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Public Member Functions | Protected Types | Protected Attributes | List of all members
HECTMover Class Referenceabstract

HECT mover. More...

#include <HECT.hh>

Inheritance diagram for HECTMover:
Inheritance graph
[legend]

Public Member Functions

 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...
 
virtual void add_frag_mover (protocols::moves::RandomMoverOP)
 default version does nothing More...
 
virtual void init_on_new_input (core::pose::Pose &pose)=0
 pure virtual version, this is where most differences between ubq and all version lie More...
 

Protected Types

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

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 Enumeration Documentation

◆ atomID

enum HECTMover::atomID
protected
Enumerator
CYS_C 
CYS_CA 
CYS_CB 
CYS_SG 
GLY_C 
GLY_CA 
GLY_N 
GLY2_C 
E3_cat_SG 
atomID_tot 

Constructor & Destructor Documentation

◆ HECTMover()

HECTMover::HECTMover ( )
inline

References fullatom_scorefunction_, basic::options::OptionKeys::in::file::native, basic::options::option, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::frags::scoring::scoring, TR, value, and xtal_pose_.

◆ ~HECTMover()

virtual HECTMover::~HECTMover ( )
inlinevirtual

Member Function Documentation

◆ add_frag_mover()

virtual void HECTMover::add_frag_mover ( protocols::moves::RandomMoverOP  )
inlinevirtual

default version does nothing

Reimplemented in HECTAllMover.

Referenced by apply().

◆ apply()

virtual void HECTMover::apply ( core::pose::Pose &  pose)
inlinevirtual

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.

References add_frag_mover(), atomIDs, create_extra_output(), basic::options::OptionKeys::cycles, fixed_starting_pose_, fragset3mer_ubq_tail_, fullatom_scorefunction_, GLY2_C, create_a3b_hbs::i, init_for_input_yet_, init_on_new_input(), mc, vancomycin::min_mover, basic::options::OptionKeys::run::min_type, basic::options::OptionKeys::MonteCarlo::MonteCarlo, movemap_, basic::options::option, option, test.Workshop6test::pack_mover, beta_nonlocal::pose, basic::options::OptionKeys::repack_cycles, test.Workshop5test::shear_mover, test.Workshop5test::small_mover, task_factory_, TR, and value.

Referenced by pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

◆ build_AtomID_vec()

void HECTMover::build_AtomID_vec ( )
inline

build_AtomID_vec builds the atomID vector used for setting up the TorsionDOFMovers and used to calculate atom distances for later scoring

References atomIDs, CYS_C, CYS_CA, CYS_CB, CYS_SG, e2_catalytic_res_, E3_cat_SG, e3_catalytic_res_, pyrosetta.toolbox.load_ligand::fa_standard, GLY2_C, GLY_C, GLY_CA, GLY_N, basic::options::OptionKeys::in::file::residue_type_set, and ubqchain_end_.

Referenced by HECTAllMover::init_on_new_input(), and HECTUBQMover::init_on_new_input().

◆ create_extra_output()

void HECTMover::create_extra_output ( core::pose::Pose const &  pose)
inline

This function is specific to the original system for which this code was written - if you are not trying to duplicate the initial results you should remove it!

References atomIDs, build_jacobian::distance, E3_cat_SG, fixed_starting_pose_, GLY_C, beta_nonlocal::pose, and xtal_pose_.

Referenced by apply().

◆ init_on_new_input()

virtual void HECTMover::init_on_new_input ( core::pose::Pose &  pose)
pure virtual

pure virtual version, this is where most differences between ubq and all version lie

Implemented in HECTUBQMover, and HECTAllMover.

Referenced by apply().

◆ make_frags()

core::fragment::FragSetCOP HECTMover::make_frags ( core::Size const  start,
core::Size const  stop,
std::string const &  seq 
)
inline

helper code for fragments generation

References basic::options::OptionKeys::debug_skip_fragment_generation, test.Workshop4test::fragset, numeric::kinematic_closure::frame(), create_a3b_hbs::j, basic::options::OptionKeys::in::file::list, basic::options::option, beta_sc_scan::seq, basic::options::OptionKeys::cutoutdomain::start, TR, and value.

Referenced by HECTAllMover::init_on_new_input(), and HECTUBQMover::init_on_new_input().

◆ parse_options()

void HECTMover::parse_options ( core::pose::Pose const &  pose)
inline

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

References e2_catalytic_res_, basic::options::OptionKeys::e2_catalytic_resnum, basic::options::OptionKeys::e2_chain, e2chain_, e2chain_end_, e2chain_num_, e2chain_start_, e3_catalytic_res_, basic::options::OptionKeys::e3_catalytic_resnum, basic::options::OptionKeys::e3_hinge_chain, e3_hinge_start_, basic::options::OptionKeys::e3_hinge_start_resnum, e3_hinge_stop_, basic::options::OptionKeys::e3_hinge_stop_resnum, e3chain_, e3chain_end_, e3chain_num_, e3chain_start_, option, beta_nonlocal::pose, runtime_assert, TR, basic::options::OptionKeys::UBQ_tail_chain, basic::options::OptionKeys::UBQ_tail_start_resnum, ubqchain_, ubqchain_end_, ubqchain_num_, ubqchain_start_, utail_start_, utail_stop_, and value.

Referenced by HECTAllMover::init_on_new_input(), and HECTUBQMover::init_on_new_input().

