def __init__(self,
references,
clones_list,
transforms,
label='',
strength=10.0,
ca_only=False):
"""Constructor
@param references Can be one of the following inputs:
IMP Hierarchy, PMI System/State/Molecule/TempResidue,
or a list/set of them
@param clones_list List of lists of the above
@param transforms Transforms moving each selection to the first
selection
@param label Label for output
@param strength The elastic bond strength
@param ca_only Optionally select so only CAlpha particles are used
"""
refs = IMP.pmi.tools.input_adaptor(references, flatten=True)
self.mdl = refs[0].get_model()
self.rs = IMP.RestraintSet(self.mdl, "Symmetry")
self.weight = 1
self.label = label
if len(clones_list) != len(transforms):
raise Exception(
'Error: There should be as many clones as transforms')
harmonic = IMP.core.Harmonic(0., strength)
for tmp_clones, trans in zip(clones_list, transforms):
clones = IMP.pmi.tools.input_adaptor(tmp_clones, flatten=True)
if len(clones) != len(refs):
raise Exception("Error: len(references)!=len(clones)")
pair_score = IMP.core.TransformedDistancePairScore(harmonic, trans)
for p0, p1 in zip(refs, clones):
if not ca_only or (IMP.atom.Atom(p0).get_atom_type()
== IMP.atom.AtomType("CA")
and IMP.atom.Atom(p1).get_atom_type()
== IMP.atom.AtomType("CA")):
r = IMP.core.PairRestraint(
self.mdl, pair_score,
[p0.get_particle_index(),
p1.get_particle_index()])
self.rs.add_restraint(r)
print('created symmetry network with',
self.rs.get_number_of_restraints(), 'restraints')
def test_xyz_particles(self):
m = IMP.Model()
ps = []
hs = []
for i in range(10):
p = IMP.Particle(m)
h = IMP.atom.Hierarchy.setup_particle(p)
d = IMP.core.XYZR.setup_particle(p)
IMP.atom.Mass.setup_particle(p, 1.0)
d.set_coordinates(
IMP.algebra.get_random_vector_in(
IMP.algebra.Sphere3D((0, 0, 0), 10)))
d.set_radius(1)
ps.append(p)
hs.append(h)
srbm = IMP.pmi.TransformMover(m, 1, 0.5)
#origin point
origin = IMP.Particle(m)
d = IMP.core.XYZR.setup_particle(origin)
d.set_coordinates((0, 0, 0))
d.set_radius(1)
rs = IMP.RestraintSet(m)
ts1 = IMP.core.Harmonic(10, 10)
dr = IMP.core.DistanceRestraint(m, ts1, ps[0], origin)
for p in ps:
srbm.add_xyz_particle(IMP.core.XYZ(p))
smv = IMP.core.SerialMover([srbm])
mc = IMP.core.MonteCarlo(m)
mc.set_scoring_function([dr])
mc.set_return_best(False)
mc.set_kt(1.0)
mc.add_mover(smv)
rh = RMF.create_rmf_file("test_transform_mover_xyz.rmf3")
IMP.rmf.add_hierarchies(rh, hs)
for n in range(10):
mc.optimize(1)
IMP.rmf.save_frame(rh)
del rh
def __init__(
self,
representation,
handleparticles_tuples,
compositeparticles_tuple_list,
cut_off=5.0,
lam=1.0,
plateau=0.0,
resolution=None,
label="None"):
# composite particles: all particles beside the handle
self.label = label
self.m = representation.prot.get_model()
self.rs = IMP.RestraintSet(self.m, 'cr')
self.handleparticles = []
for s in handleparticles_tuples:
self.handleparticles += IMP.pmi.tools.select_by_tuple(representation, s,
resolution=resolution, name_is_ambiguous=True)
self.compositeparticles=[]
compositeparticle_list = []
for list in compositeparticles_tuple_list:
tmplist = []
for s in list:
tmplist += IMP.pmi.tools.select_by_tuple(
representation, s,
resolution=resolution, name_is_ambiguous=True)
compositeparticle_list.append(tmplist)
self.compositeparticles+=tmplist
ln = IMP.pmi.CompositeRestraint(
self.m,
self.handleparticles,
cut_off,
lam,
True,
plateau)
for ps in compositeparticle_list:
# composite particles is a list of list of particles
ln.add_composite_particle(ps)
