def test_log_targets(self):
"""Test python flags"""
IMP.add_string_flag(
"mystringflag",
"mydefault",
"Some string text")
IMP.add_int_flag("myintflag", 3, "Some int text")
IMP.add_bool_flag("myboolflag", "Some bool text")
IMP.add_float_flag("myfloatflag", 10, "Some float text")
extra = IMP.setup_from_argv(["python", "--mystringflag=hi",
"--log_level=VERBOSE",
"--myintflag=6", "--myfloatflag=-6.0",
"--myboolflag", "zero", "one"],
"test things",
"arg0 arg1", 2)
print(IMP.get_string_flag("mystringflag"))
print(IMP.get_int_flag("myintflag"))
print(IMP.get_float_flag("myfloatflag"))
print(IMP.get_bool_flag("myboolflag"))
print(IMP.get_log_level())
print(extra)
self.assertEqual(IMP.get_string_flag("mystringflag"), "hi")
self.assertEqual(IMP.get_int_flag("myintflag"), 6)
self.assertEqual(IMP.get_float_flag("myfloatflag"), -6.0)
self.assertEqual(IMP.get_bool_flag("myboolflag"), True)
self.assertEqual(extra[0], "zero")
self.assertEqual(extra[1], "one")
def test_log_targets(self):
"""Test python flags"""
IMP.add_string_flag("mystringflag", "mydefault", "Some string text")
IMP.add_int_flag("myintflag", 3, "Some int text")
IMP.add_bool_flag("myboolflag", "Some bool text")
IMP.add_float_flag("myfloatflag", 10, "Some float text")
extra = IMP.setup_from_argv([
"python", "--mystringflag=hi", "--log_level=VERBOSE",
"--myintflag=6", "--myfloatflag=-6.0", "--myboolflag", "zero",
"one"
], "test things", "arg0 arg1", 2)
print(IMP.get_string_flag("mystringflag"))
print(IMP.get_int_flag("myintflag"))
print(IMP.get_float_flag("myfloatflag"))
print(IMP.get_bool_flag("myboolflag"))
print(IMP.get_log_level())
print(extra)
self.assertEqual(IMP.get_string_flag("mystringflag"), "hi")
self.assertEqual(IMP.get_int_flag("myintflag"), 6)
self.assertEqual(IMP.get_float_flag("myfloatflag"), -6.0)
self.assertEqual(IMP.get_bool_flag("myboolflag"), True)
self.assertEqual(extra[0], "zero")
self.assertEqual(extra[1], "one")
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
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)
DEBUG=False
if DEBUG and f_id >= 5*skip_n_frames:
break
def main():
IMP.add_string_flag("input_rmf", "", "The input RMF file.")
IMP.add_string_flag("output_pdb", "", "The output PDB file")
IMP.add_string_flag("ref_output", "", "reference output file from which info e.g. fg nup types can be extracted")
IMP.add_int_flag("skip_n_frames", 1,
"skip every n frames of output; if 0, include only first frame")
IMP.setup_from_argv(sys.argv, "Prettify a movie")
in_fname= IMP.get_string_flag("input_rmf")
out_fname= IMP.get_string_flag("output_pdb")
ref_output = IMP.get_string_flag("ref_output")
# Prepare out file with same static info as in file:
in_fh = RMF.open_rmf_file_read_only(in_fname)
rff = RMF.ReferenceFrameFactory(in_fh)
tf = RMF.TypedFactory(in_fh)
bf = RMF.BallFactory(in_fh)
ipf = RMF.IntermediateParticleFactory(in_fh)
fg_types, kap_types, inert_types = _get_fg_and_floater_types( ref_output )
type2chains={}
for i, fg_type in enumerate(fg_types):
print i, fg_type
type2chains[fg_type] = _add_nodes(in_fh.get_root_node(), tf, [fg_type])
skip_n_frames=IMP.get_int_flag("skip_n_frames")
if(skip_n_frames>0):
print "Skip interval:", skip_n_frames, "frames"
else:
print "Showing only first frame"
for f_id, f in enumerate(in_fh.get_frames()):
is_write= (skip_n_frames==0) or (f_id%skip_n_frames == 0)
in_fh.set_current_frame(f)
if not is_write:
print("skipping frame", f, f_id)
continue
fname= "%s_f%d.pdb" % (os.path.splitext(out_fname)[0],f_id)
F= open(fname, 'w')
# print("COMMENT writing frame", f, f_id)
chain_id="A"
atom_id=1
model_id=1
spoke_id=1
for fg_type, chains in type2chains.iteritems():
print >>F, "MODEL %d" % model_id
for chain in chains:
if chain_id=='I': # no more than 8 chains per model
chain_id='A'
print >>F, "ENDMDL"
model_id=model_id+1
print >>F, "MODEL %d" % model_id
for i,node in enumerate(chain):
res_id=i+1
coord = rff.get(node).get_translation()
print >>F, "ATOM %5d CA GLY %c%4d %8.2f%8.2f%8.2f 1.0 # %s" \
% (atom_id, chain_id, res_id,
coord[0], coord[1], coord[2],
fg_type + " spoke%d" % spoke_id)
atom_id=atom_id+1
print >>F, "TER"
chain_id=chr(ord(chain_id)+1)
spoke_id = 1 + (spoke_id % 8)
chain_id='A'
print >>F, "ENDMDL"
model_id=model_id+1
if skip_n_frames==0:
break
DEBUG=False
if (DEBUG and f_id >= 5*skip_n_frames):
break
def main():
IMP.add_string_flag("input_rmf", "", "The input RMF file.")
