMP to Modeller"""
    xkey = IMP.FloatKey("x")
    ykey = IMP.FloatKey("y")
    zkey = IMP.FloatKey("z")
    for idx in range(0, len(dvx)):
        dvx[idx] = particles[idx].get_derivative(xkey)
        dvy[idx] = particles[idx].get_derivative(ykey)
        dvz[idx] = particles[idx].get_derivative(zkey)


# Generators to create IMP UnaryFunction objects from Modeller parameters:
def _HarmonicLowerBoundGenerator(parameters, modalities):
    (mean, stdev) = parameters
    k = IMP.core.Harmonic.get_k_from_standard_deviation(stdev)
    return IMP.core.HarmonicLowerBound(mean, k)

def _HarmonicUpperBoundGenerator(parameters, modalities):
    (mean, stdev) = parameters
    k = IMP.core.Harmonic.get_k_from_standard_deviation(stdev)
    return IMP.core.HarmonicUpperBound(mean, k)

def _HarmonicGenerator(parameters, modalities):
    (mean, stdev) = parameters
    k = IMP.core.Harmonic.get_k_from_standard_deviation(stdev)
    return IMP.core.Harmonic(mean, k)

def _CosineGenerator(parameters, modalities):
    (phase, force_constant) = parameters
    (periodicity,) = modalities
    return IMP.core.Cosine(force_constant, periodicity, phase)

def _LinearGenerator(parameters, modalities):
    (scale,) = parameters
    return IMP.core.Linear(0, scale)

def _SplineGenerator(parameters, modalities):
    (open, low, high, delta, lowderiv, highderiv) = parameters[:6]
    values = []
    for v in parameters[6:]:
        values.append(v)
    if open < 0.0:
        return IMP.core.ClosedCubicSpline(values, low, delta)
    else:
        return IMP.core.OpenCubicSpline(values, low, delta)

#: Mapping from Modeller math form number to a unary function generator
_unary_func_generators = {
    1: _HarmonicLowerBoundGenerator,
    2: _HarmonicUpperBoundGenerator,
    3: _HarmonicGenerator,
    7: _CosineGenerator,
    8: _LinearGenerator,
    10: _SplineGenerator,
}

# Generators to make IMP Restraint objects from Modeller features
def _DistanceRestraintGenerator(form, modalities, atoms, parameters):
    unary_func_gen = _unary_func_generators[form]
    return IMP.core.DistanceRestraint(atoms[0].get_model(),
                                      unary_func_gen(parameters, modalities),
                                      atoms[0], atoms[1])

def _AngleRestraintGenerator(form, modalities, atoms, parameters):
    unary_func_gen = _unary_func_generators[form]
    return IMP.core.AngleRestraint(atoms[0].get_model(),
                                   unary_func_gen(parameters, modalities),
                                   atoms[0], atoms[1], atoms[2])

def _MultiBinormalGenerator(form, modalities, atoms, parameters):
    nterms = modalities[0]
    if len(parameters) != nterms * 6:
        raise ValueError("Incorrect number of parameters (%d) for multiple "
                         "binormal restraint - expecting %d (%d terms * 6)" \
                         % (len(parameters), nterms * 6, nterms))
    r = IMP.core.MultipleBinormalRestraint(atoms[0].get_model(),
                                           atoms[:4], atoms[4:8])
    for i in range(nterms):
        t = IMP.core.BinormalTerm()
        t.set_weight(parameters[i])
        t.set_means((parameters[nterms + i * 2],
                     parameters[nterms + i * 2 + 1]))
        t.set_standard_deviations((parameters[nterms * 3 + i * 2],
                                   parameters[nterms * 3 + i * 2 + 1]))
        t.set_correlation(parameters[nterms * 5 + i])
        r.add_term(t)
    return r

def _DihedralRestraintGenerator(form, modalities, atoms, parameters):
    if form == 9:
        return _MultiBinormalGenerator(form, modalities, atoms, parameters)
    unary_func_gen = _unary_func_generators[form]
    return IMP.core.DihedralRestraint(atoms[0].get_model(),
                                      unary_func_gen(parameters, modalities),
                                      atoms[0], atoms[1], atoms[2], atoms[3])

