Application-level code for simple_cycpep_predict application. More...
#include <SimpleCycpepPredictApplication.hh>
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 (std::string const &binfile_in) |
| Set the bin transitions file. 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... | |
| void | find_first_and_last_thioether_lariat_residues (core::pose::PoseCOP pose, core::Size &firstres, core::Size &lastres) const |
| Given a pose, find the first and last thioether lariat 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::simple_moves::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::simple_moves::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::simple_moves::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::simple_moves::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::simple_moves::DeclareBondOP termini, core::pose::PoseCOP pose) const |
| Set up the mover that creates sidechain isopeptide bonds. More... | |
| void | set_up_thioether_lariat_cyclization_mover (protocols::simple_moves::DeclareBondOP termini, core::pose::PoseCOP pose) const |
| Set up the mover that creates thioether lariat bonds. More... | |
| void | set_up_cyclization_mover (protocols::simple_moves::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_thioether_lariat_cyclic_constraints (core::pose::PoseOP pose, core::Size n_index, core::Size c_index) const |
| Function to add thioether lariat 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... | |
| protocols::filters::FilterOP | set_up_hbond_filter (core::Size const min_hbonds) const |
| Set up the filters for the mainchain hydrogen bonds that will be used to discard solutions with too few mainchain hydrogen bonds. 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_thioether_lariat (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::FilterOP 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, paraBBMB, 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 | find_first_and_last_polymer_residues (core::pose::Pose const &pose, core::Size &first_polymer_res, core::Size &last_polymer_res) const |
| Find the first and last polymer residues in a pose. 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... | |
| core::Size | set_up_terminal_thioether_lariat_variants (core::pose::PoseOP pose) const |
| Given a pose, add sidechain conjugation variant types to the C-terminal cysteine and add a special acetyl terminus to the N-terminal residue. 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 worker 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_binfile_ = "ABBA.bin_params" |
| Filename for the bin transitions data. 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 > > | parabbmb_positions_ |
| List of positions linked by 1,4-bis(bromomethyl)benzene. More... | |
| bool | link_all_cys_with_parabbmb_ = false |
| Should all cysteine residues be linked with 1,3,5-tris(bromomethyl)benzene? More... | |
| bool | use_parabbmb_filters_ = true |
| If true, filters are applied based on distance between paraBBMB cysteines and on constraints to discard GenKIC solutions that can't be crosslinked easily. More... | |
| core::Real | parabbmb_sidechain_distance_filter_multiplier_ = 1.0 |
| Multiplier to make the paraBBMB distance filter more permissive. More... | |
| core::Real | parabbmb_constraints_energy_filter_multiplier_ = 1.0 |
| Multiplier to make the paraBBMB constraints energy filter more permissive. 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... | |
| std::string | out_prefix_ = "" |
| Output prefix for PDB files. More... | |
| std::string | out_suffix_ = "" |
| Output suffix for PDB files. More... | |
| std::string | out_path_ = "" |
| Output directory for PDB files. More... | |
Detailed Description
Application-level code for simple_cycpep_predict application.
Also called by the BOINC minirosetta app.
Constructor & Destructor Documentation
◆ SimpleCycpepPredictApplication() [1/2]
| 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(), and protocols::cyclic_peptide_predict::register_with_citation_manager().
◆ ~SimpleCycpepPredictApplication()
|
overridedefault |
Explicit virtual destructor.
◆ SimpleCycpepPredictApplication() [2/2]
| protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::SimpleCycpepPredictApplication | ( | SimpleCycpepPredictApplication const & | src | ) |
Explicit copy constructor.
References scorefxn_.
Member Function Documentation
◆ add_amide_bond_cyclic_constraints()
|
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::chemical::ICoorAtomID::atomno(), core::id::AtomID::atomno(), core::chemical::ResidueType::icoor(), core::chemical::ResidueType::lower_connect_atom(), core::chemical::ResidueType::mainchain_atoms(), core::chemical::ResidueType::n_possible_residue_connections(), core::chemical::ResidueType::residue_connect_atom_index(), core::id::AtomID::rsd(), sequence_length(), SimpleCycpepPredictApplication_PEPBOND_C_ANGLE, SimpleCycpepPredictApplication_PEPBOND_LENGTH, SimpleCycpepPredictApplication_PEPBOND_N_ANGLE, core::chemical::AtomICoor::stub_atom1(), protocols::TR(), and core::chemical::ResidueType::upper_connect_atom().
Referenced by add_cyclic_constraints().
◆ add_bondangle_perturbation()
|
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(), core::chemical::ResidueType::atom_name(), 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().
◆ add_bondlength_perturbation()
|
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(), core::chemical::ResidueType::atom_name(), 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().
