CHARMMParameters* get_all_atom_CHARMM_parameters() {
static IMP::Pointer<CHARMMParameters> ret
=new CHARMMParameters(get_data_path("top.lib"),
get_data_path("par.lib"));
ret->set_log_level(SILENT);
return ret;
}
IMP::ParticlesTemp add_bonds(IMP::atom::Hierarchy mhd) {
IMP::atom::CHARMMParameters *ff =
IMP::atom::get_heavy_atom_CHARMM_parameters();
IMP::Pointer<IMP::atom::CHARMMTopology> topology =
ff->create_topology(mhd);
topology->add_atom_types(mhd);
IMP::ParticlesTemp bonds = topology->add_bonds(mhd);
return bonds;
}
void add_radii(Hierarchy d, const ForceFieldParameters* ffp,
FloatKey radius_key)
{
// Temporary hack to maintain old interface for SAXS
const CHARMMParameters *cp = dynamic_cast<const CHARMMParameters *>(ffp);
if (cp) {
IMP::Pointer<CHARMMTopology> top = cp->create_topology(d);
top->apply_default_patches();
top->add_atom_types(d);
}
ffp->add_radii(d, 1.0, radius_key);
}
IMPSPB_BEGIN_NAMESPACE
IMP::Pointer<core::MonteCarlo> setup_SPBMonteCarlo(Model *m,
core::MonteCarloMovers &mvs,
double temp,
SPBParameters myparam) {
IMP::Pointer<core::MonteCarlo> mc;
if (myparam.MC.do_wte) {
double w0 = myparam.MC.wte_w0 * temp / myparam.MC.tmin;
mc = new spb::MonteCarloWithWte(
m, myparam.MC.wte_emin, myparam.MC.wte_emax, myparam.MC.wte_sigma,
myparam.MC.wte_gamma, w0);
} else {
mc = new core::MonteCarlo(m);
}
mc->set_return_best(false);
mc->set_kt(temp);
mc->add_mover(new core::SerialMover(get_as<core::MonteCarloMoversTemp>(mvs)));
return mc.release();
}
int main(int argc, char *argv[]) {
IMP::setup_from_argv(argc, argv, "Test ConsecutivePairContainer.");
IMP_NEW(IMP::Model, m, ());
IMP::ParticleIndexes ps;
IMP::algebra::BoundingBox3D bb(IMP::algebra::Vector3D(0, 0, 0),
IMP::algebra::Vector3D(10, 10, 10));
for (unsigned int i = 0; i < 15; ++i) {
ps.push_back(m->add_particle("P"));
IMP::core::XYZ::setup_particle(m, ps.back(),
IMP::algebra::get_random_vector_in(bb));
}
IMP_NEW(IMP::container::ConsecutivePairContainer, cpc, (m, ps));
IMP_NEW(IMP::core::HarmonicDistancePairScore, hdps, (0, 1));
IMP::Pointer<IMP::Restraint> r =
IMP::container::create_restraint(hdps.get(), cpc.get());
IMP_USAGE_CHECK(r->evaluate(false) > 0, "zero evaluate");
IMP::Pointer<IMP::Restraint> rd = r->create_decomposition();
IMP::RestraintsTemp rds = IMP::get_restraints(IMP::RestraintsTemp(1, rd));
IMP_USAGE_CHECK(rds.size() == ps.size() - 1,
"Bad lengths: " << rds.size() << " vs " << ps.size() - 1);
double re = r->evaluate(false);
double rde = rd->evaluate(false);
IMP_CHECK_VARIABLE(re);
IMP_CHECK_VARIABLE(rde);
IMP_USAGE_CHECK(std::abs(rde - re) < .1,
"Invalid decomposed score: " << re << " vs " << rde);
return 0;
}
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;
}
int main(int argc, char **argv)
{
// output arguments
for(int i=0; i<argc; i++) std::cerr << argv[i] << " "; std::cerr << std::endl;
int number_of_iterations = 100;
int number_of_nodes = 100;
int save_configuration_number = 10;
int number_of_models_in_pdb = 100;
int number_of_active_dofs = 0;
float radii_scaling = 0.5;
bool reset_angles = false;
std::string configuration_file;
std::string connect_chains_file;
po::options_description desc("Options");
desc.add_options()
("help", "PDB file and Rotatable Angles file")
("version", "Written by Dina Schneidman.")
