def test_xlinks(self):
"""
Test the Xlinks class
"""
for p in self.pairs:
xlist = self.xlinks.get_xlinks_for_pair(p)
# build manually the list that xlist should build
manual_xlist = []
xl = None
for c in self.crosslinks:
if p == (c[0], c[3]) or p == (c[3], c[0]):
xl = bx.Xlink(*c)
if p == (c[3], c[0]):
xl.swap()
manual_xlist.append(xl)
# check the number of crosslinks for the pair
self.assertEqual(len(manual_xlist), len(xlist))
# check amino acids and distances
aa = [(xl.first_residue, xl.second_residue, xl.distance)
for xl in xlist]
ll = [(xl.first_residue, xl.second_residue, xl.distance)
for xl in manual_xlist]
for x in ll:
self.assertTrue(x in aa)
xlistDE = self.xlinks.get_xlinks_for_pair(("subunitD", "subunitE"))
xlistED = self.xlinks.get_xlinks_for_pair(("subunitE", "subunitD"))
self.assertEqual(len(xlistDE), 4)
self.assertEqual(len(xlistED), 4)
for y, x in zip(xlistDE, xlistED):
self.assertEqual(x.first_residue, y.second_residue)
self.assertEqual(y.first_residue, x.second_residue)
self.assertEqual(x.distance, y.distance)
def setUp(self):
IMP.test.TestCase.setUp(self)
if bx is None:
self.skipTest(bxerr)
self.crosslinks = [
("subunitA", "A", 1, "subunitB", "B", 1, 10),
("subunitA", "A", 2, "subunitB", "B", 2, 20),
("subunitB", "B", 3, "subunitA", "A", 3, 30),
("subunitB", "B", 4, "subunitC", "C", 1, 40),
("subunitB", "B", 5, "subunitC", "C", 2, 20),
("subunitD", "D", 6, "subunitC", "C", 1, 10),
("subunitC", "C", 3, "subunitD", "D", 2, 70),
("subunitC", "C", 4, "subunitD", "D", 3, 80),
("subunitD", "D", 4, "subunitE", "E", 1, 10),
("subunitE", "E", 5, "subunitD", "D", 2, 30),
("subunitD", "D", 6, "subunitE", "E", 3, 40),
("subunitD", "D", 7, "subunitE", "E", 4, 50),
]
# get different pairs of subunits
self.xlinks = bx.XlinksDict()
for c in self.crosslinks:
x = bx.Xlink(*c)
self.xlinks.add(x)
self.pairs = set()
for c in self.crosslinks:
self.pairs.add((c[0], c[3]))
def set_xlink_restraint(self, id1, chain1, residue1, id2, chain2, residue2,
distance, weight, stddev, max_score=False):
"""
Set a restraint on the maximum distance between 2 residues
@param id1 Name of the first component
@param chain1
@param residue1 Residue number for the aminoacid in the first
component.The number is the number in the PDB file, not the
number relative to the beginning of the chain
@param id2 Name of the second component
@param chain2
@param residue2 Residue number for the aminoacid in the second
component.
@param distance Maximum distance tolerated
@param weight Weight of the restraint
@param stddev Standard deviation used to approximate the
HarmonicUpperBound function to a Gaussian
@param max_score See help for add_restraint(). If none is given,
the maximum score is set to allow a maximum distance of 10 Angstrom
greater than the parameter "distance".
