#include <GeneralizedKICperturber.hh>
Public Member Functions | |
| GeneralizedKICperturber () | |
| Creator for GeneralizedKICperturber. More... | |
| GeneralizedKICperturber (GeneralizedKICperturber const &src) | |
| Copy constructor for GeneralizedKICperturber. More... | |
| ~GeneralizedKICperturber () override | |
| Destructor for GeneralizedKICperturber mover. More... | |
| GeneralizedKICperturberOP | clone () const |
| Clone function for GeneralizedKICperturber: More... | |
| std::string | get_name () const |
| Returns the name of this class ("GeneralizedKICperturber"). More... | |
| perturber_effect | get_perturber_effect () const |
| Returns the enum type for the effect of this perturber. More... | |
| void | set_perturber_effect (perturber_effect const &effect) |
| Sets the effect of this perturber. More... | |
| void | set_perturber_effect (std::string const &effectname) |
| Sets the effect of this perturber using the perturber effect name. Exits with an error message if the name is unknown. More... | |
| void | add_inputvalue (core::Real const &inputvalue) |
| Adds a real value to the list of real input values. More... | |
| void | add_residue (core::Size const residue_index) |
| Adds a residue to the list of residues on which this perturber should act. More... | |
| void | clear_residues () |
| Clears the residue list for this perturber. More... | |
| void | add_atom_set (utility::vector1< core::id::NamedAtomID > const &atomset) |
| Adds a set of atoms defining a bond length, bond angle, or dihedral angle to the list of sets of atoms on which this perturber should act. More... | |
| void | load_bin_params (std::string const &bin_params_file) |
| Initializes the BinTransitionCalculator object and loads a bin_params file. More... | |
| void | set_iterations (core::Size const val) |
| Set the number of iterations for this perturber. More... | |
| core::Size | iterations () const |
| Return the number of iterations for this perturber. More... | |
| void | set_must_switch_bins (bool const val) |
| Set whether the perturb_backbone_by_bins perturber requires residues to change their torsion bins every move, or whether they can stay within the same bin. More... | |
| bool | must_switch_bins () const |
| Return whether the perturb_backbone_by_bins perturber requires residues to change their torsion bins every move, or whether they can stay within the same bin. More... | |
| void | set_bin (std::string const &bin) |
| Set the bin that the set_backbone_bin perturber will use. More... | |
| std::string | bin () const |
| Get the bin that the set_backbone_bin perturber will use. More... | |
| void | apply (core::pose::Pose const &original_pose, core::pose::Pose const &loop_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< core::Real > &torsions, utility::vector1< core::Real > &bondangles, utility::vector1< core::Real > &bondlengths) const |
| Applies the perturbation to the vectors of desired torsions, desired angles, and desired bond lengths. More... | |
| void | init_bbgmover (core::pose::Pose const &loop_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map) |
| void | set_attach_boinc_ghost_observer (bool const setting) |
| Sets whether we are attaching a BOINC "ghost" pose observer. More... | |
| bool | attach_boinc_ghost_observer () const |
| Gets whether we are attaching a BOINC "ghost" pose observer. More... | |
| core::scoring::Rama_Table_Type | custom_rama_table () const |
| Get the custom Ramachandran table (by enum) for the perturb_alpha_backbone_by_rama perturber. More... | |
| void | set_custom_rama_table (core::scoring::Rama_Table_Type const type) |
| Set the custom Ramachandran table (by enum) for the perturb_alpha_backbone_by_rama perturber. More... | |
| void | set_custom_rama_table (std::string const &name) |
| Set the custom Ramachandran table (by name) for the perturb_alpha_backbone_by_rama perturber. More... | |
Static Public Member Functions | |
| static perturber_effect | get_perturber_effect_from_name (std::string const &name) |
| Returns the enum type for the effect of a pertuber based on a perturber name. Returns unknown_effect if can't find a match for the name. More... | |
| static std::string | get_perturber_effect_name (core::Size &effect) |
| Returns the name of a perturber given the enum type. Returns "unknown_effect" if no such effect exists. More... | |
| static void | define_valid_perturber_name_enumeration (utility::tag::XMLSchemaDefinition &xsd) |
Private Member Functions | |
| core::Size | get_loop_index (core::Size const original_pose_index, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, bool const fail_if_not_found=true) const |
| Given an index in the original pose and a mapping from loop to pose, return the index in the loop. More... | |
| void | reindex_AtomIDs (utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< utility::vector1< core::id::AtomID > > &AtomIDs_reindexed, core::pose::Pose const &original_pose) const |
| Given a list of lists of AtomIDs, where residue indices are based on the original pose, and a mapping of original pose residue ID values to loop residue ID values, generate a new list of lists of AtomIDs, where the residue indices are based on the loop pose. More... | |
| void | apply_set_dihedral (utility::vector1< utility::vector1< core::id::AtomID > > const &dihedrallist, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< core::Real > const &inputvalues_real, utility::vector1< core::Real > &torsions, GenKICPerturberEffect const effect) const |
| Applies a set_dihedral perturbation to a list of torsions. More... | |
| void | apply_set_bondangle (utility::vector1< utility::vector1< core::id::AtomID > > const &bondanglelist, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< core::Real > const &inputvalues_real, utility::vector1< core::Real > &bondangles, GenKICPerturberEffect const effect) const |
