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Rosetta 3.5
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Rosetta 3.5
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#include <IterativeOptEDriver.hh>
Public Types | |
| typedef core::Real | Real |
| typedef core::Size | Size |
| typedef core::scoring::ScoreTypes | ScoreTypes |
| typedef core::scoring::EnergyMap | EnergyMap |
Public Member Functions | |
| IterativeOptEDriver () | |
| Main constructor for the IterativeOptEDriver class. Note that mpi_rank and mpi_nprocs get set even if USEMPI is not defined. These values are then used to set MPI_rank_ and MPI_nprocs_. Also calls the initialize_free_and_fixed_terms method. More... | |
| ~IterativeOptEDriver () | |
| void | task_factory (core::pack::task::TaskFactoryCOP) |
| take care when using a custom TaskFactory: TaskOperations must not 'accumulate state' as they will be reused repeatedly More... | |
| void | go () |
| Main loop for the optE protocol. This is function the apps call to do optE. More... | |
Private Member Functions | |
| Size | num_outer_iterations () const |
| Size | num_inner_iterations () const |
| void | read_tagfile_to_taskfactory (std::string tagfile_name, core::pack::task::TaskFactoryOP task_factory) |
| Reads in an XML formatted task operation and puts builds a task factory from it. More... | |
| void | load_pose (core::pose::Pose &pose, std::string const &filename, bool ignore_centroid_input_flag) |
| loads structure into pose - decides between silent or pdb More... | |
| void | divide_up_pdbs () |
| The head node has to send out to all the work nodes the list of pdb files they have to do their thing on. It itself doesn't do any of the calculations, right? Work nodes get their list of pdb to work on. More... | |
| void | intialize_free_and_fixed_energy_terms () |
| Calls the method initialize_free_and_fixed() which reads in the files free and fixed and sets the EnergyMap vectors free_parameters_ and fixed_parameters_. Also here the reference energies array gets init'd. Finally, setup_derived_free_and_fixed_data gets called which. More... | |
| void | setup_derived_free_and_fixed_data () |
| include_terms_ is an EnergyMap, as well. I think this function sets up the free and fixed score lists which are just a vector1 of ScoreType objects. include_, fixed_ and free_count_ are just (Size) member variables. More... | |
| void | collect_rotamer_energies () |
| void | compute_rotamer_energies_for_assigned_pdbs () |
| Computes the rotamer energies for all positions for all pdbs given (in the call to get_nat_aa_opte_data()). Also, optionally, does the same for native rotamer recovery data. Creates an unweighted score function using the the class method 'create_unweighed_scorefunction'. The scorefunction used to get the interaction energies of the rotamers is the one that's created here. More... | |
| void | collect_rotamer_energies_from_slave_cpus () |
| Helper method for collecting energies. Calls collect_rotamer_energies_from_slave_cpu for all CPU's being used. More... | |
| void | collect_rotamer_energies_from_slave_cpu (Size const which_cpu) |
| For a calling master node, collects the rotamer energies that were calculated on a slave CPU. More... | |
| void | send_rotamer_energies_to_master_cpu () |
| Used by all slave nodes; sends the rotamer energies (according to the protocol we've set up here) to the master node. More... | |
| void | optimize_weights () |
| Optimizes weights using either a standard minimizer or a ParticleSwarmMinimizer (which is significantly better!). More... | |
| void | score_position_data () |
| utility::vector1< Real > | read_reference_energies_from_file (std::string const &fname) const |
| void | write_new_scorefile () |
| send new score file via MPI instead of writing to disk. More... | |
| void | test_sequence_recovery () |
| Calls run_design on all pdbs and collects the results from slave cpus if MPI is in use. More... | |
| void | collect_sequence_recovery_data_from_slave_cpus () |
| Helper method for master node. Calls collect_recovery_data_from_slave_cpu on all slave CPUs. More... | |
| void | collect_sequence_recovery_data_from_slave_cpu (Size const which_cpu) |
| void | run_design_on_assigned_pdbs () |
| Runs design on the pdbs assigned to this node/cpu. More... | |
| void | send_sequence_recovery_data_to_master_cpu () |
| void | repack_assigned_pdbs () |
| void | collect_rotamer_recovery_data_from_slave_cpus () |
| Helper method for master node. Calls collect_rotamer_recovery_data_from_slave_cpu on all slave CPUs. More... | |
| void | collect_rotamer_recovery_data_from_slave_cpu (Size const which_cpu) |
| void | send_rotamer_recovery_data_to_master_cpu () |
| bool | decide_if_sequence_recovery_improved () |
| The final function call of the go() method. After all the pdbs have been designed and repacked, and the recovery data collected, decide if this new set of weights improved the sequence recovery. More... | |
| void | test_weight_sensitivity (OptEMultifunc const &func, core::optimization::Multivec const &dofs) const |
| std::string | get_scorefile_name () |
| void | barrier () |
| void | exit_gracefully () |
| utility::vector1< std::string > | get_native_pdb_names () |
| Reads in the list of pdb file names to use for the optimization. Uses basic::options::start_file which returns a vector1 of strings. Unfortunately, this method reads data out of the return value of start_file() which is why you have to use a listfile with the -s option for things to work correctly. More... | |
| void | zero_aa_counts () |
| Set the counts for the amino acid frequencies (observed and expected) to zero. More... | |
| Real | measure_sequence_recovery (utility::vector1< std::string > const &native_pdb_names, utility::vector1< std::string > const &names_for_output_pdbs, core::scoring::ScoreFunctionOP sfxn, Size &npos, Size &nrecovered) |
| Real | measure_rotamer_recovery (utility::vector1< std::string > const &native_pdb_names, utility::vector1< std::string > const &names_for_output_pdbs, core::scoring::ScoreFunctionOP sfxn, Size &npos, Size &nrecovered) |
| Real | opte_weight_mixing_factor (Size outer_loop_counter, Size inner_loop_counter) |
| void | initialize_free_and_fixed (core::scoring::EnergyMap &free_parameters, core::scoring::EnergyMap &fixed_parameters) |
| Reads in the files specified by opt_e::free and opt_e::fixed. Figures out what ScoreType the user placed on each line of the file and then sets the free_parameters array with that ScoreType. If the user does not place a starting weight, a random starting weight is given for that type. Also sets the fixed terms in fixed_parameters. Both of these EnergyMap references that are passed in are actually vectors of EnergyMaps? Either way, the free and fixed params are set in this method. If no fixed or free files are found, then there are some hardcoded defaults that get used. More... | |
| bool | converged (core::scoring::EnergyMap &free_parameters_prev, core::scoring::EnergyMap &free_parameters_curr, utility::vector1< Real > const &reference_energies_prev, utility::vector1< Real > const &reference_energies_curr) |
| This function is not used. More... | |
| void | setup_pdbnames_next_round (Size const outer_loop_counter, utility::vector1< std::string > &pdbs_next_round, utility::vector1< std::string > const &native_pdb_names) |
| void | write_parameters_to_std_out (core::scoring::EnergyMap &free_parameters, utility::vector1< Real > const &reference_energies) |
| void | get_nat_aa_opte_data (std::string const &pdb_name, core::pose::Pose &pose, core::pose::Pose &native_pose, core::scoring::ScoreFunction const &scorefxn, ScoreTypes &score_list, ScoreTypes &fixed_score_vec, OptEData &opte_data) |
| refactor this into an optE common... More... | |
| void | get_nat_rot_opte_data (std::string const &pdb_name, core::pose::Pose &pose, core::pose::Pose &native_pose, utility::vector1< bool > include_rsd, core::scoring::ScoreFunction const &scorefxn, ScoreTypes &score_list, ScoreTypes &fixed_score_vec, OptEData &opte_data) |
| Similar to get_nat_aa_opte_data. See comments there for more info. More... | |
| void | set_aa_periodicity (PNatRotOptEPositionDataOP pos_data, core::chemical::AA aa) const |
| bool | residue_has_unacceptably_bad_dunbrack_energy (core::pose::Pose const &pose, Size const resid) const |
| True/False: a particular residue be skipped for inclusion into the native-rotamer recovery test because its dunbrack energy is really high. More... | |
| bool | residue_has_bad_bfactor (core::pose::Pose const &pose, Size const resid) const |
