#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_fa_elec. This excludes protein_protein_fa_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...

Private Attributes
core::pack::task::TaskFactoryOP	task_factory_

utility::vector1< std::string >	native_pdbs_

utility::vector1 < core::pose::Pose >	native_poses_

utility::vector1 < core::pose::Pose >	context_poses_

utility::vector1< std::string >	pdbs_this_round_

utility::vector1< std::string >	next_iteration_pdbs_

utility::vector1 < core::pose::Pose >	rotamer_recovery_context_poses_

utility::vector1< std::string >	ligand_repack_pdbs_
	For rotamer recovery around ligands. More...

utility::vector1 < core::pose::Pose >	ligand_repack_native_poses_

utility::vector1< std::pair < std::string, std::string > >	decdisc_native_decoy_pairs_

utility::vector1< std::string >	decdisc_crystal_natives_

utility::vector1 < utility::vector1 < core::pose::Pose > >	decdisc_native_poses_

utility::vector1 < utility::vector1 < core::pose::Pose > >	decdisc_decoy_poses_

utility::vector1 < core::pose::Pose >	decdisc_xtal_natives_

utility::vector1< std::pair < std::string, std::string > >	ligand_native_decoy_pairs_

utility::vector1< std::string >	ligand_crystal_natives_

utility::vector1< std::pair < std::string, std::string > >	ddg_mut_wt_pairs_

utility::vector1< Real >	ddGs_

utility::vector1 < utility::vector1 < std::string > >	ddG_bind_files_
	A list of lists for use in optimizing ddG binding predictions. More...

utility::vector1< Real >	ddGs_binding_

utility::vector1< std::pair < std::string, std::string > >	dG_bound_unbound_pairs_

utility::vector1< Real >	dG_binding_

OptEDataOP	decoy_discrim_data_
	preserve the decoy scores by component between iterations to minimize I/O. More...

OptEDataOP	ligand_discrim_data_
	preserve the decoy scores by component between iterations to minimize I/O. More...

OptEDataOP	dG_binding_data_
	preserve the dGbinding data between iterations to minimize I/O More...

OptEDataOP	ddG_mutation_data_
	preserve the ddMutation data between iterations to minimize I/O More...

OptEDataOP	ddG_bind_optE_data_
	preserve the ddG bind mutation data between iterations to minimize I/O More...

EnergyMap	free_parameters_
	These two get set by the user. More...

EnergyMap	fixed_parameters_

EnergyMap	include_terms_
	These get updated from the above two. More...

Size	include_count_

Size	fixed_count_

Size	free_count_

ScoreTypes	free_score_list_

ScoreTypes	fixed_score_list_

utility::vector1< Real >	component_weights_

utility::vector1 < utility::vector1< std::pair < core::chemical::AA, utility::vector1< Real > > > >	all_pssm_data_
	store the PSSM data so it's only read once. More...

utility::vector1< std::pair < core::chemical::AA, utility::vector1< Real > > >	pssm_data_

Size	MPI_rank_

Size	MPI_nprocs_

Size	outer_loop_counter_

Size	inner_loop_counter_

OptEDataOP	optE_data_

Size	total_positions_

Size	count_recovered_

utility::vector1< Size >	aa_obs_

utility::vector1< Size >	aa_exp_
	the counts for each amino acid from the previous round of design (observed) More...

utility::vector1< Real >	aa_freq_obs_
	the counts for each amino acid in the input data set (expected) More...

utility::vector1< Real >	aa_freq_exp_
	the frequency for each amino acid from the previous round of design More...

Size	total_rotamer_positions_
	the frequency for each amino acid in the input data set More...

Size	count_rotamers_recovered_

utility::vector1< Real >	before_minimization_reference_energies_

utility::vector1< Real >	after_minimization_reference_energies_

utility::vector1< Real >	reference_energies_inner_loop_

WrapperOptEMultifuncOP	wrapped_opt_min_

utility::vector1< Real >	minimizer_dofs_before_minimization_

utility::vector1< Real >	minimizer_dofs_after_minimization_

utility::vector1< Real >	minimizer_dofs_mixed_

EnergyMap	free_weights_before_minimization_

EnergyMap	free_weights_after_minimization_

EnergyMap	free_weights_inner_loop_

Real	mixing_factor_

Real	outer_loop_last_sequence_recovery_rate_

Real	outer_loop_seq_profile_cross_entropy_

Real	inner_loop_sequence_recovery_rate_

Real	inner_loop_rotamer_recovery_rate_

bool	using_unfolded_energy_term_

Member Typedef Documentation

typedef core::scoring::EnergyMap protocols::optimize_weights::IterativeOptEDriver::EnergyMap

typedef core::Real protocols::optimize_weights::IterativeOptEDriver::Real

typedef core::scoring::ScoreTypes protocols::optimize_weights::IterativeOptEDriver::ScoreTypes

typedef core::Size protocols::optimize_weights::IterativeOptEDriver::Size

Constructor & Destructor Documentation

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.