def _get_protein_atom_particles(protein):
    """Given a protein particle, get the flattened list of all child atoms"""
    atom_particles = []
    for ichain in range(protein.get_number_of_children()):
        chain = protein.get_child(ichain)
        for ires in range(chain.get_number_of_children()):
            residue = chain.get_child(ires)
            for iatom in range(residue.get_number_of_children()):
                atom = residue.get_child(iatom)
                atom_particles.append(atom.get_particle())
    return atom_particles

def _load_restraints_line(line, atom_particles):
    """Parse a single Modeller restraints file line and return the
       corresponding IMP restraint."""
    spl = line.split()
    typ = spl.pop(0)
    if typ == 'MODELLER5':
        return
    elif typ != 'R':
        raise NotImplementedError("Only 'R' lines currently read from " + \
                                  "Modeller restraints files")
    form = int(spl.pop(0))
    modalities = [int(spl.pop(0))]
    features = [int(spl.pop(0))]
# Discard group
    spl.pop(0)
    natoms = [int(spl.pop(0))]
    nparam = int(spl.pop(0))
    nfeat = int(spl.pop(0))
    for i in range(nfeat - 1):
        modalities.append(int(spl.pop(0)))
        features.append(int(spl.pop(0)))
        natoms.append(int(spl.pop(0)))
    atoms = [int(spl.pop(0)) for x in range(natoms[0])]
    for i in range(len(atoms)):
        atoms[i] = atom_particles[atoms[i] - 1]
    parameters = [float(spl.pop(0)) for x in range(nparam)]
    restraint_generators = {
        1 : _DistanceRestraintGenerator,
        2 : _AngleRestraintGenerator,
        3 : _DihedralRestraintGenerator,
        4 : _DihedralRestraintGenerator,
    }
    restraint_gen = restraint_generators[features[0]]
    return restraint_gen(form, modalities, atoms, parameters)


def _load_entire_restraints_file(filename, protein):
    """Yield a set of IMP restraints from a Modeller restraints file."""
    atoms = _get_protein_atom_particles(protein)
    with open(filename, 'r') as fh:
        for line in fh:
            try:
                rsr = _load_restraints_line(line, atoms)
                if rsr is not None:
                    yield rsr
            except Exception as err:
                print("Cannot read restraints file line:\n" + line)
                raise


def _copy_residue(r, model):
    """Copy residue information from modeller to imp"""
#print "residue "+str(r)
    p=IMP.Particle(model)
    rp= IMP.atom.Residue.setup_particle(p, IMP.atom.ResidueType(r.pdb_name),
                                         r.index)
    p.set_name(str("residue "+r.num));
    return p


def _copy_atom(a, model):
    """Copy atom information from modeller"""
#print "atom "+str(a)
    p=IMP.Particle(model)
    ap= IMP.atom.Atom.setup_particle(p,IMP.atom.AtomType(a.name))
    xyzd= IMP.core.XYZ.setup_particle(p, IMP.algebra.Vector3D(a.x, a.y, a.z))
# Alignment structures don't have charges or atom types; models do
    if hasattr(a, 'charge'):
        IMP.atom.Charged.setup_particle(p, a.charge)
    if hasattr(a, 'type'):
        IMP.atom.CHARMMAtom.setup_particle(p, a.type.name)
    ap.set_input_index(a.index)
    return p

def _copy_chain(c, model):
    """Copy chain information from modeller"""
#print "atom "+str(a)
    p=IMP.Particle(model)
#set the chain name
    cp = IMP.atom.Chain.setup_particle(p,c.name)
    return p

def _get_forcefield(submodel):
    if submodel == 3:
        ff = IMP.atom.CHARMMParameters(
                 IMP.atom.get_data_path('top_heav.lib'),
                 IMP.atom.get_data_path('par.lib'))
    else:
        ff = IMP.atom.CHARMMParameters(
                 IMP.atom.get_data_path('top.lib'),
                 IMP.atom.get_data_path('par.lib'))
    return ff