| True/False: a particular residue be skipped for inclusion into the native-rotamer recovery test because it contains an atom with a high B-factor. More... | |
| core::scoring::EnergyMap | free_terms_energy_map_from_dofs (core::optimization::Multivec const &dofs) const |
| Expand free variables and combine with fixed to make an Energy Map. More... | |
| void | free_weights_and_refEs_from_vars (utility::vector1< Real > const &vars, core::scoring::EnergyMap &weights, utility::vector1< Real > &reference_energies) const |
| core::scoring::ScoreFunctionOP | configure_new_scorefunction () const |
| Sets functional forms (e.g. soft-rep) but doesn't set any weights. If the option -optE::optE_soft_rep is specified, then an empty scorefunction with the FA_STANDARD_SOFT etable is returned. Another option is -optE::optE_no_protein_hack_elec. This excludes protein_protein_hack_elec in the the scorefunction energy method options. More... | |
| core::scoring::ScoreFunctionOP | create_unweighted_scorefunction () const |
| Takes a std::string and a destination and constructs the MPI_Send call. Does this include the reference energy term somehow? I don't believe it does. More... | |
| core::scoring::ScoreFunctionOP | create_weighted_scorefunction () const |
| void | collect_decoy_discrimination_data () |
| Collect optE data for decoy discrimination. Similar to the get_nat_aa_opte_data method. More... | |
| SingleStructureDataOP | single_structure_data_for_pose (core::scoring::ScoreFunctionOP scorefxn, core::pose::Pose &pose, core::pose::Pose const &crystal_native, utility::vector1< Real > &free_data, utility::vector1< Real > &fixed_data, std::string const &structure_tag="") const |
| AddStatus | add_structure_based_on_rms (SingleStructureDataOP ssd, PNatStructureOptEDataOP structure_data, bool intended_native) const |
| void | compute_rotamers_around_ligands () |
| Ligand stuff. More... | |
| void | collect_ligand_discrimination_data () |
| Ligand stuff. More... | |
| core::scoring::EnergyMap | score_ligand_interface (core::scoring::ScoreFunction const &scorefxn, core::pose::Pose &pose) |
| Ligand stuff. More... | |
| SingleStructureDataOP | make_simple_ssd_from_pdb (std::string const &pdb_filename, core::scoring::ScoreFunctionOP sfxn, bool pretend_no_fa_rep=false) const |
| Helper function to reduce code duplication. More... | |
| void | collect_dG_of_binding_data () |
| dG optimization optE data collection. More... | |
| void | collect_ddG_of_mutation_data () |
| ddG optimization optE data collection. More... | |
| void | collect_ddG_of_binding_data () |
| The calculations for ddG of binding for interfaces doesn't really fit with the ddG stability and dG binding optE modes. This functions loads all of the necessary structures for optimization of ddG of binding into the optE framework. More... | |
| void | load_pssm_data (std::string const &native_filename, Size const which_protein) |
| core::pack::task::PackerTaskOP | copy_native_packertask_logic (core::pose::Pose native_pose, core::pose::Pose context_pose, core::pack::task::TaskFactoryOP native_taskfactory) |
| Copies the logic in the native task factory from the native_pose to the context pose The context pose should be filled with a parsable file that does NOT restrict any residues that might be packable in the native. More... | |
| void | repack_and_minimize_pose (core::pose::Pose &pose, core::scoring::ScoreFunctionOP sfxn) const |
| std::string | node_name (int rank) |
| void | print_energies (core::pose::Pose &, core::scoring::ScoreFunctionOP, std::ostream &os=std::cout) |
| void | output_weighted_unfolded_energies () |
| Multiply out the unweighted unfolded energies with the current free and fixed term weights. More... | |
Definition at line 65 of file IterativeOptEDriver.hh.
Definition at line 70 of file IterativeOptEDriver.hh.
Definition at line 67 of file IterativeOptEDriver.hh.
Definition at line 69 of file IterativeOptEDriver.hh.
Definition at line 68 of file IterativeOptEDriver.hh.
| protocols::optimize_weights::IterativeOptEDriver::IterativeOptEDriver | ( | ) |
Main constructor for the IterativeOptEDriver class. Note that mpi_rank and mpi_nprocs get set even if USEMPI is not defined. These values are then used to set MPI_rank_ and MPI_nprocs_. Also calls the initialize_free_and_fixed_terms method.
IterativeOptEDriver::IterativeOptEDriver()
Definition at line 200 of file IterativeOptEDriver.cc.
References after_minimization_reference_energies_, before_minimization_reference_energies_, component_weights_, fixed_score_list_, free_score_list_, intialize_free_and_fixed_energy_terms(), protocols::optimize_weights::load_component_weights(), MPI_nprocs_, protocols::wum::mpi_rank(), MPI_rank_, core::scoring::name_from_score_type(), core::chemical::num_canonical_aas, read_tagfile_to_taskfactory(), reference_energies_inner_loop_, task_factory_, protocols::optimize_weights::TR(), and using_unfolded_energy_term_.
| protocols::optimize_weights::IterativeOptEDriver::~IterativeOptEDriver | ( | ) |
IterativeOptEDriver::~IterativeOptEDriver()
Definition at line 283 of file IterativeOptEDriver.cc.
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IterativeOptEDriver::add_structure_based_on_rms()
Returns 1 if added as intended, 0 if not added at all, and -1 if added in the opposite of its intention.
Definition at line 1497 of file IterativeOptEDriver.cc.
References protocols::optimize_weights::ADDED_STRUCTURE_AS_INTENDED, protocols::optimize_weights::ADDED_STRUCTURE_OPPOSITE_AS_INTENDED, protocols::optimize_weights::DID_NOT_ADD_STRUCTURE, and protocols::optimize_weights::PNatStructureOptEData::nativeness_high().
Referenced by collect_decoy_discrimination_data().
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Definition at line 3564 of file IterativeOptEDriver.cc.
Referenced by exit_gracefully(), go(), and optimize_weights().
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The calculations for ddG of binding for interfaces doesn't really fit with the ddG stability and dG binding optE modes. This functions loads all of the necessary structures for optimization of ddG of binding into the optE framework.
IterativeOptEDriver::collect_ddG_of_binding_data()
Definition at line 4497 of file IterativeOptEDriver.cc.
References core::chemical::aa_from_oneletter_code(), create_unweighted_scorefunction(), ddG_bind_files_, ddG_bind_optE_data_, ddGs_binding_, core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), core::scoring::fa_rep, fixed_score_list_, free_score_list_, MPI_rank_, protocols::optimize_weights::DDGBindOptEData::MUT_COMPLEXES_LIST_FILE, protocols::optimize_weights::DDGBindOptEData::MUT_UNBOUNDS_LIST_FILE, optE_data_, core::import_pose::pose_from_pdb(), core::pose::Pose::sequence(), core::scoring::Energies::total_energies(), protocols::optimize_weights::TR(), protocols::optimize_weights::TR_VERBOSE(), protocols::optimize_weights::DDGBindOptEData::WT_COMPLEXES_LIST_FILE, and protocols::optimize_weights::DDGBindOptEData::WT_UNBOUNDS_LIST_FILE.
Referenced by collect_rotamer_energies().
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ddG optimization optE data collection.
IterativeOptEDriver::collect_ddG_of_mutation_data()
Definition at line 4143 of file IterativeOptEDriver.cc.
References core::chemical::aa_from_oneletter_code(), core::import_pose::centroid_pose_from_pdb(), create_unweighted_scorefunction(), ddg_mut_wt_pairs_, ddG_mutation_data_, ddGs_, core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), core::scoring::fa_rep, core::chemical::FA_STANDARD, fixed_score_list_, free_score_list_, core::chemical::ChemicalManager::get_instance(), core::scoring::ScoringManager::get_instance(), core::scoring::ScoringManager::get_UnfoldedStatePotential(), MPI_rank_, optE_data_, core::import_pose::pose_from_pdb(), core::scoring::UnfoldedStatePotential::pose_raw_unfolded_state_energymap(), core::io::silent::SilentFileData::read_file(), core::chemical::ChemicalManager::residue_type_set(), core::pose::Pose::sequence(), core::io::silent::SilentFileData::set_filename(), core::scoring::surface, core::io::silent::SilentFileData::tags(), core::scoring::Energies::total_energies(), protocols::optimize_weights::TR(), protocols::optimize_weights::TR_VERBOSE(), core::scoring::UNFOLDED_SCORE12, and using_unfolded_energy_term_.
Referenced by collect_rotamer_energies().
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Collect optE data for decoy discrimination. Similar to the get_nat_aa_opte_data method.
IterativeOptEDriver::collect_decoy_discrimination_data()
Definition at line 1210 of file IterativeOptEDriver.cc.
