Application-level code for simple_cycpep_predict application. More...

#include <SimpleCycpepPredictApplication.hh>

Inheritance diagram for protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication:

Public Member Functions
	SimpleCycpepPredictApplication (bool const allow_file_read=true)
	Constructor. More...

	~SimpleCycpepPredictApplication () override
	Explicit virtual destructor. More...

	SimpleCycpepPredictApplication (SimpleCycpepPredictApplication const &src)
	Explicit copy constructor. More...

void	initialize_from_options ()
	Initialize the application. More...

void	set_cyclization_type (SCPA_cyclization_type const type_in)
	Set the cyclization type. More...

void	set_use_chainbreak_energy (bool const setting)
	Set whether we should use the chainbreak energy (true) or constraints (false) to enforce terminal amide bond geometry. More...

void	set_scorefxn (core::scoring::ScoreFunctionCOP sfxn_in)
	Sets the default scorefunction to use. More...

void	set_native (core::pose::PoseCOP native)
	Allows external code to provide a native, so that the SimpleCycpepPredictApplication doesn't have to read directly from disk. More...

void	set_sequence (std::string const &seq)
	Allows external code to provide a sequence, so that the SimpleCycpepPredictApplication doesn't have to read directly from disk. More...

void	set_allowed_residues_by_position (std::map< core::Size, utility::vector1< std::string > > const &allowed_canonicals, std::map< core::Size, utility::vector1< std::string > > const &allowed_noncanonicals)
	Allows external code to set the allowed residues by position, so that this needn't be read directly from disk. More...

void	set_silentstructure_outputlist (utility::vector1< core::io::silent::SilentStructOP > silentlist, utility::vector1< HierarchicalHybridJD_JobResultsSummaryOP > summarylist)
	Allows external code to specify that output should be appended to a list of SilentStructureOPs, so that the SimpleCycpepPredictApplication doesn't have to write directly to disk. More...

void	set_suppress_checkpoints (bool const suppress_checkpoints)
	Allows external code to suppress checkpointing, to prevent direct file I/O from disk. More...

void	set_my_rank (int const rank_in)
	If called by MPI code, the rank of the current process can be stored here. More...

void	set_already_completed_job_count (core::Size const count_in)
	Set the number of jobs that this process has already completed. More...

void	set_nstruct (core::Size const nstruct_in)
	Allows external code to override the number of structures that this should generate (otherwise set by options system. More...

void	set_L_alpha_compfile_contents (std::string const &contents_in)
	Allows external code to set the file contents for the L-alpha aa_composition file. More...

void	set_D_alpha_compfile_contents (std::string const &contents_in)
	Allows external code to set the file contents for the D-alpha aa_composition file. More...

void	set_L_beta_compfile_contents (std::string const &contents_in)
	Allows external code to set the file contents for the L-beta aa_composition file. More...

void	set_D_beta_compfile_contents (std::string const &contents_in)
	Allows external code to set the file contents for the D-beta aa_composition file. More...

void	set_abba_bins_binfile_contents (std::string const &contents_in)
	Allows external code to set the ABBA bin parameters without having to read the bin params file directly from disk. More...

void	set_sample_cis_pro_frequency (core::Real const &freq_in)
	Set the frequency with which we sample cis proline. More...

void	disable_cis_pro_sampling ()
	Set cis proline sampling OFF. More...

void	set_total_energy_cutoff (core::Real const &value_in)
	Set the total energy cutoff. More...

void	disable_total_energy_cutoff ()
	Sets use_total_energy_cutoff_ to 'false'. More...

void	set_angle_relax_rounds (core::Size const rounds_in)
	Set the number of rounds of relaxation with flexible bond angles. More...

void	set_angle_length_relax_rounds (core::Size const rounds_in)
	Set the number of rounds of relaxation with flexible bond angles and bond lengths. More...

void	set_cartesian_relax_rounds (core::Size const rounds_in)
	Set the number of rounds of Cartesian relaxation. More...

void	set_trigonal_pyramidal_metal_positions_from_string_vector (utility::vector1< std::string > const &vect)
	Given an input vector of strings of the form "res1,res2,res3,metal_name", parse this and populate the trigonal_pyramidal_metal_positions_ vector. More...

void	set_trigonal_planar_metal_positions_from_string_vector (utility::vector1< std::string > const &vect)
	Given an input vector of strings of the form "res1,res2,res3,metal_name", parse this and populate the trigonal_planar_metal_positions_ vector. More...

void	set_square_pyramidal_metal_positions_from_string_vector (utility::vector1< std::string > const &vect)
	Given an input vector of strings of the form "res1,res2,res3,res4,res5,metal_name", parse this and populate the square_pyramidal_metal_positions_ vector. More...

void	set_square_planar_metal_positions_from_string_vector (utility::vector1< std::string > const &vect)
	Given an input vector of strings of the form "res1,res2,res3,res4,metal_name", parse this and populate the square_pyramidal_metal_positions_ vector. More...

void	set_tetrahedral_metal_positions_from_string_vector (utility::vector1< std::string > const &vect)
	Given an input vector of strings of the form "res1,res2,res3,res4,metal_name", parse this and populate the tetrahedral_metal_positions_ vector. More...

void	set_octahedral_metal_positions_from_string_vector (utility::vector1< std::string > const &vect)
	Given an input vector of strings of the form "res1,res2,res3,res4,metal_name", parse this and populate the octahedral_metal_positions_ vector. More...

void	reset_trigonal_pyramidal_metal_positions ()
	Resets the trigonal_pyramidal_metal_positions_ vector. More...

void	reset_trigonal_planar_metal_positions ()
	Resets the trigonal_planar_metal_positions_ vector. More...

void	reset_square_pyramidal_metal_positions ()
	Resets the square_pyramidal_metal_positions_ vector. More...

void	reset_square_planar_metal_positions ()
	Resets the square_planar_metal_positions_ vector. More...

void	reset_tetrahedral_metal_positions ()
	Resets the tetrahedral_metal_positions_ vector. More...

void	reset_octahedral_metal_positions ()
	Resets the octahedral_metal_positions_ vector. More...

void	add_entry_to_trigonal_pyramidal_metal_positions (core::Size const res1, core::Size const res2, core::Size const res3, std::string const &metal_type)
	Adds an entry to the trigonal_pyramidal_metal_positions_ vector. More...

void	add_entry_to_trigonal_planar_metal_positions (core::Size const res1, core::Size const res2, core::Size const res3, std::string const &metal_type)
	Adds an entry to the trigonal_planar_metal_positions_ vector. More...

void	add_entry_to_square_pyramidal_metal_positions (core::Size const res1, core::Size const res2, core::Size const res3, core::Size const res4, core::Size const res5, std::string const &metal_type)
	Adds an entry to the square_pyramidal_metal_positions_ vector. More...

void	add_entry_to_square_planar_metal_positions (core::Size const res1, core::Size const res2, core::Size const res3, core::Size const res4, std::string const &metal_type)
	Adds an entry to the square_planar_metal_positions_ vector. More...

void	add_entry_to_tetrahedral_metal_positions (core::Size const res1, core::Size const res2, core::Size const res3, core::Size const res4, std::string const &metal_type)
	Adds an entry to the tetrahedral_metal_positions_ vector. More...

void	add_entry_to_octahedral_metal_positions (core::Size const res1, core::Size const res2, core::Size const res3, core::Size const res4, core::Size const res5, core::Size const res6, std::string const &metal_type)
	Adds an entry to the octahedral_metal_positions_ vector. More...

void	set_use_rama_prepro_for_sampling (bool const setting)
	Set whether we're using RamaPrePro tables for sampling. More...

core::Real	align_and_calculate_rmsd (core::pose::Pose &pose, core::pose::Pose const &native_pose, bool const skip_seq_comparison=false) const
	Align pose to native_pose, and return the RMSD between the two poses. More...

void	run () const
	Actually run the application. More...

Static Public Member Functions
static SCPA_cyclization_type	get_cyclization_type_from_name (std::string const &name)
	Given a cyclization type enum, return its name string. More...

static std::string	get_cyclization_name_from_type (SCPA_cyclization_type const type)
	Given a cyclization name string, return its type enum. More...

static void	register_options ()
	Register the set of options that this application uses (for the help menu). More...

Private Member Functions
bool	is_supported_restype (core::chemical::ResidueType const &restype) const
	-------—— Methods ----------------------—— More...

bool	is_residue_ignored_in_rms (core::Size const res_index) const
	Is this residue to be ignored in calculating RMSDs? More...

bool	is_lariat_type (SCPA_cyclization_type const type_in) const
	Is a given cyclization type a lariat type (i.e. one where a side-chain connects to backbone)? More...

bool	position_backbone_is_randomizable (core::Size const res_index) const
	Can a position's backbone be randomized? More...

void	check_loop_length (utility::vector1< std::string > const &resnames) const
	Check that the loop formed is long enough. More...

void	find_first_and_last_isopeptide_residues (core::pose::PoseCOP pose, core::Size &firstres, core::Size &lastres) const
	Given a pose, find the first and last isopeptide bond-forming residues. More...

core::Size	count_cis_peptide_bonds (core::pose::PoseCOP pose) const
	Count the number of cis-peptide bonds in the pose. More...

void	do_final_fastrelax (core::pose::PoseOP pose, core::scoring::ScoreFunctionOP sfxn, core::Size const relax_rounds, bool const angle_min, bool const length_min, bool const cartesian_min) const
	Carry out the final FastRelax. More...

void	build_polymer (core::pose::PoseOP pose, utility::vector1< std::string > const &restypes) const
	Actually build the geometry that we'll be working with. More...

void	add_n_methylation (core::pose::PoseOP pose, core::Size const cyclic_offset) const
	Add N-methylation. More...

void	set_default_rama_table_type (std::string const &type_name)
	Given the name of a Rama_Table_Type, set the default Rama_Table_Type. More...

void	set_rama_table_type_by_res (utility::vector1< std::string > const &type_name_vector)
	Given a string vector that we need to parse, populate the rama_table_type_by_res_ map. More...

core::scoring::Rama_Table_Type	get_rama_table_type_from_name (std::string const &type_name) const
	Given a Rama_Table_Type name, return the Rama_Table_Type, or an informative error message on failure. More...

void	read_sequence (std::string const &seqfile, utility::vector1< std::string > &resnames) const
	Read a sequence (as a series of full names, separated by whitespace) and store it in a string vector. More...

void	set_up_n_to_c_cyclization_mover (protocols::cyclic_peptide::DeclareBondOP termini, core::pose::PoseCOP pose, bool const native, core::Size const last_res) const
	Set up the mover that creates N-to-C amide bonds, and which updates the atoms dependent on the amide bond. More...

void	set_up_terminal_disulfide_cyclization_mover (protocols::cyclic_peptide::DeclareBondOP termini, core::pose::PoseCOP pose, bool const native, core::Size const last_disulf_res, core::Size const first_disulf_res) const
	Set up the mover that creates terminal disulfide bonds. More...

void	set_up_nterm_isopeptide_cyclization_mover (protocols::cyclic_peptide::DeclareBondOP termini, core::pose::PoseCOP pose) const
	Set up the mover that creates N-terminal isopeptide bonds. More...

void	set_up_cterm_isopeptide_cyclization_mover (protocols::cyclic_peptide::DeclareBondOP termini, core::pose::PoseCOP pose) const
	Set up the mover that creates C-terminal isopeptide bonds. More...

void	set_up_sidechain_isopeptide_cyclization_mover (protocols::cyclic_peptide::DeclareBondOP termini, core::pose::PoseCOP pose) const
	Set up the mover that creates sidechain isopeptide bonds. More...

void	set_up_cyclization_mover (protocols::cyclic_peptide::DeclareBondOP termini, core::pose::PoseCOP pose, bool const native=false, core::Size const last_res=0, core::Size const first_res=0) const
	Set up the DeclareBond mover used to connect the termini, or whatever atoms are involved in the cyclization. (Handles different cyclization modes). More...

core::Size	do_cyclic_permutation (utility::vector1< std::string > const &resnames, utility::vector1< std::string > &resnames_copy) const
	Takes a vector of residue names, chooses a random number for cyclic offset, and does a cyclic permutation. More...

void	import_and_set_up_native (std::string const &native_file, core::pose::PoseOP native_pose, core::Size const expected_residue_count) const
	Imports the native pose and sets up a terminial peptide bond. More...

void	set_up_native (core::pose::PoseOP native_pose, core::Size const expected_residue_count) const
	Sets up a terminial peptide bond and does some checks. More...

void	add_cutpoint_variants_at_termini (core::pose::PoseOP pose) const
	Add cutpoint variants to the terminal residues of an N-to-C cyclic peptide. More...

void	add_amide_bond_cyclic_constraints (core::pose::PoseOP pose, core::Size n_index, core::Size c_index) const
	Function to add cyclic constraints to a pose. More...

void	add_cyclic_constraints (core::pose::PoseOP pose) const
	Function to add cyclic constraints to a pose. More...

void	set_mainchain_torsions (core::pose::PoseOP pose, core::Size const cyclic_offset) const
	Sets all omega values to 180, and randomizes mainchain torsions. More...

void	set_up_hbond_filter (protocols::filters::CombinedFilterOP total_hbond, core::Size const nres, core::scoring::ScoreFunctionOP sfxn, core::Real const &min_hbonds) const
	Set up the filters for the mainchain hydrogen bonds that will be used to discard solutions with too little mainchain hydrogen bonding. More...

void	add_closebond_logic_n_to_c_amide_bond (core::pose::PoseCOP pose, core::Size const cyclization_point_start, core::Size const cyclization_point_end, protocols::generalized_kinematic_closure::GeneralizedKICOP genkic) const
	Set up the logic to close the bond at the cyclization point. More...

void	add_closebond_logic_terminal_disulfide (core::pose::PoseCOP pose, core::Size const cyclization_point_start, core::Size const cyclization_point_end, protocols::generalized_kinematic_closure::GeneralizedKICOP genkic) const
	Set up the logic to close the bond at the cyclization point. More...

void	add_closebond_logic_isopeptide (core::pose::PoseCOP pose, core::Size const cyclization_point_start, core::Size const cyclization_point_end, protocols::generalized_kinematic_closure::GeneralizedKICOP genkic) const
	Set up the logic to close the bond at the cyclization point. More...

void	add_closebond_logic (core::pose::PoseCOP pose, core::Size const cyclization_point_start, core::Size const cyclization_point_end, protocols::generalized_kinematic_closure::GeneralizedKICOP genkic) const
	Set up the logic to close the bond at the cyclization point. More...

