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save_assignments.py
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## \example domino/save_assignments.py
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# It can often be useful to save the assignments to a file. \imp provides support to do this to an a data set in an hdf5 file.
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#
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# You can use \c h5dump to view the contents of the created file.
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import
IMP.domino
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# create a model and some particles, they are just used as markers here
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m =
IMP.kernel.Model
()
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ps = [
IMP.kernel.Particle
(m)
for
i
in
range(0, 10)]
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# create a subset with a few of the particles
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ss =
IMP.domino.Subset
([ps[3], ps[5], ps[7]])
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file_name = IMP.create_temporary_file_name(
"assignments"
,
".asn"
)
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print
"File name is"
, file_name
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# create a list of assignments
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IMP.base.set_log_level
(IMP.base.MEMORY)
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asl =
IMP.domino.WriteAssignmentContainer
(file_name, ss, ps,
"writer"
)
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written = []
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for
i
in
range(0, 5):
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for
j
in
range(0, 5):
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for
k
in
range(0, 5):
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a =
IMP.domino.Assignment
([i, j, k])
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written.append(a)
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asl.add_assignment(a)
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del asl
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# to check, we can read it back immediately
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back_asl =
IMP.domino.ReadAssignmentContainer
(file_name, ss, ps,
"reader"
)
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if
back_asl.get_assignments() == written:
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print
"They match!"
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else
:
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print
back_asl.get_assignments()
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print
written
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raise
RuntimeError(
"They don't match :-("
)
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# More interestingly, we can create a new model and read back the
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# assignments for that
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mp =
IMP.kernel.Model
()
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psp = [
IMP.kernel.Particle
(mp)
for
i
in
range(0, 10)]
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# create a subset with a few of the particles
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ssp =
IMP.domino.Subset
([psp[3], psp[5], psp[7]])
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print
"Note the subsets are differently ordered (most of the time): "
, ss, ssp
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back_aslp =
IMP.domino.ReadAssignmentContainer
(file_name, ssp, psp,
"reader2"
)
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# however, the states are demuxed so they match the particles
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print
[str(a)
for
a
in
back_aslp.get_assignments()]
IMP::base::set_log_level
void set_log_level(LogLevel l)
Set the current global log level.
IMP::domino::Subset
Represent a subset of the particles being optimized.
Definition:
Subset.h:33
IMP::kernel::Particle
Class to handle individual model particles.
Definition:
kernel/Particle.h:34
IMP::domino::ReadAssignmentContainer
Definition:
assignment_containers.h:274
IMP::domino::Assignment
Store a configuration of a subset.
Definition:
Assignment.h:32
IMP::domino::WriteAssignmentContainer
Definition:
assignment_containers.h:241
IMP::domino
See IMP.domino for more information.
Definition:
analysis.h:15
IMP::kernel::Model
Class for storing model, its restraints, constraints, and particles.
Definition:
kernel/Model.h:72