self.rs.add_restraint(ln)
def __init__(self,
representation,
selection_tuple,
distance=3.78,
strength=10.0,
jitter=None):
"""Constructor
@param representation
@param selection_tuple Requested selection
@param distance Resting distance for restraint
@param strength Bond constant
@param jitter Defines the +- added to the optimal distance in the harmonic well restraint
used to increase the tolerance
"""
self.m = representation.prot.get_model()
self.rs = IMP.RestraintSet(self.m, "Bonds")
self.weight = 1
self.label = "None"
self.pairslist = []
particles = IMP.pmi.tools.select_by_tuple(
representation,
selection_tuple,
resolution=1)
if not jitter:
ts = IMP.core.Harmonic(distance, strength)
else:
ts = IMP.core.HarmonicWell(
(distance - jitter, distance + jitter), strength)
for ps in IMP.pmi.tools.sublist_iterator(particles, 2, 2):
pair = []
if len(ps) != 2:
raise ValueError("wrong length of pair")
for p in ps:
if not IMP.atom.Residue.get_is_setup(p):
raise TypeError("not a residue")
else:
pair.append(p)
print("ResidueBondRestraint: adding a restraint between %s %s" % (pair[0].get_name(), pair[1].get_name()))
self.rs.add_restraint(
IMP.core.DistanceRestraint(self.m, ts, pair[0], pair[1]))
self.pairslist.append(IMP.ParticlePair(pair[0], pair[1]))
self.pairslist.append(IMP.ParticlePair(pair[1], pair[0]))
def test_some_scores(self):
pdb_fn = self.get_input_file_name('helix2.pdb')
mdl = IMP.Model()
mh = IMP.atom.read_pdb(pdb_fn, mdl, IMP.atom.NonWaterPDBSelector())
ps = IMP.atom.Selection(
mh, atom_type=IMP.atom.AtomType("CA")).get_selected_particles()
strength = 10.0
rs = IMP.RestraintSet(mdl, "ElasticNetwork")
for pidx in itertools.combinations(range(len(ps)), 2):
pair = [ps[pidx[0]], ps[pidx[1]]]
distance = IMP.algebra.get_distance(
IMP.core.XYZ(pair[0]).get_coordinates(),
IMP.core.XYZ(pair[1]).get_coordinates())
ts = IMP.core.Harmonic(distance, strength)
rs.add_restraint(IMP.core.DistanceRestraint(ts, pair[0], pair[1]))
mdl.add_restraint(rs)
print(rs.evaluate(False))
def __init__(
self,
representation,
images,
resolution=None):
self.weight=1.0
self.m = representation.prot.get_model()
self.rs = IMP.RestraintSet(self.m, 'em2d')
self.label = "None"
# IMP.atom.get_by_type
particles = IMP.pmi.tools.select(
representation,
resolution=resolution)
em2d = None
self.rs.add_restraint(em2d)
def test_decomposition_4(self):
"""Test cache with decomposition with nested sets"""
(m, ps, r, pst, ik, cache) = self._create_stuff()
rs = IMP.RestraintSet(m, 1.0, "outer")
rs.set_maximum_score(2)
rs.add_restraint(r)
r.set_weight(3)
cache.add_restraints([rs])
subset = IMP.domino.Subset(ps)
rsb = cache.get_restraints(subset,
[IMP.domino.Subset([p]) for p in ps])
self.assertEqual(len(rsb), 1)
slc = cache.get_slice(rsb[0], subset)
self.assertEqual(len(slc), len(ps))
aslc = slc.get_sliced(IMP.domino.Assignment(range(len(ps))))
self.assertEqual(len(aslc), len(ps))
score = cache.get_score(rsb[0], aslc)
self.assert_(score > 1000)
def init_model_NOEs_marginal(self,
prot,
seqfile,
tblfile,
name='NOE',
verbose=True,
sequence_match=(1, 1)):
"""read TBL file and store NOE restraints, using the marginal of the
lognormal with one sigma and one gamma, for the whole dataset.
- prot: protein hierarchy
- seqfile: a file with 3-letter sequence
- tblfile: a TBL file with the restraints
- name: an optional name for the restraintset
- verbose: be verbose (default True)
- sequence_match : (noe_start, sequence_start)
Returns: data_rs
"""
# likelihood
rs = IMP.RestraintSet(self._m, 1.0, name)