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 ( )

default

Member Function Documentation

AddStatus protocols::optimize_weights::IterativeOptEDriver::add_structure_based_on_rms	(	SingleStructureDataOP	ssd,
		PNatStructureOptEDataOP	structure_data,
		bool	intended_native
	)		const

private

Returns 1 if added as intended, 0 if not added at all, and -1 if added in the opposite of its intention.

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().

void protocols::optimize_weights::IterativeOptEDriver::barrier ( )

private

Referenced by exit_gracefully(), go(), and optimize_weights().

void protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_binding_data ( )

private

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.

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::PDB_file, core::import_pose::pose_from_file(), 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().

void protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data ( )

private

ddG optimization optE data collection.

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_, MPI_rank_, optE_data_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), core::scoring::UnfoldedStatePotential::pose_raw_unfolded_state_energymap(), core::io::silent::SilentFileData::read_file(), 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().

void protocols::optimize_weights::IterativeOptEDriver::collect_decoy_discrimination_data ( )

private

Collect optE data for decoy discrimination. Similar to the get_nat_aa_opte_data method.

References add_structure_based_on_rms(), protocols::optimize_weights::ADDED_STRUCTURE_AS_INTENDED, protocols::optimize_weights::ADDED_STRUCTURE_OPPOSITE_AS_INTENDED, 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_, core::scoring::PRE_TALARIS_2013_STANDARD_WTS, 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::pose::Pose::size(), core::id::to_string(), and protocols::optimize_weights::TR_VERBOSE().

Referenced by collect_rotamer_energies().

void protocols::optimize_weights::IterativeOptEDriver::collect_dG_of_binding_data ( )

private

dG optimization optE data collection.

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().

void protocols::optimize_weights::IterativeOptEDriver::collect_ligand_discrimination_data ( )

private

Ligand stuff.

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::PDB_file, core::import_pose::pose_from_file(), score_ligand_interface(), core::pose::Pose::size(), and protocols::optimize_weights::TR().

Referenced by collect_rotamer_energies().

void protocols::optimize_weights::IterativeOptEDriver::collect_rotamer_energies ( )

private

void protocols::optimize_weights::IterativeOptEDriver::collect_rotamer_energies_from_slave_cpu ( Size const which_cpu )

private

For a calling master node, collects the rotamer energies that were calculated on a slave CPU.

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().

void protocols::optimize_weights::IterativeOptEDriver::collect_rotamer_energies_from_slave_cpus ( )

private

Helper method for collecting energies. Calls collect_rotamer_energies_from_slave_cpu for all CPU's being used.

References collect_rotamer_energies_from_slave_cpu(), MPI_nprocs_, optE_data_, protocols::analysis::total, and protocols::optimize_weights::TR().

Referenced by collect_rotamer_energies(), optimize_weights(), and score_position_data().

void protocols::optimize_weights::IterativeOptEDriver::collect_rotamer_recovery_data_from_slave_cpu ( Size const which_cpu )

private

References count_rotamers_recovered_, and total_rotamer_positions_.

Referenced by collect_rotamer_recovery_data_from_slave_cpus().

void protocols::optimize_weights::IterativeOptEDriver::collect_rotamer_recovery_data_from_slave_cpus ( )

private

Helper method for master node. Calls collect_rotamer_recovery_data_from_slave_cpu on all slave CPUs.

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().

void protocols::optimize_weights::IterativeOptEDriver::collect_sequence_recovery_data_from_slave_cpu ( Size const which_cpu )

private

References aa_exp_, aa_obs_, count_recovered_, core::chemical::num_canonical_aas, and total_positions_.

Referenced by collect_sequence_recovery_data_from_slave_cpus().

void protocols::optimize_weights::IterativeOptEDriver::collect_sequence_recovery_data_from_slave_cpus ( )

private

Helper method for master node. Calls collect_recovery_data_from_slave_cpu on all slave CPUs.

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().

void protocols::optimize_weights::IterativeOptEDriver::compute_rotamer_energies_for_assigned_pdbs ( )

private

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.

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

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::ResidueTypeBase::is_protein(), load_pssm_data(), MPI_rank_, native_pdbs_, native_poses_, node_name(), optE_data_, outer_loop_counter_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), core::pose::Pose::residue_type(), rotamer_recovery_context_poses_, core::pose::Pose::size(), protocols::optimize_weights::TR(), and protocols::optimize_weights::TR_VERBOSE().