bool	genkic_close (core::pose::PoseOP pose, core::scoring::ScoreFunctionOP sfxn_highhbond, core::scoring::ScoreFunctionOP sfxn_highhbond_cart, core::scoring::ScoreFunctionCOP sfxn_default, protocols::filters::CombinedFilterOP total_hbond, core::Size const cyclic_offset) const
	Use GeneralizedKIC to close the pose. More...

void	set_up_design_taskoperations (protocols::denovo_design::movers::FastDesignOP fdes, core::Size const cyclic_offset, core::Size const nres, core::pose::PoseCOP pose) const
	Set up the TaskOperations that conrol the design process, given user inputs. More...

std::string	get_oneletter_codes (utility::vector1< std::string > const &fullnames) const
	Given a vector of full residue names of canonical residues, give me a concatenated list of one-letter codes. More...

std::string	get_nc_name_codes (utility::vector1< std::string > const &fullnames) const
	Given a vector of full residue names, give me a string of the form "X[<fullname1>]X[<fullname2>]X[<fullname3>] ...". More...

void	store_disulfides (core::pose::PoseCOP pose, utility::vector1< std::pair< core::Size, core::Size > > &old_disulfides) const
	Given a pose, store a list of the disulfides in the pose. More...

void	break_disulfides (core::pose::PoseOP pose, utility::vector1< std::pair< core::Size, core::Size > > const &disulfides) const
	Given a pose and a list of the disulfides in the pose, break the disulfides. More...

void	rebuild_disulfides (core::pose::PoseOP pose, utility::vector1< std::pair< core::Size, core::Size > > const &disulfides) const
	Given a pose and a list of the disulfides that should be in the pose, form the disulfides. More...

void	depermute_disulfide_list (utility::vector1< std::pair< core::Size, core::Size > > const &old_disulfides, utility::vector1< std::pair< core::Size, core::Size > > &new_disulfides, core::Size const offset, core::Size const nres) const
	Given a list of old disulfide positions, generate a list of new disulfide positions based on the offset. More...

void	depermute (core::pose::PoseOP pose, core::Size const offset) const
	Given a pose that has undergone an N-residue cyclic permutation, restore the original pose, without the permutation. More...

void	new_checkpoint_file () const
	Create a new checkpoint file. More...

void	initialize_checkpointing (core::Size &lastjob, core::Size &successes) const
	Initialize checkpointing for this run. More...

void	checkpoint (core::Size const curjob, core::Size const successes) const
	Add a checkpoint to the checkpoint file. More...

void	end_checkpointing () const
	End checkpointing and delete the checkpoint file. More...

void	get_random_seed_info () const
	Restore the state of the random generator from a previous run. More...

void	store_random_seed_info () const
	Store the state of the random generator from a previous run. More...

void	erase_random_seed_info () const
	Erase the stored state of the random generator from a previous run. More...

core::Size	current_position (core::Size const absolute_position, core::Size const permutation_offset, core::Size const nresidue) const
	Given an absolute position in the sequence and the current cyclic permuation offset, return the position in the current pose corresponding to that absolute postion. More...

core::Size	original_position (core::Size const curr_position, core::Size const permutation_offset, core::Size const nresidue) const
	Given an position in the current (perturbed) pose, return the position in the original (unperturbed) pose. More...

bool	custom_rama_table_defined (core::Size const absolute_position) const
	Does a position have a custom Rama table defined? More...

core::scoring::Rama_Table_Type	rama_table_type_by_res (core::Size const absolute_position) const
	Custom Rama table for a position. More...

core::scoring::Rama_Table_Type	default_rama_table_type () const
	Get the default custom Rama table type. More...

bool	use_rama_filter () const
	Are we using a rama filter? Defaults to true. More...

bool	sample_cis_pro () const
	Are we sampling cis-prolines? More...

core::Real const &	sample_cis_pro_frequency () const
	Frequency for sampling cis prolines. More...

core::Size	angle_relax_rounds () const
	Bond angle relax rounds. More...

core::Size	angle_length_relax_rounds () const
	Bond angle / bond length relax rounds. More...

core::Size	cartesian_relax_rounds () const
	Cartesian relax rounds. More...

bool	use_rama_prepro_for_sampling () const
	Are we using RamaPrePro tables for sampling? More...

core::Size	sequence_length () const
	The length of the sequence, excluding crosslinkers. More...

void	re_append_linker_residues (core::pose::PoseCOP pose, core::pose::PoseOP newpose, core::Size const offset, utility::vector1< utility::vector1< core::Size > > const &linker_positions, std::string const &linker_name) const
	Given a pose with a linker (e.g. TBMB, TMA) in it and another pose without the linker, copy the linker residues from the first to the second, and add back covalent bonds. More...

void	re_append_trigonal_metal_residues (core::pose::PoseCOP pose, core::pose::PoseOP newpose, bool const planar) const
	Given a pose with trigonal pyramidal or trigonal planar metal variants and another pose without the variants, add back the variants to the latter. More...

void	re_append_square_pyramidal_metal_residues (core::pose::PoseCOP pose, core::pose::PoseOP newpose) const
	Given a pose with square pyramidal metal variants and another pose without the variants, add back the variants to the latter. More...

void	re_append_square_planar_metal_residues (core::pose::PoseCOP pose, core::pose::PoseOP newpose) const
	Given a pose with square planar metal variants and another pose without the variants, add back the variants to the latter. More...

void	re_append_tetrahedral_metal_residues (core::pose::PoseCOP pose, core::pose::PoseOP newpose) const
	Given a pose with tetrahedral metal variants and another pose without the variants, add back the variants to the latter. More...

void	re_append_octahedral_metal_residues (core::pose::PoseCOP pose, core::pose::PoseOP newpose) const
	Given a pose with octahedral metal variants and another pose without the variants, add back the variants to the latter. More...

SCPA_cyclization_type	cyclization_type () const
	Get the cyclization type (N-to-C cyclic, terminal disulfide, etc.). More...

bool	use_chainbreak_energy () const
	Should we use the chainbreak energy (true) or constraints (false) to enforce terminal amide bond geometry? More...

core::Size	find_first_disulf_res (core::pose::PoseCOP pose) const
	Given a pose, return the index of the first residue that can form a disulfide. More...

core::Size	find_last_disulf_res (core::pose::PoseCOP pose) const
	Given a pose, return the index of the last residue that can form a disulfide. More...

void	set_up_terminal_disulfide_variants (core::pose::PoseOP pose) const
	Given a pose, add disulfide variant types to the first and last cysteine residues in the pose. More...

void	set_up_isopeptide_variants (core::pose::PoseOP pose) const
	Given a pose, add sidechain conjugation variant types to sidechains involved in making an isopeptide bond, and strip termini from termini involved in the isopeptide bond. More...

bool	is_isopeptide_forming_amide_type (std::string const &basename) const
	Given the basename of a residue type, return true if this is a type that can donate the nitrogen to an isopeptide bond, false otherwise. More...

bool	is_isopeptide_forming_carbonyl_type (core::chemical::AA const aa) const
	Given the AA of a residue type, return true if this is a type that can donate the carbonyl to an isopeptide bond, false otherwise. More...

void	add_bondlength_perturbation (protocols::generalized_kinematic_closure::GeneralizedKIC &genkic, core::Real const bondlength_perturbation_magnitude, core::pose::Pose const &pose, core::Size const anchor_res) const
	Given a GenKIC object, a pose, and a bond length perturbation magnitude, add bond length perturbation to all bond lengths in the pose. More...

void	add_bondangle_perturbation (protocols::generalized_kinematic_closure::GeneralizedKIC &genkic, core::Real const bondangle_perturbation_magnitude, core::pose::Pose const &pose, core::Size const anchor_res) const
	Given a GenKIC object, a pose, and a bond angle perturbation magnitude, add bond angle perturbation to all bond angles in the pose. More...

Private Attributes
int	my_rank_
	If this is called by MPI code, this can store the rank of the current process. Zero otherwise. More...

core::Size	already_completed_job_count_
	The number of jobs that this slave process has already completed. Only used in MPI mode; zero otherwise. More...

SCPA_cyclization_type	cyclization_type_
	The type of cyclization. More...

bool	use_chainbreak_energy_
	Should we use the chainbreak energy (true) or constraints (false) to enforce terminal amide bond geometry? More...

core::scoring::ScoreFunctionOP	scorefxn_
	The default ScoreFunction to use. The high h-bond version is constructed from this. More...

bool	suppress_checkpoints_
	Allows external code to suppress checkpointing, so that the SimpleCycpepPredictApplication doesn't write directly to disk. More...

bool	silent_out_
	Should this application produce silent file output? More...

bool	silentlist_out_
	Should this application produce silent structure OP output, appending to a list? More...

utility::vector1 < core::io::silent::SilentStructOP > *	silentlist_
	If silentlist_out_ is used, this is the list to append SilentStructurOPs to. More...

utility::vector1 < HierarchicalHybridJD_JobResultsSummaryOP > *	summarylist_
	If silentlist_out_ is used, this is the list of job summaries to which summaries should be appended. More...

core::pose::PoseCOP	native_pose_
	A native pose, provided by external code. More...

std::string	out_filename_
	The prefix for the output filename. More...

std::string	out_scorefilename_
	The output score file name. More...

std::string	sequence_file_
	Filename for the text file containing the sequence of the peptide. More...

std::string	sequence_string_
	The string that would be read from a sequence file. More...

core::Size	sequence_length_
	The length of the sequence, excluding any cross-linkers. More...

core::Size	genkic_closure_attempts_
	The number of attempts that will be made by the generalized kinematic closure machinery. More...

core::Size	genkic_min_solution_count_
	The minimum number of solutions that must be found by the generalized kinematic closure machinery before a single solution is chosen. More...

bool	cyclic_permutations_
	Should we consider cyclic permutations? More...

bool	use_rama_filter_
	Should solutions be filtered by Ramachandran energy (in the case of alpha-amino acids)? More...

core::Real	rama_cutoff_
	The energy cutoff for the rama filter. More...

core::Real	high_hbond_weight_multiplier_
	For parts of the protocol that upweight the hydrogen bond terms, this is the factor by which these terms are upweighted. More...

core::Real	min_genkic_hbonds_
	The minimum number of mainchain hydrogen bonds that a generalized kinematic closure solution must have. More...

core::Real	min_final_hbonds_
	The minimum number of mainchain hydrogen bonds that a final solution must have. More...

core::Real	total_energy_cutoff_
	The total energy cutoff above which solutions are discarded. More...

bool	use_total_energy_cutoff_
	Determines whether the total energy cutoff should be used. More...

core::Real	hbond_energy_cutoff_
	The hbond energy cutoff above which a hbond is no longer counted. More...

core::Size	fast_relax_rounds_
	The number of FastReleax rounds to be applied whenever FastRelax is used. More...

bool	count_sc_hbonds_
	Should sidechain-mainchain hydrogen bonds be counted when counting hydrogen bonds? More...

bool	native_exists_
	Has the user specified a native structure? More...

std::string	native_filename_
	Filename for the native, if one is provided. More...

core::Size	nstruct_
	Max number of structures to generate. More...

std::string	checkpoint_job_identifier_
	A unique job name for checkpointing. More...

std::string	checkpoint_filename_
	The name of the checkpoint file. More...

core::scoring::Rama_Table_Type	default_rama_table_type_
	A default custom Ramachandran table to be used for sampling. More...

std::map< core::Size, core::scoring::Rama_Table_Type >	rama_table_type_by_res_
	Custom Ramachandran tables to be used for sampling, listed by residue. More...

std::string	rand_checkpoint_file_
	The name of the checkpoint file for the random number generator. More...

bool	try_all_disulfides_
	Should we try all disulfide combinations during structure prediction? More...

core::Real	disulf_energy_cutoff_prerelax_
	The cutoff dslf_fa13 energy, pre-relaxation, above which closure solutions are rejected. More...

core::Real	disulf_energy_cutoff_postrelax_
	The cutoff dslf_fa13 energy, post-relaxation, above which closure solutions are rejected. More...

std::map< core::Size, utility::vector1< core::Real > >	user_set_alpha_dihedrals_
	Map of (seqpos -> phi/psi/omega triplet). More...

core::Real	user_set_dihedral_perturbation_ = 0.0
	A small random value added to all user-set dihedral values. Defaults to 0. More...

core::Real	bondlength_perturbation_magnitude_ = 0.0
	A small random value added to all backbone bond lengths. Defaults to 0. More...

core::Real	bondangle_perturbation_magnitude_ = 0.0
	A small random value added to all backbone bond angles. Defaults to 0. More...

bool	filter_oversaturated_hbond_acceptors_
	Should we filter out solutions that have more than the allowed number of hydrogen bonds to an acceptor? More...

core::Real	oversaturated_hbond_cutoff_energy_
	The energy above which we no longer count a hydrogen bond to an acceptor for the filter. More...

bool	sample_cis_pro_
	At residues that are more likely to have cis omega values, sample cis some fraction of the time. More...

core::Real	sample_cis_pro_frequency_
	At residues that are more likely to have cis omega values, sample cis this fraction of the time. More...

bool	design_peptide_
	Should we design the peptide after sampling the conformation, or just relax it? More...

std::string	design_filename_
	If we're designing, this is the filename for the file that tells us what residues are allowed at what postion. More...

bool	prevent_design_file_read_
	Used to prevent this process from directly reading the input file if it has been read by another process and the information has been transmitted to this process. More...

std::map< core::Size, utility::vector1< std::string > >	allowed_canonicals_by_position_
	Allowed canonical residues at each position. More...

std::map< core::Size, utility::vector1< std::string > >	allowed_noncanonicals_by_position_
	Allowed noncanonical residues at each position. More...

bool	prohibit_D_at_negative_phi_
	Should D-residues be prohibited at positions with negative phi values? More...

bool	prohibit_L_at_positive_phi_
	Should L-residues be prohibited at positions with positive phi values? More...

bool	use_aa_comp_
	Should we use the aa_composition score term in design? More...

bool	L_alpha_comp_file_exists_
	Has an aa_composition setup file ben provided for residues in the L-alpha helix region of Ramachadran space? More...

bool	D_alpha_comp_file_exists_
	Has an aa_composition setup file ben provided for residues in the D-alpha helix region of Ramachadran space? More...

bool	L_beta_comp_file_exists_
	Has an aa_composition setup file ben provided for residues in the L-beta strand region of Ramachadran space? More...