# use the TBLReader to parse the TBL file.
sequence = IMP.isd.utils.read_sequence_file(
seqfile, first_residue_number=sequence_match[1])
tblr = IMP.isd.TBLReader.TBLReader(sequence,
sequence_match=sequence_match)
restraints = tblr.read_distances(tblfile, 'NOE')['NOE']
ln = IMP.isd.MarginalNOERestraint()
for i, restraint in enumerate(restraints):
if verbose and i % 100 == 0:
print("\r%d" % i, end=' ')
sys.stdout.flush()
# a restraint is (contributions, dist, upper, lower, volume)
# where contributions is a tuple of contributing pairs
# and a pair is (c1, c2), where c1 is of the form (resno, atname)
# residue numbers start at 0
pairs = [(self.find_atom(i, prot).get_particle(),
self.find_atom(j, prot).get_particle())
for (i, j) in restraint[0]]
pairs = IMP.container.ListPairContainer(pairs)
ln.add_contribution(pairs, restraint[4])
rs.add_restraint(ln)
if verbose:
print("\r%d NOE contributions added" % (len(restraints)))
self._m.add_restraint(rs)
return rs
def test_global_min2(self):
"""Testing finding minima with rigid bodies"""
m = IMP.Model()
rbs = [self._create_rb("1", m), self._create_rb("2", m)]
trs = [
ReferenceFrame3D(
Transformation3D(get_identity_rotation_3d(), Vector3D(0, 0,
0))),
ReferenceFrame3D(
Transformation3D(get_identity_rotation_3d(), Vector3D(2, 0,
0))),
ReferenceFrame3D(
Transformation3D(get_identity_rotation_3d(), Vector3D(4, 0,
0)))
]
ps = IMP.core.HarmonicSphereDistancePairScore(0, 1)
r = IMP.core.PairRestraint(
m, ps,
(rbs[0].get_rigid_members()[0], rbs[1].get_rigid_members()[0]))
r.set_name("restraint")
rs = IMP.RestraintSet(m)
rs.add_restraint(r)
r.set_maximum_score(.5)
pst = IMP.domino.ParticleStatesTable()
pstate = IMP.domino.RigidBodyStates(trs)
pst.set_particle_states(rbs[0], pstate)
pst.set_particle_states(rbs[1], pstate)
rg = IMP.domino.get_restraint_graph(rs, pst)
# rg.show_dotty()
print("ig")
ig = IMP.domino.get_interaction_graph([rs], pst)
# IMP.show_graphviz(ig)
print("dg")
IMP.set_log_level(IMP.VERBOSE)
dg = IMP.get_dependency_graph(m)
# IMP.show_graphviz(dg)
print("jt")
jt = IMP.domino.get_junction_tree(ig)
# jt.show_dotty()
s = IMP.domino.DominoSampler(m, pst)
s.set_restraints([rs])
s.set_log_level(IMP.VERBOSE)
cg = s.create_sample()
self.assertEqual(cg.get_number_of_configurations(), 4)
def __init__(self,
ps,
dmap,
resolution,
origin=None,
voxel_size=None,
weight=1.0,
label=""):
"""Constructor
@param ps The particles to restrain. Currently these must be atomic particles.
@param map_fn The EM density map to fit to
@param resolution Map resolution
@param origin In case you need to tell IMP the correct origin
@param voxel_size In case you need to tell IMP the angstroms per pixel
@param weight The data weight
@param label Extra PMI label
"""
print('FitRestraint: setup')
#print('\tmap_fn',map_fn)
print('\tresolution',resolution)
print('\tvoxel_size',voxel_size)
print('\torigin',origin)
print('\tweight',weight)
# some parameters
self.mdl = ps[0].get_model()
self.label = label
self.dmap = dmap #IMP.em.read_map(map_fn,IMP.em.MRCReaderWriter())
#dh = self.dmap.get_header()
#dh.set_resolution(resolution)
if voxel_size:
self.dmap.update_voxel_size(voxel_size)
if origin is not None:
if type(origin)==IMP.algebra.Vector3D:
self.dmap.set_origin(origin)
elif type(origin)==list:
self.dmap.set_origin(*origin)
else:
print('FitRestraint did not recognize format of origin')
exit()
fr = IMP.em.FitRestraint(ps,self.dmap)
self.rs = IMP.RestraintSet(self.mdl,weight,"FitRestraint")
self.rs.add_restraint(fr)
self.set_weight(weight)
def __init__(self,
representation,
tuple_selection1,
tuple_selection2,
distancemin,
distancemax,