"""
xlink = buildxlinks.Xlink(
id1,
chain1,
residue1,
id2,
chain2,
residue2,
distance)
log.info("Setting cross-linking restraint ")
log.info("%s", xlink.show())
self.xlinks_dict.add(xlink)
# setup restraint
A = representation.get_component(self.assembly, xlink.first_id)
s1 = IMP.atom.Selection(A, chain=xlink.first_chain,
residue_index=xlink.first_residue)
p1 = s1.get_selected_particles()[0]
B = representation.get_component(self.assembly, xlink.second_id)
s2 = IMP.atom.Selection(B, chain=xlink.second_chain,
residue_index=xlink.second_residue)
p2 = s2.get_selected_particles()[0]
k = core.Harmonic.get_k_from_standard_deviation(stddev)
score = core.HarmonicUpperBound(xlink.distance, k)
pair_score = IMP.core.DistancePairScore(score)
r = IMP.core.PairRestraint(pair_score, IMP.ParticlePair(p1, p2))
if not max_score:
error_distance_allowed = 100
max_score = weight * \
score.evaluate(distance + error_distance_allowed)
log.info("%s, max_score %s", xlink.show(), max_score)
self.add_restraint(r, xlink.get_name(), weight, max_score)
def test_filter_transformations(self):
"""
Check if the filtered conformation are the conformations that I
computed before
"""
try:
import subprocess
import IMP.EMageFit.buildxlinks as bx
except ImportError as e:
self.skipTest(str(e))
dock = self.import_python_application('emagefit_dock')
sel = atom.NonWaterNonHydrogenPDBSelector()
ligand = IMP.kernel.Model()
fn_ligand = self.get_input_file_name("3sfdB-3sfdA_initial_docking.pdb")
h_ligand = atom.read_pdb(fn_ligand, ligand, sel)
rb_ligand = atom.create_rigid_body(h_ligand)
receptor = IMP.kernel.Model()
fn_receptor = self.get_input_file_name("3sfdB.pdb")
h_receptor = atom.read_pdb(fn_receptor, receptor, sel)
# read_hex_transformations
fn = self.get_input_file_name("hex_solutions_3sfdB-3sfdA.txt")
residue_receptor = 23
residue_ligand = 456
distance = 30
xl = bx.Xlink("3sfdB", "B", residue_receptor, "3sfdA", "A",
residue_ligand, distance)
xlinks_list = [xl]
fn_filtered = "filtered_transforms.txt"
dock.filter_docking_results(h_receptor, h_ligand, xlinks_list, fn,
fn_filtered)
fn_stored = self.get_input_file_name(
"hex_solutions_3sfdB-3sfdA_filtered.txt")
filtered = dock.read_hex_transforms(fn_filtered)
stored = dock.read_hex_transforms(fn_stored)
# check that the filtered transforms match the stored ones
self.assertEqual(len(filtered), len(stored))
for Tf, Ts in zip(filtered, stored):
tf = Tf.get_translation()
ts = Ts.get_translation()
qf = Tf.get_rotation().get_quaternion()
qs = Ts.get_rotation().get_quaternion()
for k in range(3):
self.assertAlmostEqual(tf[k], ts[k])
for k in range(4):
self.assertAlmostEqual(qf[k], qs[k])
os.remove(fn_filtered)
def setUp(self):
IMP.test.TestCase.setUp(self)
if bx is None:
self.skipTest(bxerr)
self.max_distance = 30
self.crosslinks = [
("3sfdB", "B", 23, "3sfdA", "A", 456, self.max_distance),
("3sfdB", "B", 241, "3sfdC", "C", 112, self.max_distance),
("3sfdB", "B", 205, "3sfdD", "D", 37, self.max_distance),
("3sfdB", "B", 177, "3sfdD", "D", 99, self.max_distance),
("3sfdC", "C", 9, "3sfdD", "D", 37, self.max_distance),
("3sfdC", "C", 78, "3sfdD", "D", 128, self.max_distance),
]
self.xlinks = bx.XlinksDict()
for c in self.crosslinks:
self.xlinks.add(bx.Xlink(*c))
def test_build_order(self):
"""
Test the order recommendation for the xlinks
"""
# Note that we don't use the same crosslinks here as the other tests,
# because the order recommendation doesn't take account of multiple
# crosslinks between a given pair of subunits.
crosslinks = [
("subunitA", "A", 1, "subunitB", "B", 1, 10),
("subunitA", "A", 1, "subunitC", "B", 1, 10),
("subunitA", "A", 1, "subunitD", "B", 1, 10),
("subunitA", "A", 1, "subunitE", "B", 1, 10),
("subunitA", "A", 1, "subunitF", "B", 1, 10),
("subunitC", "A", 1, "subunitE", "B", 1, 10),
("subunitC", "A", 1, "subunitD", "B", 1, 10),
("subunitB", "A", 1, "subunitF", "B", 1, 10),
]
xlinks = bx.XlinksDict()
for c in crosslinks:
xlinks.add(bx.Xlink(*c))
dock_order = bx.DockOrder()
dock_order.set_xlinks(xlinks)
docking_pairs = dock_order.get_docking_order()
# Optimal order should be:
# - First, pick the most linked subunit (A) and dock everything
# that's linked to it (in any order)
# - Repeat with the remaining subunits in order of most links (C, B)
optimal_order = [('subunitA', 'subunitB'), ('subunitA', 'subunitC'),
('subunitA', 'subunitD'), ('subunitA', 'subunitE'),
('subunitA', 'subunitF'), ('subunitC', 'subunitD'),
('subunitC', 'subunitE'), ('subunitF', 'subunitB')]
docking_pairs = sorted(docking_pairs[:5]) + sorted(docking_pairs[5:7]) \
+ [docking_pairs[7]]
for p, q in zip(docking_pairs, optimal_order):
self.assertEqual(p, q)