| Applies a set_bondangle perturbation to a list of bond angles. More... | |
| void | apply_set_bondlength (utility::vector1< utility::vector1< core::id::AtomID > > const &bondlengthlist, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< core::Real > const &inputvalues_real, utility::vector1< core::Real > &bondlengths, GenKICPerturberEffect const effect) const |
| Applies a set_bondlength perturbation to a list of bond lengths. More... | |
| void | apply_set_backbone_bin (core::pose::Pose const &original_pose, core::pose::Pose const &loop_pose, utility::vector1< core::Size > const &residues, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map, utility::vector1< core::Real > &torsions) const |
| Applies a set_backbone_bin perturbation to the list of torsions. More... | |
| void | apply_randomize_alpha_backbone_by_rama (core::pose::Pose const &original_pose, core::pose::Pose const &loop_pose, utility::vector1< core::Size > const &residues, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map, utility::vector1< core::Real > &torsions) const |
| Applies a randomize_alpha_backbone_by_rama perturbation to the list of torsions. More... | |
| void | apply_randomize_backbone_by_rama_prepro (core::pose::Pose const &original_pose, core::pose::Pose const &loop_pose, utility::vector1< core::Size > const &residues, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map, utility::vector1< core::Real > &torsions) const |
| Applies a randomize_backbone_by_rama_prepro perturbation to the list of torsions. More... | |
| void | apply_randomize_backbone_by_bins (core::pose::Pose const &original_pose, core::pose::Pose const &loop_pose, utility::vector1< core::Size > const &residues, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map, utility::vector1< core::Real > &torsions) const |
| Applies a randomize_backbone_by_bins perturbation to the list of torsions. More... | |
| void | apply_perturb_dihedral_bbg (core::pose::Pose const &original_pose, core::pose::Pose const &loop_pose, utility::vector1< core::Size > const &residues, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< core::Real > &torsions) const |
| Applies a perturb_dihedral_bbg perturbation to a list of torsions. More... | |
| void | apply_perturb_backbone_by_bins (core::pose::Pose const &original_pose, core::pose::Pose const &loop_pose, utility::vector1< core::Size > const &residues, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map, utility::vector1< core::Real > &torsions) const |
| Applies a perturb_backbone_by_bins perturbation to the list of torsions. More... | |
| void | apply_copy_backbone_dihedrals (core::pose::Pose const &original_pose, core::pose::Pose const &loop_pose, utility::vector1< core::Size > const &residues, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map, utility::vector1< core::Real > &torsions, bool const mirror) const |
| Applies a copy_backbone_dihedrals perturbation to the list of torsions. More... | |
| void | apply_sample_cis_peptide_bond (core::pose::Pose const &loop_pose, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< core::Size > const &residues, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map, utility::vector1< core::Real > &torsions) const |
| Applies a sample_cis_peptide_bond perturbation to the list of torsions. More... | |
| bool | is_in_list (core::Size const val, utility::vector1< core::Size > const &vect) const |
| Is a value in a list? More... | |
Private Attributes | |
| simple_moves::BBGaussianMoverOP | bbgmover_ |
| bbgmover More... | |
| core::scoring::bin_transitions::BinTransitionCalculatorCOP | bin_transition_calculator_ |
| A BinTransitionCalculatorOP. This will be null by default, and will only point to a BinTransitionCalculator object in the case of those perturbers that use torsion bin transition probabilities. More... | |
| perturber_effect | effect_ |
| The effect of this perturber. See the perturber_effect enum type for more information. More... | |
| utility::vector1< core::Real > | inputvalues_real_ |
| Real input values for the operation. For example, a set_dihedral operation would take a single real value (the value that the dihedral will be set to). More... | |
| utility::vector1< core::Size > | residues_ |
| The list of residues on which this operation should be carried out. More... | |
| utility::vector1< utility::vector1< core::id::NamedAtomID > > | atoms_ |
| A list of sets of atoms defining bond lenghts, bond angles, or dihedral angles on which this perturber will work. More... | |
| core::Size | iterations_ |
| Number of iterations of perturbation for certain perturbers. More... | |
| bool | must_switch_bins_ |
| A parameter specifically for the perturb_backbone_by_bins perturber. If true, the perturber ALWAYS changes the torsion bin of the residue. If false, it MAY change the torsion bin of the residue, or it MAY keep it the same, based on the relative bin probabilities. More... | |
| std::string | bin_ |
| A parameter specifically for the set_backbone_bin perturber. The bin that will be assigned. More... | |
| bool | attach_boinc_ghost_observer_ |
| Should poses generated by the perturber be used for ghost display in BOINC? More... | |
| core::scoring::Rama_Table_Type | custom_rama_table_ |
| A parameter specifically for the perturb_alpha_backbone_by_rama perturber. An optional custom Ramachandran map for sampling. Defaults to unknown_ramatable_type (unused – use default Ramachandran map for the amino acid residue in question. More... | |
Constructor & Destructor Documentation
◆ GeneralizedKICperturber() [1/2]
| protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::GeneralizedKICperturber | ( | ) |
Creator for GeneralizedKICperturber.