bool	D_beta_comp_file_exists_
	Has an aa_composition setup file ben provided for residues in the D-beta strand region of Ramachadran space? More...

std::string	comp_file_contents_L_alpha_
	Storage for the composition constraint setup for the L-alpha helix region of Ramachandran space. More...

std::string	comp_file_contents_D_alpha_
	Storage for the composition constraint setup for the D-alpha helix region of Ramachandran space. More...

std::string	comp_file_contents_L_beta_
	Storage for the composition constraint setup for the L-beta strand region of Ramachandran space. More...

std::string	comp_file_contents_D_beta_
	Storage for the composition constraint setup for the D-beta strand region of Ramachandran space. More...

std::string	abba_bins_
	Storage for a bin definition file. More...

bool	do_not_count_adjacent_res_hbonds_
	Prevent counting of hydrogen bonds to adjacent residues? More...

core::Size	angle_relax_rounds_
	Number of rounds of relaxation with flexible bond angles. More...

core::Size	angle_length_relax_rounds_
	Number of rounds of relaxation with flexible bond angles and bond lengths. More...

core::Size	cartesian_relax_rounds_
	Number of rounds of Cartesian-space relaxation. More...

bool	use_rama_prepro_for_sampling_
	Should we use rama_prepro tables for sampling? More...

utility::vector1< core::Size >	n_methyl_positions_
	List of positions (in original sequence indexing – not permuted) that are N-methylated. More...

utility::vector1 < utility::vector1< core::Size > >	tbmb_positions_
	List of positions linked by 1,3,5-tris(bromomethyl)benzene. More...

bool	link_all_cys_with_tbmb_
	Should all cysteine residues be linked with 1,3,5-tris(bromomethyl)benzene? More...

bool	use_tbmb_filters_
	If true, filters are applied based on distance between TBMB cysteines and on constraints to discard GenKIC solutions that can't be crosslinked easily. More...

core::Real	tbmb_sidechain_distance_filter_multiplier_
	Multiplier to make the TBMB distance filter more permissive. More...

core::Real	tbmb_constraints_energy_filter_multiplier_
	Multiplier to make the TBMB constraints energy filter more permissive. More...

utility::vector1 < utility::vector1< core::Size > >	tma_positions_
	List of positions linked by trimesic acid. More...

bool	use_tma_filters_
	If true, filters are applied based on distance between trimesic acid-conjugated residues and on constraints to discard GenKIC solutions that can't be crosslinked easily. More...

core::Real	tma_sidechain_distance_filter_multiplier_
	Multiplier to make the trimesic acid distance filter more permissive. More...

core::Real	tma_constraints_energy_filter_multiplier_
	Multiplier to make the trimesic acid constraints energy filter more permissive. More...

utility::vector1< std::pair < utility::fixedsizearray1 < core::Size, 3 >, std::string > >	trigonal_pyramidal_metal_positions_
	List of positions linked by a metal coordinated with trigonal pyramidal geometry. More...

bool	use_trigonal_pyramidal_metal_filters_
	If true, filters are applied based on distance between metal-conjugated residues and on constraints to discard GenKIC solutions that can't be crosslinked easily. More...

core::Real	trigonal_pyramidal_metal_sidechain_distance_filter_multiplier_
	Multiplier to make the trigonal pyramidal metal distance filter more permissive. More...

core::Real	trigonal_pyramidal_metal_constraints_energy_filter_multiplier_
	Multiplier to make the trigonal pyramidal metal constraints energy filter more permissive. More...

utility::vector1< std::pair < utility::fixedsizearray1 < core::Size, 3 >, std::string > >	trigonal_planar_metal_positions_
	List of positions linked by a metal coordinated with trigonal planar geometry. More...

bool	use_trigonal_planar_metal_filters_
	If true, filters are applied based on distance between metal-conjugated residues and on constraints to discard GenKIC solutions that can't be crosslinked easily. More...

core::Real	trigonal_planar_metal_sidechain_distance_filter_multiplier_
	Multiplier to make the trigonal planar metal distance filter more permissive. More...

core::Real	trigonal_planar_metal_constraints_energy_filter_multiplier_
	Multiplier to make the trigonal planar metal constraints energy filter more permissive. More...

utility::vector1< std::pair < utility::fixedsizearray1 < core::Size, 5 >, std::string > >	square_pyramidal_metal_positions_
	List of positions linked by a metal with square pyramidal geometry. More...

bool	use_square_pyramidal_metal_filters_
	If true, filters are applied based on distance between metal-conjugated residues and on constraints to discard GenKIC solutions that can't be crosslinked easily. More...

core::Real	square_pyramidal_metal_sidechain_distance_filter_multiplier_
	Multiplier to make the square pyramidal metal distance filter more permissive. More...

core::Real	square_pyramidal_metal_constraints_energy_filter_multiplier_
	Multiplier to make the square pyramidal metal constraints energy filter more permissive. More...

utility::vector1< std::pair < utility::fixedsizearray1 < core::Size, 4 >, std::string > >	square_planar_metal_positions_
	List of positions linked by a metal with square planar geometry. More...

bool	use_square_planar_metal_filters_
	If true, filters are applied based on distance between metal-conjugated residues and on constraints to discard GenKIC solutions that can't be crosslinked easily. More...

core::Real	square_planar_metal_sidechain_distance_filter_multiplier_
	Multiplier to make the square planar metal distance filter more permissive. More...

core::Real	square_planar_metal_constraints_energy_filter_multiplier_
	Multiplier to make the square planar metal constraints energy filter more permissive. More...

utility::vector1< std::pair < utility::fixedsizearray1 < core::Size, 4 >, std::string > >	tetrahedral_metal_positions_
	List of positions linked by a tetrahedrally-coordinated metal. More...

bool	use_tetrahedral_metal_filters_
	If true, filters are applied based on distance between metal-conjugated residues and on constraints to discard GenKIC solutions that can't be crosslinked easily. More...

core::Real	tetrahedral_metal_sidechain_distance_filter_multiplier_
	Multiplier to make the tetrahedral metal distance filter more permissive. More...

core::Real	tetrahedral_metal_constraints_energy_filter_multiplier_
	Multiplier to make the tetrahedral metal constraints energy filter more permissive. More...

utility::vector1< std::pair < utility::fixedsizearray1 < core::Size, 6 >, std::string > >	octahedral_metal_positions_
	List of positions linked by a octahedrally-coordinated metal. More...

bool	use_octahedral_metal_filters_
	If true, filters are applied based on distance between metal-conjugated residues and on constraints to discard GenKIC solutions that can't be crosslinked easily. More...

core::Real	octahedral_metal_sidechain_distance_filter_multiplier_
	Multiplier to make the octahedral metal distance filter more permissive. More...

core::Real	octahedral_metal_constraints_energy_filter_multiplier_
	Multiplier to make the octahedral metal constraints energy filter more permissive. More...

core::Size	required_symmetry_repeats_
	If this option is used, then only backbones that are cN (or sN, if mirror symmetry is required) symmetric will be accepted. For example, if set to 2, then only c2-symmetric backbones will be accepted. More...

bool	required_symmetry_mirroring_
	If this option is used, then only backbones with mirror symmetry are accepted. Must be used with the -cyclic_peptide:require_symmetry_repeats flag. More...

core::Real	required_symmetry_angle_threshold_
	The cutoff, in degrees, to use when comparing mainchain torsion values to determine whether symmetry repeats are truely symmetric. Defaults to 10 degrees. More...

core::Real	required_symmetry_perturbation_
	The random perturbation, in degrees, to be applied when copying mainchain torsion values to produce symmetric conformations. More...

utility::vector1< core::Size >	exclude_residues_from_rms_
	Residues to exclude from the RMSD calculation. Defaults to empty list. More...

core::Size	lariat_sidechain_index_
	If the cyclization type is a lariat type, this is the index of the residue that provides the sidechain that connects to the N- or C-terminus. More...

std::pair< core::Size, core::Size >	sidechain_isopeptide_indices_
	If the cyclization type is sidechain_isopeptide, these are the indices of the residues forming the sidechain-sidechain isopeptide bond. More...

Detailed Description

Application-level code for simple_cycpep_predict application.

Also called by the BOINC minirosetta app.

Author: Vikram K. Mulligan, Baker laboratory (vmull.nosp@m.ig@u.nosp@m.w.edu)

Constructor & Destructor Documentation

protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::SimpleCycpepPredictApplication ( bool const allow_file_read = true )

Constructor.

If allow_file_read is true, initialization triggers reads from the filesystem.

References initialize_from_options().

protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::~SimpleCycpepPredictApplication ( )

overridedefault

Explicit virtual destructor.

protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::SimpleCycpepPredictApplication ( SimpleCycpepPredictApplication const & src )

Explicit copy constructor.

References scorefxn_.

Member Function Documentation

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_amide_bond_cyclic_constraints	(	core::pose::PoseOP	pose,
		core::Size	n_index,
		core::Size	c_index
	)		const

private

Function to add cyclic constraints to a pose.

This version does this for N-to-C amide bonds and isopeptide bonds.

Parameters

[in]	pose	The pose to modify.
[in]	n_index	The index of the N-terminal sidechain for an isopeptide bond. Set to 0 for N-terminus.
[in]	c_index	The index of the C-terminal sidechain for an isopeptide bond. Set to 0 for C-terminus.

References core::id::AtomID::atomno(), core::id::AtomID::rsd(), sequence_length(), SimpleCycpepPredictApplication_PEPBOND_C_ANGLE, SimpleCycpepPredictApplication_PEPBOND_LENGTH, SimpleCycpepPredictApplication_PEPBOND_N_ANGLE, and protocols::TR().

Referenced by add_cyclic_constraints().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_bondangle_perturbation	(	protocols::generalized_kinematic_closure::GeneralizedKIC &	genkic,
		core::Real const	bondangle_perturbation_magnitude,
		core::pose::Pose const &	pose,
		core::Size const	anchor_res
	)		const

private

Given a GenKIC object, a pose, and a bond angle perturbation magnitude, add bond angle perturbation to all bond angles in the pose.

References protocols::generalized_kinematic_closure::GeneralizedKIC::add_atomset_to_perturber_atomset_list(), protocols::generalized_kinematic_closure::GeneralizedKIC::add_perturber(), protocols::generalized_kinematic_closure::GeneralizedKIC::add_value_to_perturber_value_list(), cyclization_type_, core::chemical::ResidueType::mainchain_atoms(), protocols::generalized_kinematic_closure::perturber::perturb_bondangle, core::pose::Pose::residue_type(), protocols::cyclic_peptide_predict::SCPA_n_to_c_amide_bond, and core::pose::Pose::total_residue().

Referenced by genkic_close().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_bondlength_perturbation	(	protocols::generalized_kinematic_closure::GeneralizedKIC &	genkic,
		core::Real const	bondlength_perturbation_magnitude,
		core::pose::Pose const &	pose,
		core::Size const	anchor_res
	)		const

private

Given a GenKIC object, a pose, and a bond length perturbation magnitude, add bond length perturbation to all bond lengths in the pose.

References protocols::generalized_kinematic_closure::GeneralizedKIC::add_atomset_to_perturber_atomset_list(), protocols::generalized_kinematic_closure::GeneralizedKIC::add_perturber(), protocols::generalized_kinematic_closure::GeneralizedKIC::add_value_to_perturber_value_list(), cyclization_type_, core::chemical::ResidueType::mainchain_atoms(), protocols::generalized_kinematic_closure::perturber::perturb_bondlength, core::pose::Pose::residue_type(), protocols::cyclic_peptide_predict::SCPA_n_to_c_amide_bond, and core::pose::Pose::total_residue().

Referenced by genkic_close().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_closebond_logic	(	core::pose::PoseCOP	pose,
		core::Size const	cyclization_point_start,
		core::Size const	cyclization_point_end,
		protocols::generalized_kinematic_closure::GeneralizedKICOP	genkic
	)		const

private

Set up the logic to close the bond at the cyclization point.

Calls different functions for different cyclization types.

References add_closebond_logic_isopeptide(), add_closebond_logic_n_to_c_amide_bond(), add_closebond_logic_terminal_disulfide(), cyclization_type(), protocols::cyclic_peptide_predict::SCPA_cterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_invalid_type, protocols::cyclic_peptide_predict::SCPA_n_to_c_amide_bond, protocols::cyclic_peptide_predict::SCPA_nterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_sidechain_isopeptide, and protocols::cyclic_peptide_predict::SCPA_terminal_disulfide.

Referenced by genkic_close().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_closebond_logic_isopeptide	(	core::pose::PoseCOP	pose,
		core::Size const	cyclization_point_start,
		core::Size const	cyclization_point_end,
		protocols::generalized_kinematic_closure::GeneralizedKICOP	genkic
	)		const

private

Set up the logic to close the bond at the cyclization point.

This version is for all types of isopeptide bond cyclization.

Note: cyclization_point_start > cyclization_point_end

References cyclization_type(), is_isopeptide_forming_amide_type(), is_isopeptide_forming_carbonyl_type(), protocols::antibody::l1, protocols::generalized_kinematic_closure::perturber::randomize_dihedral, protocols::cyclic_peptide_predict::SCPA_cterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_nterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_sidechain_isopeptide, SimpleCycpepPredictApplication_PEPBOND_C_ANGLE, SimpleCycpepPredictApplication_PEPBOND_LENGTH, and SimpleCycpepPredictApplication_PEPBOND_N_ANGLE.

Referenced by add_closebond_logic().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_closebond_logic_n_to_c_amide_bond	(	core::pose::PoseCOP	pose,
		core::Size const	cyclization_point_start,
		core::Size const	cyclization_point_end,
		protocols::generalized_kinematic_closure::GeneralizedKICOP	genkic
	)		const

private

Set up the logic to close the bond at the cyclization point.

This version is for N-to-C amide bond cyclization.

References cyclization_type(), protocols::cyclic_peptide_predict::SCPA_n_to_c_amide_bond, sequence_length(), SimpleCycpepPredictApplication_PEPBOND_C_ANGLE, SimpleCycpepPredictApplication_PEPBOND_LENGTH, and SimpleCycpepPredictApplication_PEPBOND_N_ANGLE.

Referenced by add_closebond_logic().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_closebond_logic_terminal_disulfide	(	core::pose::PoseCOP	pose,
		core::Size const	cyclization_point_start,
		core::Size const	cyclization_point_end,
		protocols::generalized_kinematic_closure::GeneralizedKICOP	genkic
	)		const

private

Set up the logic to close the bond at the cyclization point.