References add_structure_based_on_rms(), protocols::optimize_weights::ADDED_STRUCTURE_AS_INTENDED, protocols::optimize_weights::ADDED_STRUCTURE_OPPOSITE_AS_INTENDED, core::scoring::ScoreFunctionFactory::create_score_function(), create_unweighted_scorefunction(), create_weighted_scorefunction(), decdisc_crystal_natives_, decdisc_decoy_poses_, decdisc_native_decoy_pairs_, decdisc_native_poses_, decdisc_xtal_natives_, decoy_discrim_data_, fixed_score_list_, free_score_list_, load_pose(), MPI_rank_, optE_data_, outer_loop_counter_, repack_and_minimize_pose(), core::scoring::SCORE12_PATCH, protocols::optimize_weights::PNatStructureOptEData::set_nativeness_high(), protocols::optimize_weights::PNatStructureOptEData::set_nativeness_low(), single_structure_data_for_pose(), core::io::serialization::size(), core::scoring::STANDARD_WTS, core::pose::Pose::total_residue(), and protocols::optimize_weights::TR_VERBOSE().
Referenced by collect_rotamer_energies().
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dG optimization optE data collection.
IterativeOptEDriver::collect_dG_of_binding_data()
Definition at line 4108 of file IterativeOptEDriver.cc.
References create_unweighted_scorefunction(), dG_binding_, dG_binding_data_, dG_bound_unbound_pairs_, make_simple_ssd_from_pdb(), and optE_data_.
Referenced by collect_rotamer_energies().
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Ligand stuff.
IterativeOptEDriver::collect_ligand_discrimination_data()
Definition at line 1644 of file IterativeOptEDriver.cc.
References create_unweighted_scorefunction(), fixed_score_list_, free_score_list_, ligand_crystal_natives_, ligand_discrim_data_, ligand_native_decoy_pairs_, MPI_rank_, optE_data_, core::import_pose::pose_from_pdb(), score_ligand_interface(), core::pose::Pose::total_residue(), and protocols::optimize_weights::TR().
Referenced by collect_rotamer_energies().
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IterativeOptEDriver::collect_rotamer_energies()
Definition at line 819 of file IterativeOptEDriver.cc.
References collect_ddG_of_binding_data(), collect_ddG_of_mutation_data(), collect_decoy_discrimination_data(), collect_dG_of_binding_data(), collect_ligand_discrimination_data(), collect_rotamer_energies_from_slave_cpus(), compute_rotamer_energies_for_assigned_pdbs(), compute_rotamers_around_ligands(), exit_gracefully(), free_parameters_, free_weights_after_minimization_, MPI_rank_, native_pdbs_, next_iteration_pdbs_, outer_loop_counter_, pdbs_this_round_, score_position_data(), send_rotamer_energies_to_master_cpu(), setup_pdbnames_next_round(), test_sequence_recovery(), and write_new_scorefile().
Referenced by go().
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For a calling master node, collects the rotamer energies that were calculated on a slave CPU.
IterativeOptEDriver::collect_rotamer_energies_from_slave_cpu()
Definition at line 1837 of file IterativeOptEDriver.cc.
References protocols::optimize_weights::OptEPositionDataFactory::create_position_data(), fixed_parameters_, free_parameters_, core::scoring::n_score_types, and optE_data_.
Referenced by collect_rotamer_energies_from_slave_cpus().
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Helper method for collecting energies. Calls collect_rotamer_energies_from_slave_cpu for all CPU's being used.
IterativeOptEDriver::collect_rotamer_energies_from_slave_cpus()
Definition at line 1181 of file IterativeOptEDriver.cc.
References collect_rotamer_energies_from_slave_cpu(), MPI_nprocs_, optE_data_, and protocols::optimize_weights::TR().
Referenced by collect_rotamer_energies(), optimize_weights(), and score_position_data().
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IterativeOptEDriver::collect_rotamer_recovery_data_from_slave_cpu()
Definition at line 3221 of file IterativeOptEDriver.cc.
References count_rotamers_recovered_, and total_rotamer_positions_.
Referenced by collect_rotamer_recovery_data_from_slave_cpus().
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Helper method for master node. Calls collect_rotamer_recovery_data_from_slave_cpu on all slave CPUs.
IterativeOptEDriver::collect_rotamer_recovery_data_from_slave_cpus()
Definition at line 3202 of file IterativeOptEDriver.cc.
References collect_rotamer_recovery_data_from_slave_cpu(), count_rotamers_recovered_, inner_loop_rotamer_recovery_rate_, MPI_nprocs_, total_rotamer_positions_, and protocols::optimize_weights::TR().
Referenced by test_sequence_recovery().
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IterativeOptEDriver::collect_sequence_recovery_data_from_slave_cpu()
Definition at line 3164 of file IterativeOptEDriver.cc.
References aa_exp_, aa_obs_, count_recovered_, core::chemical::num_canonical_aas, and total_positions_.
Referenced by collect_sequence_recovery_data_from_slave_cpus().
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Helper method for master node. Calls collect_recovery_data_from_slave_cpu on all slave CPUs.
IterativeOptEDriver::collect_sequence_recovery_data_from_slave_cpus()
Definition at line 3116 of file IterativeOptEDriver.cc.
References aa_exp_, aa_freq_exp_, aa_freq_obs_, aa_obs_, collect_sequence_recovery_data_from_slave_cpu(), count_recovered_, inner_loop_sequence_recovery_rate_, MPI_nprocs_, core::chemical::num_canonical_aas, core::chemical::oneletter_code_from_aa(), total_positions_, and protocols::optimize_weights::TR().
Referenced by test_sequence_recovery().
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Computes the rotamer energies for all positions for all pdbs given (in the call to get_nat_aa_opte_data()). Also, optionally, does the same for native rotamer recovery data. Creates an unweighted score function using the the class method 'create_unweighed_scorefunction'. The scorefunction used to get the interaction energies of the rotamers is the one that's created here.
IterativeOptEDriver::compute_rotamer_energies_for_assigned_pdbs()
Note: Surface is a PackerTask option. No repacking/design is done here. Just scoring. So the surface energies would not be included here in the optEdata. If surface was made into a ScoreType, then it could be added. -ronj Update: Surface score is now it's own EnergyMethod. If 'surface' is detected in the ScoreFunction, then the EnergyMethod calculates the surface energy of the pose. You don't get per-residue surface energies this way, but you do get the total pose surface energy. -ronj
Definition at line 942 of file IterativeOptEDriver.cc.
References core::import_pose::centroid_pose_from_pdb(), context_poses_, create_unweighted_scorefunction(), fixed_score_list_, free_score_list_, get_nat_aa_opte_data(), get_nat_rot_opte_data(), core::chemical::ResidueType::is_protein(), load_pssm_data(), MPI_rank_, native_pdbs_, native_poses_, node_name(), optE_data_, outer_loop_counter_, core::import_pose::pose_from_pdb(), core::pose::Pose::residue_type(), rotamer_recovery_context_poses_, core::pose::Pose::total_residue(), protocols::optimize_weights::TR(), and protocols::optimize_weights::TR_VERBOSE().
Referenced by collect_rotamer_energies().
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Ligand stuff.
IterativeOptEDriver::compute_rotamers_around_ligands()
Definition at line 1570 of file IterativeOptEDriver.cc.
References create_unweighted_scorefunction(), fixed_score_list_, core::pose::Pose::fold_tree(), free_score_list_, get_nat_rot_opte_data(), core::conformation::Residue::is_protein(), ligand_repack_native_poses_, ligand_repack_pdbs_, core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::num_jump(), optE_data_, outer_loop_counter_, core::kinematics::FoldTree::partition_by_jump(), core::import_pose::pose_from_pdb(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().
Referenced by collect_rotamer_energies().
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Sets functional forms (e.g. soft-rep) but doesn't set any weights. If the option -optE::optE_soft_rep is specified, then an empty scorefunction with the FA_STANDARD_SOFT etable is returned. Another option is -optE::optE_no_protein_hack_elec. This excludes protein_protein_hack_elec in the the scorefunction energy method options.
IterativeOptEDriver::configure_new_scorefunction
Definition at line 2994 of file IterativeOptEDriver.cc.
References core::scoring::methods::EnergyMethodOptions::etable_type(), core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_hack_elec(), core::scoring::FA_STANDARD_SOFT, core::scoring::methods::EnergyMethodOptions::hbond_options(), core::scoring::methods::EnergyMethodOptions::unfolded_energies_type(), core::scoring::UNFOLDED_SCORE12, core::scoring::hbonds::HBondOptions::use_hb_env_dep(), core::scoring::hbonds::HBondOptions::use_hb_env_dep_DNA(), and using_unfolded_energy_term_.
Referenced by create_unweighted_scorefunction(), create_weighted_scorefunction(), repack_assigned_pdbs(), and run_design_on_assigned_pdbs().
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This function is not used.
IterativeOptEDriver::converged
Definition at line 5249 of file IterativeOptEDriver.cc.