◆ add_closebond_logic()
|
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(), add_closebond_logic_thioether_lariat(), 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, and protocols::cyclic_peptide_predict::SCPA_thioether_lariat.
Referenced by genkic_close().
◆ add_closebond_logic_isopeptide()
|
private |
Set up the logic to close the bond at the cyclization point.
This version is for all types of isopeptide bond cyclization.
This version is for all types of isopeptide bond cyclization.
- Note
- cyclization_point_start > cyclization_point_end
References core::chemical::ResidueTypeBase::aa(), core::chemical::ResidueType::atom_name(), core::chemical::ICoorAtomID::atomno(), cyclization_type(), core::chemical::ResidueType::icoor(), is_isopeptide_forming_amide_type(), is_isopeptide_forming_carbonyl_type(), protocols::antibody::l1, core::chemical::ResidueType::lower_connect_atom(), core::chemical::ResidueType::n_possible_residue_connections(), core::chemical::ResidueTypeBase::name3(), protocols::generalized_kinematic_closure::perturber::randomize_dihedral, core::chemical::ResidueType::residue_connect_atom_index(), 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, SimpleCycpepPredictApplication_PEPBOND_N_ANGLE, core::chemical::AtomICoor::stub_atom1(), and core::chemical::ResidueType::upper_connect_atom().
Referenced by add_closebond_logic().
◆ add_closebond_logic_n_to_c_amide_bond()
|
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().
◆ add_closebond_logic_terminal_disulfide()
|
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().
◆ add_closebond_logic_thioether_lariat()
|
private |
Set up the logic to close the bond at the cyclization point.
This version is for all types of thioether lariat cyclization.
This version is for thioether lariat cyclization.
- Note
- cyclization_point_start > cyclization_point_end
References core::chemical::ResidueType::atom_name(), core::chemical::ICoorAtomID::atomno(), cyclization_type(), core::chemical::ResidueTypeBase::get_disulfide_atom_name(), core::chemical::ResidueType::icoor(), core::chemical::ResidueType::n_possible_residue_connections(), protocols::generalized_kinematic_closure::perturber::randomize_dihedral, core::chemical::ResidueType::residue_connect_atom_index(), protocols::cyclic_peptide_predict::SCPA_thioether_lariat, core::chemical::AtomICoor::stub_atom1(), protocols::cyclic_peptide::crosslinker::THIOETHER_UTIL_THIOETHER_BOND_C_ANGLE, protocols::cyclic_peptide::crosslinker::THIOETHER_UTIL_THIOETHER_BOND_LENGTH, and protocols::cyclic_peptide::crosslinker::THIOETHER_UTIL_THIOETHER_BOND_N_ANGLE.
Referenced by add_closebond_logic().
◆ add_cutpoint_variants_at_termini()
|
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().
◆ add_cyclic_constraints()
|
private |
Function to add cyclic constraints to a pose.
Calls functions that do this for particular cyclization types.
References add_amide_bond_cyclic_constraints(), add_thioether_lariat_cyclic_constraints(), cyclization_type(), find_first_and_last_isopeptide_residues(), find_first_and_last_thioether_lariat_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, protocols::cyclic_peptide_predict::SCPA_terminal_disulfide, and protocols::cyclic_peptide_predict::SCPA_thioether_lariat.
Referenced by run().
◆ add_entry_to_octahedral_metal_positions()
| 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().
◆ add_entry_to_square_planar_metal_positions()
| 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().
◆ add_entry_to_square_pyramidal_metal_positions()
| 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().
◆ add_entry_to_tetrahedral_metal_positions()
| 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().
◆ add_entry_to_trigonal_planar_metal_positions()
| 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().
◆ add_entry_to_trigonal_pyramidal_metal_positions()
| 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().
◆ add_n_methylation()
|
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().
◆ add_thioether_lariat_cyclic_constraints()
|
private |
Function to add thioether lariat constraints to a pose.
Function to add thioether lariat cyclic constraints to a pose.
This version does this for thioether lariats.
- 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 protocols::cyclic_peptide::crosslinker::set_up_thioether_constraints().
Referenced by add_cyclic_constraints().
◆ align_and_calculate_rmsd()
| 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(), core::pose::Pose::total_residue(), and protocols::TR().
Referenced by run().
◆ angle_length_relax_rounds()
|
inlineprivate |
Bond angle / bond length relax rounds.
References angle_length_relax_rounds_.
Referenced by genkic_close(), and run().
◆ angle_relax_rounds()
|
inlineprivate |
◆ break_disulfides()
|
private |
Given a pose and a list of the disulfides in the pose, break the disulfides.
References core::conformation::break_disulfide().
Referenced by depermute().
◆ build_polymer()
|
private |
Actually build the geometry that we'll be working with.