This version is for terminal disulfide cyclization.

References cyclization_type(), protocols::antibody::l1, protocols::generalized_kinematic_closure::perturber::randomize_dihedral, protocols::cyclic_peptide_predict::SCPA_terminal_disulfide, SimpleCycpepPredictApplication_DISULFBOND_ANGLE, and SimpleCycpepPredictApplication_DISULFBOND_LENGTH.

Referenced by add_closebond_logic().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_cutpoint_variants_at_termini ( core::pose::PoseOP pose ) const

private

Add cutpoint variants to the terminal residues of an N-to-C cyclic peptide.

References core::pose::correctly_add_cutpoint_variants(), core::pose::correctly_remove_variants_incompatible_with_lower_cutpoint_variant(), core::pose::correctly_remove_variants_incompatible_with_upper_cutpoint_variant(), and protocols::TR().

Referenced by run().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_cyclic_constraints ( core::pose::PoseOP pose ) const

private

Function to add cyclic constraints to a pose.

Calls functions that do this for particular cyclization types.

References add_amide_bond_cyclic_constraints(), cyclization_type(), find_first_and_last_isopeptide_residues(), protocols::cyclic_peptide_predict::SCPA_cterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_invalid_type, protocols::cyclic_peptide_predict::SCPA_n_to_c_amide_bond, protocols::cyclic_peptide_predict::SCPA_nterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_sidechain_isopeptide, and protocols::cyclic_peptide_predict::SCPA_terminal_disulfide.

Referenced by run().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_entry_to_octahedral_metal_positions	(	core::Size const	res1,
		core::Size const	res2,
		core::Size const	res3,
		core::Size const	res4,
		core::Size const	res5,
		core::Size const	res6,
		std::string const &	metal_type
	)

Adds an entry to the octahedral_metal_positions_ vector.

References octahedral_metal_positions_.

Referenced by set_octahedral_metal_positions_from_string_vector().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_entry_to_square_planar_metal_positions	(	core::Size const	res1,
		core::Size const	res2,
		core::Size const	res3,
		core::Size const	res4,
		std::string const &	metal_type
	)

Adds an entry to the square_planar_metal_positions_ vector.

References square_planar_metal_positions_.

Referenced by set_square_planar_metal_positions_from_string_vector().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_entry_to_square_pyramidal_metal_positions	(	core::Size const	res1,
		core::Size const	res2,
		core::Size const	res3,
		core::Size const	res4,
		core::Size const	res5,
		std::string const &	metal_type
	)

Adds an entry to the square_pyramidal_metal_positions_ vector.

References square_pyramidal_metal_positions_.

Referenced by set_square_pyramidal_metal_positions_from_string_vector().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_entry_to_tetrahedral_metal_positions	(	core::Size const	res1,
		core::Size const	res2,
		core::Size const	res3,
		core::Size const	res4,
		std::string const &	metal_type
	)

Adds an entry to the tetrahedral_metal_positions_ vector.

References tetrahedral_metal_positions_.

Referenced by set_tetrahedral_metal_positions_from_string_vector().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_entry_to_trigonal_planar_metal_positions	(	core::Size const	res1,
		core::Size const	res2,
		core::Size const	res3,
		std::string const &	metal_type
	)

Adds an entry to the trigonal_planar_metal_positions_ vector.

References trigonal_planar_metal_positions_.

Referenced by set_trigonal_planar_metal_positions_from_string_vector().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_entry_to_trigonal_pyramidal_metal_positions	(	core::Size const	res1,
		core::Size const	res2,
		core::Size const	res3,
		std::string const &	metal_type
	)

Adds an entry to the trigonal_pyramidal_metal_positions_ vector.

References trigonal_pyramidal_metal_positions_.

Referenced by set_trigonal_pyramidal_metal_positions_from_string_vector().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_n_methylation	(	core::pose::PoseOP	pose,
		core::Size const	cyclic_offset
	)		const

private

Add N-methylation.

Must be called after pose is cyclized.

References protocols::simple_moves::ModifyVariantTypeMover::apply(), n_methyl_positions_, sequence_length(), protocols::simple_moves::ModifyVariantTypeMover::set_additional_type_to_add(), protocols::simple_moves::ModifyVariantTypeMover::set_residue_selector(), and protocols::TR().

Referenced by run().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::align_and_calculate_rmsd	(	core::pose::Pose &	pose,
		core::pose::Pose const &	native_pose,
		bool const	skip_seq_comparison = `false`
	)		const

Align pose to native_pose, and return the RMSD between the two poses.

Assumes that the pose has already been de-permuted (i.e. the native and the pose line up). Only uses alpha-amino acids for the alignment, currently.

References core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_is_hydrogen(), core::chemical::ResidueType::atom_name(), core::id::AtomID::BOGUS_ATOM_ID(), exclude_residues_from_rms_, core::chemical::ResidueType::first_sidechain_atom(), core::pose::initialize_atomid_map(), is_residue_ignored_in_rms(), is_supported_restype(), core::chemical::ResidueType::is_virtual(), core::pose::Pose::residue_type(), sequence_length(), core::scoring::superimpose_pose(), core::id::to_string(), and core::pose::Pose::total_residue().

Referenced by run().

core::Size protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::angle_length_relax_rounds ( ) const

inlineprivate

Bond angle / bond length relax rounds.

References angle_length_relax_rounds_.

Referenced by genkic_close(), and run().

core::Size protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::angle_relax_rounds ( ) const

inlineprivate

Bond angle relax rounds.

References angle_relax_rounds_.

Referenced by genkic_close(), and run().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::break_disulfides	(	core::pose::PoseOP	pose,
		utility::vector1< std::pair< core::Size, core::Size > > const &	disulfides
	)		const

private

Given a pose and a list of the disulfides in the pose, break the disulfides.

References core::conformation::break_disulfide().

Referenced by depermute().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::build_polymer	(	core::pose::PoseOP	pose,
		utility::vector1< std::string > const &	restypes
	)		const

private

Actually build the geometry that we'll be working with.

References protocols::cyclic_peptide::PeptideStubMover::set_reset_mode(), and protocols::TR().

Referenced by check_loop_length(), and run().

core::Size protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::cartesian_relax_rounds ( ) const

inlineprivate

Cartesian relax rounds.

References cartesian_relax_rounds_.

Referenced by genkic_close(), and run().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::check_loop_length ( utility::vector1< std::string > const & resnames ) const

private

Check that the loop formed is long enough.

References build_polymer(), cyclization_type(), find_first_and_last_isopeptide_residues(), find_first_disulf_res(), find_last_disulf_res(), protocols::cyclic_peptide_predict::SCPA_cterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_nterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_sidechain_isopeptide, and protocols::cyclic_peptide_predict::SCPA_terminal_disulfide.

Referenced by run().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::checkpoint	(	core::Size const	curjob,
		core::Size const	successes
	)		const

private

Add a checkpoint to the checkpoint file.

The checkpoint file must already exist. Does nothing if checkpointing is disabled.

Parameters

[in]	curjob	The index of the current job just run, for writing to the checkpoint file.
[in]	successes	The number of successes so far, for writing to the checkpoint file.

References checkpoint_filename_, checkpoint_job_identifier_, store_random_seed_info(), suppress_checkpoints_, and protocols::boinc::Boinc::update_pct_complete().

Referenced by run().

core::Size protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::count_cis_peptide_bonds ( core::pose::PoseCOP pose ) const

private

Count the number of cis-peptide bonds in the pose.

Counts as cis if in the range (-90,90].

References sequence_length(), and protocols::TR().

Referenced by run().

core::Size protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::current_position	(	core::Size const	absolute_position,
		core::Size const	permutation_offset,
		core::Size const	nresidue
	)		const

inlineprivate

Given an absolute position in the sequence and the current cyclic permuation offset, return the position in the current pose corresponding to that absolute postion.

Referenced by genkic_close().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::custom_rama_table_defined ( core::Size const absolute_position ) const

inlineprivate

Does a position have a custom Rama table defined?

Does not include a default custom Rama table – only position-specific Rama tables are checked.

References rama_table_type_by_res_.

Referenced by genkic_close(), rama_table_type_by_res(), and set_mainchain_torsions().

SCPA_cyclization_type protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::cyclization_type ( ) const

inlineprivate

Get the cyclization type (N-to-C cyclic, terminal disulfide, etc.).

Const-access only.

References cyclization_type_.

Referenced by add_closebond_logic(), add_closebond_logic_isopeptide(), add_closebond_logic_n_to_c_amide_bond(), add_closebond_logic_terminal_disulfide(), add_cyclic_constraints(), check_loop_length(), depermute(), find_first_and_last_isopeptide_residues(), genkic_close(), initialize_from_options(), position_backbone_is_randomizable(), run(), set_mainchain_torsions(), set_up_cterm_isopeptide_cyclization_mover(), set_up_cyclization_mover(), set_up_design_taskoperations(), set_up_isopeptide_variants(), set_up_native(), set_up_nterm_isopeptide_cyclization_mover(), and set_up_sidechain_isopeptide_cyclization_mover().

core::scoring::Rama_Table_Type protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::default_rama_table_type ( ) const

inlineprivate

Get the default custom Rama table type.

Defaults to unknown_ramatable_type if not set.

References default_rama_table_type_.

Referenced by genkic_close(), and set_mainchain_torsions().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::depermute	(	core::pose::PoseOP	pose,
		core::Size const	offset
	)		const

private

Given a pose that has undergone an N-residue cyclic permutation, restore the original pose, without the permutation.

References break_disulfides(), cyclization_type(), depermute_disulfide_list(), octahedral_metal_positions_, re_append_linker_residues(), re_append_octahedral_metal_residues(), re_append_square_planar_metal_residues(), re_append_square_pyramidal_metal_residues(), re_append_tetrahedral_metal_residues(), re_append_trigonal_metal_residues(), rebuild_disulfides(), protocols::cyclic_peptide_predict::SCPA_terminal_disulfide, sequence_length(), set_up_cyclization_mover(), set_up_terminal_disulfide_variants(), square_planar_metal_positions_, square_pyramidal_metal_positions_, store_disulfides(), tbmb_positions_, tetrahedral_metal_positions_, tma_positions_, trigonal_planar_metal_positions_, and trigonal_pyramidal_metal_positions_.

Referenced by run().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::depermute_disulfide_list	(	utility::vector1< std::pair< core::Size, core::Size > > const &	old_disulfides,
		utility::vector1< std::pair< core::Size, core::Size > > &	new_disulfides,
		core::Size const	offset,
		core::Size const	nres
	)		const

private

Given a list of old disulfide positions, generate a list of new disulfide positions based on the offset.

Replaces the new_disulfides list.

Referenced by depermute().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::disable_cis_pro_sampling ( )

Set cis proline sampling OFF.

References sample_cis_pro_, and sample_cis_pro_frequency_.

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::disable_total_energy_cutoff ( )

Sets use_total_energy_cutoff_ to 'false'.

References use_total_energy_cutoff_.

core::Size protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::do_cyclic_permutation	(	utility::vector1< std::string > const &	resnames,
		utility::vector1< std::string > &	resnames_copy
	)		const

private

Takes a vector of residue names, chooses a random number for cyclic offset, and does a cyclic permutation.

Returns the offset and stores the new string vector in resnames_copy.

References core::scoring::rg, and protocols::TR().

Referenced by run().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::do_final_fastrelax	(	core::pose::PoseOP	pose,
		core::scoring::ScoreFunctionOP	sfxn,
		core::Size const	relax_rounds,
		bool const	angle_min,
		bool const	length_min,
		bool const	cartesian_min
	)		const

private

Carry out the final FastRelax.

References set_up_cyclization_mover(), and protocols::TR().

Referenced by run().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::end_checkpointing ( ) const

private

End checkpointing and delete the checkpoint file.

Does nothing if checkpointing is disabled.

References checkpoint_filename_, checkpoint_job_identifier_, erase_random_seed_info(), and suppress_checkpoints_.

Referenced by run().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::erase_random_seed_info ( ) const

private

Erase the stored state of the random generator from a previous run.

References rand_checkpoint_file_, and suppress_checkpoints_.

Referenced by end_checkpointing(), and new_checkpoint_file().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::find_first_and_last_isopeptide_residues	(	core::pose::PoseCOP	pose,
		core::Size &	firstres,
		core::Size &	lastres
	)		const

private

Given a pose, find the first and last isopeptide bond-forming residues.

Bases this on lariat_sidechain_index_ for lariat types, unless set to 0, in which case it finds the suitable type closest to the opposite terminus. Bases this on sidechain_isopeptide_indices_ for sidechain isopeptide cyclization, unless set to 0, in which case it finds the suitable types that are furthest apart.

References cyclization_type(), is_isopeptide_forming_amide_type(), is_isopeptide_forming_carbonyl_type(), lariat_sidechain_index_, protocols::cyclic_peptide_predict::SCPA_cterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_nterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_sidechain_isopeptide, sequence_length(), and sidechain_isopeptide_indices_.

Referenced by add_cyclic_constraints(), check_loop_length(), genkic_close(), set_up_cterm_isopeptide_cyclization_mover(), set_up_design_taskoperations(), set_up_isopeptide_variants(), set_up_nterm_isopeptide_cyclization_mover(), and set_up_sidechain_isopeptide_cyclization_mover().

core::Size protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::find_first_disulf_res ( core::pose::PoseCOP pose ) const

private

Given a pose, return the index of the first residue that can form a disulfide.

Throws an error if no residue is found.

Referenced by check_loop_length(), genkic_close(), set_up_terminal_disulfide_cyclization_mover(), and set_up_terminal_disulfide_variants().

core::Size protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::find_last_disulf_res ( core::pose::PoseCOP pose ) const

private

Given a pose, return the index of the last residue that can form a disulfide.

Throws an error if no residue is found.

Referenced by check_loop_length(), genkic_close(), set_up_terminal_disulfide_cyclization_mover(), and set_up_terminal_disulfide_variants().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::genkic_close	(	core::pose::PoseOP	pose,
		core::scoring::ScoreFunctionOP	sfxn_highhbond,
		core::scoring::ScoreFunctionOP	sfxn_highhbond_cart,
		core::scoring::ScoreFunctionCOP	sfxn_default,
		protocols::filters::CombinedFilterOP	total_hbond,
		core::Size const	cyclic_offset
	)		const

private

Use GeneralizedKIC to close the pose.