◆ GeneralizedKICperturber() [2/2]
| protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::GeneralizedKICperturber | ( | GeneralizedKICperturber const & | src | ) |
Copy constructor for GeneralizedKICperturber.
References bbgmover_, and bin_transition_calculator_.
◆ ~GeneralizedKICperturber()
|
overridedefault |
Destructor for GeneralizedKICperturber mover.
Member Function Documentation
◆ add_atom_set()
|
inline |
Adds a set of atoms defining a bond length, bond angle, or dihedral angle to the list of sets of atoms on which this perturber should act.
These are indices based on the original structure, NOT based on the loop to be closed. Some effects act on a list of residues, while others act on a list of atoms.
References atoms_.
◆ add_inputvalue()
|
inline |
Adds a real value to the list of real input values.
References inputvalues_real_.
◆ add_residue()
|
inline |
Adds a residue to the list of residues on which this perturber should act.
These are indices based on the original structure, NOT based on the loop to be closed. Some effects act on a list of residues, while others act on a list of AtomIDs.
References residues_.
◆ apply()
| void protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply | ( | core::pose::Pose const & | original_pose, |
| core::pose::Pose const & | loop_pose, | ||
| utility::vector1< std::pair< core::Size, core::Size > > const & | residue_map, | ||
| utility::vector1< std::pair< core::Size, core::Size > > const & | tail_residue_map, | ||
| utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const & | atomlist, | ||
| utility::vector1< core::Real > & | torsions, | ||
| utility::vector1< core::Real > & | bondangles, | ||
| utility::vector1< core::Real > & | bondlengths | ||
| ) | const |
Applies the perturbation to the vectors of desired torsions, desired angles, and desired bond lengths.
- Parameters
-
[in] original_pose - The original pose. [in] loop_pose - A pose consisting of just the loop to be perturbed, plus one residue on each side establishing the frame. [in] residue_map - Mapping of (loop residue, original pose residue). [in] tail_residue_map - Mapping of (tail residue in loop pose, original pose tail residue). [in] atomlist - List of atoms (residue indices are based on the loop_pose). [in,out] torsions - Desired torsions for each atom; can be set or altered by the apply() function. [in,out] bondangles - Desired bond angles for each atom; can be set or altered by the apply() function. [in,out] bondlengths - Desired bond lengths for each atom; can be set or altered by the apply() function.
References apply_copy_backbone_dihedrals(), apply_perturb_backbone_by_bins(), apply_perturb_dihedral_bbg(), apply_randomize_alpha_backbone_by_rama(), apply_randomize_backbone_by_bins(), apply_randomize_backbone_by_rama_prepro(), apply_sample_cis_peptide_bond(), apply_set_backbone_bin(), apply_set_bondangle(), apply_set_bondlength(), apply_set_dihedral(), protocols::generalized_kinematic_closure::perturber::copy_backbone_dihedrals, effect_, inputvalues_real_, protocols::generalized_kinematic_closure::perturber::mirror_backbone_dihedrals, protocols::generalized_kinematic_closure::perturber::perturb, protocols::generalized_kinematic_closure::perturber::perturb_backbone_by_bins, protocols::generalized_kinematic_closure::perturber::perturb_bondangle, protocols::generalized_kinematic_closure::perturber::perturb_bondlength, protocols::generalized_kinematic_closure::perturber::perturb_dihedral, protocols::generalized_kinematic_closure::perturber::perturb_dihedral_bbg, protocols::generalized_kinematic_closure::perturber::randomize, protocols::generalized_kinematic_closure::perturber::randomize_alpha_backbone_by_rama, protocols::generalized_kinematic_closure::perturber::randomize_backbone_by_bins, protocols::generalized_kinematic_closure::perturber::randomize_backbone_by_rama_prepro, protocols::generalized_kinematic_closure::perturber::randomize_dihedral, reindex_AtomIDs(), residues_, protocols::generalized_kinematic_closure::perturber::sample_cis_peptide_bond, protocols::generalized_kinematic_closure::perturber::set, protocols::generalized_kinematic_closure::perturber::set_backbone_bin, protocols::generalized_kinematic_closure::perturber::set_bondangle, protocols::generalized_kinematic_closure::perturber::set_bondlength, and protocols::generalized_kinematic_closure::perturber::set_dihedral.
◆ apply_copy_backbone_dihedrals()
|
private |
Applies a copy_backbone_dihedrals perturbation to the list of torsions.
- Parameters
-
[in] original_pose - The input pose. [in] loop_pose - A pose that is just the loop to be closed (possibly with other things hanging off of it). [in] residues - A vector of the indices of residues affected by this perturber. [in] atomlist - A vector of pairs of AtomID, xyz coordinate. Residue indices are based on the loop pose, NOT the original pose. [in] residue_map - A vector of pairs of (loop pose index, original pose index). [in] tail_residue_map - A vector of pairs of (loop pose index of tail residue, original pose index of tail residue). [in,out] torsions - A vector of desired torsions, some of which are randomized by this function. [in] mirror - If true, then backbone dihedrals are copied with inversion (multiplied by -1). If false, then they copied faithfully.
