IMPCORE_BEGIN_NAMESPACE
Float TypedPairScore::evaluate_index(Model *m,
const ParticleIndexPair &pip,
DerivativeAccumulator *da) const {
ParticlePair p(m->get_particle(pip[0]), m->get_particle(pip[1]));
PairScore *ps = get_pair_score(p);
if (!ps) {
if (!allow_invalid_types_) {
IMP_THROW(
"Attempt to evaluate TypedPairScore on "
"particles with invalid types ("
<< p[0]->get_value(typekey_) << ", " << p[1]->get_value(typekey_)
<< ")",
ValueException);
} else {
return 0.0;
}
} else {
return ps->evaluate_index(m, pip, da);
}
}
int main(int argc, char *argv[]) {
IMP::Strings args = IMP::setup_from_argv(argc, argv,
"Score a protein-ligand complex",
"file.mol2 file.pdb [libfile]", -1);
IMP::set_log_level(IMP::SILENT);
std::string mol2name, pdbname;
for (size_t i = 0; i < args.size(); ++i) {
std::string nm(args[i]);
if (nm.rfind(".mol2") == nm.size() - 5) {
mol2name = nm;
} else if (nm.rfind(".pdb") == nm.size() - 4) {
pdbname = nm;
} else {
break;
}
}
if (mol2name.empty() || pdbname.empty()) {
std::cerr << "Usage: " << argv[0] << " file.mol2 file.pdb [libfile]"
<< std::endl;
return EXIT_FAILURE;
}
IMP::TextInput lib;
if (args.size() == 3) {
lib = IMP::TextInput(args[2]);
}
{
int lib_requested = 0;
if (lib) lib_requested++;
if (pose_score) lib_requested++;
if (rank_score) lib_requested++;
if (lib_requested > 1) {
std::cerr << "Can only specify one of --pose, --rank, "
<< "or a library name" << std::endl;
return EXIT_FAILURE;
}
}
IMP_NEW(IMP::Model, m, ());
IMP::atom::Hierarchy p, l;
{
IMP::SetLogState ss(IMP::SILENT);
p = IMP::atom::read_pdb(pdbname, m, new IMP::atom::ATOMPDBSelector());
IMP::atom::add_protein_ligand_score_data(p);
l = IMP::atom::read_mol2(mol2name, m);
IMP::atom::add_protein_ligand_score_data(l);
}
IMP::atom::Hierarchies mols =
IMP::atom::get_by_type(l, IMP::atom::RESIDUE_TYPE);
IMP::Pointer<IMP::atom::ProteinLigandAtomPairScore> ps
= get_pair_score(lib);
double d = ps->get_maximum_distance();
IMP_NEW(IMP::core::GridClosePairsFinder, gcpf, ());
gcpf->set_distance(d);
IMP::ParticlesTemp patoms = IMP::atom::get_leaves(p);
IMP::ParticleIndexes ipatoms = IMP::get_indexes(patoms);
for (unsigned int i = 0; i < mols.size(); ++i) {
// IMP::SetLogState ss(i==0? TERSE: IMP::SILENT);
IMP::ParticlesTemp latoms = IMP::atom::get_leaves(mols[i]);
IMP::ParticleIndexes ilatoms = IMP::get_indexes(latoms);
IMP::ParticleIndexPairs ppt =
gcpf->get_close_pairs(m, ipatoms, ilatoms);
double score = ps->evaluate_indexes(m, ppt, NULL, 0, ppt.size());
std::cout << "Score for " << mols[i]->get_name() << " is " << score
<< std::endl;
}
ps->set_was_used(true);
return EXIT_SUCCESS;
}