Referenced by run().

std::string protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::get_cyclization_name_from_type ( SCPA_cyclization_type const type )

static

Given a cyclization name string, return its type enum.

References protocols::cyclic_peptide_predict::SCPA_cterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_invalid_type, protocols::cyclic_peptide_predict::SCPA_n_to_c_amide_bond, protocols::cyclic_peptide_predict::SCPA_nterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_sidechain_isopeptide, and protocols::cyclic_peptide_predict::SCPA_terminal_disulfide.

Referenced by get_cyclization_type_from_name().

protocols::cyclic_peptide_predict::SCPA_cyclization_type protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::get_cyclization_type_from_name ( std::string const & name )

static

Given a cyclization type enum, return its name string.

References get_cyclization_name_from_type(), protocols::cyclic_peptide_predict::SCPA_invalid_type, and protocols::cyclic_peptide_predict::SCPA_number_of_types.

Referenced by initialize_from_options().

std::string protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::get_nc_name_codes ( utility::vector1< std::string > const & fullnames ) const

private

Given a vector of full residue names, give me a string of the form "X[<fullname1>]X[<fullname2>]X[<fullname3>] ...".

Does no checking for duplicates. Will fail gracelessly with invalid names.

References core::chemical::FA_STANDARD, core::chemical::ResidueTypeFinder::get_representative_type(), and core::chemical::ResidueTypeFinder::residue_base_name().

Referenced by set_up_design_taskoperations().

std::string protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::get_oneletter_codes ( utility::vector1< std::string > const & fullnames ) const

private

Given a vector of full residue names of canonical residues, give me a concatenated list of one-letter codes.

Does no checking for duplicates.

References core::chemical::aa_from_name(), and core::chemical::oneletter_code_from_aa().

Referenced by set_up_design_taskoperations().

core::scoring::Rama_Table_Type protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::get_rama_table_type_from_name ( std::string const & type_name ) const

private

Given a Rama_Table_Type name, return the Rama_Table_Type, or an informative error message on failure.

References core::scoring::Ramachandran::get_ramatable_name_by_type(), core::scoring::Ramachandran::get_ramatable_type_by_name(), core::scoring::rama, and core::scoring::unknown_ramatable_type.

Referenced by set_default_rama_table_type(), and set_rama_table_type_by_res().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::get_random_seed_info ( ) const

private

Restore the state of the random generator from a previous run.

References rand_checkpoint_file_, and core::scoring::rg.

Referenced by initialize_checkpointing().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::import_and_set_up_native	(	std::string const &	native_file,
		core::pose::PoseOP	native_pose,
		core::Size const	expected_residue_count
	)		const

private

Imports the native pose and sets up a terminial peptide bond.

References core::import_pose::PDB_file, core::import_pose::pose_from_file(), set_up_native(), and protocols::TR().

Referenced by run().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::initialize_checkpointing	(	core::Size &	lastjob,
		core::Size &	successes
	)		const

private

Initialize checkpointing for this run.

This function does several things. First, it checks for an existing checkpoint file. If one exists, it checks whether the unique job name in the file matches the current job. If it does, then this job has already been attempted, and we're somewhere in the middle of it. The function reads the last attempt number and success count from the checkpoint file, and returns these values. Otherwise, it creates a new checkpoint file with the current job name and returns (0,0). If checkpointing is disabled, this function does nothing, and returns (0,0).

Parameters

[out]	lastjob	The index of the last job run. Set to zero if checkpointing is disabled or if we're creating a new checkpoint file (first job run).
[out]	successes	The number of successes so far. Set to zero if checkpointing is disabled or if we're creating a new checkpoint file (first job run).

References checkpoint_filename_, checkpoint_job_identifier_, get_random_seed_info(), new_checkpoint_file(), suppress_checkpoints_, and protocols::TR().

Referenced by run().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::initialize_from_options ( )

Initialize the application.

Initializes using the option system.

Referenced by SimpleCycpepPredictApplication().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::is_isopeptide_forming_amide_type ( std::string const & basename ) const

private

Given the basename of a residue type, return true if this is a type that can donate the nitrogen to an isopeptide bond, false otherwise.

Referenced by add_closebond_logic_isopeptide(), and find_first_and_last_isopeptide_residues().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::is_isopeptide_forming_carbonyl_type ( core::chemical::AA const aa ) const

private

Given the AA of a residue type, return true if this is a type that can donate the carbonyl to an isopeptide bond, false otherwise.

References core::chemical::aa_asp, core::chemical::aa_das, core::chemical::aa_dgu, and core::chemical::aa_glu.

Referenced by add_closebond_logic_isopeptide(), and find_first_and_last_isopeptide_residues().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::is_lariat_type ( SCPA_cyclization_type const type_in ) const

private

Is a given cyclization type a lariat type (i.e. one where a side-chain connects to backbone)?

References protocols::cyclic_peptide_predict::SCPA_cterm_isopeptide_lariat, and protocols::cyclic_peptide_predict::SCPA_nterm_isopeptide_lariat.

Referenced by initialize_from_options().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::is_residue_ignored_in_rms ( core::Size const res_index ) const

private

Is this residue to be ignored in calculating RMSDs?

References exclude_residues_from_rms_.

Referenced by align_and_calculate_rmsd().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::is_supported_restype ( core::chemical::ResidueType const & restype ) const

private

-------—— Methods ----------------------——

Is a residue type supported for macrocycle structure prediction?

Currently returns true for alpha-, beta-, or gamma-amino acids and for peptoids, false otherwise. This will be expanded in the future.

References core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_beta_aa(), core::chemical::ResidueType::is_gamma_aa(), core::chemical::ResidueType::is_oligourea(), and core::chemical::ResidueTypeBase::is_peptoid().

Referenced by align_and_calculate_rmsd(), set_mainchain_torsions(), and set_up_native().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::new_checkpoint_file ( ) const

private

Create a new checkpoint file.

References checkpoint_filename_, checkpoint_job_identifier_, erase_random_seed_info(), store_random_seed_info(), and suppress_checkpoints_.

Referenced by initialize_checkpointing().

core::Size protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::original_position	(	core::Size const	curr_position,
		core::Size const	permutation_offset,
		core::Size const	nresidue
	)		const

inlineprivate

Given an position in the current (perturbed) pose, return the position in the original (unperturbed) pose.

Referenced by genkic_close(), and set_mainchain_torsions().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::position_backbone_is_randomizable ( core::Size const res_index ) const

private

Can a position's backbone be randomized?

Returns false for disulfide or isopeptide positions, true otherwise.

References cyclization_type(), protocols::cyclic_peptide_predict::SCPA_cterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_nterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_sidechain_isopeptide, protocols::cyclic_peptide_predict::SCPA_terminal_disulfide, and sequence_length().

Referenced by genkic_close().

core::scoring::Rama_Table_Type protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::rama_table_type_by_res ( core::Size const absolute_position ) const

inlineprivate

Custom Rama table for a position.

Returns unknown_ramatable_type if none defined for the position.

References custom_rama_table_defined(), rama_table_type_by_res_, and core::scoring::unknown_ramatable_type.

Referenced by genkic_close(), and set_mainchain_torsions().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::re_append_linker_residues	(	core::pose::PoseCOP	pose,
		core::pose::PoseOP	newpose,
		core::Size const	offset,
		utility::vector1< utility::vector1< core::Size > > const &	linker_positions,
		std::string const &	linker_name
	)		const

private

Given a pose with a linker (e.g. TBMB, TMA) in it and another pose without the linker, copy the linker residues from the first to the second, and add back covalent bonds.

This function is called at the end of the protocol, and therefore doesn't bother to add back constraints.

Referenced by depermute().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::re_append_octahedral_metal_residues	(	core::pose::PoseCOP	pose,
		core::pose::PoseOP	newpose
	)		const

private

Given a pose with octahedral metal variants and another pose without the variants, add back the variants to the latter.

This function is called at the end of the protocol, and therefore doesn't bother to add back contraints.

References protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_linker_asymmetric(), and octahedral_metal_positions_.

Referenced by depermute().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::re_append_square_planar_metal_residues	(	core::pose::PoseCOP	pose,
		core::pose::PoseOP	newpose
	)		const

private

Given a pose with square planar metal variants and another pose without the variants, add back the variants to the latter.

This function is called at the end of the protocol, and therefore doesn't bother to add back contraints.

References protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_linker_asymmetric(), and square_planar_metal_positions_.

Referenced by depermute().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::re_append_square_pyramidal_metal_residues	(	core::pose::PoseCOP	pose,
		core::pose::PoseOP	newpose
	)		const

private

Given a pose with square pyramidal metal variants and another pose without the variants, add back the variants to the latter.

This function is called at the end of the protocol, and therefore doesn't bother to add back contraints.

References protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_linker_asymmetric(), and square_pyramidal_metal_positions_.

Referenced by depermute().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::re_append_tetrahedral_metal_residues	(	core::pose::PoseCOP	pose,
		core::pose::PoseOP	newpose
	)		const

private

Given a pose with tetrahedral metal variants and another pose without the variants, add back the variants to the latter.

This function is called at the end of the protocol, and therefore doesn't bother to add back contraints.

References protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_linker_asymmetric(), and tetrahedral_metal_positions_.

Referenced by depermute().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::re_append_trigonal_metal_residues	(	core::pose::PoseCOP	pose,
		core::pose::PoseOP	newpose,
		bool const	planar
	)		const

private

Given a pose with trigonal pyramidal or trigonal planar metal variants and another pose without the variants, add back the variants to the latter.

This function is called at the end of the protocol, and therefore doesn't bother to add back contraints. If planar is true, it calls the trigonal planar code; otherwise it calls the trigonal pyramidal.

References protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_linker_asymmetric(), trigonal_planar_metal_positions_, and trigonal_pyramidal_metal_positions_.

Referenced by depermute().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::read_sequence	(	std::string const &	seqfile,
		utility::vector1< std::string > &	resnames
	)		const

private

Read a sequence (as a series of full names, separated by whitespace) and store it in a string vector.

References sequence_string_, and protocols::TR().

Referenced by run().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::rebuild_disulfides	(	core::pose::PoseOP	pose,
		utility::vector1< std::pair< core::Size, core::Size > > const &	disulfides
	)		const

private

Given a pose and a list of the disulfides that should be in the pose, form the disulfides.

References core::conformation::form_disulfide().

Referenced by depermute().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::register_options ( )

static

Register the set of options that this application uses (for the help menu).

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::reset_octahedral_metal_positions ( )

Resets the octahedral_metal_positions_ vector.

References octahedral_metal_positions_.

Referenced by set_octahedral_metal_positions_from_string_vector().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::reset_square_planar_metal_positions ( )

Resets the square_planar_metal_positions_ vector.

References square_planar_metal_positions_.

Referenced by set_square_planar_metal_positions_from_string_vector().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::reset_square_pyramidal_metal_positions ( )

Resets the square_pyramidal_metal_positions_ vector.

References square_pyramidal_metal_positions_.

Referenced by set_square_pyramidal_metal_positions_from_string_vector().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::reset_tetrahedral_metal_positions ( )

Resets the tetrahedral_metal_positions_ vector.

References tetrahedral_metal_positions_.

Referenced by set_tetrahedral_metal_positions_from_string_vector().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::reset_trigonal_planar_metal_positions ( )

Resets the trigonal_planar_metal_positions_ vector.

References trigonal_planar_metal_positions_.

Referenced by set_trigonal_planar_metal_positions_from_string_vector().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::reset_trigonal_pyramidal_metal_positions ( )

Resets the trigonal_pyramidal_metal_positions_ vector.

References trigonal_pyramidal_metal_positions_.

Referenced by set_trigonal_pyramidal_metal_positions_from_string_vector().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::run ( ) const

Actually run the application.

The initialize_from_options() function must be called before calling this. (Called by default constructor.)

References core::scoring::aa_composition, add_cutpoint_variants_at_termini(), add_cyclic_constraints(), add_n_methylation(), align_and_calculate_rmsd(), already_completed_job_count_, core::scoring::angle_constraint, angle_length_relax_rounds(), angle_relax_rounds(), core::scoring::atom_pair_constraint, build_polymer(), core::scoring::cart_bonded, cartesian_relax_rounds(), core::scoring::chainbreak, check_loop_length(), checkpoint(), count_cis_peptide_bonds(), cyclic_permutations_, cyclization_type(), depermute(), core::scoring::dihedral_constraint, do_cyclic_permutation(), do_final_fastrelax(), end_checkpointing(), fast_relax_rounds_, genkic_close(), core::scoring::hbond_lr_bb, core::scoring::hbond_sr_bb, high_hbond_weight_multiplier_, import_and_set_up_native(), core::io::silent::SilentFileOptions::in_fullatom(), initialize_checkpointing(), link_all_cys_with_tbmb_, min_final_hbonds_, min_genkic_hbonds_, protocols::boinc::BoincSharedMemory::model_count, my_rank_, native_exists_, native_filename_, native_pose_, nstruct_, out_filename_, core::scoring::pro_close, read_sequence(), required_symmetry_angle_threshold_, required_symmetry_mirroring_, required_symmetry_repeats_, protocols::noesy_assign::round(), scorefxn_, protocols::cyclic_peptide_predict::SCPA_cterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_n_to_c_amide_bond, protocols::cyclic_peptide_predict::SCPA_nterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_sidechain_isopeptide, protocols::cyclic_peptide_predict::SCPA_terminal_disulfide, sequence_file_, sequence_length(), sequence_length_, set_mainchain_torsions(), set_up_cyclization_mover(), set_up_hbond_filter(), set_up_isopeptide_variants(), set_up_terminal_disulfide_variants(), silent_out_, silentlist_, silentlist_out_, summarylist_, tbmb_positions_, total_energy_cutoff_, protocols::TR(), use_aa_comp_, use_chainbreak_energy(), use_total_energy_cutoff_, and protocols::boinc::Boinc::worker_is_finished().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::sample_cis_pro ( ) const

inlineprivate

Are we sampling cis-prolines?

Defaults to false.

References sample_cis_pro_.

Referenced by genkic_close().

core::Real const& protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::sample_cis_pro_frequency ( ) const

inlineprivate

Frequency for sampling cis prolines.

References sample_cis_pro_frequency_.

Referenced by genkic_close().

core::Size protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::sequence_length ( ) const

inlineprivate

The length of the sequence, excluding crosslinkers.

This is also the index of the last sequence residue. Crosslinker residues follow this position.