References protocols::cyclic_peptide::PeptideStubMover::add_residue(), protocols::cyclic_peptide::PeptideStubMover::apply(), protocols::cyclic_peptide::PeptideStubMover::reset_mover_data(), protocols::cyclic_peptide::PeptideStubMover::set_reset_mode(), and protocols::TR().
Referenced by check_loop_length(), and run().
◆ cartesian_relax_rounds()
|
inlineprivate |
Cartesian relax rounds.
References cartesian_relax_rounds_.
Referenced by genkic_close(), and run().
◆ check_loop_length()
|
private |
Check that the loop formed is long enough.
References build_polymer(), cyclization_type(), find_first_and_last_isopeptide_residues(), find_first_and_last_thioether_lariat_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, protocols::cyclic_peptide_predict::SCPA_terminal_disulfide, and protocols::cyclic_peptide_predict::SCPA_thioether_lariat.
Referenced by run().
◆ checkpoint()
|
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().
◆ count_cis_peptide_bonds()
|
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().
◆ current_position()
|
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().
◆ custom_rama_table_defined()
|
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().
◆ cyclization_type()
|
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_closebond_logic_thioether_lariat(), add_cyclic_constraints(), check_loop_length(), depermute(), find_first_and_last_isopeptide_residues(), find_first_and_last_thioether_lariat_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(), set_up_sidechain_isopeptide_cyclization_mover(), set_up_terminal_thioether_lariat_variants(), and set_up_thioether_lariat_cyclization_mover().
◆ default_rama_table_type()
|
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().
◆ depermute()
|
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_, parabbmb_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().
◆ depermute_disulfide_list()
|
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().
◆ disable_cis_pro_sampling()
| void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::disable_cis_pro_sampling | ( | ) |
Set cis proline sampling OFF.
References sample_cis_pro_, and sample_cis_pro_frequency_.
◆ disable_total_energy_cutoff()
| void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::disable_total_energy_cutoff | ( | ) |
Sets use_total_energy_cutoff_ to 'false'.
References use_total_energy_cutoff_.
◆ do_cyclic_permutation()
|
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().
◆ do_final_fastrelax()
|
private |
Carry out the final FastRelax.
References set_up_cyclization_mover(), and protocols::TR().
Referenced by run().
◆ end_checkpointing()
|
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().
◆ erase_random_seed_info()
|
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().
◆ find_first_and_last_isopeptide_residues()
|
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().
◆ find_first_and_last_polymer_residues()
|
private |
Find the first and last polymer residues in a pose.
References core::chemical::ResidueTypeBase::is_polymer(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().
Referenced by set_up_isopeptide_variants(), set_up_terminal_disulfide_variants(), and set_up_terminal_thioether_lariat_variants().
◆ find_first_and_last_thioether_lariat_residues()
|
private |
Given a pose, find the first and last thioether lariat bond-forming residues.
First residue is 1 by definition (chloroacetyl goes where??); last is TYPICALLY C-term in the classic peptidream approach but does not have to be. n.b. Suga has methods for incorporating additional cysteines into bicyclic peptides, but for the moment "closest to the opposite terminus" is sufficient.
References cyclization_type(), find_last_disulf_res(), lariat_sidechain_index_, and protocols::cyclic_peptide_predict::SCPA_thioether_lariat.
Referenced by add_cyclic_constraints(), check_loop_length(), genkic_close(), set_up_terminal_thioether_lariat_variants(), and set_up_thioether_lariat_cyclization_mover().
◆ find_first_disulf_res()
|
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().
◆ find_last_disulf_res()
|
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(), find_first_and_last_thioether_lariat_residues(), genkic_close(), set_up_terminal_disulfide_cyclization_mover(), and set_up_terminal_disulfide_variants().
◆ genkic_close()
|
private |
Use GeneralizedKIC to close the pose.
