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IMP Reference Guide  2.6.1
The Integrative Modeling Platform
bipartite_nonbonded_interactions.py
1 ## \example container/bipartite_nonbonded_interactions.py
2 # This example shows how set up excluded volume interactions between two
3 # sets of particles.
4 
5 import IMP
6 import IMP.core
7 import IMP.container
8 import sys
9 
10 IMP.setup_from_argv(sys.argv, "bipartite nonbonded interactions")
11 
12 # This example addes a restraint on bipartite nonbonded interactions
13 # after excluding a set of bonded interactions.
14 
15 m = IMP.Model()
16 # The set of particles
21 
22 # Set up the nonbonded list
24 
25 # Set up excluded volume
27 evr = IMP.container.PairsRestraint(ps, nbl)
28 
29 # Set up optimizer
31 o.set_scoring_function([evr])
32 
33 o.optimize(1000)
Lower bound harmonic function (non-zero when feature < mean)
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)
Various classes to hold sets of particles.
XYZRs create_xyzr_particles(Model *m, unsigned int num, Float radius, Float box_side=10)
Create a set of particles with random coordinates.
Simple conjugate gradients optimizer.
A score on the distance between the surfaces of two spheres.
Return all close ordered pairs of particles taken from the two SingletonContainers.
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:72
Store a list of ParticleIndexes.
Basic functionality that is expected to be used by a wide variety of IMP users.
Applies a PairScore to each Pair in a list.