References core::scoring::n_score_types, core::scoring::name_from_score_type(), and protocols::optimize_weights::TR().
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Copies the logic in the native task factory from the native_pose to the context pose The context pose should be filled with a parsable file that does NOT restrict any residues that might be packable in the native.
copy_native_packertask_logic
Definition at line 5426 of file IterativeOptEDriver.cc.
References read_tagfile_to_taskfactory().
Referenced by get_nat_aa_opte_data(), get_nat_rot_opte_data(), measure_rotamer_recovery(), and measure_sequence_recovery().
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Takes a std::string and a destination and constructs the MPI_Send call. Does this include the reference energy term somehow? I don't believe it does.
IterativeOptEDriver::create_unweighted_scorefunction
Definition at line 3034 of file IterativeOptEDriver.cc.
References configure_new_scorefunction(), include_terms_, and core::scoring::n_score_types.
Referenced by collect_ddG_of_binding_data(), collect_ddG_of_mutation_data(), collect_decoy_discrimination_data(), collect_dG_of_binding_data(), collect_ligand_discrimination_data(), compute_rotamer_energies_for_assigned_pdbs(), and compute_rotamers_around_ligands().
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Construct a score function: set etable type, set weights, set reference weights.
Definition at line 3047 of file IterativeOptEDriver.cc.
References configure_new_scorefunction(), fixed_parameters_, free_weights_inner_loop_, core::scoring::n_score_types, core::scoring::ref, and reference_energies_inner_loop_.
Referenced by collect_decoy_discrimination_data().
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The final function call of the go() method. After all the pdbs have been designed and repacked, and the recovery data collected, decide if this new set of weights improved the sequence recovery.
IterativeOptEDriver::decide_if_sequence_recovery_improved()
Definition at line 3404 of file IterativeOptEDriver.cc.
References aa_freq_exp_, aa_freq_obs_, before_minimization_reference_energies_, free_parameters_, free_weights_before_minimization_, free_weights_inner_loop_, inner_loop_counter_, inner_loop_sequence_recovery_rate_, mixing_factor_, MPI_nprocs_, MPI_rank_, core::chemical::num_canonical_aas, num_inner_iterations(), outer_loop_counter_, outer_loop_last_sequence_recovery_rate_, outer_loop_seq_profile_cross_entropy_, reference_energies_inner_loop_, core::scoring::EMapVector::show_nonzero(), and protocols::optimize_weights::TR().
Referenced by go().
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The head node has to send out to all the work nodes the list of pdb files they have to do their thing on. It itself doesn't do any of the calculations, right? Work nodes get their list of pdb to work on.
IterativeOptEDriver::divide_up_pdbs()
Definition at line 361 of file IterativeOptEDriver.cc.
References ddG_bind_files_, ddg_mut_wt_pairs_, ddGs_, ddGs_binding_, decdisc_crystal_natives_, decdisc_native_decoy_pairs_, dG_binding_, dG_bound_unbound_pairs_, get_native_pdb_names(), ligand_crystal_natives_, ligand_native_decoy_pairs_, ligand_repack_pdbs_, MPI_nprocs_, MPI_rank_, protocols::optimize_weights::DDGBindOptEData::MUT_COMPLEXES_LIST_FILE, protocols::optimize_weights::DDGBindOptEData::MUT_UNBOUNDS_LIST_FILE, native_pdbs_, next_iteration_pdbs_, setup_pdbnames_next_round(), protocols::optimize_weights::TR_VERBOSE(), protocols::optimize_weights::DDGBindOptEData::WT_COMPLEXES_LIST_FILE, and protocols::optimize_weights::DDGBindOptEData::WT_UNBOUNDS_LIST_FILE.
Referenced by go().
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Definition at line 880 of file IterativeOptEDriver.cc.
References barrier().
Referenced by collect_rotamer_energies(), and test_sequence_recovery().
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Expand free variables and combine with fixed to make an Energy Map.
IterativeOptEDriver::free_terms_energy_map_from_dofs
This dofs Multivec is the list of weights that the OptEMultifunc sees; do not confuse this set of dofs with the set of dofs that the Minimizer and the WrappedOptEMultifunc use.
Definition at line 2945 of file IterativeOptEDriver.cc.
References free_score_list_.
Referenced by free_weights_and_refEs_from_vars().
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IterativeOptEDriver::free_weights_and_refEs_from_vars
Definition at line 2967 of file IterativeOptEDriver.cc.
References free_count_, free_terms_energy_map_from_dofs(), core::chemical::num_canonical_aas, and core::scoring::EMapVector::zero().
Referenced by write_new_scorefile().
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refactor this into an optE common...
This function is the heart of the optE protocol. For each position of the protein, we're going to create a new PackerTask that only tries all of the various amino acids at that position. (It also uses any packer task related flags on the command line.) opte_data is a container class for optE data objects. So each position is going to have a PNatAAOptEPositionData object. For each rotamer that's built for each position, the energies for the fixed and free energy terms are stored in a PNatAAOptERotamerData object which gets added to the PNatAAOptEPositionData object. So at the end of this function we have one optEData object which has position info for all position and rotamer data for all rotamers at each position.
IterativeOptEDriver::get_nat_aa_opte_data
Definition at line 3617 of file IterativeOptEDriver.cc.
References core::conformation::Residue::aa(), protocols::optimize_weights::OptEData::add_position_data(), core::pack::task::operation::InitializeFromCommandline::apply(), copy_native_packertask_logic(), core::pack::create_packer_graph(), core::pack::rotamer_set::RotamerSetFactory::create_rotamer_set(), core::pose::Pose::energies(), core::scoring::fa_rep, core::scoring::ScoringManager::get_instance(), core::graph::Graph::get_node(), core::scoring::ScoringManager::get_UnfoldedStatePotential(), core::conformation::Residue::is_protein(), core::chemical::ResidueType::name3(), core::chemical::name_from_aa(), core::chemical::num_canonical_aas, core::graph::Node::num_neighbors_counting_self(), core::pose::Pose::pdb_info(), core::scoring::ScoreFunction::prepare_rotamers_for_packing(), pssm_data_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::set_unfolded_energy_emap_vector(), core::scoring::ScoreFunction::setup_for_packing(), task_factory_, core::scoring::Energies::tenA_neighbor_graph(), core::pose::Pose::total_residue(), protocols::optimize_weights::TR(), core::scoring::UNFOLDED_SCORE12, and using_unfolded_energy_term_.
Referenced by compute_rotamer_energies_for_assigned_pdbs().
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Similar to get_nat_aa_opte_data. See comments there for more info.
IterativeOptEDriver::get_nat_rot_opte_data
Definition at line 3795 of file IterativeOptEDriver.cc.
References core::chemical::ResidueType::aa(), core::conformation::Residue::aa(), protocols::optimize_weights::OptEData::add_position_data(), core::pack::task::operation::InitializeFromCommandline::apply(), core::conformation::Residue::chi(), copy_native_packertask_logic(), core::pack::create_packer_graph(), core::pack::rotamer_set::RotamerSetFactory::create_rotamer_set(), core::scoring::fa_rep, core::pack::dunbrack::RotamerLibrary::get_instance(), core::chemical::ResidueType::name3(), core::chemical::oneletter_code_from_aa(), core::pose::Pose::pdb_info(), core::pose::Pose::phi(), core::scoring::ScoreFunction::prepare_rotamers_for_packing(), core::pose::Pose::psi(), core::pose::Pose::residue(), residue_has_bad_bfactor(), core::pose::Pose::residue_type(), set_aa_periodicity(), core::scoring::ScoreFunction::setup_for_packing(), task_factory_, core::pose::Pose::total_residue(), and protocols::optimize_weights::TR().
Referenced by compute_rotamer_energies_for_assigned_pdbs(), and compute_rotamers_around_ligands().
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Reads in the list of pdb file names to use for the optimization. Uses basic::options::start_file which returns a vector1 of strings. Unfortunately, this method reads data out of the return value of start_file() which is why you have to use a listfile with the -s option for things to work correctly.
IterativeOptEDriver::get_native_pdb_names
Definition at line 3582 of file IterativeOptEDriver.cc.
Referenced by divide_up_pdbs().
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IterativeOptEDriver::get_scorefile_name()
Definition at line 3073 of file IterativeOptEDriver.cc.
References outer_loop_counter_.
Referenced by write_new_scorefile().
| void protocols::optimize_weights::IterativeOptEDriver::go | ( | ) |
Main loop for the optE protocol. This is function the apps call to do optE.
Definition at line 3530 of file IterativeOptEDriver.cc.