References core::chemical::aa_dpr, core::chemical::aa_pro, abba_bins_binfile_, add_bondangle_perturbation(), add_bondlength_perturbation(), add_closebond_logic(), protocols::generalized_kinematic_closure::filter::alpha_aa_rama_check, angle_length_relax_rounds(), angle_relax_rounds(), bondangle_perturbation_magnitude_, bondlength_perturbation_magnitude_, cartesian_relax_rounds(), comp_file_contents_D_alpha_, comp_file_contents_D_beta_, comp_file_contents_L_alpha_, comp_file_contents_L_beta_, protocols::generalized_kinematic_closure::perturber::copy_backbone_dihedrals, current_position(), custom_rama_table_defined(), cyclization_type(), D_alpha_comp_file_exists_, D_beta_comp_file_exists_, default_rama_table_type(), design_peptide_, disulf_energy_cutoff_postrelax_, disulf_energy_cutoff_prerelax_, core::scoring::dslf_fa13, fast_relax_rounds_, filter_oversaturated_hbond_acceptors_, find_first_and_last_isopeptide_residues(), find_first_and_last_thioether_lariat_residues(), find_first_disulf_res(), find_last_disulf_res(), genkic_closure_attempts_, genkic_min_solution_count_, L_alpha_comp_file_exists_, L_beta_comp_file_exists_, protocols::generalized_kinematic_closure::filter::loop_bump_check, protocols::generalized_kinematic_closure::selector::lowest_energy_selector, min_genkic_hbonds_, protocols::generalized_kinematic_closure::perturber::mirror_backbone_dihedrals, octahedral_metal_constraints_energy_filter_multiplier_, octahedral_metal_positions_, octahedral_metal_sidechain_distance_filter_multiplier_, original_position(), oversaturated_hbond_cutoff_energy_, parabbmb_constraints_energy_filter_multiplier_, parabbmb_positions_, parabbmb_sidechain_distance_filter_multiplier_, protocols::generalized_kinematic_closure::perturber::perturb_dihedral, position_backbone_is_randomizable(), rama_cutoff_, protocols::generalized_kinematic_closure::filter::rama_prepro_check, rama_table_type_by_res(), protocols::generalized_kinematic_closure::perturber::randomize_alpha_backbone_by_rama, protocols::generalized_kinematic_closure::perturber::randomize_backbone_by_rama_prepro, required_symmetry_angle_threshold_, required_symmetry_mirroring_, required_symmetry_perturbation_, required_symmetry_repeats_, core::scoring::rg, protocols::generalized_kinematic_closure::perturber::sample_cis_peptide_bond, sample_cis_pro(), sample_cis_pro_frequency(), 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, protocols::cyclic_peptide_predict::SCPA_thioether_lariat, sequence_length(), protocols::generalized_kinematic_closure::perturber::set_dihedral, set_up_cyclization_mover(), set_up_design_taskoperations(), square_planar_metal_constraints_energy_filter_multiplier_, square_planar_metal_positions_, square_planar_metal_sidechain_distance_filter_multiplier_, square_pyramidal_metal_constraints_energy_filter_multiplier_, square_pyramidal_metal_positions_, square_pyramidal_metal_sidechain_distance_filter_multiplier_, tbmb_constraints_energy_filter_multiplier_, tbmb_positions_, tbmb_sidechain_distance_filter_multiplier_, tetrahedral_metal_constraints_energy_filter_multiplier_, tetrahedral_metal_positions_, tetrahedral_metal_sidechain_distance_filter_multiplier_, tma_constraints_energy_filter_multiplier_, tma_positions_, tma_sidechain_distance_filter_multiplier_, protocols::TR(), trigonal_planar_metal_constraints_energy_filter_multiplier_, trigonal_planar_metal_positions_, trigonal_planar_metal_sidechain_distance_filter_multiplier_, trigonal_pyramidal_metal_constraints_energy_filter_multiplier_, trigonal_pyramidal_metal_positions_, trigonal_pyramidal_metal_sidechain_distance_filter_multiplier_, try_all_disulfides_, core::scoring::unknown_ramatable_type, use_octahedral_metal_filters_, use_parabbmb_filters_, use_rama_filter(), use_rama_prepro_for_sampling(), use_square_planar_metal_filters_, use_square_pyramidal_metal_filters_, use_tbmb_filters_, use_tetrahedral_metal_filters_, use_tma_filters_, use_trigonal_planar_metal_filters_, use_trigonal_pyramidal_metal_filters_, user_set_alpha_dihedrals_, and user_set_dihedral_perturbation_.
Referenced by run().
◆ get_cyclization_name_from_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, protocols::cyclic_peptide_predict::SCPA_terminal_disulfide, and protocols::cyclic_peptide_predict::SCPA_thioether_lariat.
Referenced by get_cyclization_type_from_name().
◆ get_cyclization_type_from_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().
◆ get_nc_name_codes()
|
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().
◆ get_oneletter_codes()
|
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().
◆ get_rama_table_type_from_name()
|
private |
Given a Rama_Table_Type name, return the Rama_Table_Type, or an informative error message on failure.
References core::scoring::rama, and core::scoring::unknown_ramatable_type.
Referenced by set_default_rama_table_type(), and set_rama_table_type_by_res().
◆ get_random_seed_info()
|
private |
Restore the state of the random generator from a previous run.
References rand_checkpoint_file_, and core::scoring::rg.
Referenced by initialize_checkpointing().
◆ import_and_set_up_native()
|
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().
◆ initialize_checkpointing()
|
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().
◆ initialize_from_options()
| void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::initialize_from_options | ( | ) |
Initialize the application.
Initializes using the option system.