resolution=1.0,
kappa=1.0):
self.m = representation.prot.get_model()
self.rs = IMP.RestraintSet(self.m, 'distance')
#ts = IMP.core.Harmonic(distance,kappa)
ts1 = IMP.core.HarmonicUpperBound(distancemax, kappa)
ts2 = IMP.core.HarmonicLowerBound(distancemin, kappa)
# IMP.atom.get_by_type
particles1 = IMP.pmi.tools.select(representation,
resolution=resolution,
name=tuple_selection1[2],
residue=tuple_selection1[0])
particles2 = IMP.pmi.tools.select(representation,
resolution=resolution,
name=tuple_selection2[2],
residue=tuple_selection2[0])
for p in particles1:
print p.get_name()
for p in particles2:
print p.get_name()
if len(particles1) > 1:
print "DistanceRestraint error: more than one particle selected"
exit()
if len(particles2) > 1:
print "DistanceRestraint error: more than one particle selected"
exit()
self.rs.add_restraint(
IMP.core.DistanceRestraint(ts1, particles1[0], particles2[0]))
self.rs.add_restraint(
IMP.core.DistanceRestraint(ts2, particles1[0], particles2[0]))
def test_refcount_director_restraints(self):
"""Refcounting should prevent director Restraints from being deleted"""
dirchk = IMP.test.DirectorObjectChecker(self)
m = IMP.Model("ref count dir restraints")
rs = IMP.RestraintSet(m)
IMP.set_log_level(IMP.VERBOSE)
r = DummyRestraint(m)
r.python_member = 'test string'
rs.add_restraint(r)
# Since C++ now holds a reference to r, it should be safe to delete the
# Python object (director objects should not be freed while C++ holds
# a reference)
del r
newr = rs.get_restraint(0)
self.assertEqual(newr.python_member, 'test string')
# Make sure that all director objects are cleaned up
dirchk.assert_number(1)
del newr, m, rs
dirchk.assert_number(0)
def test_global_min3(self):
"""Testing splitting restraints with rigid bodies and interestings scores"""
m = IMP.Model()
rbs = [
self._create_rb("1", m, 4),
self._create_rb("2", m, 4),
self._create_rb("3", m, 4)
]
trs = [
ReferenceFrame3D(
Transformation3D(get_identity_rotation_3d(), Vector3D(0, 0,
0))),
ReferenceFrame3D(
Transformation3D(get_identity_rotation_3d(), Vector3D(2, 0,
0))),
ReferenceFrame3D(
Transformation3D(get_identity_rotation_3d(), Vector3D(4, 0,
0)))
]
lps = IMP.core.SphereDistancePairScore(
IMP.core.HarmonicUpperBound(0, 1))
ps = IMP.core.KClosePairsPairScore(lps, IMP.core.RigidMembersRefiner())
pl = IMP.container.ListPairContainer(m, [(rbs[0], rbs[1]),
(rbs[1], rbs[2])])
r = IMP.container.PairsRestraint(ps, pl)
r.set_name("restraint")
rs = IMP.RestraintSet(m)
rs.add_restraint(r)
r.set_maximum_score(.5)
dg = IMP.get_dependency_graph(m)
# dg.show_dotty()
pst = IMP.domino.ParticleStatesTable()
pstate = IMP.domino.RigidBodyStates(trs)
pst.set_particle_states(rbs[0], pstate)
pst.set_particle_states(rbs[1], pstate)
pst.set_particle_states(rbs[2], pstate)
#occ= IMP.domino.OptimizeRestraints(m.get_root_restraint_set(), pst)
rc = IMP.domino.RestraintCache(pst)
rc.add_restraints([rs])
allr = rc.get_restraints()
for r in allr:
print(r.get_name())
self.assertEqual(len(allr), 3)
def __init__(self, representation,
hierarchies=None,
other_hierarchies=None,
resolution=None, kappa=1.0):
self.m = representation.prot.get_model()
self.rs = IMP.RestraintSet(self.m, 'excluded_volume')
self.weight = 1.0
self.kappa = kappa
self.label = "None"
self.cpc = None
ssps = IMP.core.SoftSpherePairScore(self.kappa)
lsa = IMP.container.ListSingletonContainer(self.m)
particles = IMP.pmi.tools.select(
representation,
resolution=resolution,
hierarchies=hierarchies)
lsa.add_particles(particles)
if other_hierarchies is None:
rbcpf = IMP.core.RigidClosePairsFinder()
self.cpc = IMP.container.ClosePairContainer(lsa, 0.0, rbcpf, 10.0)