def add_soft_sphere_radii(hierarchy, submodel, scale=1.0, filename=None):
    """Add radii to the hierarchy using the Modeller radius library, radii.lib.
       Each radius is scaled by the given scale (Modeller usually scales radii
       by a factor of 0.82). submodel specifies the topology submodel, which is
       the column in radii.lib to use."""
    if filename is None:
        filename = IMP.atom.get_data_path('radii.lib')
    radii = {}
    with open(filename) as fh:
        for line in fh:
            if line.startswith('#'): continue
            spl = line.split()
            if len(spl) > 11:
                radii[spl[0]] = float(spl[submodel])
    atoms = IMP.atom.get_by_type(hierarchy, IMP.atom.ATOM_TYPE)
    for a in atoms:
        p = a.get_particle()
        ct = IMP.atom.CHARMMAtom(p).get_charmm_type()
        if ct in radii:
            radius = radii[ct] * scale
            if IMP.core.XYZR.get_is_setup(p):
                IMP.core.XYZR(p).set_radius(radius)
            else:
                IMP.core.XYZR.setup_particle(p, radius)


class ModelLoader(object):
    """Read a Modeller model into IMP. After creating this object, the atoms
       in the Modeller model can be loaded into IMP using the load_atoms()
       method, then optionally any Modeller static restraints can be read in
       with load_static_restraints() or load_static_restraints_file().

       This class can also be used to read Modeller alignment structures;
       however, only load_atoms() will be useful in such a case (since
       alignment structures don't have restraints or other information).

    """

    def __init__(self, modeller_model):
        """Constructor.
           @param modeller_model The Modeller model or alignment structure
                                 object to read.
        """
        self._modeller_model = modeller_model

    def load_atoms(self, model):
        """Construct an IMP::atom::Hierarchy that contains the same atoms as
           the Modeller model or alignment structure.

           IMP atoms created from a Modeller model will be given charges and
           CHARMM types, extracted from the model. Alignment structures don't
           contain this information, so the IMP atoms won't either.

           @param model The IMP::Model object in which the hierarchy will be
                        created. The highest level hierarchy node is a PROTEIN.
           @return the newly-created root IMP::atom::Hierarchy.
        """
        pp = IMP.Particle(model)
        hpp = IMP.atom.Hierarchy.setup_particle(pp)
        self._atoms = {}
        for chain in self._modeller_model.chains:
            cp = IMP.Particle(model)
            hcp = IMP.atom.Chain.setup_particle(cp, chain.name)
# We don't really know the type yet
            hpp.add_child(hcp)
            for residue in chain.residues:
                rp = _copy_residue(residue, model)
                hrp = IMP.atom.Hierarchy(rp)
                hcp.add_child(hrp)
                for atom in residue.atoms:
                    ap = _copy_atom(atom, model)
                    hap = IMP.atom.Hierarchy(ap)
                    hrp.add_child(hap)
                    self._atoms[atom.index] = ap
                lastres = hrp
        self._modeller_hierarchy = hpp
        return hpp

    def _get_nonbonded_list(self, atoms, pair_filter, edat, distance):
        nbl = IMP.container.ClosePairContainer(atoms, distance,
                                               edat.update_dynamic)

# Exclude the same sets of atoms as Modeller
        if pair_filter is None:
            pair_filter = IMP.atom.StereochemistryPairFilter()
            if edat.excl_local[0]:
                pair_filter.set_bonds(list(self.load_bonds()))
            if edat.excl_local[1]:
                pair_filter.set_angles(list(self.load_angles()))
            if edat.excl_local[2]:
                pair_filter.set_dihedrals(list(self.load_dihedrals()))
        nbl.add_pair_filter(pair_filter)
        return nbl

    def load_bonds(self):
        """Load the Modeller bond topology into the IMP model. Each bond is
           represented in IMP as an IMP::atom::Bond, with no defined length
           or stiffness. These bonds are primarily useful as input to
           IMP::atom::StereochemistryPairFilter, to exclude bond interactions
           from the nonbonded list. Typically the contribution to the scoring
           function from the bonds is included in the Modeller static restraints
           (use load_static_restraints() or load_static_restraints_file() to
           load these). If you want to regenerate the stereochemistry in IMP,
           do not use these functions (as then stereochemistry scoring terms
           and exclusions would be double-counted) and instead use the
           IMP::atom::CHARMMTopology class.