Referenced by collect_rotamer_energies().

void protocols::optimize_weights::IterativeOptEDriver::compute_rotamers_around_ligands ( )

private

ScoreFunctionOP protocols::optimize_weights::IterativeOptEDriver::configure_new_scorefunction ( ) const

private

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_fa_elec. This excludes protein_protein_fa_elec in the the scorefunction energy method options.

References core::scoring::methods::EnergyMethodOptions::atom_vdw_atom_type_set_name(), core::scoring::methods::EnergyMethodOptions::etable_type(), core::scoring::methods::EnergyMethodOptions::exclude_intra_res_protein(), core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_fa_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_DNA(), and using_unfolded_energy_term_.

Referenced by create_unweighted_scorefunction(), create_weighted_scorefunction(), repack_assigned_pdbs(), and run_design_on_assigned_pdbs().

bool protocols::optimize_weights::IterativeOptEDriver::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
	)

private

This function is not used.

References core::scoring::n_score_types, core::scoring::name_from_score_type(), and protocols::optimize_weights::TR().

core::pack::task::PackerTaskOP protocols::optimize_weights::IterativeOptEDriver::copy_native_packertask_logic	(	core::pose::Pose	native_pose,
		core::pose::Pose	context_pose,
		core::pack::task::TaskFactoryOP	native_taskfactory
	)

private

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.

References read_tagfile_to_taskfactory().

Referenced by get_nat_aa_opte_data(), get_nat_rot_opte_data(), measure_rotamer_recovery(), and measure_sequence_recovery().

ScoreFunctionOP protocols::optimize_weights::IterativeOptEDriver::create_unweighted_scorefunction ( ) const

private

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.

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().

core::scoring::ScoreFunctionOP protocols::optimize_weights::IterativeOptEDriver::create_weighted_scorefunction ( ) const

private

Construct a score function: set etable type, set weights, set reference weights.

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().

bool protocols::optimize_weights::IterativeOptEDriver::decide_if_sequence_recovery_improved ( )

private

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.

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().

void protocols::optimize_weights::IterativeOptEDriver::divide_up_pdbs ( )

private

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.

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().

void protocols::optimize_weights::IterativeOptEDriver::exit_gracefully ( )

private

References barrier().

Referenced by collect_rotamer_energies(), and test_sequence_recovery().

core::scoring::EnergyMap protocols::optimize_weights::IterativeOptEDriver::free_terms_energy_map_from_dofs ( core::optimization::Multivec const & dofs ) const

private

Expand free variables and combine with fixed to make an Energy Map.

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.

References free_score_list_.

Referenced by free_weights_and_refEs_from_vars().

void protocols::optimize_weights::IterativeOptEDriver::free_weights_and_refEs_from_vars	(	utility::vector1< Real > const &	vars,
		core::scoring::EnergyMap &	weights,
		utility::vector1< Real > &	reference_energies
	)		const

private

References free_count_, free_terms_energy_map_from_dofs(), core::chemical::num_canonical_aas, and core::scoring::EMapVector::zero().

Referenced by write_new_scorefile().

void protocols::optimize_weights::IterativeOptEDriver::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
	)

private

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.

References protocols::cluster::calibur::aa, 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::pose::Pose::energies(), core::scoring::fa_rep, core::conformation::Residue::is_protein(), core::chemical::ResidueTypeBase::name3(), core::chemical::name_from_aa(), core::chemical::num_canonical_aas, core::pose::Pose::pdb_info(), core::scoring::ScoreFunction::prepare_rotamers_for_packing(), pssm_data_, core::scoring::UnfoldedStatePotential::raw_unfolded_state_energymap(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::scoring::ScoreFunction::setup_for_packing(), core::pose::Pose::size(), task_factory_, core::scoring::Energies::tenA_neighbor_graph(), protocols::optimize_weights::TR(), core::scoring::UNFOLDED_SCORE12, and using_unfolded_energy_term_.

Referenced by compute_rotamer_energies_for_assigned_pdbs().

void protocols::optimize_weights::IterativeOptEDriver::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
	)

private

Similar to get_nat_aa_opte_data. See comments there for more info.

References core::chemical::ResidueTypeBase::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::scoring::fa_rep, core::chemical::ResidueTypeBase::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(), core::pose::Pose::size(), task_factory_, core::id::to_string(), and protocols::optimize_weights::TR().

Referenced by compute_rotamer_energies_for_assigned_pdbs(), and compute_rotamers_around_ligands().

utility::vector1< std::string > protocols::optimize_weights::IterativeOptEDriver::get_native_pdb_names ( )

private

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.

Referenced by divide_up_pdbs().

std::string protocols::optimize_weights::IterativeOptEDriver::get_scorefile_name ( )

private

Remarks: IMPORTANT IMPORTANT IMPORTANT: requires weightdir having been created before launching the program.

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.