("number_of_iterations,i", po::value<int>(&number_of_iterations)->default_value(100),
"number of iterations (default = 100)")
("number_of_nodes,n", po::value<int>(&number_of_nodes)->default_value(100),
"number of nodes (default = 100)")
("number_of_path_configurations_saved,p", po::value<int>(&save_configuration_number)->default_value(10),
"if the path between two nodes is feasible, each Nth configuration on the path will be added to the tree (default = 10?)")
("number_of_active_dofs,a", po::value<int>(&number_of_active_dofs)->default_value(0),
"for many dofs use this option with 10-50 dofs (default = 0)")
("radii_scaling,s", po::value<float>(&radii_scaling)->default_value(0.5),
"radii scaling parameter (0.5 < s < 1.0, default = 0.5)")
("reset_angles", "set initial values in rotatable angles to PI (default = false)")
("connect_chains_file,c",
po::value<std::string>(&connect_chains_file),
"connect chains into one rigid body by adding bonds between specified atoms")
("number_of_models_in_pdb,m", po::value<int>(&number_of_models_in_pdb)->default_value(100),
"number of models in output PDB files (default = 100)")
;
po::options_description hidden("Hidden options");
hidden.add_options()
("input-files", po::value< std::vector<std::string> >(),
"input PDB and rotatable angles files")
("target_configurations,t", po::value<std::string>(&configuration_file),
"target_configurations")
;
po::options_description cmdline_options;
cmdline_options.add(desc).add(hidden);
po::options_description visible("Usage: <pdb_file> <rotatable_angles_file>");
visible.add(desc);
po::positional_options_description p;
p.add("input-files", -1);
po::variables_map vm;
po::store(po::command_line_parser(argc,
argv).options(cmdline_options).positional(p).run(), vm);
po::notify(vm);
std::vector<std::string> files;
if(vm.count("input-files")) {
files = vm["input-files"].as< std::vector<std::string> >();
}
if(vm.count("help") || files.size() == 0) {
std::cout << visible << "\n";
return 0;
}
if(radii_scaling < 0.5 || radii_scaling > 1.0) {
std::cerr << "radii_scaling parameter outside allowed range" << radii_scaling << std::endl;
}
if(vm.count("reset_angles")) reset_angles=true;
std::string pdb_name = files[0];
std::string angle_file_name;
if(files.size() > 1) angle_file_name = files[1];
// read in the input protein
IMP::Pointer<IMP::Model> model = new IMP::Model();
std::cerr << "Starting reading pdb file " << pdb_name << std::endl;
IMP::atom::Hierarchy mhd =
IMP::atom::read_pdb(pdb_name, model,
new IMP::atom::NonWaterNonHydrogenPDBSelector(),
// don't add radii
true, true);
IMP::ParticlesTemp atoms = IMP::atom::get_by_type(mhd, IMP::atom::ATOM_TYPE);
IMP::ParticlesTemp residues = IMP::atom::get_by_type(mhd, IMP::atom::RESIDUE_TYPE);
const std::string topology_file_name = IMP::atom::get_data_path("top_heav.lib");
const std::string parameter_file_name = IMP::atom::get_data_path("par.lib");
std::ifstream test(topology_file_name.c_str());
if(!test) {
std::cerr << "Please provide topology file " << topology_file_name
<< std::endl;
exit(1);
}
std::ifstream test1(parameter_file_name.c_str());
if(!test1) {
std::cerr << "Please provide parameter file " << parameter_file_name
<< std::endl;
exit(1);
}
IMP::atom::CHARMMParameters* ff =
new IMP::atom::CHARMMParameters(topology_file_name, parameter_file_name);
IMP::Pointer<IMP::atom::CHARMMTopology> topology =
ff->create_topology(mhd);
// We don't want to add/remove any atoms, so we only add atom types
topology->apply_default_patches();
// topology->setup_hierarchy(mhd); //removes atoms
topology->add_atom_types(mhd);
IMP::ParticlesTemp bonds = topology->add_bonds(mhd);
// create phi/psi joints
IMP::atom::Residues flexible_residues;
std::vector<IMP::atom::Atoms> dihedral_angles;
if(angle_file_name.length()>0) {