References apply_set_dihedral(), core::conformation::Residue::connect_atom(), core::conformation::Residue::connected_residue_at_resconn(), get_loop_index(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::chemical::ResidueType::lower_connect_id(), core::conformation::Residue::mainchain_torsions(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::generalized_kinematic_closure::perturber::set, and core::chemical::ResidueType::upper_connect_id().
Referenced by apply().
◆ apply_perturb_backbone_by_bins()
|
private |
Applies a perturb_backbone_by_bins perturbation to the list of torsions.
- Parameters
-
[in] original_pose - The input pose. [in] loop_pose - A pose that is just the loop to be closed (possibly with other things hanging off of it). [in] residues - A vector of the indices of residues affected by this perturber. [in] atomlist - A vector of pairs of AtomID, xyz coordinate. Residue indices are based on the loop pose, NOT the original pose. [in] residue_map - A vector of pairs of (loop pose index, original pose index). [in] tail_residue_map - A vector of pairs of (loop pose index of tail residue, original pose index of tail residue). [in,out] torsions - A vector of desired torsions, some of which are randomized by this function.
References apply_set_dihedral(), attach_boinc_ghost_observer(), bin_transition_calculator_, core::pose::Pose::conformation(), core::conformation::Residue::connect_map(), core::chemical::ResConnID::connid(), get_loop_index(), core::conformation::Residue::is_polymer_bonded(), iterations(), core::conformation::Residue::mainchain_atoms(), must_switch_bins(), core::chemical::ResConnID::resid(), core::pose::Pose::residue(), core::conformation::Conformation::residue(), core::conformation::Residue::residue_connect_atom_index(), core::scoring::rg, protocols::generalized_kinematic_closure::perturber::set, protocols::generalized_kinematic_closure::set_loop_pose(), core::pose::Pose::size(), core::conformation::Residue::type(), and core::chemical::ResidueType::upper_connect_id().
Referenced by apply().
◆ apply_perturb_dihedral_bbg()
|
private |
Applies a perturb_dihedral_bbg perturbation to a list of torsions.
Backbone Gaussian Perturbation
- Parameters
-
[in] original_pose - The input pose. [in] loop_pose - A pose that is just the loop to be closed (possibly with other things hanging off of it). [in] residues - A vector of the indices of residues affected by this perturber. Note that [in] atomlist - A vector of pairs of AtomID, xyz coordinate. Residue indices are based on the loop pose, NOT the original pose. [in] residue_map - A vector of pairs of (loop pose index, original pose index). [in,out] torsions - A vector of desired torsions, some of which are randomized by this function.
References core::conformation::Residue::atom_index(), attach_boinc_ghost_observer(), bbgmover_, get_loop_index(), core::chemical::ResidueType::is_alpha_aa(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::generalized_kinematic_closure::perturber::TR(), core::conformation::Residue::type(), and core::pose::Pose::xyz().
Referenced by apply().
◆ apply_randomize_alpha_backbone_by_rama()
|
private |
Applies a randomize_alpha_backbone_by_rama perturbation to the list of torsions.
This checks whether each residue is an alpha-amino acid.
- Parameters
-
[in] original_pose - The input pose. [in] loop_pose - A pose that is just the loop to be closed (possibly with other things hanging off of it). [in] residues - A vector of the indices of residues affected by this perturber. [in] atomlist - A vector of pairs of AtomID, xyz coordinate. Residue indices are based on the loop pose, NOT the original pose. [in] residue_map - A vector of pairs of (loop pose index, original pose index). [in] tail_residue_map - A vector of pairs of (loop pose index of tail residue, original pose index of tail residue). [in,out] torsions - A vector of desired torsions, some of which are randomized by this function.
This checks whether each residue is an alpha-amino acid.
- Parameters
-
[in] original_pose - The input pose. [in] loop_pose - A pose that is just the loop to be closed (possibly with other things hanging off of it). [in] residues - A vector of the indices of residues affected by this perturber. Note that [in] atomlist - A vector of pairs of AtomID, xyz coordinate. Residue indices are based on the loop pose, NOT the original pose. [in] residue_map - A vector of pairs of (loop pose index, original pose index). [in] tail_residue_map - A vector of pairs of (loop pose index of tail residue, original pose index of tail residue). [in,out] torsions - A vector of desired torsions, some of which are randomized by this function.
References core::pose::Pose::aa(), core::chemical::aa_unk, core::conformation::Residue::atom_index(), attach_boinc_ghost_observer(), core::conformation::Residue::backbone_aa(), custom_rama_table(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), get_loop_index(), core::chemical::ResidueType::is_alpha_aa(), core::scoring::rama, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), protocols::generalized_kinematic_closure::perturber::TR(), core::scoring::unknown_ramatable_type, and core::pose::Pose::xyz().
Referenced by apply().
◆ apply_randomize_backbone_by_bins()
|
private |
Applies a randomize_backbone_by_bins perturbation to the list of torsions.