References allowed_canonicals_by_position_, allowed_noncanonicals_by_position_, bondangle_perturbation_magnitude_, bondlength_perturbation_magnitude_, checkpoint_filename_, checkpoint_job_identifier_, comp_file_contents_D_alpha_, comp_file_contents_D_beta_, comp_file_contents_L_alpha_, comp_file_contents_L_beta_, count_sc_hbonds_, cyclic_permutations_, cyclization_type(), cyclization_type_, D_alpha_comp_file_exists_, D_beta_comp_file_exists_, design_filename_, design_peptide_, disulf_energy_cutoff_postrelax_, disulf_energy_cutoff_prerelax_, do_not_count_adjacent_res_hbonds_, exclude_residues_from_rms_, fast_relax_rounds_, filter_oversaturated_hbond_acceptors_, genkic_closure_attempts_, genkic_min_solution_count_, get_cyclization_type_from_name(), core::scoring::get_score_function(), hbond_energy_cutoff_, high_hbond_weight_multiplier_, is_lariat_type(), L_alpha_comp_file_exists_, L_beta_comp_file_exists_, lariat_sidechain_index_, link_all_cys_with_parabbmb_, link_all_cys_with_tbmb_, min_final_hbonds_, min_genkic_hbonds_, n_methyl_positions_, native_exists_, native_filename_, nstruct_, octahedral_metal_constraints_energy_filter_multiplier_, octahedral_metal_sidechain_distance_filter_multiplier_, out_filename_, out_path_, out_prefix_, out_scorefilename_, out_suffix_, oversaturated_hbond_cutoff_energy_, parabbmb_constraints_energy_filter_multiplier_, parabbmb_positions_, parabbmb_sidechain_distance_filter_multiplier_, protocols::hybridization::path, prevent_design_file_read_, prohibit_D_at_negative_phi_, prohibit_L_at_positive_phi_, rama_cutoff_, rand_checkpoint_file_, protocols::cyclic_peptide_predict::read_file_into_string(), protocols::cyclic_peptide_predict::read_peptide_design_file(), required_symmetry_angle_threshold_, required_symmetry_mirroring_, required_symmetry_perturbation_, required_symmetry_repeats_, scorefxn_, 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, protocols::cyclic_peptide_predict::SCPA_thioether_lariat, sequence_file_, set_angle_length_relax_rounds(), set_angle_relax_rounds(), set_cartesian_relax_rounds(), set_cyclization_type(), set_default_rama_table_type(), set_octahedral_metal_positions_from_string_vector(), set_rama_table_type_by_res(), set_sample_cis_pro_frequency(), set_square_planar_metal_positions_from_string_vector(), set_square_pyramidal_metal_positions_from_string_vector(), set_tetrahedral_metal_positions_from_string_vector(), set_total_energy_cutoff(), set_trigonal_planar_metal_positions_from_string_vector(), set_trigonal_pyramidal_metal_positions_from_string_vector(), set_use_chainbreak_energy(), set_use_rama_prepro_for_sampling(), sidechain_isopeptide_indices_, silent_out_, square_planar_metal_constraints_energy_filter_multiplier_, square_planar_metal_sidechain_distance_filter_multiplier_, square_pyramidal_metal_constraints_energy_filter_multiplier_, square_pyramidal_metal_sidechain_distance_filter_multiplier_, tbmb_constraints_energy_filter_multiplier_, tbmb_positions_, tbmb_sidechain_distance_filter_multiplier_, tetrahedral_metal_constraints_energy_filter_multiplier_, tetrahedral_metal_sidechain_distance_filter_multiplier_, tma_constraints_energy_filter_multiplier_, tma_positions_, tma_sidechain_distance_filter_multiplier_, protocols::TR(), trigonal_planar_metal_constraints_energy_filter_multiplier_, trigonal_planar_metal_sidechain_distance_filter_multiplier_, trigonal_pyramidal_metal_constraints_energy_filter_multiplier_, trigonal_pyramidal_metal_sidechain_distance_filter_multiplier_, try_all_disulfides_, use_aa_comp_, use_octahedral_metal_filters_, use_parabbmb_filters_, use_rama_filter_, use_square_planar_metal_filters_, use_square_pyramidal_metal_filters_, use_tbmb_filters_, use_tetrahedral_metal_filters_, use_tma_filters_, use_trigonal_planar_metal_filters_, use_trigonal_pyramidal_metal_filters_, user_set_alpha_dihedrals_, and user_set_dihedral_perturbation_.
Referenced by SimpleCycpepPredictApplication().
◆ is_isopeptide_forming_amide_type()
|
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().
◆ is_isopeptide_forming_carbonyl_type()
|
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 protocols::cluster::calibur::aa, 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().
