18 topology = ff.create_topology(prot)
23 topology.apply_default_patches()
28 topology.add_atom_types(prot)
33 topology.add_missing_atoms(prot)
36 topology.add_coordinates(prot)
45 bonds = topology.add_bonds(prot)
46 angles = ff.create_angles(bonds)
47 dihedrals = ff.create_dihedrals(bonds)
48 impropers = topology.add_impropers(prot)
90 ff.add_well_depths(prot)
106 pair_filter.set_bonds(bonds)
107 pair_filter.set_angles(angles)
108 pair_filter.set_dihedrals(dihedrals)
109 nbl.add_pair_filter(pair_filter)
119 print m.evaluate(
False)
Applies a SingletonScore to each Singleton in a list.
Select non water and non hydrogen atoms.
CHARMMParameters * get_heavy_atom_CHARMM_parameters()
Score the angle based on a UnaryFunction,.
void remove_charmm_untyped_atoms(Hierarchy hierarchy)
Remove any atom from the Hierarchy that does not have a CHARMM type.
Various classes to hold sets of particles.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
std::string get_example_path(std::string file_name)
Return the path to installed example data for this module.
Return all close unordered pairs of particles taken from the SingletonContainer.
Lennard-Jones score between a pair of particles.
Store a kernel::ParticleIndexes.
Hierarchies get_by_type(Hierarchy mhd, GetByType t)
Score the improper dihedral based on a UnaryFunction,.
Score the bond based on a UnaryFunction,.
A filter that excludes bonds, angles and dihedrals.
Smooth interaction scores by switching the derivatives (force switch).
Functionality for loading, creating, manipulating and scoring atomic structures.
void read_pdb(base::TextInput input, int model, Hierarchy h)
Applies a PairScore to each Pair in a list.
Class for storing model, its restraints, constraints, and particles.
Score the dihedral angle.
Harmonic function (symmetric about the mean)