- Parameters
-
[in] original_pose - The input pose. [in] loop_pose - A pose that is just the loop to be closed (possibly with other things hanging off of it). [in] residues - A vector of the indices of residues affected by this perturber. [in] atomlist - A vector of pairs of AtomID, xyz coordinate. Residue indices are based on the loop pose, NOT the original pose. [in] residue_map - A vector of pairs of (loop pose index, original pose index). [in] tail_residue_map - A vector of pairs of (loop pose index of tail residue, original pose index of tail residue). [in,out] torsions - A vector of desired torsions, some of which are randomized by this function.
This randomly assigns torsion bins based on transition probabilities of i->i+1 residues, then picks mainchain torsion angles within each bin randomly or in a biased manner (if Ramachandran information is available, for example, in the case of alpha-amino acids).
- Parameters
-
[in] original_pose - The input pose. [in] loop_pose - A pose that is just the loop to be closed (possibly with other things hanging off of it). [in] residues - A vector of the indices of residues affected by this perturber. [in] atomlist - A vector of pairs of AtomID, xyz coordinate. Residue indices are based on the loop pose, NOT the original pose. [in] residue_map - A vector of pairs of (loop pose index, original pose index). [in] tail_residue_map - A vector of pairs of (loop pose index of tail residue, original pose index of tail residue). [in,out] torsions - A vector of desired torsions, some of which are randomized by this function.
References apply_set_dihedral(), bin_transition_calculator_, core::pose::Pose::conformation(), core::conformation::Residue::connect_map(), core::chemical::ResConnID::connid(), get_loop_index(), core::conformation::Residue::is_polymer_bonded(), core::conformation::Residue::mainchain_atoms(), core::chemical::ResConnID::resid(), core::pose::Pose::residue(), core::conformation::Conformation::residue(), core::conformation::Residue::residue_connect_atom_index(), protocols::generalized_kinematic_closure::perturber::set, core::pose::Pose::size(), core::conformation::Residue::type(), and core::chemical::ResidueType::upper_connect_id().
Referenced by apply().
◆ apply_randomize_backbone_by_rama_prepro()
|
private |
Applies a randomize_backbone_by_rama_prepro perturbation to the list of torsions.
This checks whether each residue is an alpha-amino acid.
- Parameters
-
[in] original_pose - The input pose. [in] loop_pose - A pose that is just the loop to be closed (possibly with other things hanging off of it). [in] residues - A vector of the indices of residues affected by this perturber. [in] atomlist - A vector of pairs of AtomID, xyz coordinate. Residue indices are based on the loop pose, NOT the original pose. [in] residue_map - A vector of pairs of (loop pose index, original pose index). [in] tail_residue_map - A vector of pairs of (loop pose index of tail residue, original pose index of tail residue). [in,out] torsions - A vector of desired torsions, some of which are randomized by this function.
This checks whether each residue is an alpha-amino acid.
- Parameters
-
[in] original_pose - The input pose. [in] loop_pose - A pose that is just the loop to be closed (possibly with other things hanging off of it). [in] residues - A vector of the indices of residues affected by this perturber. Note that [in] atomlist - A vector of pairs of AtomID, xyz coordinate. Residue indices are based on the loop pose, NOT the original pose. [in] residue_map - A vector of pairs of (loop pose index, original pose index). [in] tail_residue_map - A vector of pairs of (loop pose index of tail residue, original pose index of tail residue). [in,out] torsions - A vector of desired torsions, some of which are randomized by this function.
References core::conformation::Residue::atom_index(), core::conformation::Residue::atom_name(), attach_boinc_ghost_observer(), core::id::BB, core::pose::Pose::conformation(), core::conformation::Residue::connected_residue_at_lower(), core::conformation::Residue::connected_residue_at_upper(), get_loop_index(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), is_in_list(), core::scoring::rama, core::pose::Pose::residue(), core::pose::Pose::residue_type_ptr(), core::pose::Pose::set_torsion(), core::pose::Pose::size(), core::id::to_string(), protocols::generalized_kinematic_closure::perturber::TR(), and core::pose::Pose::xyz().
Referenced by apply().
◆ apply_sample_cis_peptide_bond()
|
private |
Applies a sample_cis_peptide_bond perturbation to the list of torsions.
This checks whether each residue specified is an alpha- or beta-amino acid. If it is, it samples the cis version of the omega angle (if omega is in the chain of atoms).
- Parameters
-
[in] loop_pose - A pose that is just the loop to be closed (possibly with other things hanging off of it). [in] atomlist - A vector of pairs of AtomID, xyz coordinate. Residue indices are based on the loop pose, NOT the original pose. [in] residues - A vector of the indices of residues affected by this perturber. [in] residue_map - A vector of pairs of (loop pose index, original pose index). [in] tail_residue_map - A vector of pairs of (loop pose index, original pose index). [in,out] torsions - A vector of desired torsions, some of which are randomized by this function.
References core::conformation::Residue::atom_index(), get_loop_index(), inputvalues_real_, core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_beta_aa(), core::chemical::ResidueType::is_gamma_aa(), core::chemical::ResidueType::is_oligourea(), core::chemical::ResidueTypeBase::is_peptoid(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::scoring::rg, and protocols::generalized_kinematic_closure::perturber::TR().
Referenced by apply().
◆ apply_set_backbone_bin()
|
private |
Applies a set_backbone_bin perturbation to the list of torsions.
