def __init__(self, fh, diameter):
self.atom_factory = RMF.AtomFactory(fh)
self.bond_factory = RMF.BondFactory(fh)
self.particle_factory = RMF.ParticleFactory(fh)
self.ball_factory = RMF.BallFactory(fh)
self.segment_factory = RMF.SegmentFactory(fh)
self.cylinder_factory = RMF.CylinderFactory(fh)
self.diameter = diameter * 1.5
def test_perturbed(self):
"""Test writing a simple hierarchy"""
m = IMP.kernel.Model()
h = IMP.atom.read_pdb(self.get_input_file_name("small_protein.pdb"), m)
hs = IMP.atom.create_simplified_along_backbone(
IMP.atom.get_by_type(h, IMP.atom.CHAIN_TYPE)[0], 1)
IMP.base.set_log_level(IMP.base.SILENT)
fname = self.get_tmp_file_name("restraint_bonds.rmf3")
fh = RMF.create_rmf_file(fname)
IMP.rmf.add_hierarchy(fh, hs)
leaves = IMP.atom.get_leaves(hs)
cpc = IMP.container.ConsecutivePairContainer(leaves)
br = IMP.container.PairsRestraint(
IMP.core.HarmonicSphereDistancePairScore(0, 1), cpc)
IMP.rmf.add_restraints_as_bonds(fh, [br])
IMP.rmf.save_frame(fh, "frame")
bf = RMF.BondFactory(fh)
count = 0
for nid in fh.get_node_ids():
n = fh.get_node(nid)
if bf.get_is(n):
count += 1
self.assertEqual(count, len(leaves) - 1)
number_of_particles = 10
number_of_frames = 100
minimum_radius = .5
maximum_radius = 3
box_size = 15
# find the name for a temporary file to use to for writing the hdf5 file
tfn = RMF._get_temporary_file_path("motion.rmf3")
print("File is", tfn)
# open the temporary file, clearing any existing contents
fh = RMF.create_rmf_file(tfn)
tf = RMF.TypedFactory(fh)
pf = RMF.ParticleFactory(fh)
bf = RMF.BondFactory(fh)
sf = RMF.SegmentFactory(fh)
rf = RMF.RepresentationFactory(fh)
scf = RMF.ScoreFactory(fh)
coords = []
radii = []
particles = []
def get_distance(v0, r0, v1, r1):
return (((v0[0] - v1[0])**2 + (v0[1] - v1[1])**2 +
(v0[1] - v1[1])**2)**.5 - r0 - r1)
def intersects(c, r, cs, rs):
pf,
acf,
af,
ccf,
cf,
bf,
prev)
return prev
fh = RMF.open_rmf_file_read_only(RMF.get_example_path("3U7W.rmf"))
fh.set_current_frame(RMF.FrameID(0))
outpath = RMF._get_temporary_file_path("3U7W-residues.rmf")
out = RMF.create_rmf_file(outpath)
out.add_frame("nothing", RMF.FRAME)
print("file is", outpath)
bf = RMF.BondFactory(out)
rcf = RMF.ResidueFactory(fh)
rf = RMF.ResidueFactory(out)
pcf = RMF.ParticleFactory(fh)
pf = RMF.ParticleFactory(out)
acf = RMF.AtomFactory(fh)
af = RMF.AtomFactory(out)
ccf = RMF.ChainFactory(fh)
cf = RMF.ChainFactory(out)
bf = RMF.BondFactory(out)
copy_to_residues(
fh.get_root_node(),
out.get_root_node(),
rcf,
rf,
# same thing
from __future__ import print_function
import RMF
file_name = RMF._get_temporary_file_path("reference_frame.rmfz")
print("file is", file_name)
fh = RMF.create_rmf_file(file_name)
fh.add_frame("first frame", RMF.FRAME)
rh = fh.get_root_node()
reference_frame_factory = RMF.ReferenceFrameFactory(fh)
ball_factory = RMF.BallFactory(fh)
particle_factory = RMF.ParticleFactory(fh)
color_factory = RMF.ColoredFactory(fh)
bond_factory = RMF.BondFactory(fh)
origin = rh.add_child("origin", RMF.REPRESENTATION)
pd = particle_factory.get(origin)
pd.set_radius(1)
pd.set_mass(2)
pd.set_coordinates(RMF.Vector3(0, 0, 0))
for i in range(0, 3):
c = rh.add_child(str(i), RMF.REPRESENTATION)
pd = particle_factory.get(c)
pd.set_radius(1)
pd.set_mass(2)
coords = [0, 0, 0]
coords[i] = 2
pd.set_coordinates(RMF.Vector3(*coords))