evr = IMP.container.PairsRestraint(ssps, self.cpc)
else:
other_lsa = IMP.container.ListSingletonContainer(self.m)
other_particles = IMP.pmi.tools.select(
representation,
resolution=resolution,
hierarchies=other_hierarchies)
other_lsa.add_particles(particles)
self.cpc = IMP.container.CloseBipartitePairContainer(
lsa,
other_lsa,
0.0,
10.0)
evr = IMP.container.PairsRestraint(ssps, self.cpc)
self.rs.add_restraint(evr)
def create_restraints_for_rmf(self):
""" create dummy harmonic restraints for each XL but don't add to model
Makes it easy to see each contribution to each XL in RMF
"""
dummy_mdl = IMP.Model()
hps = IMP.core.HarmonicDistancePairScore(self.length, 1.0)
dummy_rs = []
for nxl in range(self.rs.get_number_of_restraints()):
xl = IMP.isd.AtomicCrossLinkMSRestraint.get_from(
self.rs.get_restraint(nxl))
rs = IMP.RestraintSet(dummy_mdl, 'atomic_xl_' + str(nxl))
for ncontr in range(xl.get_number_of_contributions()):
ps = xl.get_contribution(ncontr)
dr = IMP.core.PairRestraint(
hps, [self.mdl.get_particle(p) for p in ps],
'xl%i_contr%i' % (nxl, ncontr))
rs.add_restraint(dr)
dummy_rs.append(MyGetRestraint(rs))
return dummy_rs
def __init__(self,
root,
map_fn,
resolution,
origin=None,
voxel_size=None,
weight=1.0,
label="",
selection_dict=None):
""" create a FitRestraint. can provide rigid bodies instead of individual particles """
print('FitRestraint: setup')
print('\tmap_fn', map_fn)
print('\tresolution', resolution)
print('\tvoxel_size', voxel_size)
print('\torigin', origin)
print('\tweight', weight)
# some parameters
self.mdl = root.get_model()
self.label = label
self.dmap = IMP.em.read_map(map_fn, IMP.em.MRCReaderWriter())
dh = self.dmap.get_header()
dh.set_resolution(resolution)
if voxel_size:
self.dmap.update_voxel_size(voxel_size)
if type(origin) == IMP.algebra.Vector3D:
self.dmap.set_origin(origin)
elif type(origin) == list:
self.dmap.set_origin(*origin)
else:
print('FitRestraint did not recognize format of origin')
exit()
if selection_dict:
ps = IMP.atom.Selection(root,
**selection_dict).get_selected_particles()
else:
ps = IMP.atom.get_leaves(root)
fr = IMP.em.FitRestraint(ps, self.dmap)
self.rs = IMP.RestraintSet(self.mdl, weight, "FitRestraint")
self.rs.add_restraint(fr)
self.set_weight(weight)
def __init__(
self,
representation,
selection_tuple,
anglemin=100.0,
anglemax=140.0,
strength=10.0):
self.m = representation.prot.get_model()
self.rs = IMP.RestraintSet(self.m, "Angles")
self.weight = 1
self.label = "None"
self.pairslist = []
particles = IMP.pmi.tools.select_by_tuple(
representation,
selection_tuple,
resolution=1)
ts = IMP.core.HarmonicWell(
(self.pi * anglemin / 180.0,
self.pi * anglemax / 180.0),
strength)
for ps in IMP.pmi.tools.sublist_iterator(particles, 3, 3):
triplet = []
if len(ps) != 3:
print "ResidueAngleRestraint: wrong length of triplet"
exit()
for p in ps:
if not IMP.atom.Residue.get_is_setup(p):
print "ResidueAngleRestraint: not a residue"
exit()
else:
triplet.append(p)
print "ResidueAngleRestraint: adding a restraint between %s %s %s" % (triplet[0].get_name(), triplet[1].get_name(), triplet[2].get_name())
self.rs.add_restraint(
IMP.core.AngleRestraint(ts,
triplet[0],
triplet[1],
triplet[2]))
self.pairslist.append(IMP.ParticlePair(triplet[0], triplet[2]))
self.pairslist.append(IMP.ParticlePair(triplet[2], triplet[0]))
def test_delete_model_accessor_2(self):
"Python Restraints from vector accessors should survive model deletion"
refcnt = IMP.test.RefCountChecker(self)
m = IMP.Model("restraint survival")
rs = IMP.RestraintSet(m)
r = IMP._ConstRestraint(m, [], 1)
rs.add_restraint(r)