References barrier(), collect_rotamer_energies(), decide_if_sequence_recovery_improved(), divide_up_pdbs(), inner_loop_counter_, MPI_rank_, node_name(), num_inner_iterations(), num_outer_iterations(), optimize_weights(), outer_loop_counter_, test_sequence_recovery(), protocols::optimize_weights::TR(), and write_new_scorefile().
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Reads in the files specified by opt_e::free and opt_e::fixed. Figures out what ScoreType the user placed on each line of the file and then sets the free_parameters array with that ScoreType. If the user does not place a starting weight, a random starting weight is given for that type. Also sets the fixed terms in fixed_parameters. Both of these EnergyMap references that are passed in are actually vectors of EnergyMaps? Either way, the free and fixed params are set in this method. If no fixed or free files are found, then there are some hardcoded defaults that get used.
IterativeOptEDriver::initialize_free_and_fixed()
Definition at line 5104 of file IterativeOptEDriver.cc.
References core::scoring::cenpack, core::scoring::dslf_ca_dih, core::scoring::dslf_cs_ang, core::scoring::dslf_ss_dih, core::scoring::dslf_ss_dst, core::scoring::env, core::scoring::envsmooth, core::scoring::fa_atr, core::scoring::fa_dun, core::scoring::fa_rep, core::scoring::hbond_lr_bb, core::scoring::hbond_sr_bb, MPI_rank_, core::scoring::n_score_types, core::scoring::name_from_score_type(), protocols::optimize_weights::optE_RG(), core::scoring::p_aa_pp, core::scoring::pair, core::scoring::rama, core::scoring::ScoreTypeManager::score_type_from_name(), core::pack::task::tokenize_line(), protocols::optimize_weights::TR_VERBOSE(), and core::scoring::vdw.
Referenced by intialize_free_and_fixed_energy_terms().
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Calls the method initialize_free_and_fixed() which reads in the files free and fixed and sets the EnergyMap vectors free_parameters_ and fixed_parameters_. Also here the reference energies array gets init'd. Finally, setup_derived_free_and_fixed_data gets called which.
IterativeOptEDriver::intialize_free_and_fixed_energy_terms()
Definition at line 1916 of file IterativeOptEDriver.cc.
References before_minimization_reference_energies_, fixed_parameters_, free_parameters_, initialize_free_and_fixed(), MPI_rank_, core::chemical::num_canonical_aas, and setup_derived_free_and_fixed_data().
Referenced by IterativeOptEDriver().
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loads structure into pose - decides between silent or pdb
IterativeOptEDriver::load_pose()
Definition at line 322 of file IterativeOptEDriver.cc.
References core::import_pose::centroid_pose_from_pdb(), core::import_pose::pose_from_pdb(), core::io::silent::SilentFileData::read_file(), and protocols::optimize_weights::TR_VERBOSE().
Referenced by collect_decoy_discrimination_data().
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IterativeOptEDriver::load_pssm_data
Definition at line 1046 of file IterativeOptEDriver.cc.
References core::chemical::aa_from_oneletter_code(), all_pssm_data_, core::chemical::num_canonical_aas, outer_loop_counter_, protocols::optimize_weights::pssm_data, pssm_data_, and protocols::optimize_weights::TR().
Referenced by compute_rotamer_energies_for_assigned_pdbs().
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Helper function to reduce code duplication.
IterativeOptEDriver::make_simple_ssd_from_pdb()
Definition at line 4069 of file IterativeOptEDriver.cc.
References core::import_pose::centroid_pose_from_pdb(), core::scoring::fa_rep, fixed_score_list_, free_score_list_, core::import_pose::pose_from_pdb(), and structure.
Referenced by collect_dG_of_binding_data().
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IterativeOptEDriver::measure_rotamer_recovery()
Definition at line 4978 of file IterativeOptEDriver.cc.
References copy_native_packertask_logic(), core::conformation::Residue::is_protein(), native_poses_, core::conformation::Residue::nchi(), core::pose::Pose::residue(), core::pack::dunbrack::rotamer_from_chi(), rotamer_recovery_context_poses_, protocols::simple_moves::PackRotamersMover::task_factory(), task_factory_, and core::pose::Pose::total_residue().
Referenced by repack_assigned_pdbs().
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IterativeOptEDriver::measure_sequence_recovery()
iterate across all the native pdbs,
Definition at line 4827 of file IterativeOptEDriver.cc.
References core::conformation::Residue::aa(), aa_exp_, aa_obs_, context_poses_, copy_native_packertask_logic(), core::pose::Pose::dump_scored_pdb(), core::scoring::fa_atr, core::conformation::Residue::is_protein(), MPI_rank_, native_poses_, outer_loop_counter_, core::import_pose::pose_from_pdb(), print_energies(), core::pose::Pose::residue(), rotamer_recovery_context_poses_, core::scoring::surface, task_factory_, core::pose::Pose::total_residue(), protocols::optimize_weights::TR(), and protocols::optimize_weights::TR_VERBOSE().
Referenced by run_design_on_assigned_pdbs().
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IterativeOptEDriver::node_name()
Definition at line 5467 of file IterativeOptEDriver.cc.
Referenced by compute_rotamer_energies_for_assigned_pdbs(), and go().
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Definition at line 1905 of file IterativeOptEDriver.cc.
Referenced by decide_if_sequence_recovery_improved(), and go().
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Definition at line 1898 of file IterativeOptEDriver.cc.
Referenced by go().
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IterativeOptEDriver::opte_weight_mixing_factor
Definition at line 5082 of file IterativeOptEDriver.cc.
Referenced by write_new_scorefile().
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Optimizes weights using either a standard minimizer or a ParticleSwarmMinimizer (which is significantly better!).
IterativeOptEDriver::optimize_weights()
Assuming the ParticleSwarmMinimizer is used... Each particle traverses weight space and comes up with a set of values, then it evaluates the fitness function (which basically calls all of the appropriate underlying get_score() methods) to see how good the new weights are. The particles then update their direction and velocity and come up with a new set of weights to evaluate. This is done with a set number of particles and a set number of cycles. Currently using on the order of 100 particles and 20 cycles. (No tests have been done to determine the optimum number of particles and/or cycles, although ronj likes to use more particles whenever possible.)
Definition at line 1959 of file IterativeOptEDriver.cc.
References after_minimization_reference_energies_, barrier(), before_minimization_reference_energies_, collect_rotamer_energies_from_slave_cpus(), component_weights_, protocols::optimize_weights::OptEMultifunc::declare_minimization_over(), protocols::optimize_weights::OptEMultifunc::fix_reference_energies(), fixed_parameters_, fixed_score_list_, free_count_, free_parameters_, free_score_list_, free_weights_after_minimization_, free_weights_before_minimization_, protocols::optimize_weights::OptEMultifunc::get_dofs_from_energy_map(), protocols::optimize_weights::OptEMultifunc::get_energy_map_from_dofs(), protocols::optimize_weights::OptEMultifunc::get_reference_energies_from_dofs(), include_terms_, inner_loop_counter_, minimizer_dofs_after_minimization_, minimizer_dofs_before_minimization_, minimizer_dofs_mixed_, MPI_rank_, protocols::optimize_weights::n_optE_data_types, core::scoring::n_score_types, core::scoring::name_from_score_type(), core::chemical::num_canonical_aas, optE_data_, protocols::optimize_weights::OptEPositionDataFactory::optE_type_name(), outer_loop_counter_, read_reference_energies_from_file(), core::optimization::ParticleSwarmMinimizer::run(), core::optimization::Minimizer::run(), send_rotamer_energies_to_master_cpu(), protocols::loops::start, test_weight_sensitivity(), protocols::optimize_weights::TR(), protocols::optimize_weights::TR_VERBOSE(), using_unfolded_energy_term_, protocols::optimize_weights::OptEMultifunc::wait_for_remote_vars(), and wrapped_opt_min_.
Referenced by go().
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Multiply out the unweighted unfolded energies with the current free and fixed term weights.
IterativeOptEDriver::output_weighted_unfolded_energies
Dots the unweighted, unfolded energies with the current free and fixed term weights and prints out the weighted unfolded energies to stdout.
Definition at line 2860 of file IterativeOptEDriver.cc.
References fixed_parameters_, fixed_score_list_, free_weights_inner_loop_, core::scoring::ScoringManager::get_instance(), core::scoring::ScoringManager::get_UnfoldedStatePotential(), core::scoring::n_score_types, core::chemical::name_from_aa(), core::scoring::name_from_score_type(), core::chemical::num_canonical_aas, core::scoring::UnfoldedStatePotential::raw_unfolded_state_energymap(), protocols::optimize_weights::TR(), protocols::optimize_weights::TR_VERBOSE(), core::scoring::unfolded, core::scoring::UNFOLDED_SCORE12, and using_unfolded_energy_term_.
