Then a second copy of the protein is loaded and they are both added to the same hierarchy to define a hypothetical assembly.
import IMP
import IMP.core
import IMP.atom
m = IMP.Model()
mp0= IMP.atom.read_pdb(IMP.atom.get_example_path('example_protein.pdb'), m)
# get the 16th residue of the first chain
hchain= IMP.atom.get_by_type(mp0, IMP.atom.CHAIN_TYPE)[0]
# decorate the chain particle with an IMP.atom.Chain decorator.
# unfortunately, our python wrapper does not handle converseions properly
# as a result you have to manually get the particle for that chain
chain=IMP.atom.Chain(hchain.get_particle())
r16 = IMP.atom.get_residue(chain, 16)
r16.show()
# get all the atoms
atoms= IMP.atom.get_by_type(mp0, IMP.atom.ATOM_TYPE)
# I didn't really have anything interesting to do with them...
# create a new version of the protein that is coarsened (one particle per residue)
smp0= IMP.atom.create_simplified_along_backbone(chain, 1)
# we don't need mp0 any more
IMP.atom.destroy(mp0)
# load another copy
mp1= IMP.atom.read_pdb(IMP.atom.get_example_path('example_protein.pdb'), m)
# make this one rigid
IMP.atom.setup_as_rigid_body(mp1)
# create a hierarchy which contains the two proteins
p = IMP.Particle(m)
rmp= IMP.atom.Hierarchy.setup_particle(p)
rmp.add_child(smp0)
rmp.add_child(mp1)
import IMP.atom
m= IMP.Model()
prot= IMP.atom.read_pdb(IMP.atom.get_example_path("example_protein.pdb"), m)
bds= IMP.atom.get_internal_bonds(prot)
bl= IMP.container.ListSingletonContainer(bds.get_particles())
h= IMP.core.Harmonic(0,1)
bs= IMP.atom.BondSingletonScore(h)
br= IMP.container.SingletonsRestraint(bs, bl)
m.add_restraint(br)
print m.evaluate(False)
import IMP.atom
import IMP.container
# Create an IMP model and add a heavy atom-only protein from a PDB file
m = IMP.Model()
prot = IMP.atom.read_pdb(IMP.atom.get_example_path("example_protein.pdb"), m,
IMP.atom.NonWaterNonHydrogenPDBSelector())
# Read in the CHARMM heavy atom topology and parameter files
ff = IMP.atom.CHARMMParameters(IMP.atom.get_data_path("top_heav.lib"),
IMP.atom.get_data_path("par.lib"))
# Using the CHARMM libraries, determine the ideal topology (atoms and their
# connectivity) for the PDB file's primary sequence
topology = ff.create_topology(prot)
# Typically this modifies the C and N termini of each chain in the protein by
# applying the CHARMM CTER and NTER patches. Patches can also be manually
# applied at this point, e.g. to add disulfide bridges.
topology.apply_default_patches(ff)
# Each atom is mapped to its CHARMM type. These are needed to look up bond
# lengths, Lennard-Jones radii etc. in the CHARMM parameter file. Atom types
# can also be manually assigned at this point using the CHARMMAtom decorator.
topology.add_atom_types(prot)
# Generate and return lists of bonds, angles, dihedrals and impropers for
# the protein. Each is a Particle in the model which defines the 2, 3 or 4
# atoms that are bonded, and adds parameters such as ideal bond length
# and force constant. Note that bonds and impropers are explicitly listed
# in the CHARMM topology file, while angles and dihedrals are generated
# automatically from an existing set of bonds. These particles only define the
# bonds, but do not score them or exclude them from the nonbonded list.
bonds = topology.add_bonds(prot, ff)
angles = ff.generate_angles(bonds)
dihedrals = ff.generate_dihedrals(bonds)
impropers = topology.add_impropers(prot, ff)
# Maintain stereochemistry by scoring bonds, angles, dihedrals and impropers
# Score all of the bonds. This is done by combining IMP 'building blocks':
# - A ListSingletonContainer simply manages a list of the bond particles.
# - A BondSingletonScore, when given a bond particle, scores the bond by
# calculating the distance between the two atoms it bonds, subtracting the
# ideal value, and weighting the result by the bond's "stiffness", such that
# an "ideal" bond scores zero, and bonds away from equilibrium score non-zero.
# It then hands off to a UnaryFunction to actually penalize the value. In
# this case, a Harmonic UnaryFunction is used with a mean of zero, so that
# bond lengths are harmonically restrained.
# - A SingletonsRestraint simply goes through each of the bonds in the
# container and scores each one in turn.
cont = IMP.container.ListSingletonContainer("bonds")
cont.add_particles(bonds)
bss = IMP.atom.BondSingletonScore(IMP.core.Harmonic(0, 1))
m.add_restraint(IMP.container.SingletonsRestraint(bss, cont))
# Score angles, dihedrals, and impropers. In the CHARMM forcefield, angles and
# impropers are harmonically restrained, so this is the same as for bonds.
# Dihedrals are scored internally by a periodic (cosine) function.
cont = IMP.container.ListSingletonContainer("angles")
cont.add_particles(angles)
bss = IMP.atom.AngleSingletonScore(IMP.core.Harmonic(0,1))
m.add_restraint(IMP.container.SingletonsRestraint(bss, cont))
cont = IMP.container.ListSingletonContainer("dihedrals")
cont.add_particles(dihedrals)
bss = IMP.atom.DihedralSingletonScore()
m.add_restraint(IMP.container.SingletonsRestraint(bss, cont))
cont = IMP.container.ListSingletonContainer("impropers")
cont.add_particles(impropers)
bss = IMP.atom.ImproperSingletonScore(IMP.core.Harmonic(0,1))
m.add_restraint(IMP.container.SingletonsRestraint(bss, cont))
# Add non-bonded interaction (in this case, Lennard-Jones). This needs to
# know the radii and well depths for each atom, so add them from the forcefield
# (they can also be assigned manually using the XYZR or LennardJones
# decorators):
ff.add_radii(prot)
ff.add_well_depths(prot)
# Get a list of all atoms in the protein, and put it in a container
atoms = IMP.atom.get_by_type(prot, IMP.atom.ATOM_TYPE)
cont = IMP.container.ListSingletonContainer(atoms)
# Add a restraint for the Lennard-Jones interaction. Again, this is built from
# a collection of building blocks. First, a ClosePairContainer maintains a list
# of all pairs of Particles that are close. A StereochemistryPairFilter is used
# to exclude atoms from this list that are bonded to each other or are involved
# in an angle or dihedral (1-3 or 1-4 interaction). Then, a
# LennardJonesPairScore scores a pair of atoms with the Lennard-Jones potential.
# Finally, a PairsRestraint is used which simply applies the
# LennardJonesPairScore to each pair in the ClosePairContainer.
nbl = IMP.container.ClosePairContainer(cont, 4.0)
pair_filter = IMP.atom.StereochemistryPairFilter()
pair_filter.set_bonds(bonds)
pair_filter.set_angles(angles)
pair_filter.set_dihedrals(dihedrals)
nbl.add_pair_filter(pair_filter)
sf = IMP.atom.ForceSwitch(6.0, 7.0)
ps = IMP.atom.LennardJonesPairScore(sf)
m.add_restraint(IMP.container.PairsRestraint(ps, nbl))
# Finally, evaluate the score of the whole system (without derivatives)
print m.evaluate(False)