del r
# Now create new Python Restraint r from a C++ vector accessor
# These accessors call specific methods in the SWIG wrapper which
# are modified by typemaps in our interface.
r = rs.get_restraints()[0]
# Python reference r plus C++ reference from m
self.assertEqual(r.get_ref_count(), 2)
del m, rs
# Now only the Python reference r should survive
self.assertEqual(r.get_ref_count(), 1)
refcnt.assert_number(1)
del r
refcnt.assert_number(0)
def test_delete_model_iterator(self):
"""Python Restraints from iterators should survive model deletion"""
refcnt = IMP.test.RefCountChecker(self)
m = IMP.Model("python restraint survival")
rs = IMP.RestraintSet(m)
r = IMP._ConstRestraint(m, [], 1)
rs.add_restraint(r)
del r
# Now create new Python Restraint r from C++ iterator
# This calls swig::from() internally, which is modified by template
# specialization in our SWIG interface.
r = rs.get_restraints()[0]
# Python reference r plus C++ reference from m
self.assertEqual(r.get_ref_count(), 2)
del m, rs
# Now only the Python reference r should survive
self.assertEqual(r.get_ref_count(), 1)
refcnt.assert_number(1)
del r
refcnt.assert_number(0)
def __init__(self, objects, kappa=10.0, resolution=1.0, label="None"):
self.weight = 1.0
self.kappa = kappa
self.label = label
if self.label == "None":
self.label = str(selection_tuples) # noqa: F821
hiers = []
for obj in objects:
hiers.append(
IMP.pmi.tools.input_adaptor(obj, resolution, flatten=True))
self.m = hiers[0][0].get_model()
cr = ConnectivityNetworkRestraint(self.m)
for hs in hiers:
cr.add_particles([h.get_particle() for h in hs])
self.rs = IMP.RestraintSet(self.m, label)
self.rs.add_restraint(cr)
def test_rescaling(self):
"""Test thermostatting by velocity rescaling"""
for i in range(100):
self.particles.append(self.create_point_particle(self.model,
-43.0, 65.0, 93.0))
self.particles[-1].add_attribute(masskey, cmass, False)
self.md.assign_velocities(100.0)
scaler = IMP.atom.VelocityScalingOptimizerState(self.model,
self.particles, 298.0)
scaler.set_period(10)
self.md.add_optimizer_state(scaler)
r = IMP.RestraintSet(self.model)
self.md.set_scoring_function(r)
self.md.optimize(10)
# Temperature should have been rescaled to 298.0 at some point:
self._check_temperature(298.0, 0.1)
# Also check immediate rescaling:
scaler.set_temperature(50.0)
scaler.rescale_velocities()
self._check_temperature(50.0, 0.1)
def save_rmf_snapshot(self, filename):
sorted_ids = None
sorted_group_ids = sorted(self.cross_link_db.data_base.keys())
list_of_pairs = []
for group in sorted_group_ids:
group_xls = []
group_dists_particles = []
for xl in self.cross_link_db.data_base[group]:
xllabel = self.cross_link_db.get_short_cross_link_string(xl)
(c1, c2, r1,
r2) = IMP.pmi.io.crosslink._ProteinsResiduesArray(xl)
try:
(mdist, p1, p2) = self._get_distance_and_particle_pair(
r1, c1, r2, c2)
except TypeError:
continue
group_dists_particles.append((mdist, p1, p2, xllabel))
if group_dists_particles:
(minmdist, minp1, minp2,
minxllabel) = min(group_dists_particles, key=lambda t: t[0])
list_of_pairs.append((minp1, minp2, xllabel))
else:
continue
m = self.prots[0].get_model()
linear = IMP.core.Linear(0, 0.0)
linear.set_slope(1.0)
dps2 = IMP.core.DistancePairScore(linear)
rslin = IMP.RestraintSet(m, 'linear_dummy_restraints')
for pair in list_of_pairs:
pr = IMP.core.PairRestraint(m, dps2, (pair[0], pair[1]))
pr.set_name(pair[2])
rslin.add_restraint(pr)
rh = RMF.create_rmf_file(filename)
IMP.rmf.add_hierarchies(rh, self.prots)
IMP.rmf.add_restraints(rh, [rslin])
IMP.rmf.save_frame(rh)
del rh
def test_interaction_graph(self):
"""Testing the interaction graph with rigid bodies"""