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().

void protocols::optimize_weights::IterativeOptEDriver::initialize_free_and_fixed	(	core::scoring::EnergyMap &	free_parameters,
		core::scoring::EnergyMap &	fixed_parameters
	)

private

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.

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(), core::scoring::p_aa_pp, core::scoring::pair, core::scoring::rama, core::scoring::rg, core::scoring::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().

void protocols::optimize_weights::IterativeOptEDriver::intialize_free_and_fixed_energy_terms ( )

private

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.

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().

void protocols::optimize_weights::IterativeOptEDriver::load_pose	(	core::pose::Pose &	pose,
		std::string const &	filename,
		bool	ignore_centroid_input_flag = `false`
	)

private

loads structure into pose - decides between silent or pdb

References core::import_pose::centroid_pose_from_pdb(), protocols::hybridization::path, core::import_pose::PDB_file, core::import_pose::pose_from_file(), core::io::silent::SilentFileData::read_file(), and protocols::optimize_weights::TR_VERBOSE().

Referenced by collect_decoy_discrimination_data().

void protocols::optimize_weights::IterativeOptEDriver::load_pssm_data	(	std::string const &	native_filename,
		Size const	which_protein
	)

private

References protocols::cluster::calibur::aa, core::chemical::aa_from_oneletter_code(), all_pssm_data_, core::chemical::num_canonical_aas, outer_loop_counter_, protocols::optimize_weights::pssm_data, pssm_data_, core::simple_metrics::metrics::sum, and protocols::optimize_weights::TR().

Referenced by compute_rotamer_energies_for_assigned_pdbs().

SingleStructureDataOP protocols::optimize_weights::IterativeOptEDriver::make_simple_ssd_from_pdb	(	std::string const &	pdb_filename,
		core::scoring::ScoreFunctionOP	sfxn,
		bool	pretend_no_fa_rep = `false`
	)		const

private

Helper function to reduce code duplication.

References core::import_pose::centroid_pose_from_pdb(), core::scoring::fa_rep, fixed_score_list_, free_score_list_, core::import_pose::PDB_file, and core::import_pose::pose_from_file().

Referenced by collect_dG_of_binding_data().

Real protocols::optimize_weights::IterativeOptEDriver::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
	)

private

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_, core::pose::Pose::size(), and task_factory_.

Referenced by repack_assigned_pdbs().

Real protocols::optimize_weights::IterativeOptEDriver::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 &	nresidues_designed,
		Size &	nresidues_recovered
	)

private

std::string protocols::optimize_weights::IterativeOptEDriver::node_name ( int rank )

private

Referenced by compute_rotamer_energies_for_assigned_pdbs(), and go().

Size protocols::optimize_weights::IterativeOptEDriver::num_inner_iterations ( ) const

private

Referenced by decide_if_sequence_recovery_improved(), and go().

Size protocols::optimize_weights::IterativeOptEDriver::num_outer_iterations ( ) const

private

Referenced by go().

Real protocols::optimize_weights::IterativeOptEDriver::opte_weight_mixing_factor	(	Size	outer_loop_counter,
		Size	inner_loop_counter
	)

private

Referenced by write_new_scorefile().

void protocols::optimize_weights::IterativeOptEDriver::optimize_weights ( )

private

Optimizes weights using either a standard minimizer or a ParticleSwarmMinimizer (which is significantly better!).

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.)

Referenced by go().

void protocols::optimize_weights::IterativeOptEDriver::output_weighted_unfolded_energies ( )

private

Multiply out the unweighted unfolded energies with the current free and fixed term weights.

Dots the unweighted, unfolded energies with the current free and fixed term weights and prints out the weighted unfolded energies to stdout.

References protocols::cluster::calibur::aa, core::chemical::element::F, fixed_parameters_, fixed_score_list_, free_weights_inner_loop_, 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().

void protocols::optimize_weights::IterativeOptEDriver::print_energies	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	sfxn,
		std::ostream &	os = `std::cout`
	)

private

utility::vector1< Real > protocols::optimize_weights::IterativeOptEDriver::read_reference_energies_from_file ( std::string const & fname ) const

private

References core::chemical::num_canonical_aas.

Referenced by optimize_weights().

void protocols::optimize_weights::IterativeOptEDriver::read_tagfile_to_taskfactory	(	std::string	tagfile_name,
		core::pack::task::TaskFactoryOP	task_factory
	)

private

Reads in an XML formatted task operation and puts builds a task factory from it.

Referenced by copy_native_packertask_logic(), and IterativeOptEDriver().

void protocols::optimize_weights::IterativeOptEDriver::repack_and_minimize_pose	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	sfxn
	)		const

private

References protocols::minimization_packing::PackRotamersMover::apply(), protocols::minimization_packing::MinMover::min_type(), and protocols::minimization_packing::PackRotamersMover::task_factory().