Sets the mainchain torsion bin for each of a list of residues, then picks random mainchain torsion values from within the bin.
- Parameters
-
[in] original_pose - The input pose. [in] loop_pose - A pose that is just the loop to be closed (possibly with other things hanging off of it). [in] residues - A vector of the indices of residues affected by this perturber. [in] atomlist - A vector of pairs of AtomID, xyz coordinate. Residue indices are based on the loop pose, NOT the original pose. [in] residue_map - A vector of pairs of (loop pose index, original pose index). [in] tail_residue_map - A vector of pairs of (loop pose index of tail residue, original pose index of tail residue). [in,out] torsions - A vector of desired torsions, some of which are randomized by this function.
References apply_set_dihedral(), bin_, bin_transition_calculator_, core::pose::Pose::conformation(), core::conformation::Residue::connect_map(), core::chemical::ResConnID::connid(), get_loop_index(), core::conformation::Residue::mainchain_atoms(), core::chemical::ResConnID::resid(), core::conformation::Conformation::residue(), core::conformation::Residue::residue_connect_atom_index(), protocols::generalized_kinematic_closure::perturber::set, core::pose::Pose::size(), core::conformation::Residue::type(), and core::chemical::ResidueType::upper_connect_id().
Referenced by apply().
◆ apply_set_bondangle()
|
private |
Applies a set_bondangle perturbation to a list of bond angles.
- Parameters
-
[in] bondanglelist - List of sets of atoms defining bond angles, indexed based on the loop_pose. [in] atomlist - List of atoms (residue indices are based on the loop_pose). [in] inputvalues_real – Vector of input values (one value or one for each bond angle to be set). [in,out] bondangles - Desired bond angles for each atom; set by this function. [in] bondanglelist - List of sets of atoms defining bond angles, indexed based on the loop_pose. [in] atomlist - List of atoms (residue indices are based on the loop_pose). [in] inputvalues_real - List of real-valued input values (one for each bondangle to be set OR one single one). [in,out] bondangles - Desired bond angles for each atom; set by this function.
References protocols::generalized_kinematic_closure::perturber::perturb, protocols::generalized_kinematic_closure::perturber::randomize, core::scoring::rg, protocols::generalized_kinematic_closure::perturber::set, core::id::to_string(), and protocols::generalized_kinematic_closure::perturber::TR().
Referenced by apply().
◆ apply_set_bondlength()
|
private |
Applies a set_bondlength perturbation to a list of bond lengths.
- Parameters
-
[in] bondlengthlist - List of sets of atoms defining bond lengths, indexed based on the loop_pose. [in] atomlist - List of atoms (residue indices are based on the loop_pose). [in] inputvalues_real – Vector of input values (one value or one for each bond angle to be set). [in,out] bondlengths - Desired bond lengths for each atom; set by this function. [in] bondlengthlist - List of sets of atoms defining bond lengths, indexed based on the loop_pose. [in] atomlist - List of atoms (residue indices are based on the loop_pose). [in] inputvalues_real - List of input values (a single one or one for each bondlength to be set). [in,out] bondlengths - Desired bond lengths for each atom; set by this function.
References protocols::generalized_kinematic_closure::perturber::perturb, protocols::generalized_kinematic_closure::perturber::randomize, core::scoring::rg, protocols::generalized_kinematic_closure::perturber::set, core::id::to_string(), and protocols::generalized_kinematic_closure::perturber::TR().
Referenced by apply().
◆ apply_set_dihedral()
|
private |
Applies a set_dihedral perturbation to a list of torsions.
Can also be used to randomize dihedral values.
- Parameters
-
[in] dihedrallist - List of sets of atoms defining dihedrals, indexed based on the loop_pose. [in] atomlist - List of atoms (residue indices are based on the loop_pose). [in] inputvalues_real – Vector of input values (one value or one for each dihedral to be set). [in,out] torsions - Desired torsions for each atom; set by this function. [in] effect - Should the specified torsions be set (0), randomized (1), or perturbed (2)?
Can also be used to randomize dihedral values.d
- Parameters
-
[in] dihedrallist - List of sets of atoms defining dihedrals, indexed based on the loop_pose. [in] atomlist - List of atoms (residue indices are based on the loop_pose). [in] inputvalues_real – Vector of input values (one value or one for each dihedral to be set). [in,out] torsions - Desired torsions for each atom; set by this function. [in] effect - Should the specified torsions be set (0), randomized (1), or perturbed (2)?
References protocols::generalized_kinematic_closure::perturber::perturb, protocols::generalized_kinematic_closure::perturber::randomize, core::scoring::rg, protocols::generalized_kinematic_closure::perturber::set, and protocols::generalized_kinematic_closure::perturber::TR().
Referenced by apply(), apply_copy_backbone_dihedrals(), apply_perturb_backbone_by_bins(), apply_randomize_backbone_by_bins(), and apply_set_backbone_bin().
◆ attach_boinc_ghost_observer()
|
inline |
Gets whether we are attaching a BOINC "ghost" pose observer.
Only does anything in the BOINC graphics build.
References attach_boinc_ghost_observer_.
Referenced by apply_perturb_backbone_by_bins(), apply_perturb_dihedral_bbg(), apply_randomize_alpha_backbone_by_rama(), and apply_randomize_backbone_by_rama_prepro().
◆ bin()
|
inline |
◆ clear_residues()
|
inline |
Clears the residue list for this perturber.
References residues_.
◆ clone()
| GeneralizedKICperturberOP protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::clone | ( | ) | const |
Clone function for GeneralizedKICperturber:
Returns an owning pointer to a copy of this perturber.
◆ custom_rama_table()
|
inline |
Get the custom Ramachandran table (by enum) for the perturb_alpha_backbone_by_rama perturber.
References custom_rama_table_.
Referenced by apply_randomize_alpha_backbone_by_rama().
◆ define_valid_perturber_name_enumeration()
|
static |
◆ get_loop_index()
|
private |
Given an index in the original pose and a mapping from loop to pose, return the index in the loop.
If fail_if_not_found is true (the default), throws an exception if the index isn't found. If false, returns zero instead.
References core::id::to_string().
Referenced by apply_copy_backbone_dihedrals(), apply_perturb_backbone_by_bins(), apply_perturb_dihedral_bbg(), apply_randomize_alpha_backbone_by_rama(), apply_randomize_backbone_by_bins(), apply_randomize_backbone_by_rama_prepro(), apply_sample_cis_peptide_bond(), apply_set_backbone_bin(), and reindex_AtomIDs().
◆ get_name()
| std::string protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::get_name | ( | ) | const |
Returns the name of this class ("GeneralizedKICperturber").
◆ get_perturber_effect()
|
inline |
Returns the enum type for the effect of this perturber.
References effect_.
◆ get_perturber_effect_from_name()
|
static |
Returns the enum type for the effect of a pertuber based on a perturber name. Returns unknown_effect if can't find a match for the name.
References protocols::generalized_kinematic_closure::perturber::end_of_effect_list, get_perturber_effect_name(), and protocols::generalized_kinematic_closure::perturber::unknown_effect.
Referenced by set_perturber_effect().
◆ get_perturber_effect_name()
|
static |
Returns the name of a perturber given the enum type. Returns "unknown_effect" if no such effect exists.
References protocols::generalized_kinematic_closure::perturber::copy_backbone_dihedrals, protocols::generalized_kinematic_closure::perturber::mirror_backbone_dihedrals, protocols::generalized_kinematic_closure::perturber::no_effect, protocols::generalized_kinematic_closure::perturber::perturb_backbone_by_bins, protocols::generalized_kinematic_closure::perturber::perturb_bondangle, protocols::generalized_kinematic_closure::perturber::perturb_bondlength, protocols::generalized_kinematic_closure::perturber::perturb_dihedral, protocols::generalized_kinematic_closure::perturber::perturb_dihedral_bbg, protocols::generalized_kinematic_closure::perturber::randomize_alpha_backbone_by_rama, protocols::generalized_kinematic_closure::perturber::randomize_backbone_by_bins, protocols::generalized_kinematic_closure::perturber::randomize_backbone_by_rama_prepro, protocols::generalized_kinematic_closure::perturber::randomize_dihedral, protocols::generalized_kinematic_closure::perturber::sample_cis_peptide_bond, protocols::generalized_kinematic_closure::perturber::set_backbone_bin, protocols::generalized_kinematic_closure::perturber::set_bondangle, protocols::generalized_kinematic_closure::perturber::set_bondlength, and protocols::generalized_kinematic_closure::perturber::set_dihedral.
Referenced by define_valid_perturber_name_enumeration(), and get_perturber_effect_from_name().
◆ init_bbgmover()
| void protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::init_bbgmover | ( | core::pose::Pose const & | loop_pose, |
| utility::vector1< std::pair< core::Size, core::Size > > const & | residue_map | ||
| ) |
References bbgmover_, residues_, and core::pose::Pose::size().
◆ is_in_list()
|
private |
Is a value in a list?
References protocols::hybridization::val.
Referenced by apply_randomize_backbone_by_rama_prepro().
◆ iterations()
|
inline |
Return the number of iterations for this perturber.
References iterations_.
Referenced by apply_perturb_backbone_by_bins().
◆ load_bin_params()
| void protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::load_bin_params | ( | std::string const & | bin_params_file | ) |
Initializes the BinTransitionCalculator object and loads a bin_params file.
References bin_transition_calculator_, and protocols::generalized_kinematic_closure::perturber::TR().
◆ must_switch_bins()
|
inline |
Return whether the perturb_backbone_by_bins perturber requires residues to change their torsion bins every move, or whether they can stay within the same bin.
References must_switch_bins_.
Referenced by apply_perturb_backbone_by_bins().
◆ reindex_AtomIDs()
|
private |
Given a list of lists of AtomIDs, where residue indices are based on the original pose, and a mapping of original pose residue ID values to loop residue ID values, generate a new list of lists of AtomIDs, where the residue indices are based on the loop pose.
Given a list of lists of atoms (as std::pair <residue_index, atom_name>) where residue indices are based on the original pose, and a mapping of original pose residue ID values to loop residue ID values, generate a new list of lists of AtomIDs, where the residue indices are based on the loop pose.
References core::conformation::Residue::atom_index(), atoms_, get_loop_index(), core::conformation::Residue::has(), core::pose::Pose::residue(), and core::pose::Pose::size().
Referenced by apply().
◆ set_attach_boinc_ghost_observer()
|
inline |
Sets whether we are attaching a BOINC "ghost" pose observer.
Only does anything in the BOINC graphics build.
References attach_boinc_ghost_observer_.
◆ set_bin()
|
inline |
◆ set_custom_rama_table() [1/2]
|
inline |
Set the custom Ramachandran table (by enum) for the perturb_alpha_backbone_by_rama perturber.
References custom_rama_table_, and core::scoring::unknown_ramatable_type.
Referenced by set_custom_rama_table().
◆ set_custom_rama_table() [2/2]
| void protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::set_custom_rama_table | ( | std::string const & | name | ) |
Set the custom Ramachandran table (by name) for the perturb_alpha_backbone_by_rama perturber.
References core::scoring::rama, set_custom_rama_table(), and core::scoring::unknown_ramatable_type.
◆ set_iterations()
|
inline |
Set the number of iterations for this perturber.
References iterations_, and protocols::hybridization::val.
◆ set_must_switch_bins()
|
inline |
Set whether the perturb_backbone_by_bins perturber requires residues to change their torsion bins every move, or whether they can stay within the same bin.
References must_switch_bins_, and protocols::hybridization::val.
◆ set_perturber_effect() [1/2]
| void protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::set_perturber_effect | ( | perturber_effect const & | effect | ) |
Sets the effect of this perturber.
References effect_, and protocols::generalized_kinematic_closure::perturber::end_of_effect_list.
Referenced by set_perturber_effect().
◆ set_perturber_effect() [2/2]
| void protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::set_perturber_effect | ( | std::string const & | effectname | ) |
Sets the effect of this perturber using the perturber effect name. Exits with an error message if the name is unknown.
References protocols::generalized_kinematic_closure::perturber::end_of_effect_list, get_perturber_effect_from_name(), and set_perturber_effect().
Member Data Documentation
◆ atoms_
|
private |
A list of sets of atoms defining bond lenghts, bond angles, or dihedral angles on which this perturber will work.
These are NamedAtomIDs (residue_index, atom_name). The residue indices are based on the original structure, NOT on the loop to be closed. Some effects act on a list of residues, while others act on a list of atoms.
Referenced by add_atom_set(), and reindex_AtomIDs().
◆ attach_boinc_ghost_observer_
|
private |
Should poses generated by the perturber be used for ghost display in BOINC?
Outside of the BOINC build, this does nothing.
Referenced by attach_boinc_ghost_observer(), and set_attach_boinc_ghost_observer().
◆ bbgmover_
|
private |
bbgmover
Referenced by apply_perturb_dihedral_bbg(), GeneralizedKICperturber(), and init_bbgmover().
◆ bin_
|
private |
A parameter specifically for the set_backbone_bin perturber. The bin that will be assigned.
Referenced by apply_set_backbone_bin(), bin(), and set_bin().
◆ bin_transition_calculator_
|
private |
A BinTransitionCalculatorOP. This will be null by default, and will only point to a BinTransitionCalculator object in the case of those perturbers that use torsion bin transition probabilities.
Referenced by apply_perturb_backbone_by_bins(), apply_randomize_backbone_by_bins(), apply_set_backbone_bin(), GeneralizedKICperturber(), and load_bin_params().
◆ custom_rama_table_
|
private |
A parameter specifically for the perturb_alpha_backbone_by_rama perturber. An optional custom Ramachandran map for sampling. Defaults to unknown_ramatable_type (unused – use default Ramachandran map for the amino acid residue in question.
Referenced by custom_rama_table(), and set_custom_rama_table().
◆ effect_
|
private |
The effect of this perturber. See the perturber_effect enum type for more information.
Referenced by apply(), get_perturber_effect(), and set_perturber_effect().
◆ inputvalues_real_
|
private |
Real input values for the operation. For example, a set_dihedral operation would take a single real value (the value that the dihedral will be set to).
Referenced by add_inputvalue(), apply(), and apply_sample_cis_peptide_bond().
◆ iterations_
|
private |
Number of iterations of perturbation for certain perturbers.
Referenced by iterations(), and set_iterations().
◆ must_switch_bins_
|
private |
A parameter specifically for the perturb_backbone_by_bins perturber. If true, the perturber ALWAYS changes the torsion bin of the residue. If false, it MAY change the torsion bin of the residue, or it MAY keep it the same, based on the relative bin probabilities.
Referenced by must_switch_bins(), and set_must_switch_bins().
◆ residues_
|
private |
The list of residues on which this operation should be carried out.
These are indices based on the original structure, NOT based on the loop to be closed. Some effects act on a list of residues, while others act on a list of AtomIDs.
Referenced by add_residue(), apply(), clear_residues(), and init_bbgmover().
The documentation for this class was generated from the following files:
- src/protocols/generalized_kinematic_closure/perturber/GeneralizedKICperturber.hh
- src/protocols/generalized_kinematic_closure/perturber/GeneralizedKICperturber.cc
