restrainer/em_restraint.py

This example shows how to use IMP::em::FitRestraint.

<!-- File: em_representation.xml -->

<Representation>
    <Protein id="Protein1">
        <Chain>
            <Fragment id="frag1">
                <GeometricShapeRep>
                    <Sphere radius="1.0" weight="1.0">
                        <InitialPosition optimize="1" x="12.0" y="12.0" z="12.0"/>
                    </Sphere>
                </GeometricShapeRep>
            </Fragment>
            <Fragment id="frag2">
                <GeometricShapeRep>
                    <Sphere radius="1.0" weight="1.0">
                        <InitialPosition optimize="1" x="15.0" y="6.0" z="6.0"/>
                    </Sphere>
                </GeometricShapeRep>
            </Fragment>
            <Fragment id="frag3">
                <GeometricShapeRep>
                    <Sphere radius="1.0" weight="1.0">
                        <InitialPosition optimize="1" x="6.0" y="15.0" z="15.0"/>
                    </Sphere>
                </GeometricShapeRep>
            </Fragment>
        </Chain>
    </Protein>
</Representation>

<!-- File: em_restraint.xml -->

<RestraintSet>
    <EM>
        <Restraint name="em_restraint" density_filename="data/in.mrc" spacing="1.0" resolution="3.0" xorigin="-6.0" yorigin="-6.0" zorigin="-6.0">
            <Particle id="frag1"/>
            <Particle id="frag2"/>
            <Particle id="frag3"/>
        </Restraint>
    </EM>
</RestraintSet>

## \example restrainer/em_restraint.py
# This example shows how to use IMP::em::FitRestraint.
#
# \include em_representation.xml
# \include em_restraint.xml
#

# -- File: em_restraint.py --#

import IMP
import IMP.restrainer

# Create restrainer object
restrainer = IMP.restrainer.Main()

# Add representation and restraint to restrainer
rep = restrainer.add_representation(
    IMP.restrainer.get_example_path('input/em_representation.xml'))
rsr = restrainer.add_restraint(
    IMP.restrainer.get_example_path('input/em_restraint.xml'))

# =======================================================================###
#  At this point all data from XML files have been placed into the model.
#  Now it is possible to perform various operations on the IMP model.
# =======================================================================###

# Get the IMP model object used by restrainer
model = restrainer.get_model()

# Get restraint by name
r = rsr.get_restraint_by_name('em_restraint')

# Get EM density map header from the restraint
dmap_header = r.dmap_header

# Get IMP::em::FitRestraint
fit_restraint = r.imp_restraint
fit_restraint.evaluate(False)