23 const double dope_threshold = 16;
24 const double spring_constant = 1;
31 for (
unsigned int i = 0; i < 2; ++i) {
51 for (
unsigned int i = 0; i < atoms.size(); ++i) {
52 for (
unsigned int j = 0; j < i; ++j) {
60 int main(
int argc,
char *argv[]) {
65 "Show how to use dope and excluded volume");
72 DopeAndExcludedVolumeDistancePairScore;
76 new DopeAndExcludedVolumeDistancePairScore(
78 SoftSphere(Harmonic(spring_constant))));
85 for (
unsigned int i = 0; i < pips.size(); ++i) {
86 std::cout <<
"Score is " << score->evaluate_index(
87 model, pips[i],
nullptr) << std::endl;
91 catch (
const std::exception &e) {
92 std::cerr <<
"ERROR: " << e.what() << std::endl;
Helper macros for implementing IMP Objects.
A Score on the distance between a pair of particles.
A Score on the distance between a pair of particles.
ParticleIndex add_particle(std::string name)
Add particle to the model.
void add_child(Hierarchy o)
Add a child and check that the types are appropriate.
static Atom setup_particle(Model *m, ParticleIndex pi, Atom other)
A Score on the distance between a pair of particles.
void add_radii(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters(), FloatKey radius_key=FloatKey("radius"))
Add vdW radius from given force field.
static Residue setup_particle(Model *m, ParticleIndex pi, ResidueType t, int index, int insertion_code)
A Score on the distance between a pair of particles.
Create efficient distance-based pair scores.
static XYZ setup_particle(Model *m, ParticleIndex pi)
Class for storing model, its restraints, constraints, and particles.
Define functions to add bonds and radii to atoms.
A decorator for a particle representing an atom.
A decorator for Residues.
A smart pointer to a ref-counted Object that is a class member.
A harmonic score on the negative directed distance between a pair of particles. The score equals zero...
A decorator for a residue.
Support for shared command line flags.
void add_dope_score_data(atom::Hierarchy h)
Score pair of atoms based on DOPE.
Store info for a chain of a protein.
void setup_from_argv(int argc, char **argv, std::string description)
Parse the command line flags and return the positional arguments.
static Chain setup_particle(Model *m, ParticleIndex pi, std::string id)
Decorator for a sphere-like particle.