           You must call load_atoms() prior to using this function.
           @see load_angles(), load_dihedrals(), load_impropers()
           @return A generator listing all of the bonds.
        """
        if not hasattr(self, '_modeller_hierarchy'):
            raise ValueError("Call load_atoms() first.")
        for (maa, mab) in self._modeller_model.bonds:
            pa = self._atoms[maa.index]
            pb = self._atoms[mab.index]
            if IMP.atom.Bonded.get_is_setup(pa):
                ba= IMP.atom.Bonded(pa)
            else:
                ba= IMP.atom.Bonded.setup_particle(pa)
            if IMP.atom.Bonded.get_is_setup(pb):
                bb= IMP.atom.Bonded(pb)
            else:
                bb= IMP.atom.Bonded.setup_particle(pb)
            yield IMP.atom.create_bond(ba, bb,
                                       IMP.atom.Bond.SINGLE).get_particle()

    def load_angles(self):
        """Load the Modeller angle topology into the IMP model.
           See load_bonds() for more details."""
        return self._internal_load_angles(self._modeller_model.angles,
                                          IMP.atom.Angle)

    def load_dihedrals(self):
        """Load the Modeller dihedral topology into the IMP model.
           See load_bonds() for more details."""
        return self._internal_load_angles(self._modeller_model.dihedrals,
                                          IMP.atom.Dihedral)

    def load_impropers(self):
        """Load the Modeller improper topology into the IMP model.
           See load_bonds() for more details."""
        return self._internal_load_angles(self._modeller_model.impropers,
                                          IMP.atom.Dihedral)

    def _internal_load_angles(self, angles, angle_class):
        if not hasattr(self, '_modeller_hierarchy'):
            raise ValueError("Call load_atoms() first.")
        for modeller_atoms in angles:
            imp_particles = [self._atoms[x.index] for x in modeller_atoms]
            p = IMP.Particle(imp_particles[0].get_model())
            a = angle_class.setup_particle(p,
                                 *[IMP.core.XYZ(x) for x in imp_particles])
            yield a.get_particle()

    def load_static_restraints_file(self, filename):
        """Convert a Modeller static restraints file into equivalent
           IMP::Restraints. load_atoms() must have been called first to read
           in the atoms that the restraints will act upon.
           @param filename Name of the Modeller restraints file. The restraints
                  in this file are assumed to act upon the model read in by
                  load_atoms(); no checking is done to enforce this.
           @return A Python generator of the newly-created IMP::Restraint
                   objects.
        """
        if not hasattr(self, '_modeller_hierarchy'):
            raise ValueError("Call load_atoms() first.")
        return _load_entire_restraints_file(filename, self._modeller_hierarchy)


    def load_static_restraints(self):
        """Convert the current set of Modeller static restraints into equivalent
           IMP::Restraints. load_atoms() must have been called first to read
           in the atoms that the restraints will act upon.
           @return A Python generator of the newly-created IMP::Restraint
                   objects.
        """
        class _RestraintGenerator(object):
            """Simple generator wrapper"""
            def __init__(self, gen):
                self._gen = gen
            def __iter__(self, *args, **keys):
                return self
            def close(self, *args, **keys):
                return self._gen.close(*args, **keys)
            def next(self):
                return next(self._gen)
            __next__ = next
            def send(self, *args, **keys):
                return self._gen.send(*args, **keys)
            def throw(self, *args, **keys):
                return self._gen.throw(*args, **keys)
# Write current restraints into a temporary file
        t = _TempDir()
        rsrfile = os.path.join(t.tmpdir, 'restraints.rsr')
        self._modeller_model.restraints.write(file=rsrfile)
# Read the file back in
        gen = self.load_static_restraints_file(rsrfile)
        wrap = _RestraintGenerator(gen)
# Ensure that tmpdir remains until we're done with the generator
        wrap._tempdir = t
        return wrap

    def load_dynamic_restraints(self, pair_filter=None):
        """Convert Modeller dynamic restraints into IMP::Restraint objects.