m = IMP.Model()
rb0 = self._create_rigid_body(m)
rb1 = self._create_rigid_body(m)
rb2 = self._create_rigid_body(m)
r = IMP.core.PairRestraint(m, IMP.core.HarmonicDistancePairScore(0, 1),
(rb0, rb1))
rs = IMP.RestraintSet(m)
rs.add_restraint(r)
dg = IMP.get_dependency_graph(m)
# IMP.show_graphviz(dg)
ig = IMP.domino.get_interaction_graph([rs], [rb0, rb1, rb2])
# IMP.show_graphviz(ig)
for v in ig.get_vertices():
if ig.get_vertex_name(v) == rb0 or ig.get_vertex_name(v) == rb1:
self.assertEqual(len(ig.get_out_neighbors(v)), 1)
self.assertEqual(len(ig.get_in_neighbors(v)), 1)
else:
self.assertEqual(len(ig.get_out_neighbors(v)), 0)
self.assertEqual(len(ig.get_in_neighbors(v)), 0)
def test_decomposition_5(self):
"""Test cache with simple restraint"""
(m, ps, r, pst, ik, cache) = self._create_stuff()
rs = IMP.RestraintSet(m, 1.0, "outer")
r = IMP._ConstRestraint(1, [ps[0]])
r.set_name("const 2")
rs.add_restraint(r)
r.set_maximum_score(.5)
cache.add_restraints([rs])
print("info:")
cache.show_restraint_information()
subset = IMP.domino.Subset([ps[0]])
rsb = cache.get_restraints(subset, [])
self.assertEqual(len(rsb), 1)
slc = cache.get_slice(rsb[0], subset)
self.assertEqual(len(slc), 1)
aslc = slc.get_sliced(IMP.domino.Assignment(range(len(ps))))
self.assertEqual(len(aslc), 1)
score = cache.get_score(rsb[0], aslc)
print(score)
self.assert_(score > 1000)
def setUp(self):
"""set up distance restraints and create optimizer """
IMP.test.TestCase.setUp(self)
self.imp_model = IMP.Model()
self.particles = []
self.restraint_sets = []
self.rsrs = []
# create particles 0 - 1
self.particles.append(self.create_point_particle(self.imp_model,
-43.0, 65.0, 93.0))
self.particles.append(self.create_point_particle(self.imp_model,
20.0, 74.0, -80.0))
self.particles.append(self.create_point_particle(self.imp_model,
4.0, -39.0, 26.0))
p1 = self.particles[0]
p1.add_attribute(radkey, 1.0, False)
p1 = self.particles[1]
p1.add_attribute(radkey, 2.0, False)
p1 = self.particles[2]
p1.add_attribute(radkey, 3.0, False)
# separate 3 particles by their radii
for pairs in ((0, 1), (1, 2), (0, 2)):
p1 = self.particles[pairs[0]]
p2 = self.particles[pairs[1]]
mean = p1.get_value(radkey) + p2.get_value(radkey)
sf = IMP.core.Harmonic(mean, 0.1)
rsr = IMP.core.DistanceRestraint(self.imp_model, sf, p1, p2)
self.rsrs.append(rsr)
# add restraints
rs = IMP.RestraintSet(self.imp_model, 1.0, "distance_rsrs")
self.restraint_sets.append(rs)
for i in range(len(self.rsrs)):
rs.add_restraint(self.rsrs[i])
self.steepest_descent = IMP.core.SteepestDescent(self.imp_model)
self.steepest_descent.set_scoring_function([rs])
def test_global_min3(self):
"""Test sampling with edge scores"""
m = IMP.Model()
m.set_log_level(IMP.SILENT)
ps = []
for i in range(0, 3):
p = IMP.Particle(m)
d = IMP.core.XYZ.setup_particle(p)
ps.append(p)
pts = [
IMP.algebra.Vector3D(0, 0, 0),
IMP.algebra.Vector3D(1, 0, 0),
IMP.algebra.Vector3D(2, 0, 0),
IMP.algebra.Vector3D(3, 0, 0)
]
particle_state = IMP.domino.XYZStates(pts)
pst = IMP.domino.ParticleStatesTable()
r = IMP.RestraintSet(m)
for p in ps:
pst.set_particle_states(p, particle_state)
r.add_restraint(IMP._ConstRestraint(1, [p]))
r.add_restraint(
IMP.core.DistanceRestraint(m, IMP.core.Harmonic(1, 1), ps[0],
ps[1]))
r.add_restraint(
IMP.core.DistanceRestraint(m, IMP.core.Harmonic(1, 1), ps[1],
ps[2]))
r.set_maximum_score(3.1)
sampler = IMP.domino.DominoSampler(m, pst)
sampler.set_restraints([r])
sampler.set_log_level(IMP.VERBOSE)
cs = sampler.create_sample()
self.assertGreater(cs.get_number_of_configurations(), 0)
for i in range(0, cs.get_number_of_configurations()):
cs.load_configuration(i)