◆ is_lariat_type()
|
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, protocols::cyclic_peptide_predict::SCPA_nterm_isopeptide_lariat, and protocols::cyclic_peptide_predict::SCPA_thioether_lariat.
Referenced by initialize_from_options().
◆ is_residue_ignored_in_rms()
|
private |
Is this residue to be ignored in calculating RMSDs?
References exclude_residues_from_rms_.
Referenced by align_and_calculate_rmsd().
◆ is_supported_restype()
|
private |
----------— Methods -------------------------—
Is a residue type supported for macrocycle structure prediction?
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.
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().
◆ new_checkpoint_file()
|
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().
◆ original_position()
|
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().
◆ position_backbone_is_randomizable()
|
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().
◆ rama_table_type_by_res()
|
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().
◆ re_append_linker_residues()
|
private |
Given a pose with a linker (e.g. TBMB, paraBBMB, 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().
◆ re_append_octahedral_metal_residues()
|
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().
◆ re_append_square_planar_metal_residues()
|
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().
◆ re_append_square_pyramidal_metal_residues()
|
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().
◆ re_append_tetrahedral_metal_residues()
|
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().
◆ re_append_trigonal_metal_residues()
|
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().
◆ read_sequence()
|
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().
◆ rebuild_disulfides()
|
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().
◆ register_options()
|
static |
Register the set of options that this application uses (for the help menu).
References protocols::hybridization::path.
◆ reset_octahedral_metal_positions()
| 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().
◆ reset_square_planar_metal_positions()
| 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().
◆ reset_square_pyramidal_metal_positions()
| 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().
◆ reset_tetrahedral_metal_positions()
| 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().
◆ reset_trigonal_planar_metal_positions()
| 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().
◆ reset_trigonal_pyramidal_metal_positions()
| 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().
◆ run()
| 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, protocols::viewer::add_conformation_viewer(), 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(), protocols::viewer::clear_conformation_viewers(), protocols::cyclic_peptide::crosslinker::correct_thioether_virtuals(), 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::pose::get_center_of_mass(), 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_parabbmb_, 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_, out_path_, out_prefix_, out_suffix_, parabbmb_positions_, 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, protocols::cyclic_peptide_predict::SCPA_thioether_lariat, 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(), set_up_terminal_thioether_lariat_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().
◆ sample_cis_pro()
|
inlineprivate |
Are we sampling cis-prolines?
Defaults to false.
References sample_cis_pro_.
Referenced by genkic_close().
◆ sample_cis_pro_frequency()
|
inlineprivate |
Frequency for sampling cis prolines.
References sample_cis_pro_frequency_.
Referenced by genkic_close().
◆ sequence_length()
|
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(), and set_up_n_to_c_cyclization_mover().
◆ set_abba_bins_binfile()
| void protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_abba_bins_binfile | ( | std::string const & | binfile_in | ) |
Set the bin transitions file.
References abba_bins_binfile_.
◆ set_allowed_residues_by_position()
| 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_.
◆ set_already_completed_job_count()
| 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_.
◆ set_angle_length_relax_rounds()
| 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().
◆ set_angle_relax_rounds()
| 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().
◆ set_cartesian_relax_rounds()
| 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().
◆ set_cyclization_type()
| 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().
◆ set_D_alpha_compfile_contents()
| 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_.
◆ set_D_beta_compfile_contents()
| 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_.
◆ set_default_rama_table_type()
|
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().
◆ set_L_alpha_compfile_contents()
| 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_.
◆ set_L_beta_compfile_contents()
| 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_.
◆ set_mainchain_torsions()
|
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::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::rg, protocols::cyclic_peptide_predict::SCPA_nterm_isopeptide_lariat, protocols::cyclic_peptide_predict::SCPA_sidechain_isopeptide, protocols::cyclic_peptide_predict::SCPA_terminal_disulfide, protocols::cyclic_peptide_predict::SCPA_thioether_lariat, sequence_length(), protocols::TR(), core::scoring::unknown_ramatable_type, and use_rama_prepro_for_sampling().
Referenced by run().
◆ set_my_rank()
| 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_.
◆ set_native()
| 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().
◆ set_nstruct()
| 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_.
◆ set_octahedral_metal_positions_from_string_vector()
| 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().
◆ set_rama_table_type_by_res()
|
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().
◆ set_sample_cis_pro_frequency()
| 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().
◆ set_scorefxn()
| 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_.
◆ set_sequence()
| 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_.
◆ set_silentstructure_outputlist()
| 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_.
◆ set_square_planar_metal_positions_from_string_vector()
| 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().
◆ set_square_pyramidal_metal_positions_from_string_vector()
| 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().
◆ set_suppress_checkpoints()
| 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_.
◆ set_tetrahedral_metal_positions_from_string_vector()
| 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().
