6 from __future__
import print_function
23 topology = ff.create_topology(prot)
28 topology.apply_default_patches()
35 topology.setup_hierarchy(prot)
46 ff.add_well_depths(prot)
49 atoms = IMP.atom.get_by_type(prot, IMP.atom.ATOM_TYPE)
60 nbl.add_pair_filter(r.get_pair_filter())
70 print(scoring_function.evaluate(
False))
Select non water and non hydrogen atoms.
CHARMMParameters * get_heavy_atom_CHARMM_parameters()
Enforce CHARMM stereochemistry on the given Hierarchy.
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)
Various classes to hold sets of particles.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Create a scoring function on a list of restraints.
Return all close unordered pairs of particles taken from the SingletonContainer.
void read_pdb(TextInput input, int model, Hierarchy h)
Class for storing model, its restraints, constraints, and particles.
Lennard-Jones score between a pair of particles.
Store a list of ParticleIndexes.
Smooth interaction scores by switching the derivatives (force switch).
Functionality for loading, creating, manipulating and scoring atomic structures.
Applies a PairScore to each Pair in a list.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.