IMP.add_string_flag("output_pdb", "", "The output PDB file")
IMP.add_string_flag(
"ref_output", "",
"reference output file from which info e.g. fg nup types can be extracted"
)
IMP.add_int_flag(
"skip_n_frames", 1,
"skip every n frames of output; if 0, include only first frame")
IMP.add_int_flag("first_frame", 0, "start from speicifed frame")
IMP.setup_from_argv(sys.argv, "Prettify a movie")
in_fname = IMP.get_string_flag("input_rmf")
out_fname = IMP.get_string_flag("output_pdb")
ref_output = IMP.get_string_flag("ref_output")
# Prepare out file with same static info as in file:
in_fh = RMF.open_rmf_file_read_only(in_fname)
rff = RMF.ReferenceFrameFactory(in_fh)
tf = RMF.TypedFactory(in_fh)
bf = RMF.BallFactory(in_fh)
ipf = RMF.IntermediateParticleFactory(in_fh)
fg_types, kap_types, inert_types = _get_fg_and_floater_types(ref_output)
type2chains = {}
print("fg_types", fg_types)
for i, fg_type in enumerate(fg_types):
type2chains[fg_type] = _add_nodes(in_fh.get_root_node(), tf, [fg_type])
print(type2chains[fg_type])
skip_n_frames = IMP.get_int_flag("skip_n_frames")
first_frame = IMP.get_int_flag("first_frame")
if (skip_n_frames > 0):
print "Skip interval:", skip_n_frames, "frames"
else:
print "Showing only first frame"
for f_id, f in enumerate(in_fh.get_frames()):
is_write = (f_id >= first_frame) and ((skip_n_frames == 0) or
(f_id % skip_n_frames == 0))
in_fh.set_current_frame(f)
if not is_write:
print("skipping frame", f, f_id)
continue
fname = "%s_f%05d.pdb" % (os.path.splitext(out_fname)[0], f_id)
F = open(fname, 'w')
print("COMMENT writing frame", f, f_id)
chain_id = "A"
atom_id = 1
model_id = 1
spoke_id = 1
for fg_type, chains in type2chains.iteritems():
print >> F, "MODEL %d" % model_id
for chain in chains:
print("Chain ", chain)
if chain_id == 'I': # no more than 8 chains per model
chain_id = 'A'
print >> F, "ENDMDL"
model_id = model_id + 1
print >> F, "MODEL %d" % model_id
for i, node in enumerate(chain):
res_id = i + 1
coord = rff.get(node).get_translation()
print >>F, "ATOM %5d CA GLY %c%4d %8.2f%8.2f%8.2f 1.0 # %s" \
% (atom_id, chain_id, res_id,
coord[0], coord[1], coord[2],
fg_type + " spoke%d" % spoke_id)
atom_id = atom_id + 1
print >> F, "TER"
chain_id = chr(ord(chain_id) + 1)
spoke_id = 1 + (spoke_id % 8)
chain_id = 'A'
print >> F, "ENDMDL"
model_id = model_id + 1
if skip_n_frames == 0:
break
DEBUG = False
if (DEBUG and f_id >= 5 * skip_n_frames):
break
## \example kernel/flags.py
# A simple example of how to use IMP flags support in a python
# executable. Run with "--help" to see all available flags.
import IMP
import sys
IMP.add_string_flag("hello", "Hello world", "How to say hello")
IMP.setup_from_argv(sys.argv, "An example for using flags in python.")
if IMP.get_string_flag("hello") == "":
IMP.write_help()
exit(1)
print(IMP.get_string_flag("hello"))