◆ set_total_energy_cutoff()
| 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().
◆ set_trigonal_planar_metal_positions_from_string_vector()
| 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().
◆ set_trigonal_pyramidal_metal_positions_from_string_vector()
| 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().
◆ set_up_cterm_isopeptide_cyclization_mover()
|
private |
Set up the mover that creates C-terminal isopeptide bonds.
References core::chemical::ResidueType::atom_name(), cyclization_type(), find_first_and_last_isopeptide_residues(), core::chemical::ResidueType::n_possible_residue_connections(), core::chemical::ResidueTypeBase::name3(), core::chemical::ResidueType::residue_connect_atom_index(), protocols::cyclic_peptide_predict::SCPA_cterm_isopeptide_lariat, and protocols::TR().
Referenced by set_up_cyclization_mover().
◆ set_up_cyclization_mover()
|
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, protocols::cyclic_peptide_predict::SCPA_thioether_lariat, 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(), set_up_terminal_disulfide_cyclization_mover(), and set_up_thioether_lariat_cyclization_mover().
Referenced by depermute(), do_final_fastrelax(), genkic_close(), run(), and set_up_native().
◆ set_up_design_taskoperations()
|
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().
◆ set_up_hbond_filter()
|
private |
Set up the filters for the mainchain hydrogen bonds that will be used to discard solutions with too few mainchain hydrogen bonds.
References count_sc_hbonds_, do_not_count_adjacent_res_hbonds_, and hbond_energy_cutoff_.
Referenced by run().
◆ set_up_isopeptide_variants()
|
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(), find_first_and_last_polymer_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, and core::chemical::SIDECHAIN_CONJUGATION.
Referenced by run().
◆ set_up_n_to_c_cyclization_mover()
|
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().
◆ set_up_native()
|
private |
Sets up a terminial peptide bond and does some checks.
References protocols::cyclic_peptide::crosslinker::correct_thioether_virtuals(), 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, protocols::cyclic_peptide_predict::SCPA_thioether_lariat, set_up_cyclization_mover(), set_up_terminal_disulfide_variants(), set_up_terminal_thioether_lariat_variants(), and protocols::TR().
Referenced by import_and_set_up_native(), and set_native().
◆ set_up_nterm_isopeptide_cyclization_mover()
|
private |
Set up the mover that creates N-terminal isopeptide bonds.
References core::chemical::ResidueType::atom_name(), cyclization_type(), find_first_and_last_isopeptide_residues(), core::chemical::ResidueType::n_possible_residue_connections(), core::chemical::ResidueTypeBase::name3(), core::chemical::ResidueType::residue_connect_atom_index(), protocols::cyclic_peptide_predict::SCPA_nterm_isopeptide_lariat, and protocols::TR().
Referenced by set_up_cyclization_mover().
◆ set_up_sidechain_isopeptide_cyclization_mover()
|
private |
Set up the mover that creates sidechain isopeptide bonds.
References core::chemical::ResidueType::atom_name(), cyclization_type(), find_first_and_last_isopeptide_residues(), core::chemical::ResidueType::n_possible_residue_connections(), core::chemical::ResidueTypeBase::name3(), core::chemical::ResidueType::residue_connect_atom_index(), protocols::cyclic_peptide_predict::SCPA_sidechain_isopeptide, and protocols::TR().
Referenced by set_up_cyclization_mover().
◆ set_up_terminal_disulfide_cyclization_mover()
|
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().
◆ set_up_terminal_disulfide_variants()
|
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_and_last_polymer_residues(), 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().
◆ set_up_terminal_thioether_lariat_variants()
|
private |
Given a pose, add sidechain conjugation variant types to the C-terminal cysteine and add a special acetyl terminus to the N-terminal residue.
- Returns
- The thioether cysteine index.
References core::pose::add_upper_terminus_type_to_pose_residue(), cyclization_type(), find_first_and_last_polymer_residues(), find_first_and_last_thioether_lariat_residues(), protocols::cyclic_peptide_predict::SCPA_thioether_lariat, and protocols::cyclic_peptide::crosslinker::set_up_thioether_variants().
Referenced by run(), and set_up_native().
◆ set_up_thioether_lariat_cyclization_mover()
|
private |
Set up the mover that creates thioether lariat bonds.
References cyclization_type(), find_first_and_last_thioether_lariat_residues(), protocols::cyclic_peptide_predict::SCPA_thioether_lariat, and protocols::cyclic_peptide::crosslinker::set_up_thioether_bond_mover().
Referenced by set_up_cyclization_mover().
◆ set_use_chainbreak_energy()
| 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().
◆ set_use_rama_prepro_for_sampling()
| 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().
◆ store_disulfides()
|
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().
