automatic.py

## \example pmi/automatic.py
"""This script shows how to use the BuildSystem macro to construct large
   systems with minimal code
"""

from __future__ import print_function
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 tempfile
import os
import sys

IMP.setup_from_argv(sys.argv, "Automatic setup of a large system")
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)

# This is the topology table format.
#  It allows you to create many components in a simple way
#  By default it sets up each molecule as a rigid body, filling in missing
#  pieces with beads
#  You can create multiple domains by specifying different segments, as
#  in Rpb1 below
#  You can also create copies of molecules by appending '.X' to the name,
#  as in Rpb4 below
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|
|Rpb1  |blue      |1WCM.fasta|1WCM:A|1WCM_fitted.pdb|A|1,100  |0 |5|0 |1|1,2| |
|Rpb1  |cyan      |1WCM.fasta|1WCM:A|BEADS          |A|101,150|0 |5|0 |2|1,2| |
|Rpb2  |red       |1WCM.fasta|1WCM:B|1WCM_fitted.pdb|B|1,END  |0 |5|0 |3|1  | |
|Rpb3  |green     |1WCM.fasta|1WCM:C|1WCM_fitted.pdb|C|1,END  |0 |5|0 |4|1  | |
|Rpb4  |orange    |1WCM.fasta|1WCM:D|1WCM_fitted.pdb|D|1,END  |0 |5|0 |5|1,3| |
|Rpb4.1|yellow    |1WCM.fasta|1WCM:D|1WCM_fitted.pdb|D|1,END  |0 |5|0 |6|1,3| |
|Rpb4.2|salmon    |1WCM.fasta|1WCM:D|1WCM_fitted.pdb|D|1,END  |0 |5|0 |7|1,3| |
|Rpb5  |gold      |1WCM.fasta|1WCM:E|BEADS          | |1,50   |  |5|0 |8|1  | |
|Rpb5  |pink      |1WCM.fasta|1WCM:E|IDEAL_HELIX    | |51,100 |  |5|0 |8|1  | |
'''

# 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()

# 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()

# ##################### 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)


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


# 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='auto_output/', output_objects=output_objects,
    monte_carlo_steps=10, number_of_best_scoring_models=0, number_of_frames=5)
rex.execute_macro()

os.remove(tf.name)