Referenced by collect_decoy_discrimination_data().

void protocols::optimize_weights::IterativeOptEDriver::repack_assigned_pdbs ( )

private

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().

bool protocols::optimize_weights::IterativeOptEDriver::residue_has_bad_bfactor	(	core::pose::Pose const &	pose,
		Size const	resid
	)		const

private

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.

pose must have been read from a pdb.

References core::pose::Pose::pdb_info().

Referenced by get_nat_rot_opte_data().

bool protocols::optimize_weights::IterativeOptEDriver::residue_has_unacceptably_bad_dunbrack_energy	(	core::pose::Pose const &	pose,
		Size const	resid
	)		const

private

True/False: a particular residue be skipped for inclusion into the native-rotamer recovery test because its dunbrack energy is really high.

Precondition: pose must have been scored

void protocols::optimize_weights::IterativeOptEDriver::run_design_on_assigned_pdbs ( )

private

Runs design on the pdbs assigned to this node/cpu.

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().

core::scoring::EnergyMap protocols::optimize_weights::IterativeOptEDriver::score_ligand_interface	(	core::scoring::ScoreFunction const &	scorefxn,
		core::pose::Pose &	pose
	)

private

Ligand stuff.

References protocols::rigid::RigidBodyTransMover::apply(), core::pose::Pose::energies(), core::scoring::n_score_types, core::pose::Pose::num_jump(), protocols::stepwise::modeler::split_pose(), protocols::rigid::RigidBodyTransMover::step_size(), and core::scoring::Energies::total_energies().

Referenced by collect_ligand_discrimination_data().

void protocols::optimize_weights::IterativeOptEDriver::score_position_data ( )

private

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_, 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::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().

void protocols::optimize_weights::IterativeOptEDriver::send_rotamer_energies_to_master_cpu ( )

private

Used by all slave nodes; sends the rotamer energies (according to the protocol we've set up here) to the master node.

References fixed_parameters_, free_parameters_, core::scoring::n_score_types, and optE_data_.

Referenced by collect_rotamer_energies(), optimize_weights(), and score_position_data().

void protocols::optimize_weights::IterativeOptEDriver::send_rotamer_recovery_data_to_master_cpu ( )

private

References count_rotamers_recovered_, and total_rotamer_positions_.

Referenced by test_sequence_recovery().

void protocols::optimize_weights::IterativeOptEDriver::send_sequence_recovery_data_to_master_cpu ( )

private

References aa_exp_, aa_obs_, count_recovered_, core::chemical::num_canonical_aas, and total_positions_.

Referenced by test_sequence_recovery().

void protocols::optimize_weights::IterativeOptEDriver::set_aa_periodicity	(	PNatRotOptEPositionDataOP	pos_data,
		core::chemical::AA	aa
	)		const

private

void protocols::optimize_weights::IterativeOptEDriver::setup_derived_free_and_fixed_data ( )

private

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.

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().

void protocols::optimize_weights::IterativeOptEDriver::setup_pdbnames_next_round	(	Size const	outer_loop_counter,
		utility::vector1< std::string > &	pdbs_next_round,
		utility::vector1< std::string > const &	native_pdb_names
	)

private

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.

Remarks: Requires workdir_{0..MPI_numprocs_ - 1 } directories already exist.

References MPI_rank_, and core::id::to_string().

Referenced by collect_rotamer_energies(), and divide_up_pdbs().

SingleStructureDataOP protocols::optimize_weights::IterativeOptEDriver::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

private

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

References task_factory_.

void protocols::optimize_weights::IterativeOptEDriver::test_sequence_recovery ( )

private

Calls run_design on all pdbs and collects the results from slave cpus if MPI is in use.

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().

void protocols::optimize_weights::IterativeOptEDriver::test_weight_sensitivity	(	OptEMultifunc const &	func,
		core::optimization::Multivec const &	dofs
	)		const

private

References free_score_list_, protocols::mean_field::max(), core::conformation::membrane::out, outer_loop_counter_, core::id::to_string(), and protocols::hybridization::val.

Referenced by optimize_weights().

void protocols::optimize_weights::IterativeOptEDriver::write_new_scorefile ( )

private

send new score file via MPI instead of writing to disk.

Remarks: The reference energy term is automatically added to the end of the scorefile with a weight of 1, so don't put it as a free or fixed param or it will be counted twice. The actual reference energies per AA are varied during the protocol and also written out here.