References sequence_length_.

Referenced by add_amide_bond_cyclic_constraints(), add_closebond_logic_n_to_c_amide_bond(), add_n_methylation(), align_and_calculate_rmsd(), count_cis_peptide_bonds(), depermute(), find_first_and_last_isopeptide_residues(), genkic_close(), position_backbone_is_randomizable(), run(), set_mainchain_torsions(), set_up_isopeptide_variants(), and set_up_n_to_c_cyclization_mover().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_abba_bins_binfile_contents ( std::string const & contents_in )

Allows external code to set the ABBA bin parameters without having to read the bin params file directly from disk.

References abba_bins_.

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_allowed_residues_by_position	(	std::map< core::Size, utility::vector1< std::string > > const &	allowed_canonicals,
		std::map< core::Size, utility::vector1< std::string > > const &	allowed_noncanonicals
	)

Allows external code to set the allowed residues by position, so that this needn't be read directly from disk.

References allowed_canonicals_by_position_, and allowed_noncanonicals_by_position_.

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_already_completed_job_count ( core::Size const count_in )

Set the number of jobs that this process has already completed.

References already_completed_job_count_.

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_angle_length_relax_rounds ( core::Size const rounds_in )

Set the number of rounds of relaxation with flexible bond angles and bond lengths.

References angle_length_relax_rounds_.

Referenced by initialize_from_options().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_angle_relax_rounds ( core::Size const rounds_in )

Set the number of rounds of relaxation with flexible bond angles.

References angle_relax_rounds_.

Referenced by initialize_from_options().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_cartesian_relax_rounds ( core::Size const rounds_in )

Set the number of rounds of Cartesian relaxation.

References cartesian_relax_rounds_.

Referenced by initialize_from_options().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_cyclization_type ( SCPA_cyclization_type const type_in )

Set the cyclization type.

References cyclization_type_, and protocols::cyclic_peptide_predict::SCPA_invalid_type.

Referenced by initialize_from_options().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_D_alpha_compfile_contents ( std::string const & contents_in )

Allows external code to set the file contents for the D-alpha aa_composition file.

References comp_file_contents_D_alpha_, and D_alpha_comp_file_exists_.

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_D_beta_compfile_contents ( std::string const & contents_in )

Allows external code to set the file contents for the D-beta aa_composition file.

References comp_file_contents_D_beta_, and D_beta_comp_file_exists_.

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_default_rama_table_type ( std::string const & type_name )

private

Given the name of a Rama_Table_Type, set the default Rama_Table_Type.

Error if unknown type.

References default_rama_table_type_, get_rama_table_type_from_name(), and protocols::TR().

Referenced by initialize_from_options().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_L_alpha_compfile_contents ( std::string const & contents_in )

Allows external code to set the file contents for the L-alpha aa_composition file.

References comp_file_contents_L_alpha_, and L_alpha_comp_file_exists_.

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_L_beta_compfile_contents ( std::string const & contents_in )

Allows external code to set the file contents for the L-beta aa_composition file.

References comp_file_contents_L_beta_, and L_beta_comp_file_exists_.

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_mainchain_torsions	(	core::pose::PoseOP	pose,
		core::Size const	cyclic_offset
	)		const

private

Sets all omega values to 180, and randomizes mainchain torsions.

For alpha-amino acids, mainchain torsions are randomized by the Ramachandran plot. For other residue types, just randomizes mainchain torsions other than peptide bonds.

References core::chemical::aa_unk, core::id::BB, custom_rama_table_defined(), cyclization_type(), default_rama_table_type(), core::scoring::Ramachandran::draw_random_phi_psi_from_extra_cdf(), core::chemical::FA_STANDARD, core::scoring::RamaPrePro::get_mainchain_torsions_covered(), is_supported_restype(), original_position(), core::scoring::rama, rama_table_type_by_res(), core::scoring::RamaPrePro::random_mainchain_torsions(), core::scoring::Ramachandran::random_phipsi_from_rama(), core::scoring::rg, protocols::cyclic_peptide_predict::SCPA_nterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_sidechain_isopeptide, protocols::cyclic_peptide_predict::SCPA_terminal_disulfide, sequence_length(), protocols::TR(), core::scoring::unknown_ramatable_type, and use_rama_prepro_for_sampling().

Referenced by run().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_my_rank ( int const rank_in )

If called by MPI code, the rank of the current process can be stored here.

Used for output of job summaries.

References my_rank_.

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_native ( core::pose::PoseCOP native )

Allows external code to provide a native, so that the SimpleCycpepPredictApplication doesn't have to read directly from disk.

References native_exists_, native_pose_, and set_up_native().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_nstruct ( core::Size const nstruct_in )

Allows external code to override the number of structures that this should generate (otherwise set by options system.

References nstruct_.

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_octahedral_metal_positions_from_string_vector ( utility::vector1< std::string > const & vect )

Given an input vector of strings of the form "res1,res2,res3,res4,metal_name", parse this and populate the octahedral_metal_positions_ vector.

Resets the octahedral_metal_positions_ vector.

References add_entry_to_octahedral_metal_positions(), reset_octahedral_metal_positions(), and protocols::TR().

Referenced by initialize_from_options().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_rama_table_type_by_res ( utility::vector1< std::string > const & type_name_vector )

private

Given a string vector that we need to parse, populate the rama_table_type_by_res_ map.

The string vector must be of the format: [integer] [rama type name] [integer] [rama type name] etc. Throws error if could not parse.

References get_rama_table_type_from_name(), rama_table_type_by_res_, and protocols::TR().

Referenced by initialize_from_options().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_sample_cis_pro_frequency ( core::Real const & freq_in )

Set the frequency with which we sample cis proline.

Implicitly sets sample_cis_pro_ to "true" if freq_in is not 0.0, "false" if it is.

References sample_cis_pro_, sample_cis_pro_frequency_, and protocols::TR().

Referenced by initialize_from_options().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_scorefxn ( core::scoring::ScoreFunctionCOP sfxn_in )

Sets the default scorefunction to use.

The scorefunction is cloned. The high-hbond version is constructed from this one. If necessary, the aa_composition score term will be turned on in that one; it needn't be turned on in this one.

References scorefxn_.

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_sequence ( std::string const & seq )

Allows external code to provide a sequence, so that the SimpleCycpepPredictApplication doesn't have to read directly from disk.

References sequence_string_.

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_silentstructure_outputlist	(	utility::vector1< core::io::silent::SilentStructOP > *	silentlist,
		utility::vector1< HierarchicalHybridJD_JobResultsSummaryOP > *	summarylist
	)

Allows external code to specify that output should be appended to a list of SilentStructureOPs, so that the SimpleCycpepPredictApplication doesn't have to write directly to disk.

References silent_out_, silentlist_, silentlist_out_, and summarylist_.

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_square_planar_metal_positions_from_string_vector ( utility::vector1< std::string > const & vect )

Given an input vector of strings of the form "res1,res2,res3,res4,metal_name", parse this and populate the square_pyramidal_metal_positions_ vector.

Given an input vector of strings of the form "res1,res2,res3,res4,metal_name", parse this and populate the square_planar_metal_positions_ vector.

Resets the square_pyramidal_metal_positions_ vector.

Resets the square_planar_metal_positions_ vector.

References add_entry_to_square_planar_metal_positions(), reset_square_planar_metal_positions(), and protocols::TR().

Referenced by initialize_from_options().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_square_pyramidal_metal_positions_from_string_vector ( utility::vector1< std::string > const & vect )

Given an input vector of strings of the form "res1,res2,res3,res4,res5,metal_name", parse this and populate the square_pyramidal_metal_positions_ vector.

Resets the square_pyramidal_metal_positions_ vector.

References add_entry_to_square_pyramidal_metal_positions(), reset_square_pyramidal_metal_positions(), and protocols::TR().

Referenced by initialize_from_options().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_suppress_checkpoints ( bool const suppress_checkpoints )

Allows external code to suppress checkpointing, to prevent direct file I/O from disk.

Useful on Blue Gene.

References suppress_checkpoints_.

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_tetrahedral_metal_positions_from_string_vector ( utility::vector1< std::string > const & vect )

Given an input vector of strings of the form "res1,res2,res3,res4,metal_name", parse this and populate the tetrahedral_metal_positions_ vector.

Resets the tetrahedral_metal_positions_ vector.

References add_entry_to_tetrahedral_metal_positions(), reset_tetrahedral_metal_positions(), and protocols::TR().

Referenced by initialize_from_options().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_total_energy_cutoff ( core::Real const & value_in )

Set the total energy cutoff.

Also sets use_total_energy_cutoff_ to 'true'.

References total_energy_cutoff_, and use_total_energy_cutoff_.

Referenced by initialize_from_options().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_trigonal_planar_metal_positions_from_string_vector ( utility::vector1< std::string > const & vect )

Given an input vector of strings of the form "res1,res2,res3,metal_name", parse this and populate the trigonal_planar_metal_positions_ vector.

Resets the trigonal_planar_metal_positions_ vector.

References add_entry_to_trigonal_planar_metal_positions(), reset_trigonal_planar_metal_positions(), and protocols::TR().

Referenced by initialize_from_options().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_trigonal_pyramidal_metal_positions_from_string_vector ( utility::vector1< std::string > const & vect )

Given an input vector of strings of the form "res1,res2,res3,metal_name", parse this and populate the trigonal_pyramidal_metal_positions_ vector.

Resets the trigonal_pyramidal_metal_positions_ vector.

References add_entry_to_trigonal_pyramidal_metal_positions(), reset_trigonal_pyramidal_metal_positions(), and protocols::TR().

Referenced by initialize_from_options().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_cterm_isopeptide_cyclization_mover	(	protocols::cyclic_peptide::DeclareBondOP	termini,
		core::pose::PoseCOP	pose
	)		const

private

Set up the mover that creates C-terminal isopeptide bonds.

References cyclization_type(), find_first_and_last_isopeptide_residues(), protocols::cyclic_peptide_predict::SCPA_cterm_isopeptide_lariat, and protocols::TR().

Referenced by set_up_cyclization_mover().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_cyclization_mover	(	protocols::cyclic_peptide::DeclareBondOP	termini,
		core::pose::PoseCOP	pose,
		bool const	native = `false`,
		core::Size const	last_res = `0`,
		core::Size const	first_res = `0`
	)		const

private

Set up the DeclareBond mover used to connect the termini, or whatever atoms are involved in the cyclization. (Handles different cyclization modes).

References cyclization_type(), protocols::cyclic_peptide_predict::SCPA_cterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_invalid_type, protocols::cyclic_peptide_predict::SCPA_n_to_c_amide_bond, protocols::cyclic_peptide_predict::SCPA_nterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_sidechain_isopeptide, protocols::cyclic_peptide_predict::SCPA_terminal_disulfide, set_up_cterm_isopeptide_cyclization_mover(), set_up_n_to_c_cyclization_mover(), set_up_nterm_isopeptide_cyclization_mover(), set_up_sidechain_isopeptide_cyclization_mover(), and set_up_terminal_disulfide_cyclization_mover().

Referenced by depermute(), do_final_fastrelax(), genkic_close(), run(), and set_up_native().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_design_taskoperations	(	protocols::denovo_design::movers::FastDesignOP	fdes,
		core::Size const	cyclic_offset,
		core::Size const	nres,
		core::pose::PoseCOP	pose
	)		const

private

Set up the TaskOperations that conrol the design process, given user inputs.

Default behaviour is designing all positions with L-canonicals and their D-equivalents EXCEPT cys and met (and gly), unless the user overrides this.

References allowed_canonicals_by_position_, allowed_noncanonicals_by_position_, cyclization_type(), find_first_and_last_isopeptide_residues(), get_nc_name_codes(), get_oneletter_codes(), prohibit_D_at_negative_phi_, prohibit_L_at_positive_phi_, protocols::cyclic_peptide_predict::SCPA_cterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_nterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_sidechain_isopeptide, and protocols::TR().

Referenced by genkic_close().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_hbond_filter	(	protocols::filters::CombinedFilterOP	total_hbond,
		core::Size const	nres,
		core::scoring::ScoreFunctionOP	sfxn,
		core::Real const &	min_hbonds
	)		const

private

Set up the filters for the mainchain hydrogen bonds that will be used to discard solutions with too little mainchain hydrogen bonding.

References count_sc_hbonds_, do_not_count_adjacent_res_hbonds_, and hbond_energy_cutoff_.

Referenced by run().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_isopeptide_variants ( core::pose::PoseOP pose ) const

private

Given a pose, add sidechain conjugation variant types to sidechains involved in making an isopeptide bond, and strip termini from termini involved in the isopeptide bond.

References core::pose::add_lower_terminus_type_to_pose_residue(), core::pose::add_upper_terminus_type_to_pose_residue(), core::pose::add_variant_type_to_pose_residue(), cyclization_type(), find_first_and_last_isopeptide_residues(), core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), protocols::cyclic_peptide_predict::SCPA_cterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_nterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_sidechain_isopeptide, sequence_length(), and core::chemical::SIDECHAIN_CONJUGATION.

Referenced by run().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_n_to_c_cyclization_mover	(	protocols::cyclic_peptide::DeclareBondOP	termini,
		core::pose::PoseCOP	pose,
		bool const	native,
		core::Size const	last_res
	)		const

private

Set up the mover that creates N-to-C amide bonds, and which updates the atoms dependent on the amide bond.

References sequence_length(), and protocols::TR().

Referenced by set_up_cyclization_mover().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_native	(	core::pose::PoseOP	native_pose,
		core::Size const	expected_residue_count
	)		const

private

Sets up a terminial peptide bond and does some checks.

References cyclization_type(), is_supported_restype(), core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), protocols::cyclic_peptide_predict::SCPA_cterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_n_to_c_amide_bond, protocols::cyclic_peptide_predict::SCPA_nterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_terminal_disulfide, set_up_cyclization_mover(), set_up_terminal_disulfide_variants(), and protocols::TR().

Referenced by import_and_set_up_native(), and set_native().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_nterm_isopeptide_cyclization_mover	(	protocols::cyclic_peptide::DeclareBondOP	termini,
		core::pose::PoseCOP	pose
	)		const

private

Set up the mover that creates N-terminal isopeptide bonds.

References cyclization_type(), find_first_and_last_isopeptide_residues(), protocols::cyclic_peptide_predict::SCPA_nterm_isopeptide_lariat, and protocols::TR().