Referenced by write_new_scorefile().
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IterativeOptEDriver::print_energies()
Definition at line 5483 of file IterativeOptEDriver.cc.
References core::pose::Pose::energies(), core::scoring::fa_atr, core::scoring::fa_dun, core::scoring::fa_intra_rep, core::scoring::fa_pair, core::scoring::fa_rep, core::scoring::fa_sol, core::scoring::hbond_bb_sc, core::scoring::hbond_lr_bb, core::scoring::hbond_sc, core::scoring::hbond_sr_bb, core::scoring::n_score_types, core::scoring::omega, core::scoring::p_aa_pp, core::scoring::pro_close, core::scoring::rama, core::scoring::ref, core::scoring::surface, core::scoring::Energies::total_energies(), core::scoring::unfolded, and core::scoring::rna::X.
Referenced by measure_sequence_recovery().
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Definition at line 2373 of file IterativeOptEDriver.cc.
References core::chemical::num_canonical_aas.
Referenced by optimize_weights().
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Reads in an XML formatted task operation and puts builds a task factory from it.
IterativeOptEDriver::read_tagfile_to_taskfactory()
Definition at line 298 of file IterativeOptEDriver.cc.
References core::pack::task::operation::TaskOperationFactory::get_instance(), and core::pack::task::operation::TaskOperationFactory::newTaskOperations().
Referenced by copy_native_packertask_logic(), and IterativeOptEDriver().
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Definition at line 5340 of file IterativeOptEDriver.cc.
References protocols::simple_moves::PackRotamersMover::apply(), protocols::simple_moves::MinMover::min_type(), core::pack::task::TaskFactory::push_back(), and protocols::simple_moves::PackRotamersMover::task_factory().
Referenced by collect_decoy_discrimination_data().
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IterativeOptEDriver::repack_assigned_pdbs()
Definition at line 3321 of file IterativeOptEDriver.cc.
References configure_new_scorefunction(), count_rotamers_recovered_, fixed_parameters_, free_weights_inner_loop_, measure_rotamer_recovery(), core::scoring::n_score_types, native_pdbs_, next_iteration_pdbs_, core::scoring::ref, reference_energies_inner_loop_, and total_rotamer_positions_.
Referenced by test_sequence_recovery().
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True/False: a particular residue be skipped for inclusion into the native-rotamer recovery test because it contains an atom with a high B-factor.
IterativeOptEDriver::residue_has_bad_bfactor
pose must have been read from a pdb.
Definition at line 4046 of file IterativeOptEDriver.cc.
References core::pose::Pose::pdb_info().
Referenced by get_nat_rot_opte_data().
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True/False: a particular residue be skipped for inclusion into the native-rotamer recovery test because its dunbrack energy is really high.
IterativeOptEDriver::residue_has_unacceptably_bad_dunbrack_energy
Precondition: pose must have been scored
Definition at line 4015 of file IterativeOptEDriver.cc.
References core::chemical::ResidueType::aa(), core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_cys, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_gly, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_trp, core::chemical::aa_tyr, core::chemical::aa_val, core::pose::Pose::energies(), core::scoring::fa_dun, core::scoring::Energies::residue_total_energies(), and core::pose::Pose::residue_type().
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Runs design on the pdbs assigned to this node/cpu.
IterativeOptEDriver::run_design_on_assigned_pdbs()
Definition at line 3248 of file IterativeOptEDriver.cc.
References configure_new_scorefunction(), count_recovered_, fixed_parameters_, free_weights_inner_loop_, measure_sequence_recovery(), MPI_rank_, core::scoring::n_score_types, native_pdbs_, next_iteration_pdbs_, core::scoring::ref, reference_energies_inner_loop_, total_positions_, protocols::optimize_weights::TR_VERBOSE(), core::scoring::unfolded, and zero_aa_counts().
Referenced by test_sequence_recovery().
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Ligand stuff.
IterativeOptEDriver::score_ligand_interface()
Definition at line 1801 of file IterativeOptEDriver.cc.
References protocols::rigid::RigidBodyTransMover::apply(), core::pose::Pose::energies(), core::scoring::n_score_types, core::pose::Pose::num_jump(), protocols::rigid::RigidBodyTransMover::step_size(), and core::scoring::Energies::total_energies().
Referenced by collect_ligand_discrimination_data().
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Definition at line 2402 of file IterativeOptEDriver.cc.
References after_minimization_reference_energies_, before_minimization_reference_energies_, collect_rotamer_energies_from_slave_cpus(), component_weights_, fixed_parameters_, fixed_score_list_, free_count_, free_parameters_, free_score_list_, core::scoring::ScoreTypeManager::is_score_type(), MPI_rank_, protocols::optimize_weights::n_optE_data_types, core::chemical::num_canonical_aas, optE_data_, protocols::optimize_weights::OptEPositionDataFactory::optE_type_name(), core::scoring::ScoreTypeManager::score_type_from_name(), send_rotamer_energies_to_master_cpu(), protocols::optimize_weights::TR(), and protocols::optimize_weights::TR_VERBOSE().
Referenced by collect_rotamer_energies().
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Used by all slave nodes; sends the rotamer energies (according to the protocol we've set up here) to the master node.
IterativeOptEDriver::send_rotamer_energies_to_master_cpu()
Definition at line 1138 of file IterativeOptEDriver.cc.
References fixed_parameters_, free_parameters_, core::scoring::n_score_types, and optE_data_.
Referenced by collect_rotamer_energies(), optimize_weights(), and score_position_data().
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IterativeOptEDriver::send_rotamer_recovery_data_to_master_cpu()
Definition at line 3386 of file IterativeOptEDriver.cc.
References count_rotamers_recovered_, and total_rotamer_positions_.
Referenced by test_sequence_recovery().
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IterativeOptEDriver::send_recovery_data_to_master_cpu()
Definition at line 3364 of file IterativeOptEDriver.cc.
References aa_exp_, aa_obs_, count_recovered_, core::chemical::num_canonical_aas, and total_positions_.
Referenced by test_sequence_recovery().
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IterativeOptEDriver::set_aa_periodicity
Definition at line 3967 of file IterativeOptEDriver.cc.
References core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_cys, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_gly, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_trp, core::chemical::aa_tyr, and core::chemical::aa_val.
Referenced by get_nat_rot_opte_data().
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include_terms_ is an EnergyMap, as well. I think this function sets up the free and fixed score lists which are just a vector1 of ScoreType objects. include_, fixed_ and free_count_ are just (Size) member variables.
IterativeOptEDriver::setup_derived_free_and_fixed_data()
Definition at line 898 of file IterativeOptEDriver.cc.
References fixed_count_, fixed_parameters_, fixed_score_list_, free_count_, free_parameters_, free_score_list_, include_count_, include_terms_, and core::scoring::n_score_types.
Referenced by intialize_free_and_fixed_energy_terms().
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IterativeOptEDriver::setup_pdbnames_next_round
This method takes the filenames from the current round and creates new filenames based on what iteration of the outer_loop_counter we're on. So, each iteration we want to use the newest pdbs. This method ensures the filename get updated.
Definition at line 5318 of file IterativeOptEDriver.cc.
References MPI_rank_.
Referenced by collect_rotamer_energies(), and divide_up_pdbs().
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IterativeOptEDriver::single_structure_data_for_pose()
Definition at line 1466 of file IterativeOptEDriver.cc.
References core::scoring::CA_rmsd(), core::pose::Pose::energies(), fixed_score_list_, free_score_list_, and core::scoring::Energies::total_energies().
Referenced by collect_decoy_discrimination_data().
| void protocols::optimize_weights::IterativeOptEDriver::task_factory | ( | core::pack::task::TaskFactoryCOP | tf) |
take care when using a custom TaskFactory: TaskOperations must not 'accumulate state' as they will be reused repeatedly
Definition at line 286 of file IterativeOptEDriver.cc.
References task_factory_.
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Calls run_design on all pdbs and collects the results from slave cpus if MPI is in use.
IterativeOptEDriver::test_sequence_recovery()
Definition at line 3087 of file IterativeOptEDriver.cc.
References collect_rotamer_recovery_data_from_slave_cpus(), collect_sequence_recovery_data_from_slave_cpus(), exit_gracefully(), MPI_rank_, repack_assigned_pdbs(), run_design_on_assigned_pdbs(), send_rotamer_recovery_data_to_master_cpu(), and send_sequence_recovery_data_to_master_cpu().
Referenced by collect_rotamer_energies(), and go().
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Definition at line 2343 of file IterativeOptEDriver.cc.
References free_score_list_, and outer_loop_counter_.
