protein_residue_binding.py

## \example pmi/protein_residue_binding.py
"""
This script shows how to simulate residue-protein
binding contacts inferred from mutagenesis studies.
This example shows protein A binding to protein B
through a set of residues predicted to be required
for binding in mutagensis studies.
"""

import IMP
import IMP.atom
import IMP.rmf
import IMP.pmi
import IMP.pmi.topology
import IMP.pmi.dof
import IMP.pmi.macros
import IMP.pmi.restraints
import IMP.pmi.restraints.stereochemistry
import IMP.pmi.restraints.basic
import tempfile
import os
import sys

IMP.setup_from_argv(sys.argv, "Simulate residue-protein binding contacts")
if IMP.get_is_quick_test():
    print("This example is too slow to test in debug mode - run without")
    print("internal tests enabled, or without the --run-quick-test flag")
    sys.exit(0)

topology = '''
|molecule_name|color|fasta_fn|fasta_id|pdb_fn|chain|residue_range|pdb_offset|bead_size|em_residues_per_gaussian|rigid_body|super_rigid_body|chain_of_super_rigid_bodies|
|Rpb4  |red   |1WCM.fasta |1WCM:D   |1WCM_fitted.pdb    |D|1,END  |0 |5|0 |1 | | ||
|Rpb7  |gold  |1WCM.fasta |1WCM:G   |1WCM_fitted.pdb    |G|1,END  |0 |5|0 |2 | | ||
'''

# Normally the topology table is kept in a text file but here we just write
# it to a temporary one
tf = tempfile.NamedTemporaryFile(delete=False, mode='w')
tf.write(topology)
tf.close()

print(IMP.pmi.get_example_path('data/'))

# The TopologyReader reads the text file, and the BuildSystem macro
# constructs it
mdl = IMP.Model()
reader = IMP.pmi.topology.TopologyReader(
    tf.name, pdb_dir=IMP.pmi.get_example_path('data/'),
    fasta_dir=IMP.pmi.get_example_path('data/'),
    gmm_dir=IMP.pmi.get_example_path('data/'))
bs = IMP.pmi.macros.BuildSystem(mdl)
# note you can call this multiple times to create a multi-state system
bs.add_state(reader)
hier, dof = bs.execute_macro()

# ################ STEREOCHEMISTRY RESTRAINTS ################

output_objects = []  # keep a list of functions that need to be reported

# Connectivity keeps things connected along the backbone (ignores if inside
# same rigid body)
crs = []
moldict = bs.get_molecules()[0]
mols = []
for molname in moldict:
    for mol in moldict[molname]:
        cr = IMP.pmi.restraints.stereochemistry.ConnectivityRestraint(mol)
        cr.add_to_model()
        output_objects.append(cr)
        crs.append(cr)
        mols.append(mol)

# Excluded volume - automatically more efficient due to rigid bodies
evr = IMP.pmi.restraints.stereochemistry.ExcludedVolumeSphere(
    included_objects=mols)
evr.add_to_model()
output_objects.append(evr)

# External barrier- Avoid proteins to drift away
eb = IMP.pmi.restraints.basic.ExternalBarrier(hierarchies=hier, radius=500)
eb.add_to_model()

# ################# PROTEIN-RESIDUE PROXIMITY ################

br = IMP.pmi.restraints.basic.ResidueProteinProximityRestraint(
    hier, selection=('Rpb7', 38, 44, 'Rpb4'), label='B38_44')

br.add_to_model()
br.set_weight(5.0)
output_objects.append(br)
br.get_output()

# ##################### SAMPLING #######################

# Fix rigid-body

part_p1 = IMP.atom.Selection(hier,
                             molecule="Rpb4").get_selected_particles()

xyzs, rbs = dof.disable_movers(part_p1,
                               mover_types=[IMP.core.RigidBodyMover])


# mix it up so it looks cool
IMP.pmi.tools.shuffle_configuration(hier)

# Quickly move all flexible beads into place
dof.optimize_flexible_beads(100)

rex = IMP.pmi.macros.ReplicaExchange(
    mdl,
    root_hier=hier,
    monte_carlo_sample_objects=dof.get_movers(),
    global_output_directory='output/',
    output_objects=output_objects,
    monte_carlo_steps=10,
    number_of_best_scoring_models=0,
    number_of_frames=500)
rex.execute_macro()

os.remove(tf.name)