◆ store_random_seed_info()
|
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().
◆ use_chainbreak_energy()
|
inlineprivate |
Should we use the chainbreak energy (true) or constraints (false) to enforce terminal amide bond geometry?
References use_chainbreak_energy_.
Referenced by run().
◆ use_rama_filter()
|
inlineprivate |
Are we using a rama filter? Defaults to true.
References use_rama_filter_.
Referenced by genkic_close().
◆ use_rama_prepro_for_sampling()
|
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
◆ abba_bins_binfile_
|
private |
Filename for the bin transitions data.
Referenced by genkic_close(), and set_abba_bins_binfile().
◆ 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().
◆ 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().
◆ already_completed_job_count_
|
private |
The number of jobs that this worker process has already completed. Only used in MPI mode; zero otherwise.
Referenced by run(), and set_already_completed_job_count().
◆ 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().
◆ 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().
◆ bondangle_perturbation_magnitude_
|
private |
A small random value added to all backbone bond angles. Defaults to 0.
Referenced by genkic_close(), and initialize_from_options().
◆ bondlength_perturbation_magnitude_
|
private |
A small random value added to all backbone bond lengths. Defaults to 0.
Referenced by genkic_close(), and initialize_from_options().
◆ cartesian_relax_rounds_
|
private |
Number of rounds of Cartesian-space relaxation.
Default 0.
Referenced by cartesian_relax_rounds(), and set_cartesian_relax_rounds().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ cyclic_permutations_
|
private |
Should we consider cyclic permutations?
Defaults to true.
Referenced by initialize_from_options(), and run().
◆ cyclization_type_
|
private |
The type of cyclization.
Referenced by add_bondangle_perturbation(), add_bondlength_perturbation(), cyclization_type(), initialize_from_options(), and set_cyclization_type().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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(), find_first_and_last_thioether_lariat_residues(), and initialize_from_options().
◆ link_all_cys_with_parabbmb_
|
private |
Should all cysteine residues be linked with 1,3,5-tris(bromomethyl)benzene?
False by default.
Referenced by initialize_from_options(), and run().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ native_exists_
|
private |
Has the user specified a native structure?
Referenced by initialize_from_options(), run(), and set_native().
◆ native_filename_
|
private |
Filename for the native, if one is provided.
Referenced by initialize_from_options(), and run().
◆ 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().
◆ nstruct_
|
private |
Max number of structures to generate.
Referenced by initialize_from_options(), run(), and set_nstruct().
◆ 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().
◆ 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().
◆ 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().
◆ out_filename_
|
private |
The prefix for the output filename.
Defaults to "S_".
Referenced by initialize_from_options(), and run().
◆ out_path_
|
private |
Output directory for PDB files.
Referenced by initialize_from_options(), and run().
◆ out_prefix_
|
private |
Output prefix for PDB files.
Referenced by initialize_from_options(), and run().
◆ out_scorefilename_
|
private |
◆ out_suffix_
|
private |
Output suffix for PDB files.
Referenced by initialize_from_options(), and run().
◆ 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().
◆ parabbmb_constraints_energy_filter_multiplier_
|
private |
Multiplier to make the paraBBMB constraints energy filter more permissive.
Default 1.0.
Referenced by genkic_close(), and initialize_from_options().
◆ parabbmb_positions_
|
mutableprivate |
List of positions linked by 1,4-bis(bromomethyl)benzene.
This is a vector of vectors of two residues.
Referenced by depermute(), genkic_close(), initialize_from_options(), and run().
◆ parabbmb_sidechain_distance_filter_multiplier_
|
private |
Multiplier to make the paraBBMB distance filter more permissive.
Default 1.0.
Referenced by genkic_close(), and initialize_from_options().
◆ 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().
◆ 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().
◆ 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().
◆ rama_cutoff_
|
private |
The energy cutoff for the rama filter.
Defaults to 0.3.
Referenced by genkic_close(), and initialize_from_options().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ silent_out_
|
private |
Should this application produce silent file output?
Referenced by initialize_from_options(), run(), and set_silentstructure_outputlist().
◆ 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().
◆ silentlist_out_
|
private |
Should this application produce silent structure OP output, appending to a list?
Referenced by run(), and set_silentstructure_outputlist().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ use_aa_comp_
|
private |
Should we use the aa_composition score term in design?
Default false.
Referenced by initialize_from_options(), and run().
◆ 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().
◆ 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().
◆ use_parabbmb_filters_
|
private |
If true, filters are applied based on distance between paraBBMB 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ user_set_dihedral_perturbation_
|
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:
- src/protocols/cyclic_peptide_predict/SimpleCycpepPredictApplication.hh
- src/protocols/cyclic_peptide_predict/SimpleCycpepPredictApplication.cc