Referenced by optimize_weights().
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send new score file via MPI instead of writing to disk.
IterativeOptEDriver::write_new_scorefile()
Definition at line 2532 of file IterativeOptEDriver.cc.
References aa_freq_exp_, aa_freq_obs_, after_minimization_reference_energies_, before_minimization_reference_energies_, core::scoring::fa_atr, fixed_parameters_, free_count_, free_weights_after_minimization_, free_weights_and_refEs_from_vars(), free_weights_before_minimization_, free_weights_inner_loop_, get_scorefile_name(), inner_loop_counter_, minimizer_dofs_after_minimization_, minimizer_dofs_before_minimization_, minimizer_dofs_mixed_, mixing_factor_, MPI_nprocs_, MPI_rank_, core::scoring::n_score_types, core::scoring::name_from_score_type(), core::chemical::num_canonical_aas, core::chemical::oneletter_code_from_aa(), optE_data_, opte_weight_mixing_factor(), outer_loop_counter_, output_weighted_unfolded_energies(), reference_energies_inner_loop_, protocols::optimize_weights::TR(), protocols::optimize_weights::TR_VERBOSE(), and wrapped_opt_min_.
Referenced by collect_rotamer_energies(), and go().
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Definition at line 5293 of file IterativeOptEDriver.cc.
References core::scoring::n_score_types, core::scoring::name_from_score_type(), and protocols::optimize_weights::TR().
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Set the counts for the amino acid frequencies (observed and expected) to zero.
IterativeOptEDriver::zero_aa_counts()
Definition at line 4813 of file IterativeOptEDriver.cc.
References aa_exp_, aa_freq_exp_, aa_freq_obs_, and aa_obs_.
Referenced by run_design_on_assigned_pdbs().
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the counts for each amino acid from the previous round of design (observed)
Definition at line 422 of file IterativeOptEDriver.hh.
Referenced by collect_sequence_recovery_data_from_slave_cpu(), collect_sequence_recovery_data_from_slave_cpus(), measure_sequence_recovery(), send_sequence_recovery_data_to_master_cpu(), and zero_aa_counts().
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the frequency for each amino acid from the previous round of design
Definition at line 424 of file IterativeOptEDriver.hh.
Referenced by collect_sequence_recovery_data_from_slave_cpus(), decide_if_sequence_recovery_improved(), write_new_scorefile(), and zero_aa_counts().
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the counts for each amino acid in the input data set (expected)
Definition at line 423 of file IterativeOptEDriver.hh.
Referenced by collect_sequence_recovery_data_from_slave_cpus(), decide_if_sequence_recovery_improved(), write_new_scorefile(), and zero_aa_counts().
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Definition at line 421 of file IterativeOptEDriver.hh.
Referenced by collect_sequence_recovery_data_from_slave_cpu(), collect_sequence_recovery_data_from_slave_cpus(), measure_sequence_recovery(), send_sequence_recovery_data_to_master_cpu(), and zero_aa_counts().
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Definition at line 432 of file IterativeOptEDriver.hh.
Referenced by IterativeOptEDriver(), optimize_weights(), score_position_data(), and write_new_scorefile().
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store the PSSM data so it's only read once.
Definition at line 404 of file IterativeOptEDriver.hh.
Referenced by load_pssm_data().
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Hold the result of minimization – interpolate between the before and after weight sets during iterative sequence recovery.
Definition at line 431 of file IterativeOptEDriver.hh.
Referenced by decide_if_sequence_recovery_improved(), intialize_free_and_fixed_energy_terms(), IterativeOptEDriver(), optimize_weights(), score_position_data(), and write_new_scorefile().
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Definition at line 401 of file IterativeOptEDriver.hh.
Referenced by IterativeOptEDriver(), optimize_weights(), and score_position_data().
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Definition at line 341 of file IterativeOptEDriver.hh.
Referenced by compute_rotamer_energies_for_assigned_pdbs(), and measure_sequence_recovery().
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Definition at line 420 of file IterativeOptEDriver.hh.
Referenced by collect_sequence_recovery_data_from_slave_cpu(), collect_sequence_recovery_data_from_slave_cpus(), run_design_on_assigned_pdbs(), and send_sequence_recovery_data_to_master_cpu().
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Definition at line 427 of file IterativeOptEDriver.hh.
Referenced by collect_rotamer_recovery_data_from_slave_cpu(), collect_rotamer_recovery_data_from_slave_cpus(), repack_assigned_pdbs(), and send_rotamer_recovery_data_to_master_cpu().
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A list of lists for use in optimizing ddG binding predictions.
Definition at line 371 of file IterativeOptEDriver.hh.
Referenced by collect_ddG_of_binding_data(), and divide_up_pdbs().
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preserve the ddG bind mutation data between iterations to minimize I/O
Definition at line 388 of file IterativeOptEDriver.hh.
Referenced by collect_ddG_of_binding_data().
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A list of file-list pairs: first = list of relaxed mutant pdbs; second = list of native pdbs
Definition at line 367 of file IterativeOptEDriver.hh.
Referenced by collect_ddG_of_mutation_data(), and divide_up_pdbs().
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preserve the ddMutation data between iterations to minimize I/O
Definition at line 386 of file IterativeOptEDriver.hh.
Referenced by collect_ddG_of_mutation_data().
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Definition at line 368 of file IterativeOptEDriver.hh.
Referenced by collect_ddG_of_mutation_data(), and divide_up_pdbs().
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Definition at line 372 of file IterativeOptEDriver.hh.
Referenced by collect_ddG_of_binding_data(), and divide_up_pdbs().
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Definition at line 355 of file IterativeOptEDriver.hh.
Referenced by collect_decoy_discrimination_data(), and divide_up_pdbs().
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Definition at line 357 of file IterativeOptEDriver.hh.
Referenced by collect_decoy_discrimination_data().
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A list of file-list pairs. first = list of relaxed-native pdbs; second = list of decoy pdbs.
Definition at line 354 of file IterativeOptEDriver.hh.
Referenced by collect_decoy_discrimination_data(), and divide_up_pdbs().
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Definition at line 356 of file IterativeOptEDriver.hh.
Referenced by collect_decoy_discrimination_data().
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Definition at line 358 of file IterativeOptEDriver.hh.
Referenced by collect_decoy_discrimination_data().
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preserve the decoy scores by component between iterations to minimize I/O.
Definition at line 380 of file IterativeOptEDriver.hh.
Referenced by collect_decoy_discrimination_data().
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Definition at line 377 of file IterativeOptEDriver.hh.
Referenced by collect_dG_of_binding_data(), and divide_up_pdbs().
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preserve the dGbinding data between iterations to minimize I/O
Definition at line 384 of file IterativeOptEDriver.hh.
Referenced by collect_dG_of_binding_data().
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A list of PDB file pairs: first = "bound" structure; second = "unbound" structure with partners well separated
Definition at line 376 of file IterativeOptEDriver.hh.
Referenced by collect_dG_of_binding_data(), and divide_up_pdbs().
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Definition at line 397 of file IterativeOptEDriver.hh.
Referenced by setup_derived_free_and_fixed_data().
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Definition at line 392 of file IterativeOptEDriver.hh.
Referenced by collect_rotamer_energies_from_slave_cpu(), create_weighted_scorefunction(), intialize_free_and_fixed_energy_terms(), optimize_weights(), output_weighted_unfolded_energies(), repack_assigned_pdbs(), run_design_on_assigned_pdbs(), score_position_data(), send_rotamer_energies_to_master_cpu(), setup_derived_free_and_fixed_data(), and write_new_scorefile().
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Definition at line 400 of file IterativeOptEDriver.hh.
Referenced by collect_ddG_of_binding_data(), collect_ddG_of_mutation_data(), collect_decoy_discrimination_data(), collect_ligand_discrimination_data(), compute_rotamer_energies_for_assigned_pdbs(), compute_rotamers_around_ligands(), IterativeOptEDriver(), make_simple_ssd_from_pdb(), optimize_weights(), output_weighted_unfolded_energies(), score_position_data(), setup_derived_free_and_fixed_data(), and single_structure_data_for_pose().
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Definition at line 398 of file IterativeOptEDriver.hh.
Referenced by free_weights_and_refEs_from_vars(), optimize_weights(), score_position_data(), setup_derived_free_and_fixed_data(), and write_new_scorefile().
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These two get set by the user.
Definition at line 391 of file IterativeOptEDriver.hh.
Referenced by collect_rotamer_energies(), collect_rotamer_energies_from_slave_cpu(), decide_if_sequence_recovery_improved(), intialize_free_and_fixed_energy_terms(), optimize_weights(), score_position_data(), send_rotamer_energies_to_master_cpu(), and setup_derived_free_and_fixed_data().