           For each currently active Modeller dynamic restraint
           (e.g. soft-sphere, electrostatics) an equivalent IMP::Restraint
           is created.
           load_atoms() must have been called first to read
           in the atoms that the restraints will act upon.

           If pair_filter is given, it is an IMP::PairFilter object to exclude
           pairs from the nonbonded lists used by the dynamic restraints.
           Otherwise, an IMP::atom::StereochemistryPairFilter object is created
           to exclude Modeller bonds, angles and dihedrals, as specified by
           edat.excl_local. (Note that this calls load_bonds(), load_angles()
           and load_dihedrals(), so will create duplicate lists of bonds if
           those methods are called manually as well.)

           @note Currently only soft-sphere, electrostatic and Lennard-Jones
                 restraints are loaded.
           @return A Python generator of the newly-created IMP::Restraint
                   objects.
        """
        if not hasattr(self, '_modeller_hierarchy'):
            raise ValueError("Call load_atoms() first.")
        edat = self._modeller_model.env.edat
        libs = self._modeller_model.env.libs
        atoms = IMP.atom.get_leaves(self._modeller_hierarchy)
        m = atoms[0].get_model()
        atoms = IMP.container.ListSingletonContainer(m, IMP.get_indexes(atoms))

        if edat.dynamic_sphere:
# Note: cannot use Modeller's cutoff distance, as that is
# center-to-center; IMP's is sphere surface-surface
            nbl = self._get_nonbonded_list(atoms, pair_filter, edat, 0.)
# No way to get Modeller radii, so we have to reassign them
            add_soft_sphere_radii(self._modeller_hierarchy,
                                  libs.topology.submodel, edat.radii_factor)
            k = \
              IMP.core.Harmonic.get_k_from_standard_deviation(edat.sphere_stdv)
            ps = IMP.core.SphereDistancePairScore(
                              IMP.core.HarmonicLowerBound(0, k))
            yield IMP.container.PairsRestraint(ps, nbl)

        if edat.dynamic_lennard or edat.dynamic_coulomb:
# 3.0 is roughly the max. atom diameter
            d = max(edat.contact_shell - 3.0, 0.0)
            nbl = self._get_nonbonded_list(atoms, pair_filter, edat, d)
            ff = _get_forcefield(libs.topology.submodel)
            ff.add_radii(self._modeller_hierarchy)

            if edat.dynamic_lennard:
                ff.add_well_depths(self._modeller_hierarchy)
                sf = IMP.atom.ForceSwitch(edat.lennard_jones_switch[0],
                                          edat.lennard_jones_switch[1])
                ps = IMP.atom.LennardJonesPairScore(sf)
                yield IMP.container.PairsRestraint(ps, nbl)

            if edat.dynamic_coulomb:
                sf = IMP.atom.ForceSwitch(edat.coulomb_switch[0],
                                          edat.coulomb_switch[1])
                ps = IMP.atom.CoulombPairScore(sf)
                ps.set_relative_dielectric(edat.relative_dielectric)
                yield IMP.container.PairsRestraint(ps, nbl)



def get_module_version():
    r"""get_module_version() -> std::string const"""
    return _IMP_modeller.get_module_version()

def get_example_path(fname):
    r"""get_example_path(std::string fname) -> std::string"""
    return _IMP_modeller.get_example_path(fname)

def get_data_path(fname):
    r"""get_data_path(std::string fname) -> std::string"""
    return _IMP_modeller.get_data_path(fname)

from . import _version_check
_version_check.check_version(get_module_version())
__version__ = get_module_version()