self.assertLess((IMP.core.get_distance(IMP.core.XYZ(
ps[0]), IMP.core.XYZ(ps[1])) - 1)**2, .1)
self.assertLess((IMP.core.get_distance(IMP.core.XYZ(
ps[1]), IMP.core.XYZ(ps[2])) - 1)**2, .1)
def test_global_min1(self):
"""Testing splitting restraints with rigid bodies"""
m = IMP.Model()
rbs = [
self._create_rb("1", m),
self._create_rb("2", m),
self._create_rb("3", m)
]
trs = [
ReferenceFrame3D(
Transformation3D(get_identity_rotation_3d(), Vector3D(0, 0,
0))),
ReferenceFrame3D(
Transformation3D(get_identity_rotation_3d(), Vector3D(2, 0,
0))),
ReferenceFrame3D(
Transformation3D(get_identity_rotation_3d(), Vector3D(4, 0,
0)))
]
ps = IMP.core.HarmonicSphereDistancePairScore(0, 1)
members = IMP.get_indexes([x.get_rigid_members()[0] for x in rbs])
pl = IMP.container.ListPairContainer(m, [(members[0], members[1]),
(members[1], members[2])])
r = IMP.container.PairsRestraint(ps, pl)
r.set_name("restraint")
rs = IMP.RestraintSet(m)
rs.add_restraint(r)
r.set_maximum_score(.5)
pst = IMP.domino.ParticleStatesTable()
pstate = IMP.domino.RigidBodyStates(trs)
pst.set_particle_states(rbs[0], pstate)
pst.set_particle_states(rbs[1], pstate)
pst.set_particle_states(rbs[2], pstate)
rc = IMP.domino.RestraintCache(pst)
rc.add_restraints([rs])
allr = rc.get_restraints()
for r in allr:
print(r.get_name())
self.assertEqual(len(allr), 3)
def __init__(self,
representation,
radius,
hierarchies=None,
resolution=None):
self.m = representation.prot.get_model()
self.rs = IMP.RestraintSet(self.m, 'barrier')
self.radius = radius
self.label = "None"
c3 = IMP.algebra.Vector3D(0, 0, 0)
ub3 = IMP.core.HarmonicUpperBound(radius, 10.0)
ss3 = IMP.core.DistanceToSingletonScore(ub3, c3)
lsc = IMP.container.ListSingletonContainer(self.m)
# IMP.atom.get_by_type
particles = IMP.pmi.tools.select(representation,
resolution=resolution,
hierarchies=hierarchies)
lsc.add_particles(particles)
r3 = IMP.container.SingletonsRestraint(ss3, lsc)
self.rs.add_restraint(r3)
def __init__(self,
representation,
images,
pixel_size,
image_resolution,
projection_number,
resolution=None):
self.weight = 1.0
self.m = representation.prot.get_model()
self.rs = IMP.RestraintSet(self.m, 'em2d')
self.label = "None"
# IMP.atom.get_by_type
particles = IMP.pmi.tools.select(representation, resolution=resolution)
#print particles
em2d = IMP.em2d.PCAFitRestraint(particles, images, pixel_size,
image_resolution, projection_number,
True)
self.rs.add_restraint(em2d)
def __init__(self, objects, distance=3.78, strength=10.0, jitter=None):
"""Constructor
@param objects Objects to restrain
@param distance Resting distance for restraint
@param strength Bond constant
@param jitter Defines the +- added to the optimal distance in
the harmonic well restraint used to increase the tolerance
"""
particles = IMP.pmi.tools.input_adaptor(objects, 1, flatten=True)
self.m = particles[0].get_model()
self.rs = IMP.RestraintSet(self.m, "Bonds")
self.weight = 1
self.label = "None"
self.pairslist = []
if not jitter:
ts = IMP.core.Harmonic(distance, strength)
else:
ts = IMP.core.HarmonicWell((distance - jitter, distance + jitter),
strength)
for ps in IMP.pmi.tools.sublist_iterator(particles, 2, 2):
pair = []
if len(ps) != 2:
raise ValueError("wrong length of pair")
for p in ps:
if not IMP.atom.Residue.get_is_setup(p):
raise TypeError("%s is not a residue" % p)
else:
pair.append(p)
print("ResidueBondRestraint: adding a restraint between %s %s" %
(pair[0].get_name(), pair[1].get_name()))
self.rs.add_restraint(
IMP.core.DistanceRestraint(self.m, ts, pair[0], pair[1]))
self.pairslist.append(IMP.ParticlePair(pair[0], pair[1]))
self.pairslist.append(IMP.ParticlePair(pair[1], pair[0]))