Referenced by set_up_cyclization_mover().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_sidechain_isopeptide_cyclization_mover	(	protocols::cyclic_peptide::DeclareBondOP	termini,
		core::pose::PoseCOP	pose
	)		const

private

Set up the mover that creates sidechain isopeptide bonds.

References cyclization_type(), find_first_and_last_isopeptide_residues(), protocols::cyclic_peptide_predict::SCPA_sidechain_isopeptide, and protocols::TR().

Referenced by set_up_cyclization_mover().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_terminal_disulfide_cyclization_mover	(	protocols::cyclic_peptide::DeclareBondOP	termini,
		core::pose::PoseCOP	pose,
		bool const	native,
		core::Size const	last_disulf_res,
		core::Size const	first_disulf_res
	)		const

private

Set up the mover that creates terminal disulfide bonds.

References find_first_disulf_res(), find_last_disulf_res(), and protocols::TR().

Referenced by set_up_cyclization_mover().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_terminal_disulfide_variants ( core::pose::PoseOP pose ) const

private

Given a pose, add disulfide variant types to the first and last cysteine residues in the pose.

This should ONLY be called on a pose just before a bond is declared between these residues.

References core::pose::add_lower_terminus_type_to_pose_residue(), core::pose::add_upper_terminus_type_to_pose_residue(), protocols::simple_moves::ModifyVariantTypeMover::apply(), find_first_disulf_res(), find_last_disulf_res(), protocols::simple_moves::ModifyVariantTypeMover::set_additional_type_to_add(), protocols::simple_moves::ModifyVariantTypeMover::set_residue_selector(), core::id::to_string(), and protocols::TR().

Referenced by depermute(), run(), and set_up_native().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_use_chainbreak_energy ( bool const setting )

Set whether we should use the chainbreak energy (true) or constraints (false) to enforce terminal amide bond geometry.

References use_chainbreak_energy_.

Referenced by initialize_from_options().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_use_rama_prepro_for_sampling ( bool const setting )

Set whether we're using RamaPrePro tables for sampling.

Setting this to "false" lets us use classic rama tables. True by default.

References use_rama_prepro_for_sampling_.

Referenced by initialize_from_options().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::store_disulfides	(	core::pose::PoseCOP	pose,
		utility::vector1< std::pair< core::Size, core::Size > > &	old_disulfides
	)		const

private

Given a pose, store a list of the disulfides in the pose.

Clears the old_disulfides list and repopulates it.

References core::conformation::disulfide_bonds().

Referenced by depermute().

void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::store_random_seed_info ( ) const

private

Store the state of the random generator from a previous run.

References rand_checkpoint_file_, core::scoring::rg, and suppress_checkpoints_.

Referenced by checkpoint(), and new_checkpoint_file().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::use_chainbreak_energy ( ) const

inlineprivate

Should we use the chainbreak energy (true) or constraints (false) to enforce terminal amide bond geometry?

References use_chainbreak_energy_.

Referenced by run().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::use_rama_filter ( ) const

inlineprivate

Are we using a rama filter? Defaults to true.

References use_rama_filter_.

Referenced by genkic_close().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::use_rama_prepro_for_sampling ( ) const

inlineprivate

Are we using RamaPrePro tables for sampling?

True if we are, false if we're using classic rama tables.

References use_rama_prepro_for_sampling_.

Referenced by genkic_close(), and set_mainchain_torsions().

Member Data Documentation

std::string protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::abba_bins_

private

Storage for a bin definition file.

Cached to prevent repeated read from disk.

Referenced by genkic_close(), initialize_from_options(), and set_abba_bins_binfile_contents().

std::map< core::Size, utility::vector1 < std::string > > protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::allowed_canonicals_by_position_

private

Allowed canonical residues at each position.

Only used for design. Map key "0" is used for default settings applied to any position not explicitly specified.

Referenced by initialize_from_options(), set_allowed_residues_by_position(), and set_up_design_taskoperations().

std::map< core::Size, utility::vector1 < std::string > > protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::allowed_noncanonicals_by_position_

private

Allowed noncanonical residues at each position.

Only used for design. Map key "0" is used for default settings applied to any position not explicitly specified.

Referenced by initialize_from_options(), set_allowed_residues_by_position(), and set_up_design_taskoperations().

core::Size protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::already_completed_job_count_

private

The number of jobs that this slave process has already completed. Only used in MPI mode; zero otherwise.

Referenced by run(), and set_already_completed_job_count().

core::Size protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::angle_length_relax_rounds_

private

Number of rounds of relaxation with flexible bond angles and bond lengths.

Default 0.

Referenced by angle_length_relax_rounds(), and set_angle_length_relax_rounds().

core::Size protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::angle_relax_rounds_

private

Number of rounds of relaxation with flexible bond angles.

Default 0.

Referenced by angle_relax_rounds(), and set_angle_relax_rounds().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::bondangle_perturbation_magnitude_ = 0.0

private

A small random value added to all backbone bond angles. Defaults to 0.

Referenced by genkic_close(), and initialize_from_options().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::bondlength_perturbation_magnitude_ = 0.0

private

A small random value added to all backbone bond lengths. Defaults to 0.

Referenced by genkic_close(), and initialize_from_options().

core::Size protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::cartesian_relax_rounds_

private

Number of rounds of Cartesian-space relaxation.

Default 0.

Referenced by cartesian_relax_rounds(), and set_cartesian_relax_rounds().

std::string protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::checkpoint_filename_

private

The name of the checkpoint file.

Defaults to "checkpoint.txt". Read from options.

Referenced by checkpoint(), end_checkpointing(), initialize_checkpointing(), initialize_from_options(), and new_checkpoint_file().

std::string protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::checkpoint_job_identifier_

private

A unique job name for checkpointing.

If none is provided, job is not checkpointed.

Referenced by checkpoint(), end_checkpointing(), initialize_checkpointing(), initialize_from_options(), and new_checkpoint_file().

std::string protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::comp_file_contents_D_alpha_

private

Storage for the composition constraint setup for the D-alpha helix region of Ramachandran space.

Cached to prevent repeated read from disk.

Referenced by genkic_close(), initialize_from_options(), and set_D_alpha_compfile_contents().

std::string protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::comp_file_contents_D_beta_

private

Storage for the composition constraint setup for the D-beta strand region of Ramachandran space.

Cached to prevent repeated read from disk.

Referenced by genkic_close(), initialize_from_options(), and set_D_beta_compfile_contents().

std::string protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::comp_file_contents_L_alpha_

private

Storage for the composition constraint setup for the L-alpha helix region of Ramachandran space.

Cached to prevent repeated read from disk.

Referenced by genkic_close(), initialize_from_options(), and set_L_alpha_compfile_contents().

std::string protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::comp_file_contents_L_beta_

private

Storage for the composition constraint setup for the L-beta strand region of Ramachandran space.

Cached to prevent repeated read from disk.

Referenced by genkic_close(), initialize_from_options(), and set_L_beta_compfile_contents().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::count_sc_hbonds_

private

Should sidechain-mainchain hydrogen bonds be counted when counting hydrogen bonds?

Defaults to false.

Referenced by initialize_from_options(), and set_up_hbond_filter().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::cyclic_permutations_

private

Should we consider cyclic permutations?

Defaults to true.

Referenced by initialize_from_options(), and run().

SCPA_cyclization_type protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::cyclization_type_

private

The type of cyclization.

Referenced by add_bondangle_perturbation(), add_bondlength_perturbation(), cyclization_type(), initialize_from_options(), and set_cyclization_type().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::D_alpha_comp_file_exists_

private

Has an aa_composition setup file ben provided for residues in the D-alpha helix region of Ramachadran space?

Referenced by genkic_close(), initialize_from_options(), and set_D_alpha_compfile_contents().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::D_beta_comp_file_exists_

private

Has an aa_composition setup file ben provided for residues in the D-beta strand region of Ramachadran space?

Referenced by genkic_close(), initialize_from_options(), and set_D_beta_compfile_contents().

core::scoring::Rama_Table_Type protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::default_rama_table_type_

private

A default custom Ramachandran table to be used for sampling.

Defaults to unknown_ramatable_type (which means that no custom Rama table is applied by default).

Referenced by default_rama_table_type(), and set_default_rama_table_type().

std::string protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::design_filename_

private

If we're designing, this is the filename for the file that tells us what residues are allowed at what postion.

If left blank, no file is read.

Referenced by initialize_from_options().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::design_peptide_

private

Should we design the peptide after sampling the conformation, or just relax it?

Default "false" (relax only; no design).

Referenced by genkic_close(), and initialize_from_options().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::disulf_energy_cutoff_postrelax_

private

The cutoff dslf_fa13 energy, post-relaxation, above which closure solutions are rejected.

Read from options.

Referenced by genkic_close(), and initialize_from_options().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::disulf_energy_cutoff_prerelax_

private

The cutoff dslf_fa13 energy, pre-relaxation, above which closure solutions are rejected.

Read from options.

Referenced by genkic_close(), and initialize_from_options().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::do_not_count_adjacent_res_hbonds_

private

Prevent counting of hydrogen bonds to adjacent residues?

Default true.

Referenced by initialize_from_options(), and set_up_hbond_filter().

utility::vector1< core::Size > protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::exclude_residues_from_rms_

private

Residues to exclude from the RMSD calculation. Defaults to empty list.

Referenced by align_and_calculate_rmsd(), initialize_from_options(), and is_residue_ignored_in_rms().

core::Size protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::fast_relax_rounds_

private

The number of FastReleax rounds to be applied whenever FastRelax is used.

Defaults to 3.

Referenced by genkic_close(), initialize_from_options(), and run().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::filter_oversaturated_hbond_acceptors_

private

Should we filter out solutions that have more than the allowed number of hydrogen bonds to an acceptor?

Default true.

Referenced by genkic_close(), and initialize_from_options().

core::Size protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::genkic_closure_attempts_

private

The number of attempts that will be made by the generalized kinematic closure machinery.

Defaults to 1.

Referenced by genkic_close(), and initialize_from_options().

core::Size protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::genkic_min_solution_count_

private

The minimum number of solutions that must be found by the generalized kinematic closure machinery before a single solution is chosen.

Defaults to 1.

Referenced by genkic_close(), and initialize_from_options().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::hbond_energy_cutoff_

private

The hbond energy cutoff above which a hbond is no longer counted.

Defaults to -0.25.

Referenced by initialize_from_options(), and set_up_hbond_filter().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::high_hbond_weight_multiplier_

private

For parts of the protocol that upweight the hydrogen bond terms, this is the factor by which these terms are upweighted.

Defaults to 10.0.

Referenced by initialize_from_options(), and run().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::L_alpha_comp_file_exists_

private

Has an aa_composition setup file ben provided for residues in the L-alpha helix region of Ramachadran space?

Referenced by genkic_close(), initialize_from_options(), and set_L_alpha_compfile_contents().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::L_beta_comp_file_exists_

private

Has an aa_composition setup file ben provided for residues in the L-beta strand region of Ramachadran space?

Referenced by genkic_close(), initialize_from_options(), and set_L_beta_compfile_contents().

core::Size protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::lariat_sidechain_index_

private

If the cyclization type is a lariat type, this is the index of the residue that provides the sidechain that connects to the N- or C-terminus.

If set to zero (default), the residue of appropriate type that's closest to the other end is used.

Referenced by find_first_and_last_isopeptide_residues(), and initialize_from_options().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::link_all_cys_with_tbmb_

private

Should all cysteine residues be linked with 1,3,5-tris(bromomethyl)benzene?

False by default.

Referenced by initialize_from_options(), and run().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::min_final_hbonds_

private

The minimum number of mainchain hydrogen bonds that a final solution must have.

Defaults to 0 (report only).

Referenced by initialize_from_options(), and run().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::min_genkic_hbonds_

private

The minimum number of mainchain hydrogen bonds that a generalized kinematic closure solution must have.

Defaults to 3.

Referenced by genkic_close(), initialize_from_options(), and run().

int protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::my_rank_

private

If this is called by MPI code, this can store the rank of the current process. Zero otherwise.

-------—— Data -------------------------—— --—— When you add new data to this class, -— --—— you must update the copy constructor -—

Referenced by run(), and set_my_rank().

utility::vector1< core::Size > protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::n_methyl_positions_

private

List of positions (in original sequence indexing – not permuted) that are N-methylated.

Defaults to empty list.

Referenced by add_n_methylation(), and initialize_from_options().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::native_exists_

private

Has the user specified a native structure?

Referenced by initialize_from_options(), run(), and set_native().

std::string protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::native_filename_

private

Filename for the native, if one is provided.

Referenced by initialize_from_options(), and run().

core::pose::PoseCOP protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::native_pose_

private

A native pose, provided by external code.

If provided, this prevents the app from reading from the filesystem in the run() function.

Referenced by run(), and set_native().

core::Size protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::nstruct_

private

Max number of structures to generate.

Referenced by initialize_from_options(), run(), and set_nstruct().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::octahedral_metal_constraints_energy_filter_multiplier_

private

Multiplier to make the octahedral metal constraints energy filter more permissive.

Default 1.0.

Referenced by genkic_close(), and initialize_from_options().

utility::vector1< std::pair< utility::fixedsizearray1< core::Size, 6 >, std::string > > protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::octahedral_metal_positions_

private

List of positions linked by a octahedrally-coordinated metal.

This is a vector of pairs of (lists of four residues, metal type string).

Referenced by add_entry_to_octahedral_metal_positions(), depermute(), genkic_close(), re_append_octahedral_metal_residues(), and reset_octahedral_metal_positions().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::octahedral_metal_sidechain_distance_filter_multiplier_

private

Multiplier to make the octahedral metal distance filter more permissive.

Default 1.0.

Referenced by genkic_close(), and initialize_from_options().

std::string protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::out_filename_

private

The prefix for the output filename.

Defaults to "S_".

Referenced by initialize_from_options(), and run().

std::string protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::out_scorefilename_

private

The output score file name.

Defaults to "default.sc".

Referenced by initialize_from_options().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::oversaturated_hbond_cutoff_energy_

private

The energy above which we no longer count a hydrogen bond to an acceptor for the filter.

Default -0.1.

Referenced by genkic_close(), and initialize_from_options().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::prevent_design_file_read_

private

Used to prevent this process from directly reading the input file if it has been read by another process and the information has been transmitted to this process.

Default false; set to true by set_allowed_residues_by_position().

Referenced by initialize_from_options().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::prohibit_D_at_negative_phi_

private

Should D-residues be prohibited at positions with negative phi values?

