def main():
IMP.base.add_string_flag("input", "", "The RMF file to add cylinders to.")
IMP.base.add_float_flag("radius", 5, "The radius of the cylinder.")
IMP.base.add_float_flag("site_radius", 2, "The radius of the sites.")
IMP.base.add_bool_flag("recolor_fgs", "recolor fg nup chains")
IMP.base.add_bool_flag("recolor_floats",
"recolor floating (diffusing) molecules")
IMP.base.setup_from_argv(sys.argv, "Prettify a movie")
fh = RMF.open_rmf_file(IMP.base.get_string_flag("input"))
radius = IMP.base.get_float_flag("radius")
print "opened", fh.get_name()
cf = RMF.CylinderFactory(fh)
rff = RMF.ReferenceFrameFactory(fh)
tf = RMF.TypedFactory(fh)
bf = RMF.BallFactory(fh)
cdf = RMF.ColoredFactory(fh)
ipf = RMF.IntermediateParticleFactory(fh)
fg_types = [
IMP.npctransport.get_type_of_fg(i).get_string()
for i in range(0, IMP.npctransport.get_number_of_types_of_fg())
]
float_types = [
IMP.npctransport.get_type_of_float(i).get_string()
for i in range(0, IMP.npctransport.get_number_of_types_of_float())
]
fh.set_current_frame(RMF.ALL_FRAMES)
if (IMP.base.get_bool_flag("recolor_fgs")):
_recolor(fh.get_root_node(), tf, cdf, fg_types, fg_color)
if (IMP.base.get_bool_flag("recolor_floats")):
_recolor(fh.get_root_node(), tf, cdf, float_types[0:1], kap_color)
_recolor(fh.get_root_node(), tf, cdf, float_types[1:], crap_color)
_resize_sites(fh.get_root_node(), bf,
IMP.base.get_float_flag("site_radius"))
cylinders = _add_nodes(fh.get_root_node(), cf, cdf, tf, fg_types, radius,
fg_color)
for i in range(0, fh.get_number_of_frames()):
print "frame", i
fh.set_current_frame(i)
for c in cylinders:
_set_cylinder(c, cf, rff)
# This simple example makes an RMF file with several rigid copies of the
# 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
def main():
IMP.add_string_flag("input_rmf", "", "The input RMF file.")
IMP.add_string_flag("output_rmf", "",
"The output RMF file in which to add cylinders.")
IMP.add_string_flag(
"ref_output", "",
"reference output file from which info e.g. fg nup types can be extracted"
)
IMP.add_float_flag("radius", 5, "The radius of the cylinder.")
IMP.add_float_flag("site_radius", 2, "The radius of the sites.")
IMP.add_bool_flag("recolor_fgs", "recolor fg nup chains")
IMP.add_bool_flag("recolor_floats",
"recolor floating (diffusing) molecules")
IMP.add_int_flag(
"smooth_n_frames", 1,
"smooth by averaging over a window of specified frames (but retaining the same number of expected frames"
)
IMP.add_int_flag("skip_n_frames", 1, "skip every n frames of output")
IMP.setup_from_argv(sys.argv, "Prettify a movie")
in_fname = IMP.get_string_flag("input_rmf")
out_fname = IMP.get_string_flag("output_rmf")
ref_output = IMP.get_string_flag("ref_output")
radius = IMP.get_float_flag("radius")
# Prepare out file with same static info as in file:
in_fh = RMF.open_rmf_file_read_only(in_fname)
out_fh = RMF.create_rmf_file(out_fname)
print("creating file", out_fname)
RMF.clone_file_info(in_fh, out_fh)
RMF.clone_hierarchy(in_fh, out_fh)
RMF.clone_static_frame(in_fh, out_fh)
print("opened", in_fh.get_name())
cf = RMF.CylinderFactory(out_fh)
rff = RMF.ReferenceFrameFactory(out_fh)
tf = RMF.TypedFactory(out_fh)
bf = RMF.BallFactory(out_fh)
cdf = RMF.ColoredFactory(out_fh)
ipf = RMF.IntermediateParticleFactory(out_fh)
fg_types, kap_types, inert_types = _get_fg_and_floater_types(ref_output)
# out_fh.set_current_frame(RMF.ALL_FRAMES)
# Modify static information:
if (IMP.get_bool_flag("recolor_floats")):
_recolor(out_fh.get_root_node(), tf, cdf, kap_types, kap_color)
_recolor(out_fh.get_root_node(), tf, cdf, inert_types, inert_color)
_resize_sites(out_fh.get_root_node(), bf,
IMP.get_float_flag("site_radius"))
cylinders = []
for i, fg_type in enumerate(fg_types):
color = IMP.display.get_display_color(i)
rgb = [color.get_red(), color.get_green(), color.get_blue()]
print("Checking fg type", fg_type)
cylinders += _add_nodes(out_fh.get_root_node(), cf, cdf, tf, [fg_type],
radius, rgb) # fg_color
if (IMP.get_bool_flag("recolor_fgs")):
# print "Recoloring",fg_type, rgb
_recolor(out_fh.get_root_node(), tf, cdf, [fg_type],
rgb) # fg_color
# Clone and modify per-frame information:
smooth_xyz_dict = {}
smooth_n_frames = IMP.get_int_flag("smooth_n_frames")
skip_n_frames = IMP.get_int_flag("skip_n_frames")
print("Skip interval:", skip_n_frames, "frames")
for f_id, f in enumerate(in_fh.get_frames()):
is_write = f_id % skip_n_frames == 0
in_fh.set_current_frame(f)
if not is_write:
if (smooth_n_frames > 1):
_smooth(in_fh.get_root_node(),
tf,
rff,
smooth_xyz_dict,
n=smooth_n_frames,
is_write=False)
print("skipping frame", f, f_id)
continue
print("cloning frame", f, f_id)
out_fh.add_frame(in_fh.get_name(f), in_fh.get_type(f))
RMF.clone_loaded_frame(in_fh, out_fh)
if (smooth_n_frames > 1):
_smooth(out_fh.get_root_node(),
tf,
rff,
smooth_xyz_dict,
n=smooth_n_frames,
is_write=True)
for c in cylinders:
_set_cylinder(c, cf, rff)
if (IMP.get_bool_flag("recolor_fgs")):
_recolor_cylinder(c, cf, cdf)
DEBUG = False
if DEBUG and f_id >= 5 * skip_n_frames:
break
# find the name for a temporary file to use to for writing the hdf5 file
tfn = RMF._get_temporary_file_path("aliases.rmf")
print("File is", tfn)
# open the temporary file, clearing any existing contents
fh = RMF.create_rmf_file(tfn)
# add a frame to the file
fh.add_frame("root", RMF.FRAME)
rh = fh.get_root_node()
# add a bunch of "molecules" with colors
mrh = rh.add_child("molecules", RMF.REPRESENTATION)
pf = RMF.ParticleFactory(fh)
cf = RMF.ColoredFactory(fh)
red = []
green = []
blue = []
for i in range(0, 10):
curph = mrh.add_child("mol" + str(i), RMF.REPRESENTATION)
for j in range(0, 10):
curh = curph.add_child("atom" + str(j), RMF.REPRESENTATION)
p = pf.get(curh)
p.set_coordinates(RMF.Vector3(3 * i, 3 * j, 0))
p.set_mass(1)
p.set_radius(1)
c = cf.get(curh)
if j % 3 == 0:
c.set_rgb_color(RMF.Vector3(1, 0, 0))