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Definition at line 399 of file IterativeOptEDriver.hh.
Referenced by collect_ddG_of_binding_data(), collect_ddG_of_mutation_data(), collect_decoy_discrimination_data(), collect_ligand_discrimination_data(), compute_rotamer_energies_for_assigned_pdbs(), compute_rotamers_around_ligands(), free_terms_energy_map_from_dofs(), IterativeOptEDriver(), make_simple_ssd_from_pdb(), optimize_weights(), score_position_data(), setup_derived_free_and_fixed_data(), single_structure_data_for_pose(), and test_weight_sensitivity().
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Definition at line 446 of file IterativeOptEDriver.hh.
Referenced by collect_rotamer_energies(), optimize_weights(), and write_new_scorefile().
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Definition at line 445 of file IterativeOptEDriver.hh.
Referenced by decide_if_sequence_recovery_improved(), optimize_weights(), and write_new_scorefile().
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Definition at line 447 of file IterativeOptEDriver.hh.
Referenced by create_weighted_scorefunction(), decide_if_sequence_recovery_improved(), output_weighted_unfolded_energies(), repack_assigned_pdbs(), run_design_on_assigned_pdbs(), and write_new_scorefile().
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Definition at line 396 of file IterativeOptEDriver.hh.
Referenced by setup_derived_free_and_fixed_data().
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These get updated from the above two.
Definition at line 395 of file IterativeOptEDriver.hh.
Referenced by create_unweighted_scorefunction(), optimize_weights(), and setup_derived_free_and_fixed_data().
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Definition at line 416 of file IterativeOptEDriver.hh.
Referenced by decide_if_sequence_recovery_improved(), go(), optimize_weights(), and write_new_scorefile().
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Definition at line 454 of file IterativeOptEDriver.hh.
Referenced by collect_rotamer_recovery_data_from_slave_cpus().
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Definition at line 453 of file IterativeOptEDriver.hh.
Referenced by collect_sequence_recovery_data_from_slave_cpus(), and decide_if_sequence_recovery_improved().
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Definition at line 363 of file IterativeOptEDriver.hh.
Referenced by collect_ligand_discrimination_data(), and divide_up_pdbs().
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preserve the decoy scores by component between iterations to minimize I/O.
Definition at line 382 of file IterativeOptEDriver.hh.
Referenced by collect_ligand_discrimination_data().
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A list of file-list pairs. first = list of relaxed-native pdbs; second = list of decoy pdbs.
Definition at line 362 of file IterativeOptEDriver.hh.
Referenced by collect_ligand_discrimination_data(), and divide_up_pdbs().
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Definition at line 349 of file IterativeOptEDriver.hh.
Referenced by compute_rotamers_around_ligands().
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For rotamer recovery around ligands.
Definition at line 348 of file IterativeOptEDriver.hh.
Referenced by compute_rotamers_around_ligands(), and divide_up_pdbs().
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Definition at line 442 of file IterativeOptEDriver.hh.
Referenced by optimize_weights(), and write_new_scorefile().
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Definition at line 441 of file IterativeOptEDriver.hh.
Referenced by optimize_weights(), and write_new_scorefile().
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Definition at line 443 of file IterativeOptEDriver.hh.
Referenced by optimize_weights(), and write_new_scorefile().
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Definition at line 449 of file IterativeOptEDriver.hh.
Referenced by decide_if_sequence_recovery_improved(), and write_new_scorefile().
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Definition at line 413 of file IterativeOptEDriver.hh.
Referenced by collect_rotamer_energies_from_slave_cpus(), collect_rotamer_recovery_data_from_slave_cpus(), collect_sequence_recovery_data_from_slave_cpus(), decide_if_sequence_recovery_improved(), divide_up_pdbs(), IterativeOptEDriver(), and write_new_scorefile().
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Definition at line 412 of file IterativeOptEDriver.hh.
Referenced by collect_ddG_of_binding_data(), collect_ddG_of_mutation_data(), collect_decoy_discrimination_data(), collect_ligand_discrimination_data(), collect_rotamer_energies(), compute_rotamer_energies_for_assigned_pdbs(), decide_if_sequence_recovery_improved(), divide_up_pdbs(), go(), initialize_free_and_fixed(), intialize_free_and_fixed_energy_terms(), IterativeOptEDriver(), measure_sequence_recovery(), optimize_weights(), run_design_on_assigned_pdbs(), score_position_data(), setup_pdbnames_next_round(), test_sequence_recovery(), and write_new_scorefile().
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Definition at line 339 of file IterativeOptEDriver.hh.
Referenced by collect_rotamer_energies(), compute_rotamer_energies_for_assigned_pdbs(), divide_up_pdbs(), repack_assigned_pdbs(), and run_design_on_assigned_pdbs().
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Definition at line 340 of file IterativeOptEDriver.hh.
Referenced by compute_rotamer_energies_for_assigned_pdbs(), measure_rotamer_recovery(), and measure_sequence_recovery().
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Definition at line 343 of file IterativeOptEDriver.hh.
Referenced by collect_rotamer_energies(), divide_up_pdbs(), repack_assigned_pdbs(), and run_design_on_assigned_pdbs().
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Definition at line 417 of file IterativeOptEDriver.hh.
Referenced by collect_ddG_of_binding_data(), collect_ddG_of_mutation_data(), collect_decoy_discrimination_data(), collect_dG_of_binding_data(), collect_ligand_discrimination_data(), collect_rotamer_energies_from_slave_cpu(), collect_rotamer_energies_from_slave_cpus(), compute_rotamer_energies_for_assigned_pdbs(), compute_rotamers_around_ligands(), optimize_weights(), score_position_data(), send_rotamer_energies_to_master_cpu(), and write_new_scorefile().
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Definition at line 415 of file IterativeOptEDriver.hh.
Referenced by collect_decoy_discrimination_data(), collect_rotamer_energies(), compute_rotamer_energies_for_assigned_pdbs(), compute_rotamers_around_ligands(), decide_if_sequence_recovery_improved(), get_scorefile_name(), go(), load_pssm_data(), measure_sequence_recovery(), optimize_weights(), test_weight_sensitivity(), and write_new_scorefile().
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Definition at line 451 of file IterativeOptEDriver.hh.
Referenced by decide_if_sequence_recovery_improved().
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Definition at line 452 of file IterativeOptEDriver.hh.
Referenced by decide_if_sequence_recovery_improved().
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Definition at line 342 of file IterativeOptEDriver.hh.
Referenced by collect_rotamer_energies().
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Definition at line 405 of file IterativeOptEDriver.hh.
Referenced by get_nat_aa_opte_data(), and load_pssm_data().
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Definition at line 433 of file IterativeOptEDriver.hh.
Referenced by create_weighted_scorefunction(), decide_if_sequence_recovery_improved(), IterativeOptEDriver(), repack_assigned_pdbs(), run_design_on_assigned_pdbs(), and write_new_scorefile().
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Definition at line 345 of file IterativeOptEDriver.hh.
Referenced by compute_rotamer_energies_for_assigned_pdbs(), measure_rotamer_recovery(), and measure_sequence_recovery().
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Definition at line 338 of file IterativeOptEDriver.hh.
Referenced by get_nat_aa_opte_data(), get_nat_rot_opte_data(), IterativeOptEDriver(), measure_rotamer_recovery(), measure_sequence_recovery(), and task_factory().
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Definition at line 419 of file IterativeOptEDriver.hh.
Referenced by collect_sequence_recovery_data_from_slave_cpu(), collect_sequence_recovery_data_from_slave_cpus(), run_design_on_assigned_pdbs(), and send_sequence_recovery_data_to_master_cpu().
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the frequency for each amino acid in the input data set
Definition at line 426 of file IterativeOptEDriver.hh.
Referenced by collect_rotamer_recovery_data_from_slave_cpu(), collect_rotamer_recovery_data_from_slave_cpus(), repack_assigned_pdbs(), and send_rotamer_recovery_data_to_master_cpu().
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Definition at line 456 of file IterativeOptEDriver.hh.
Referenced by collect_ddG_of_mutation_data(), configure_new_scorefunction(), get_nat_aa_opte_data(), IterativeOptEDriver(), optimize_weights(), and output_weighted_unfolded_energies().
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When using the optEMultifunc wrapper, hold on to the dofs that the minimizer has access to and interpolate in the space of those dofs; then convert the interpolated dofs into weights. Interpolating the weights directly might result in weights that violate the mixing rules for the wrapper.
Definition at line 440 of file IterativeOptEDriver.hh.
Referenced by optimize_weights(), and write_new_scorefile().
1.8.4