References aa_freq_exp_, aa_freq_obs_, after_minimization_reference_energies_, before_minimization_reference_energies_, core::chemical::element::F, 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().

void protocols::optimize_weights::IterativeOptEDriver::write_parameters_to_std_out	(	core::scoring::EnergyMap &	free_parameters,
		utility::vector1< Real > const &	reference_energies
	)

private

References core::scoring::n_score_types, core::scoring::name_from_score_type(), and protocols::optimize_weights::TR().

void protocols::optimize_weights::IterativeOptEDriver::zero_aa_counts ( )

private

Set the counts for the amino acid frequencies (observed and expected) to zero.

References aa_exp_, aa_freq_exp_, aa_freq_obs_, and aa_obs_.

Referenced by run_design_on_assigned_pdbs().

Member Data Documentation

utility::vector1< Size > protocols::optimize_weights::IterativeOptEDriver::aa_exp_

private

the counts for each amino acid from the previous round of design (observed)

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().

utility::vector1< Real > protocols::optimize_weights::IterativeOptEDriver::aa_freq_exp_

private

the frequency for each amino acid from the previous round of design

Referenced by collect_sequence_recovery_data_from_slave_cpus(), decide_if_sequence_recovery_improved(), write_new_scorefile(), and zero_aa_counts().

utility::vector1< Real > protocols::optimize_weights::IterativeOptEDriver::aa_freq_obs_

private

the counts for each amino acid in the input data set (expected)

Referenced by collect_sequence_recovery_data_from_slave_cpus(), decide_if_sequence_recovery_improved(), write_new_scorefile(), and zero_aa_counts().

utility::vector1< Size > protocols::optimize_weights::IterativeOptEDriver::aa_obs_

private

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().

utility::vector1< Real > protocols::optimize_weights::IterativeOptEDriver::after_minimization_reference_energies_

private

Referenced by IterativeOptEDriver(), optimize_weights(), score_position_data(), and write_new_scorefile().

utility::vector1< utility::vector1< std::pair< core::chemical::AA, utility::vector1< Real > > > > protocols::optimize_weights::IterativeOptEDriver::all_pssm_data_

private

store the PSSM data so it's only read once.

Referenced by load_pssm_data().

utility::vector1< Real > protocols::optimize_weights::IterativeOptEDriver::before_minimization_reference_energies_

private

Hold the result of minimization – interpolate between the before and after weight sets during iterative sequence recovery.

Referenced by decide_if_sequence_recovery_improved(), intialize_free_and_fixed_energy_terms(), IterativeOptEDriver(), optimize_weights(), score_position_data(), and write_new_scorefile().

utility::vector1< Real > protocols::optimize_weights::IterativeOptEDriver::component_weights_

private

Referenced by IterativeOptEDriver(), optimize_weights(), and score_position_data().

utility::vector1< core::pose::Pose > protocols::optimize_weights::IterativeOptEDriver::context_poses_

private

Referenced by compute_rotamer_energies_for_assigned_pdbs(), and measure_sequence_recovery().

Size protocols::optimize_weights::IterativeOptEDriver::count_recovered_

private

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().

Size protocols::optimize_weights::IterativeOptEDriver::count_rotamers_recovered_

private

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().

utility::vector1< utility::vector1< std::string > > protocols::optimize_weights::IterativeOptEDriver::ddG_bind_files_

private

A list of lists for use in optimizing ddG binding predictions.

Referenced by collect_ddG_of_binding_data(), and divide_up_pdbs().

OptEDataOP protocols::optimize_weights::IterativeOptEDriver::ddG_bind_optE_data_

private

preserve the ddG bind mutation data between iterations to minimize I/O

Referenced by collect_ddG_of_binding_data().

utility::vector1< std::pair< std::string, std::string > > protocols::optimize_weights::IterativeOptEDriver::ddg_mut_wt_pairs_

private

A list of file-list pairs: first = list of relaxed mutant pdbs; second = list of native pdbs

Referenced by collect_ddG_of_mutation_data(), and divide_up_pdbs().

OptEDataOP protocols::optimize_weights::IterativeOptEDriver::ddG_mutation_data_

private

preserve the ddMutation data between iterations to minimize I/O

Referenced by collect_ddG_of_mutation_data().

utility::vector1< Real > protocols::optimize_weights::IterativeOptEDriver::ddGs_

private

Referenced by collect_ddG_of_mutation_data(), and divide_up_pdbs().

utility::vector1< Real > protocols::optimize_weights::IterativeOptEDriver::ddGs_binding_

private

Referenced by collect_ddG_of_binding_data(), and divide_up_pdbs().

utility::vector1< std::string > protocols::optimize_weights::IterativeOptEDriver::decdisc_crystal_natives_

private

Referenced by collect_decoy_discrimination_data(), and divide_up_pdbs().

utility::vector1< utility::vector1< core::pose::Pose > > protocols::optimize_weights::IterativeOptEDriver::decdisc_decoy_poses_

private

Referenced by collect_decoy_discrimination_data().

utility::vector1< std::pair< std::string, std::string > > protocols::optimize_weights::IterativeOptEDriver::decdisc_native_decoy_pairs_

private

A list of file-list pairs. first = list of relaxed-native pdbs; second = list of decoy pdbs.