Default true.

Referenced by initialize_from_options(), and set_up_design_taskoperations().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::prohibit_L_at_positive_phi_

private

Should L-residues be prohibited at positions with positive phi values?

Default true.

Referenced by initialize_from_options(), and set_up_design_taskoperations().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::rama_cutoff_

private

The energy cutoff for the rama filter.

Defaults to 0.3.

Referenced by genkic_close(), and initialize_from_options().

std::map<core::Size, core::scoring::Rama_Table_Type> protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::rama_table_type_by_res_

private

Custom Ramachandran tables to be used for sampling, listed by residue.

Defaults to an empty map. Only mapped indicies have custom rama tables applied. Overrides default_rama_table_type_ (if used) at the residue indices in the map.

Referenced by custom_rama_table_defined(), rama_table_type_by_res(), and set_rama_table_type_by_res().

std::string protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::rand_checkpoint_file_

private

The name of the checkpoint file for the random number generator.

Defaults to "rng.state.gz". Read from options.

Referenced by erase_random_seed_info(), get_random_seed_info(), initialize_from_options(), and store_random_seed_info().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::required_symmetry_angle_threshold_

private

The cutoff, in degrees, to use when comparing mainchain torsion values to determine whether symmetry repeats are truely symmetric. Defaults to 10 degrees.

Referenced by genkic_close(), initialize_from_options(), and run().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::required_symmetry_mirroring_

private

If this option is used, then only backbones with mirror symmetry are accepted. Must be used with the -cyclic_peptide:require_symmetry_repeats flag.

Referenced by genkic_close(), initialize_from_options(), and run().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::required_symmetry_perturbation_

private

The random perturbation, in degrees, to be applied when copying mainchain torsion values to produce symmetric conformations.

Defaults to 0.0 (no perturbation).

Referenced by genkic_close(), and initialize_from_options().

core::Size protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::required_symmetry_repeats_

private

If this option is used, then only backbones that are cN (or sN, if mirror symmetry is required) symmetric will be accepted. For example, if set to 2, then only c2-symmetric backbones will be accepted.

Referenced by genkic_close(), initialize_from_options(), and run().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::sample_cis_pro_

private

At residues that are more likely to have cis omega values, sample cis some fraction of the time.

Currently applies only to L-proline and D-proline. Could be extended to beta-3-proline and to N-methylated amino acids, once those are added. Read from database.

Referenced by disable_cis_pro_sampling(), sample_cis_pro(), and set_sample_cis_pro_frequency().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::sample_cis_pro_frequency_

private

At residues that are more likely to have cis omega values, sample cis this fraction of the time.

Read from database.

Referenced by disable_cis_pro_sampling(), sample_cis_pro_frequency(), and set_sample_cis_pro_frequency().

core::scoring::ScoreFunctionOP protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::scorefxn_

private

The default ScoreFunction to use. The high h-bond version is constructed from this.

Referenced by initialize_from_options(), run(), set_scorefxn(), and SimpleCycpepPredictApplication().

std::string protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::sequence_file_

private

Filename for the text file containing the sequence of the peptide.

Must be provided with the -cyclic_peptide:sequence_file flag.

Referenced by initialize_from_options(), and run().

core::Size protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::sequence_length_

mutableprivate

The length of the sequence, excluding any cross-linkers.

Computed internally and stored for reference. This is also the index of the last sequence residue (with cross-linkers following in linear sequence).

Referenced by run(), and sequence_length().

std::string protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::sequence_string_

private

The string that would be read from a sequence file.

If provided by external code, prevents filesystem read in run() function.

Referenced by read_sequence(), and set_sequence().

std::pair< core::Size, core::Size > protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::sidechain_isopeptide_indices_

private

If the cyclization type is sidechain_isopeptide, these are the indices of the residues forming the sidechain-sidechain isopeptide bond.

If (0, 0), the default, then the most widely-separated pair of appropriate type is automatically chosen.

Referenced by find_first_and_last_isopeptide_residues(), and initialize_from_options().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::silent_out_

private

Should this application produce silent file output?

Referenced by initialize_from_options(), run(), and set_silentstructure_outputlist().

utility::vector1< core::io::silent::SilentStructOP >* protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::silentlist_

private

If silentlist_out_ is used, this is the list to append SilentStructurOPs to.

Note that this is a non-const pointer to a vector.

Referenced by run(), and set_silentstructure_outputlist().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::silentlist_out_

private

Should this application produce silent structure OP output, appending to a list?

Referenced by run(), and set_silentstructure_outputlist().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::square_planar_metal_constraints_energy_filter_multiplier_

private

Multiplier to make the square planar metal constraints energy filter more permissive.

Default 1.0.

Referenced by genkic_close(), and initialize_from_options().

utility::vector1< std::pair< utility::fixedsizearray1< core::Size, 4 >, std::string > > protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::square_planar_metal_positions_

private

List of positions linked by a metal with square planar geometry.

This is a vector of pairs of (lists of four residues, metal type string).

Referenced by add_entry_to_square_planar_metal_positions(), depermute(), genkic_close(), re_append_square_planar_metal_residues(), and reset_square_planar_metal_positions().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::square_planar_metal_sidechain_distance_filter_multiplier_

private

Multiplier to make the square planar metal distance filter more permissive.

Default 1.0.

Referenced by genkic_close(), and initialize_from_options().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::square_pyramidal_metal_constraints_energy_filter_multiplier_

private

Multiplier to make the square pyramidal metal constraints energy filter more permissive.

Default 1.0.

Referenced by genkic_close(), and initialize_from_options().

utility::vector1< std::pair< utility::fixedsizearray1< core::Size, 5 >, std::string > > protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::square_pyramidal_metal_positions_

private

List of positions linked by a metal with square pyramidal geometry.

This is a vector of pairs of (lists of five residues, metal type string).

Referenced by add_entry_to_square_pyramidal_metal_positions(), depermute(), genkic_close(), re_append_square_pyramidal_metal_residues(), and reset_square_pyramidal_metal_positions().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::square_pyramidal_metal_sidechain_distance_filter_multiplier_

private

Multiplier to make the square pyramidal metal distance filter more permissive.

Default 1.0.

Referenced by genkic_close(), and initialize_from_options().

utility::vector1< HierarchicalHybridJD_JobResultsSummaryOP >* protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::summarylist_

private

If silentlist_out_ is used, this is the list of job summaries to which summaries should be appended.

Note that this is a non-const pointer to a vector.

Referenced by run(), and set_silentstructure_outputlist().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::suppress_checkpoints_

private

Allows external code to suppress checkpointing, so that the SimpleCycpepPredictApplication doesn't write directly to disk.

Referenced by checkpoint(), end_checkpointing(), erase_random_seed_info(), initialize_checkpointing(), new_checkpoint_file(), set_suppress_checkpoints(), and store_random_seed_info().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::tbmb_constraints_energy_filter_multiplier_

private

Multiplier to make the TBMB constraints energy filter more permissive.

Default 1.0.

Referenced by genkic_close(), and initialize_from_options().

utility::vector1< utility::vector1 < core::Size > > protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::tbmb_positions_

mutableprivate

List of positions linked by 1,3,5-tris(bromomethyl)benzene.

This is a vector of lists of three residues.

Referenced by depermute(), genkic_close(), initialize_from_options(), and run().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::tbmb_sidechain_distance_filter_multiplier_

private

Multiplier to make the TBMB distance filter more permissive.

Default 1.0.

Referenced by genkic_close(), and initialize_from_options().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::tetrahedral_metal_constraints_energy_filter_multiplier_

private

Multiplier to make the tetrahedral metal constraints energy filter more permissive.

Default 1.0.

Referenced by genkic_close(), and initialize_from_options().

utility::vector1< std::pair< utility::fixedsizearray1< core::Size, 4 >, std::string > > protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::tetrahedral_metal_positions_

private

List of positions linked by a tetrahedrally-coordinated metal.

This is a vector of pairs of (lists of four residues, metal type string).

Referenced by add_entry_to_tetrahedral_metal_positions(), depermute(), genkic_close(), re_append_tetrahedral_metal_residues(), and reset_tetrahedral_metal_positions().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::tetrahedral_metal_sidechain_distance_filter_multiplier_

private

Multiplier to make the tetrahedral metal distance filter more permissive.

Default 1.0.

Referenced by genkic_close(), and initialize_from_options().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::tma_constraints_energy_filter_multiplier_

private

Multiplier to make the trimesic acid constraints energy filter more permissive.

Default 1.0.

Referenced by genkic_close(), and initialize_from_options().

utility::vector1< utility::vector1 < core::Size > > protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::tma_positions_

private

List of positions linked by trimesic acid.

This is a vector of lists of three residues.

Referenced by depermute(), genkic_close(), and initialize_from_options().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::tma_sidechain_distance_filter_multiplier_

private

Multiplier to make the trimesic acid distance filter more permissive.

Default 1.0.

Referenced by genkic_close(), and initialize_from_options().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::total_energy_cutoff_

private

The total energy cutoff above which solutions are discarded.

Defaults to 0.0.

Referenced by run(), and set_total_energy_cutoff().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::trigonal_planar_metal_constraints_energy_filter_multiplier_

private

Multiplier to make the trigonal planar metal constraints energy filter more permissive.

Default 1.0.

Referenced by genkic_close(), and initialize_from_options().

utility::vector1< std::pair< utility::fixedsizearray1< core::Size, 3 >, std::string > > protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::trigonal_planar_metal_positions_

private

List of positions linked by a metal coordinated with trigonal planar geometry.

This is a vector of pairs of (lists of four residues, metal type string).

Referenced by add_entry_to_trigonal_planar_metal_positions(), depermute(), genkic_close(), re_append_trigonal_metal_residues(), and reset_trigonal_planar_metal_positions().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::trigonal_planar_metal_sidechain_distance_filter_multiplier_

private

Multiplier to make the trigonal planar metal distance filter more permissive.

Default 1.0.

Referenced by genkic_close(), and initialize_from_options().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::trigonal_pyramidal_metal_constraints_energy_filter_multiplier_

private

Multiplier to make the trigonal pyramidal metal constraints energy filter more permissive.

Default 1.0.

Referenced by genkic_close(), and initialize_from_options().

utility::vector1< std::pair< utility::fixedsizearray1< core::Size, 3 >, std::string > > protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::trigonal_pyramidal_metal_positions_

private

List of positions linked by a metal coordinated with trigonal pyramidal geometry.

This is a vector of pairs of (lists of four residues, metal type string).

Referenced by add_entry_to_trigonal_pyramidal_metal_positions(), depermute(), genkic_close(), re_append_trigonal_metal_residues(), and reset_trigonal_pyramidal_metal_positions().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::trigonal_pyramidal_metal_sidechain_distance_filter_multiplier_

private

Multiplier to make the trigonal pyramidal metal distance filter more permissive.

Default 1.0.

Referenced by genkic_close(), and initialize_from_options().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::try_all_disulfides_

private

Should we try all disulfide combinations during structure prediction?

Default false. Read from options.

Referenced by genkic_close(), and initialize_from_options().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::use_aa_comp_

private

Should we use the aa_composition score term in design?

Default false.

Referenced by initialize_from_options(), and run().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::use_chainbreak_energy_

private

Should we use the chainbreak energy (true) or constraints (false) to enforce terminal amide bond geometry?

True by default (use chainbreak energy).

Referenced by set_use_chainbreak_energy(), and use_chainbreak_energy().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::use_octahedral_metal_filters_

private

If true, filters are applied based on distance between metal-conjugated residues and on constraints to discard GenKIC solutions that can't be crosslinked easily.

True by default.

Referenced by genkic_close(), and initialize_from_options().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::use_rama_filter_

private

Should solutions be filtered by Ramachandran energy (in the case of alpha-amino acids)?

Defaults to true.

Referenced by initialize_from_options(), and use_rama_filter().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::use_rama_prepro_for_sampling_

private

Should we use rama_prepro tables for sampling?

Default true.

Referenced by set_use_rama_prepro_for_sampling(), and use_rama_prepro_for_sampling().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::use_square_planar_metal_filters_

private

If true, filters are applied based on distance between metal-conjugated residues and on constraints to discard GenKIC solutions that can't be crosslinked easily.

True by default.

Referenced by genkic_close(), and initialize_from_options().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::use_square_pyramidal_metal_filters_

private

If true, filters are applied based on distance between metal-conjugated residues and on constraints to discard GenKIC solutions that can't be crosslinked easily.

True by default.

Referenced by genkic_close(), and initialize_from_options().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::use_tbmb_filters_

private

If true, filters are applied based on distance between TBMB cysteines and on constraints to discard GenKIC solutions that can't be crosslinked easily.

True by default.

Referenced by genkic_close(), and initialize_from_options().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::use_tetrahedral_metal_filters_

private

If true, filters are applied based on distance between metal-conjugated residues and on constraints to discard GenKIC solutions that can't be crosslinked easily.

True by default.

Referenced by genkic_close(), and initialize_from_options().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::use_tma_filters_

private

If true, filters are applied based on distance between trimesic acid-conjugated residues and on constraints to discard GenKIC solutions that can't be crosslinked easily.

True by default.

Referenced by genkic_close(), and initialize_from_options().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::use_total_energy_cutoff_

private

Determines whether the total energy cutoff should be used.

Defaults to 'false'.

Referenced by disable_total_energy_cutoff(), run(), and set_total_energy_cutoff().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::use_trigonal_planar_metal_filters_

private

If true, filters are applied based on distance between metal-conjugated residues and on constraints to discard GenKIC solutions that can't be crosslinked easily.

True by default.

Referenced by genkic_close(), and initialize_from_options().

bool protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::use_trigonal_pyramidal_metal_filters_

private

If true, filters are applied based on distance between metal-conjugated residues and on constraints to discard GenKIC solutions that can't be crosslinked easily.

True by default.

Referenced by genkic_close(), and initialize_from_options().

std::map< core::Size, utility::vector1 < core::Real > > protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::user_set_alpha_dihedrals_

private

Map of (seqpos -> phi/psi/omega triplet).

The user can set certain alpha-amino acid mainchain dihedral values, if he or she so wishes.

Referenced by genkic_close(), and initialize_from_options().

core::Real protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::user_set_dihedral_perturbation_ = 0.0

private

A small random value added to all user-set dihedral values. Defaults to 0.

Referenced by genkic_close(), and initialize_from_options().

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