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IMP Reference Guide
2.8.0
The Integrative Modeling Platform
IMP Manual
Reference Guide
Modules
Classes
Examples
doc
examples
domino
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
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# support to do this to 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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7
import
IMP.domino
8
import
sys
9
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IMP.setup_from_argv
(sys.argv,
"save assignments"
)
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# create a model and some particles; they are just used as markers here
13
m =
IMP.Model
()
14
ps = [
IMP.Particle
(m)
for
i
in
range(0, 10)]
15
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# create a subset with a few of the particles
17
ss =
IMP.domino.Subset
([ps[3], ps[5], ps[7]])
18
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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.set_log_level
(IMP.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
38
back_asl =
IMP.domino.ReadAssignmentContainer
(file_name, ss, ps,
"reader"
)
39
40
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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.Model
()
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psp = [
IMP.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::setup_from_argv
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)
IMP::domino::Subset
Represent a subset of the particles being optimized.
Definition:
Subset.h:33
IMP::Model
Class for storing model, its restraints, constraints, and particles.
Definition:
Model.h:72
IMP::set_log_level
void set_log_level(LogLevel l)
Set the current global log level.
IMP::domino::ReadAssignmentContainer
Read the assignments from binary data on disk.
Definition:
assignment_containers.h:274
IMP::domino::Assignment
Store a configuration of a subset.
Definition:
Assignment.h:32
IMP::Particle
Class to handle individual particles of a Model object.
Definition:
Particle.h:41
IMP::domino::WriteAssignmentContainer
Store the assignments on disk as binary data.
Definition:
assignment_containers.h:241
IMP::domino
Divide-and-conquer inferential optimization in discrete space.
IMP::create_temporary_file_name
std::string create_temporary_file_name(std::string prefix="imp_temp", std::string suffix="")
Create a temporary file.