Referenced by collect_decoy_discrimination_data(), and divide_up_pdbs().

utility::vector1< utility::vector1< core::pose::Pose > > protocols::optimize_weights::IterativeOptEDriver::decdisc_native_poses_

private

Referenced by collect_decoy_discrimination_data().

utility::vector1< core::pose::Pose > protocols::optimize_weights::IterativeOptEDriver::decdisc_xtal_natives_

private

Referenced by collect_decoy_discrimination_data().

OptEDataOP protocols::optimize_weights::IterativeOptEDriver::decoy_discrim_data_

private

preserve the decoy scores by component between iterations to minimize I/O.

Referenced by collect_decoy_discrimination_data().

utility::vector1< Real > protocols::optimize_weights::IterativeOptEDriver::dG_binding_

private

Referenced by collect_dG_of_binding_data(), and divide_up_pdbs().

OptEDataOP protocols::optimize_weights::IterativeOptEDriver::dG_binding_data_

private

preserve the dGbinding data between iterations to minimize I/O

Referenced by collect_dG_of_binding_data().

utility::vector1< std::pair< std::string, std::string > > protocols::optimize_weights::IterativeOptEDriver::dG_bound_unbound_pairs_

private

A list of PDB file pairs: first = "bound" structure; second = "unbound" structure with partners well separated

Referenced by collect_dG_of_binding_data(), and divide_up_pdbs().

Size protocols::optimize_weights::IterativeOptEDriver::fixed_count_

private

Referenced by setup_derived_free_and_fixed_data().

EnergyMap protocols::optimize_weights::IterativeOptEDriver::fixed_parameters_

private

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().

ScoreTypes protocols::optimize_weights::IterativeOptEDriver::fixed_score_list_

private

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().

Size protocols::optimize_weights::IterativeOptEDriver::free_count_

private

Referenced by free_weights_and_refEs_from_vars(), optimize_weights(), score_position_data(), setup_derived_free_and_fixed_data(), and write_new_scorefile().

EnergyMap protocols::optimize_weights::IterativeOptEDriver::free_parameters_

private

These two get set by the user.

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().

ScoreTypes protocols::optimize_weights::IterativeOptEDriver::free_score_list_

private

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().

EnergyMap protocols::optimize_weights::IterativeOptEDriver::free_weights_after_minimization_

private

Referenced by collect_rotamer_energies(), optimize_weights(), and write_new_scorefile().

EnergyMap protocols::optimize_weights::IterativeOptEDriver::free_weights_before_minimization_

private

Referenced by decide_if_sequence_recovery_improved(), optimize_weights(), and write_new_scorefile().

EnergyMap protocols::optimize_weights::IterativeOptEDriver::free_weights_inner_loop_

private

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().

Size protocols::optimize_weights::IterativeOptEDriver::include_count_

private

Referenced by setup_derived_free_and_fixed_data().

EnergyMap protocols::optimize_weights::IterativeOptEDriver::include_terms_

private

These get updated from the above two.

Referenced by create_unweighted_scorefunction(), optimize_weights(), and setup_derived_free_and_fixed_data().

Size protocols::optimize_weights::IterativeOptEDriver::inner_loop_counter_

private

Referenced by decide_if_sequence_recovery_improved(), go(), optimize_weights(), and write_new_scorefile().

Real protocols::optimize_weights::IterativeOptEDriver::inner_loop_rotamer_recovery_rate_

private

Referenced by collect_rotamer_recovery_data_from_slave_cpus().

Real protocols::optimize_weights::IterativeOptEDriver::inner_loop_sequence_recovery_rate_

private

Referenced by collect_sequence_recovery_data_from_slave_cpus(), and decide_if_sequence_recovery_improved().

utility::vector1< std::string > protocols::optimize_weights::IterativeOptEDriver::ligand_crystal_natives_

private

Referenced by collect_ligand_discrimination_data(), and divide_up_pdbs().

OptEDataOP protocols::optimize_weights::IterativeOptEDriver::ligand_discrim_data_

private

preserve the decoy scores by component between iterations to minimize I/O.

Referenced by collect_ligand_discrimination_data().

utility::vector1< std::pair< std::string, std::string > > protocols::optimize_weights::IterativeOptEDriver::ligand_native_decoy_pairs_

private

A list of file-list pairs. first = list of relaxed-native pdbs; second = list of decoy pdbs.