read_angle_file(angle_file_name, residues, atoms,
flexible_residues, dihedral_angles);
} else {
flexible_residues = residues;
}
std::vector<IMP::atom::Atoms> connect_chains_atoms;
if(connect_chains_file.length() > 0) {
read_connect_chains_file(connect_chains_file, atoms, connect_chains_atoms);
for(unsigned i=0; i<connect_chains_atoms.size(); i++) {
IMP::atom::Bond bond = create_bond(connect_chains_atoms[i]);
if(bond != IMP::atom::Bond()) bonds.push_back(bond);
}
}
IMP::ParticlesTemp angles = ff->create_angles(bonds);
IMP::ParticlesTemp dihedrals = ff->create_dihedrals(bonds);
std::cerr << "# atoms " << atoms.size()
<< " # bonds " << bonds.size()
<< " # angles " << angles.size()
<< " # dihedrals " << dihedrals.size() << std::endl;
add_missing_bonds(atoms, bonds);
std::cerr << "# atoms " << atoms.size()
<< " # bonds " << bonds.size()
<< " # angles " << angles.size()
<< " # dihedrals " << dihedrals.size() << std::endl;
// add radius
ff->add_radii(mhd, radii_scaling);
// prepare exclusions list
IMP_NEW(IMP::atom::StereochemistryPairFilter, pair_filter, ());
pair_filter->set_bonds(bonds);
pair_filter->set_angles(angles);
pair_filter->set_dihedrals(dihedrals);
// close pair container
IMP_NEW(IMP::container::ListSingletonContainer, lsc, (atoms));
IMP_NEW(IMP::container::ClosePairContainer, cpc, (lsc, 15.0));
cpc->add_pair_filter(pair_filter);
IMP_NEW(IMP::core::SoftSpherePairScore, score,(1));
IMP_NEW(IMP::container::PairsRestraint, pr, (score, cpc));
// TODO: check why not working: should be much faster
//IMP::Pointer<IMP::Restraint> pr=
// IMP::container::create_restraint(score, cpc);
ProteinKinematics pk(mhd, flexible_residues, dihedral_angles);
std::cerr << "ProteinKinematics done" << std::endl;
DihedralAngleRevoluteJoints joints = pk.get_ordered_joints();
IMP_NEW(KinematicForestScoreState, kfss, (pk.get_kinematic_forest(),
pk.get_rigid_bodies(),
atoms));
model->add_score_state(kfss);
// create dofs
DOFs dofs;
for(unsigned int i=0; i<joints.size(); i++) {
std::cerr << "Angle = " << joints[i]->get_angle() << " " << 180 * joints[i]->get_angle()/IMP::algebra::PI << std::endl;
if(reset_angles) joints[i]->set_angle(IMP::algebra::PI);
IMP_NEW(DOF, dof, (joints[i]->get_angle(),
-IMP::algebra::PI,
IMP::algebra::PI,
IMP::algebra::PI/360));
dofs.push_back(dof);
}
DOFValues val(dofs);
if(reset_angles) {
kfss->do_before_evaluate();
for(unsigned int i=0; i<joints.size(); i++) {
std::cerr << "Angle = " << joints[i]->get_angle() << " " << 180 * joints[i]->get_angle()/IMP::algebra::PI << std::endl;
}
}
DirectionalDOF dd(dofs);
IMP_NEW(UniformBackboneSampler, ub_sampler, (joints, dofs));
IMP_NEW(PathLocalPlanner, planner, (model, ub_sampler, &dd,
save_configuration_number));
std::cerr << "Init RRT" << std::endl;
IMP_NEW(RRT, rrt, (model, ub_sampler, planner, dofs, number_of_iterations,
number_of_nodes, number_of_active_dofs));
rrt->set_scoring_function(pr);
std::cerr << "Start RRT run" << std::endl;
std::string filename = "node_begin.pdb";
IMP::atom::write_pdb(mhd, filename);
rrt->run();
std::cerr << "Done RRT " << rrt->get_DOFValues().size() << std::endl;
// output PDBs
std::ofstream *out = NULL;
int file_counter = 1;
int model_counter = 0;
std::vector<DOFValues> dof_values = rrt->get_DOFValues();
for(unsigned int i = 0; i<dof_values.size(); i++) {
ub_sampler->apply(dof_values[i]);
kfss->do_before_evaluate();
// open new file if needed
if(model_counter % number_of_models_in_pdb == 0) { // open new file
if(out !=NULL) out->close();
std::string file_name = "nodes" + std::string(boost::lexical_cast<std::string>(file_counter)) + ".pdb";
out = new std::ofstream(file_name.c_str());
file_counter++;
model_counter=0;
}
IMP::atom::write_pdb(mhd, *out, model_counter+1);
model_counter++;
}
out->close();
return 0;
}