HECT mover. More...
Public Member Functions | |
| HECTAllMover () | |
| virtual void | init_on_new_input (core::pose::Pose &pose) |
| init_on_new_input system allows for initializing these details the first time apply() is called. the job distributor will reinitialize the whole mover when the input changes (a freshly constructed mover, which will re-run this on first apply(). More... | |
| virtual | ~HECTAllMover () |
| virtual void | add_frag_mover (protocols::moves::RandomMoverOP random_mover) |
| default version does nothing More... | |
| virtual protocols::moves::MoverOP | fresh_instance () const |
 Public Member Functions inherited from HECTMover | |
| HECTMover () | |
| core::fragment::FragSetCOP | make_frags (core::Size const start, core::Size const stop, std::string const &seq) |
| helper code for fragments generation More... | |
| void | parse_options (core::pose::Pose const &pose) |
| parse_options will grab things from the option system and store them in local data - the stored data are used in the later setup functions More... | |
| void | set_up_foldtree (core::pose::Pose &pose) |
| set_up_foldtree More... | |
| void | set_up_taskfactory () |
| some shared setup of task factory More... | |
| void | ubq_constraints (core::pose::Pose &pose) |
| ubq_constraints will set up some ubiquitin to E3 constraints based on the input crystal structures. To refresh your memory, this code runs on the PDBs 3JW0 and 3JVZ, from reference Kamadurai HB, Souphron J, Scott DC, Duda DM, Miller DJ, Stringer D, Piper RC, Schulman BA. Insights into ubiquitin transfer cascades from a structure of a UbcH5B approximately ubiquitin-HECT(NEDD4L) complex. Mol Cell. 2009 Dec 25;36(6):1095-102. Anyway, the constraints are drawn from some mutational experiments in the paper, which showed that these interactions matter for functionality. More... | |
| void | build_AtomID_vec () |
| build_AtomID_vec builds the atomID vector used for setting up the TorsionDOFMovers and used to calculate atom distances for later scoring More... | |
| virtual | ~HECTMover () |
| virtual bool | reinitialize_for_each_job () const |
| virtual bool | reinitialize_for_new_input () const |
| void | create_extra_output (core::pose::Pose const &pose) |
| virtual void | apply (core::pose::Pose &pose) |
| this apply function holds the main apply for BOTH HECT_UBQ and HECT_ALL. It has a function call to a function which will handle the different aspect for those two peices of code; the remainder of the differences are encoded in the setup function defined by each subclass. More... | |
Private Types | |
| typedef HECTMover | parent |
Additional Inherited Members | |
| Protected Types inherited from HECTMover | |
| enum | atomID { CYS_C = 1 , CYS_CA = 2 , CYS_CB = 3 , CYS_SG = 4 , GLY_C = 5 , GLY_CA = 6 , GLY_N = 7 , GLY2_C = 8 , E3_cat_SG = 9 , atomID_tot = E3_cat_SG } |
| Protected Attributes inherited from HECTMover | |
| bool | init_for_input_yet_ |
| flag for when init function has run. More... | |
| char | e3chain_ |
| variables for points of interest in the protein (brackets for movers) - this may be overkill More... | |
| char | e2chain_ |
| char | ubqchain_ |
| core::Size | e3chain_num_ |
| core::Size | e3chain_start_ |
| core::Size | e3chain_end_ |
| core::Size | e3_hinge_start_ |
| core::Size | e3_hinge_stop_ |
| core::Size | e3_catalytic_res_ |
| core::Size | ubqchain_num_ |
| core::Size | ubqchain_start_ |
| core::Size | ubqchain_end_ |
| core::Size | utail_start_ |
| core::Size | utail_stop_ |
| core::Size | e2chain_num_ |
| core::Size | e2chain_start_ |
| core::Size | e2chain_end_ |
| core::Size | e2_catalytic_res_ |
| core::scoring::ScoreFunctionOP | fullatom_scorefunction_ |
| core::pack::task::TaskFactoryOP | task_factory_ |
| core::kinematics::MoveMapOP | movemap_ |
| core::fragment::FragSetCOP | fragset3mer_e3_hinge_ |
| fragment sets for hinge region and tail region More... | |
| core::fragment::FragSetCOP | fragset3mer_ubq_tail_ |
| core::pose::PoseCOP | fixed_starting_pose_ |
| this mover ignores the apply-passed PDB, instead returning to the starting pose set up by the init function. Under the assumption that the starting pose is not changing this lets up skip running the setup code every time. More... | |
| core::pose::PoseCOP | xtal_pose_ |
| utility::vector1< core::id::AtomID > | atomIDs |
| vector contains atomIDs for thioester bond and atoms before/after bond to determine various torsions - indexed by enum More... | |
Detailed Description
HECT mover.
Member Typedef Documentation
◆ parent
|
private |
Constructor & Destructor Documentation
◆ HECTAllMover()
|
inline |
Referenced by fresh_instance().
◆ ~HECTAllMover()
|
inlinevirtual |
Member Function Documentation
◆ add_frag_mover()
|
inlinevirtual |
default version does nothing
Reimplemented from HECTMover.
References HECTMover::fragset3mer_e3_hinge_, and HECTMover::movemap_.
◆ fresh_instance()
|
inlinevirtual |
References HECTAllMover().
◆ init_on_new_input()
|
inlinevirtual |
init_on_new_input system allows for initializing these details the first time apply() is called. the job distributor will reinitialize the whole mover when the input changes (a freshly constructed mover, which will re-run this on first apply().
Implements HECTMover.
References HECTMover::build_AtomID_vec(), basic::options::OptionKeys::catalytic_cst_sd, basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, basic::options::OptionKeys::debug, basic::options::OptionKeys::msd::debug, HECTMover::e2_catalytic_res_, HECTMover::E3_cat_SG, HECTMover::e3_catalytic_res_, HECTMover::e3_hinge_start_, HECTMover::e3_hinge_stop_, pyrosetta.toolbox.load_ligand::fa_standard, HECTMover::fixed_starting_pose_, HECTMover::fragset3mer_e3_hinge_, HECTMover::fragset3mer_ubq_tail_, create_a3b_hbs::i, HECTMover::init_for_input_yet_, HECTMover::make_frags(), HECTMover::movemap_, option, HECTMover::parse_options(), beta_nonlocal::pose, basic::options::OptionKeys::in::file::residue_type_set, beta_sc_scan::seq, HECTMover::set_up_foldtree(), HECTMover::set_up_taskfactory(), TR, HECTMover::ubq_constraints(), HECTMover::ubqchain_end_, HECTMover::utail_start_, and value.
The documentation for this class was generated from the following file:
- src/apps/pilot/smlewis/hect/HECT_all.cc