Referenced by collect_ligand_discrimination_data(), and divide_up_pdbs().

utility::vector1< core::pose::Pose > protocols::optimize_weights::IterativeOptEDriver::ligand_repack_native_poses_

private

Referenced by compute_rotamers_around_ligands().

utility::vector1< std::string > protocols::optimize_weights::IterativeOptEDriver::ligand_repack_pdbs_

private

For rotamer recovery around ligands.

Referenced by compute_rotamers_around_ligands(), and divide_up_pdbs().

utility::vector1< Real > protocols::optimize_weights::IterativeOptEDriver::minimizer_dofs_after_minimization_

private

Referenced by optimize_weights(), and write_new_scorefile().

utility::vector1< Real > protocols::optimize_weights::IterativeOptEDriver::minimizer_dofs_before_minimization_

private

Referenced by optimize_weights(), and write_new_scorefile().

utility::vector1< Real > protocols::optimize_weights::IterativeOptEDriver::minimizer_dofs_mixed_

private

Referenced by optimize_weights(), and write_new_scorefile().

Real protocols::optimize_weights::IterativeOptEDriver::mixing_factor_

private

Referenced by decide_if_sequence_recovery_improved(), and write_new_scorefile().

Size protocols::optimize_weights::IterativeOptEDriver::MPI_nprocs_

private

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().

utility::vector1< std::string > protocols::optimize_weights::IterativeOptEDriver::native_pdbs_

private

Referenced by collect_rotamer_energies(), compute_rotamer_energies_for_assigned_pdbs(), divide_up_pdbs(), repack_assigned_pdbs(), and run_design_on_assigned_pdbs().

utility::vector1< core::pose::Pose > protocols::optimize_weights::IterativeOptEDriver::native_poses_

private

Referenced by compute_rotamer_energies_for_assigned_pdbs(), measure_rotamer_recovery(), and measure_sequence_recovery().

utility::vector1< std::string > protocols::optimize_weights::IterativeOptEDriver::next_iteration_pdbs_

private

Referenced by collect_rotamer_energies(), divide_up_pdbs(), repack_assigned_pdbs(), and run_design_on_assigned_pdbs().

OptEDataOP protocols::optimize_weights::IterativeOptEDriver::optE_data_

private

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().

Size protocols::optimize_weights::IterativeOptEDriver::outer_loop_counter_

private

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().

Real protocols::optimize_weights::IterativeOptEDriver::outer_loop_last_sequence_recovery_rate_

private

Referenced by decide_if_sequence_recovery_improved().

Real protocols::optimize_weights::IterativeOptEDriver::outer_loop_seq_profile_cross_entropy_

private

Referenced by decide_if_sequence_recovery_improved().

utility::vector1< std::string > protocols::optimize_weights::IterativeOptEDriver::pdbs_this_round_

private

Referenced by collect_rotamer_energies().

utility::vector1< std::pair< core::chemical::AA, utility::vector1< Real > > > protocols::optimize_weights::IterativeOptEDriver::pssm_data_

private

Referenced by get_nat_aa_opte_data(), and load_pssm_data().

utility::vector1< Real > protocols::optimize_weights::IterativeOptEDriver::reference_energies_inner_loop_

private

Referenced by create_weighted_scorefunction(), decide_if_sequence_recovery_improved(), IterativeOptEDriver(), repack_assigned_pdbs(), run_design_on_assigned_pdbs(), and write_new_scorefile().

utility::vector1< core::pose::Pose > protocols::optimize_weights::IterativeOptEDriver::rotamer_recovery_context_poses_

private

Referenced by compute_rotamer_energies_for_assigned_pdbs(), measure_rotamer_recovery(), and measure_sequence_recovery().

core::pack::task::TaskFactoryOP protocols::optimize_weights::IterativeOptEDriver::task_factory_

private

Referenced by get_nat_aa_opte_data(), get_nat_rot_opte_data(), IterativeOptEDriver(), measure_rotamer_recovery(), measure_sequence_recovery(), and task_factory().

Size protocols::optimize_weights::IterativeOptEDriver::total_positions_

private

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().

Size protocols::optimize_weights::IterativeOptEDriver::total_rotamer_positions_

private

the frequency for each amino acid in the input data set

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().

bool protocols::optimize_weights::IterativeOptEDriver::using_unfolded_energy_term_

private

Referenced by collect_ddG_of_mutation_data(), configure_new_scorefunction(), get_nat_aa_opte_data(), IterativeOptEDriver(), optimize_weights(), and output_weighted_unfolded_energies().

WrapperOptEMultifuncOP protocols::optimize_weights::IterativeOptEDriver::wrapped_opt_min_

private

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.

Referenced by optimize_weights(), and write_new_scorefile().

The documentation for this class was generated from the following files:

src/protocols/optimize_weights/IterativeOptEDriver.hh
src/protocols/optimize_weights/IterativeOptEDriver.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation