Adds charged residues to a protein surface. More...
#include <Supercharge.hh>
Public Types | |
| using | SizeSet = std::set< core::Size > |
 Public Types inherited from protocols::moves::Mover | |
| typedef utility::tag::TagCOP | TagCOP |
| typedef core::pose::Pose | Pose |
| typedef core::pose::PoseCOP | PoseCOP |
| typedef std::list< std::string > | Strings |
Public Member Functions | |
| Supercharge ()=default | |
| ~Supercharge () override=default | |
| void | AvNAPSA_positive (bool s) |
| void | AvNAPSA_negative (bool s) |
| void | target_net_charge_active (bool s) |
| void | target_net_charge (int s) |
| void | surface_atom_cutoff (core::Size s) |
| void | surface_residue_cutoff (core::Size s) |
| void | include_arg (bool s) |
| void | include_lys (bool s) |
| void | include_asp (bool s) |
| void | include_glu (bool s) |
| void | refweight_arg (core::Real s) |
| void | refweight_lys (core::Real s) |
| void | refweight_asp (core::Real s) |
| void | refweight_glu (core::Real s) |
| void | dont_mutate_glyprocys (bool s) |
| void | dont_mutate_correct_charge (bool s) |
| void | dont_mutate_hbonded_sidechains (bool s) |
| void | pre_packminpack (bool s) |
| void | local_nstruct (core::Size s) |
| void | compare_residue_energies_all (bool s) |
| void | compare_residue_energies_mut (bool s) |
| void | apply (Pose &pose) override |
| Main Method. More... | |
| virtual void | AvNAPSA_values (Pose const &pose) |
| average number of neighboring atoms per sidechain atom More... | |
| virtual void | set_resfile_AvNAPSA (Pose const &pose) |
| virtual void | design_supercharge_AvNAPSA (Pose const &starting_pose, Pose &pose) |
| virtual void | prepack_input_structure (Pose &pose) |
| void | set_surface (Pose const &pose) |
| void | set_resfile (Pose const &pose) |
| utility::vector1< core::Real > | set_reference_energies () |
| void | design_supercharge (Pose const &starting_pose, Pose &pose) |
| void | print_netcharge_and_mutations (Pose const &starting_pose, Pose const &pose) |
| int | get_net_charge (Pose const &pose) |
| void | energy_comparison (Pose &native, Pose &pose) |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| Public Member Functions inherited from protocols::moves::Mover | |
| Mover () | |
| virtual MoverOP | create () |
| MoverCOP | get_self_ptr () const |
| MoverOP | get_self_ptr () |
| MoverCAP | get_self_weak_ptr () const |
| MoverAP | get_self_weak_ptr () |
| Mover (std::string const &type_name) | |
| sets the type for a mover; name_ has been removed (2010/05/14) More... | |
| virtual void | test_move (Pose &pose) |
| : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More... | |
| virtual MoverOP | clone () const |
| Return a clone of the Mover object. More... | |
| virtual bool | reinitialize_for_each_job () const |
| Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More... | |
| virtual bool | reinitialize_for_new_input () const |
| Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More... | |
| virtual MoverOP | fresh_instance () const |
| Generates a new Mover object freshly created with the default ctor. More... | |
| MoverStatus | get_last_move_status () const |
| end parser interface, start Job Distributor interface///////////// More... | |
| void | reset_status () |
| resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More... | |
| virtual core::pose::PoseOP | get_additional_output () |
| Mechanism by which a mover may return multiple output poses from a single input pose. More... | |
| void | set_type (std::string const &setting) |
| Set the 'type' string. More... | |
| std::string | get_type () const |
| void | type (const std::string &type_in) |
| Set the 'type' string. More... | |
| std::string const & | type () const |
| Get the set 'type' string. More... | |
| virtual void | set_input_pose (PoseCOP pose) |
| setter for poses contained for rms More... | |
| virtual void | set_native_pose (PoseCOP pose) |
| setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More... | |
| PoseCOP | get_input_pose () const |
| PoseCOP | get_native_pose () const |
| virtual void | parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
| virtual void | set_current_tag (std::string const &new_tag) |
| std::string | get_current_tag () const |
| A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More... | |
| virtual void | show (std::ostream &output=std::cout) const |
| Outputs details about the Mover, including current settings. More... | |
| virtual core::Real | last_proposal_density_ratio () |
| virtual void | clear_info () |
| Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More... | |
| virtual Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor More... | |
| virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
| Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Private Attributes | |
| bool | AvNAPSA_positive_ = false |
| bool | AvNAPSA_negative_ = false |
| bool | target_net_charge_active_ = false |
| int | target_net_charge_ = 0 |
| core::Size | surface_atom_cutoff_ = 120 |
| bool | surface_atom_cutoff_set_ = false |
| core::Size | surface_residue_cutoff_ = 16 |
| bool | include_arg_ = false |
| bool | include_lys_ = false |
| bool | include_asp_ = false |
| bool | include_glu_ = false |
| core::Real | refweight_arg_ = -0.14916 |
| core::Real | refweight_lys_ = -0.287374 |
| core::Real | refweight_asp_ = -1.28682 |
| core::Real | refweight_glu_ = -1.55374 |
| bool | dont_mutate_glyprocys_ = true |
| bool | dont_mutate_correct_charge_ = true |
| bool | dont_mutate_hbonded_sidechains_ = true |
| bool | pre_packminpack_ = false |
| core::Size | local_nstruct_ = 1 |
| bool | compare_residue_energies_all_ = false |
| bool | compare_residue_energies_mut_ = true |
| SizeSet | surface_res_ |
| std::string | outputname_ |
| std::string | out_path_ |
| utility::vector1< core::Real > | AvNAPSA_values_ |
| core::Size | largest_mutated_AvNAPSA_ |
| core::scoring::ScoreFunctionOP | scorefxn_ |
Additional Inherited Members | |
| Static Public Member Functions inherited from protocols::moves::Mover | |
| static std::string | name () |
| static void | register_options () |
| Overload this static method if you access options within the mover. More... | |
| Protected Member Functions inherited from protocols::moves::Mover | |
| void | set_last_move_status (MoverStatus status) |
| nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More... | |
Detailed Description
Adds charged residues to a protein surface.
There are two modes for supercharging. The first is called AvNAPSA developed by the David Liu lab at Harvard. In this approach, surface residues are defined by the Average # Neighbor Atoms Per Sidechain Atom (AvNAPSA value), with a cutoff of 150. I think 100 is a safer cutoff. Arg, Lys, Asp, Glu, Asn, Gln are the only residues allowed to mutated. Lys is always chosen for positive, Glu is always chosen for negative, unless the native is Asn, then Asp is chosen. Thus, the sequence is deterministic. If one desires a particular net charge, the residues would be sorted from low to high AvNAPSA value and mutated one at a time until the target charge is achieved - this ignores the ceiling of 150 or 100. The second approach uses the Rosetta score function to guide the surface mutagenesis. The user must specifiy if Arg, Lys, or Asp, Glu are desired, and what the reference weights are. Alternatively, the user can specify a target net charge, and the reference weights of the charged residues will be incremented/decremented until the net charge is reached.
AvNAPSA-mode, target charge
- Define surface. sort NQ and RK/DE residues by AvNAPSA value (low to high)
- Next residue in sorted list: Positive: mutate DENQ-->K, Negative: mutate RKQ-->E and N-->D
- If net charge = target net charge, output pdb
AvNAPSA-mode, no target charge
- Define surface by AvNAPSA value (<100 default)
- For each NQ and DE/RK residue in the surface: Positive: mutate DENQ-->K, Negative: mutate RKQ-->E and N-->D
- Output pdb
Rosetta-mode, target charge
- Define surface. Neighbor by distance calculator (CB dist.), <16 neighbors default or Define surface by AvNAPSA value (<100 default)
- Set design task read user resfile, if provided dont_mutate gly, pro, cys dont_mutate h-bonded sidechains dont_mutate correct charge residues
- Set reference energies for RK/DE, starting at user input values
- pack rotamers mover
- check net charge, increment/decrement reference energies (back to step 3.)
- Once a pack rotamers run results in the correct net charge, output pdb
Rosetta-mode, no target charge
- Define surface. Neighbor by distance calculator (CB dist.), <16 neighbors default or Define surface by AvNAPSA value (<100 default)
- Set design task read user resfile, if provided dont_mutate gly, pro, cys dont_mutate h-bonded sidechains dont_mutate correct charge residues
- Set reference energies for RK/DE, using the user input values
- pack rotamers mover
- Output pdb
Note: either mode will read a user input resfile, but be sure to use ALLAA as the default, because NATAA default will make the surface residues undesignable. Either mode will make a second resfile with NATAA as default.
CAUTION: Supercharge does it's own output.
Member Typedef Documentation
◆ SizeSet
| using protocols::design_opt::Supercharge::SizeSet = std::set<core::Size> |
Constructor & Destructor Documentation
◆ Supercharge()
|
default |
◆ ~Supercharge()
|
overridedefault |
Member Function Documentation
◆ apply()
|
overridevirtual |
Main Method.
Implements protocols::moves::Mover.
References core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies(), protocols::moves::FAIL_DO_NOT_RETRY, core::scoring::get_score_function(), core::scoring::methods::EnergyMethodOptions::hbond_options(), protocols::hybridization::path, core::pose::Pose::pdb_info(), core::pose::Pose::size(), and protocols::design_opt::TR().
◆ AvNAPSA_negative()
|
inline |
References AvNAPSA_negative_.
◆ AvNAPSA_positive()
|
inline |
References AvNAPSA_positive_.
◆ AvNAPSA_values()
|
virtual |
average number of neighboring atoms per sidechain atom
References core::conformation::Residue::atom(), core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::name3(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::design_opt::TR(), and core::conformation::Atom::xyz().
◆ compare_residue_energies_all()
|
inline |
References compare_residue_energies_all_.
◆ compare_residue_energies_mut()
|
inline |
References compare_residue_energies_mut_.
◆ design_supercharge()
| void protocols::design_opt::Supercharge::design_supercharge | ( | Pose const & | starting_pose, |
| Pose & | pose | ||
| ) |
References core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies(), core::pose::Pose::dump_scored_pdb(), core::scoring::get_score_function(), core::scoring::methods::EnergyMethodOptions::hbond_options(), core::conformation::membrane::out, core::pose::Pose::pdb_info(), core::scoring::ref, and protocols::design_opt::TR().
◆ design_supercharge_AvNAPSA()
◆ dont_mutate_correct_charge()
|
inline |
References dont_mutate_correct_charge_.
◆ dont_mutate_glyprocys()
|
inline |
References dont_mutate_glyprocys_.
◆ dont_mutate_hbonded_sidechains()
|
inline |
References dont_mutate_hbonded_sidechains_.
◆ energy_comparison()
References core::scoring::dslf_fa13, core::pose::Pose::energies(), core::scoring::fa_atr, core::scoring::fa_dun, core::scoring::fa_elec, core::scoring::fa_intra_rep, core::scoring::fa_intra_sol_xover4, core::scoring::fa_rep, core::scoring::fa_sol, core::scoring::hbond_bb_sc, core::scoring::hbond_lr_bb, core::scoring::hbond_sc, core::scoring::hbond_sr_bb, core::scoring::lk_ball_wtd, core::conformation::Residue::name3(), core::scoring::omega, core::scoring::p_aa_pp, core::pose::Pose::pdb_info(), core::scoring::pro_close, core::scoring::rama_prepro, core::scoring::ref, core::pose::Pose::residue(), core::scoring::Energies::residue_total_energies(), core::scoring::Energies::residue_total_energy(), core::pose::Pose::size(), protocols::analysis::total, protocols::design_opt::TR(), and core::scoring::yhh_planarity.
◆ get_name()
|
inlineoverridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
◆ get_net_charge()
| int protocols::design_opt::Supercharge::get_net_charge | ( | Pose const & | pose | ) |
◆ include_arg()
|
inline |
References include_arg_.
◆ include_asp()
|
inline |
References include_asp_.
◆ include_glu()
|
inline |
References include_glu_.
◆ include_lys()
|
inline |
References include_lys_.
◆ local_nstruct()
|
inline |
References local_nstruct_.
◆ pre_packminpack()
|
inline |
References pre_packminpack_.
◆ prepack_input_structure()
|
virtual |
◆ print_netcharge_and_mutations()
◆ refweight_arg()
|
inline |
References refweight_arg_.
◆ refweight_asp()
|
inline |
References refweight_asp_.
◆ refweight_glu()
|
inline |
References refweight_glu_.
◆ refweight_lys()
|
inline |
References refweight_lys_.
◆ set_reference_energies()
| utility::vector1< Real > protocols::design_opt::Supercharge::set_reference_energies | ( | ) |
◆ set_resfile()
| void protocols::design_opt::Supercharge::set_resfile | ( | Pose const & | pose | ) |
References core::scoring::hbonds::HBond::get_self_ptr(), core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbond, core::conformation::Residue::name1(), core::scoring::hbonds::HBondSet::nhbonds(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies(), and protocols::design_opt::TR().
◆ set_resfile_AvNAPSA()
|
virtual |
◆ set_surface()
| void protocols::design_opt::Supercharge::set_surface | ( | Pose const & | pose | ) |
References core::conformation::Residue::atom(), core::conformation::Residue::first_sidechain_atom(), core::pose::metrics::CalculatorFactory::Instance(), core::pose::Pose::metric(), core::conformation::Residue::name3(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::pdb_info(), core::pose::metrics::CalculatorFactory::register_calculator(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::design_opt::TR(), and core::conformation::Atom::xyz().
◆ surface_atom_cutoff()
|
inline |
if target_net_charge is specified, the AvNAPSA cutoff is ignored
References surface_atom_cutoff_, and surface_atom_cutoff_set_.
◆ surface_residue_cutoff()
|
inline |
References surface_residue_cutoff_.
◆ target_net_charge()
|
inline |
References target_net_charge_.
◆ target_net_charge_active()
|
inline |
References target_net_charge_active_.
Member Data Documentation
◆ AvNAPSA_negative_
|
private |
Referenced by AvNAPSA_negative().
◆ AvNAPSA_positive_
|
private |
Referenced by AvNAPSA_positive().
◆ AvNAPSA_values_
|
private |
◆ compare_residue_energies_all_
|
private |
Referenced by compare_residue_energies_all().
◆ compare_residue_energies_mut_
|
private |
Referenced by compare_residue_energies_mut().
◆ dont_mutate_correct_charge_
|
private |
Referenced by dont_mutate_correct_charge().
◆ dont_mutate_glyprocys_
|
private |
Referenced by dont_mutate_glyprocys().
◆ dont_mutate_hbonded_sidechains_
|
private |
Referenced by dont_mutate_hbonded_sidechains().
◆ include_arg_
|
private |
Referenced by include_arg().
◆ include_asp_
|
private |
Referenced by include_asp().
◆ include_glu_
|
private |
Referenced by include_glu().
◆ include_lys_
|
private |
Referenced by include_lys().
◆ largest_mutated_AvNAPSA_
|
private |
◆ local_nstruct_
|
private |
Referenced by local_nstruct().
◆ out_path_
|
private |
◆ outputname_
|
private |
◆ pre_packminpack_
|
private |
Referenced by pre_packminpack().
◆ refweight_arg_
|
private |
Referenced by refweight_arg().
◆ refweight_asp_
|
private |
Referenced by refweight_asp().
◆ refweight_glu_
|
private |
Referenced by refweight_glu().
◆ refweight_lys_
|
private |
Referenced by refweight_lys().
◆ scorefxn_
|
private |
◆ surface_atom_cutoff_
|
private |
Referenced by surface_atom_cutoff().
◆ surface_atom_cutoff_set_
|
private |
Referenced by surface_atom_cutoff().
◆ surface_res_
|
private |
◆ surface_residue_cutoff_
|
private |
Referenced by surface_residue_cutoff().
◆ target_net_charge_
|
private |
Referenced by target_net_charge().
◆ target_net_charge_active_
|
private |
Referenced by target_net_charge_active().
The documentation for this class was generated from the following files:
- src/protocols/design_opt/Supercharge.hh
- src/protocols/design_opt/Supercharge.cc