◆ reinitialize_for_each_job()

virtual bool HECTMover::reinitialize_for_each_job ( ) const
inlinevirtual

◆ reinitialize_for_new_input()

virtual bool HECTMover::reinitialize_for_new_input ( ) const
inlinevirtual

◆ set_up_foldtree()

void HECTMover::set_up_foldtree ( core::pose::Pose &  pose)
inline

set_up_foldtree

References e2_catalytic_res_, e2chain_end_, e2chain_start_, e3chain_end_, e3chain_start_, beta_nonlocal::pose, TR, ubqchain_end_, and ubqchain_start_.

Referenced by HECTAllMover::init_on_new_input(), and HECTUBQMover::init_on_new_input().

◆ set_up_taskfactory()

void HECTMover::set_up_taskfactory ( )
inline

some shared setup of task factory

References e2_catalytic_res_, e2chain_end_, e2chain_start_, e3_hinge_start_, e3_hinge_stop_, e3chain_end_, e3chain_start_, create_a3b_hbs::i, option, packing::resfile(), vancomycin::task, task_factory_, ubqchain_end_, ubqchain_start_, basic::options::OptionKeys::inout::dbms::user, and utail_start_.

Referenced by HECTAllMover::init_on_new_input(), and HECTUBQMover::init_on_new_input().

◆ ubq_constraints()

void HECTMover::ubq_constraints ( core::pose::Pose &  pose)
inline

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.

References basic::options::OptionKeys::constraints::constraints, e3chain_, pyrosetta.toolbox.load_ligand::fa_standard, fullatom_scorefunction_, basic::options::OptionKeys::mp::scoring::hbond, option, beta_nonlocal::pose, basic::options::OptionKeys::in::file::residue_type_set, basic::options::OptionKeys::ubq_cst_sd, ubqchain_, and value.

Referenced by HECTAllMover::init_on_new_input(), and HECTUBQMover::init_on_new_input().

Member Data Documentation

◆ atomIDs

utility::vector1< core::id::AtomID > HECTMover::atomIDs
protected

vector contains atomIDs for thioester bond and atoms before/after bond to determine various torsions - indexed by enum

Referenced by apply(), build_AtomID_vec(), and create_extra_output().

◆ e2_catalytic_res_

core::Size HECTMover::e2_catalytic_res_
protected

Referenced by build_AtomID_vec(), HECTAllMover::init_on_new_input(), HECTUBQMover::init_on_new_input(), parse_options(), set_up_foldtree(), and set_up_taskfactory().

◆ e2chain_

char HECTMover::e2chain_
protected

Referenced by parse_options().

◆ e2chain_end_

core::Size HECTMover::e2chain_end_
protected

Referenced by parse_options(), set_up_foldtree(), and set_up_taskfactory().

◆ e2chain_num_

core::Size HECTMover::e2chain_num_
protected

Referenced by parse_options().

◆ e2chain_start_

core::Size HECTMover::e2chain_start_
protected

Referenced by parse_options(), set_up_foldtree(), and set_up_taskfactory().

◆ e3_catalytic_res_

core::Size HECTMover::e3_catalytic_res_
protected

Referenced by build_AtomID_vec(), HECTAllMover::init_on_new_input(), HECTUBQMover::init_on_new_input(), and parse_options().

◆ e3_hinge_start_

core::Size HECTMover::e3_hinge_start_
protected

Referenced by HECTAllMover::init_on_new_input(), parse_options(), and set_up_taskfactory().

◆ e3_hinge_stop_

core::Size HECTMover::e3_hinge_stop_
protected

Referenced by HECTAllMover::init_on_new_input(), parse_options(), and set_up_taskfactory().

◆ e3chain_

char HECTMover::e3chain_
protected

variables for points of interest in the protein (brackets for movers) - this may be overkill

Referenced by parse_options(), and ubq_constraints().

◆ e3chain_end_

core::Size HECTMover::e3chain_end_
protected

Referenced by parse_options(), set_up_foldtree(), and set_up_taskfactory().

◆ e3chain_num_

core::Size HECTMover::e3chain_num_
protected

Referenced by parse_options().

◆ e3chain_start_

core::Size HECTMover::e3chain_start_
protected

Referenced by parse_options(), set_up_foldtree(), and set_up_taskfactory().

◆ fixed_starting_pose_

core::pose::PoseCOP HECTMover::fixed_starting_pose_
protected

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.

Referenced by apply(), create_extra_output(), HECTAllMover::init_on_new_input(), and HECTUBQMover::init_on_new_input().

◆ fragset3mer_e3_hinge_

core::fragment::FragSetCOP HECTMover::fragset3mer_e3_hinge_
protected

fragment sets for hinge region and tail region

Referenced by HECTAllMover::add_frag_mover(), and HECTAllMover::init_on_new_input().

◆ fragset3mer_ubq_tail_

core::fragment::FragSetCOP HECTMover::fragset3mer_ubq_tail_
protected

Referenced by apply(), HECTAllMover::init_on_new_input(), and HECTUBQMover::init_on_new_input().

◆ fullatom_scorefunction_

core::scoring::ScoreFunctionOP HECTMover::fullatom_scorefunction_
protected

Referenced by apply(), HECTMover(), and ubq_constraints().

◆ init_for_input_yet_

bool HECTMover::init_for_input_yet_
protected

flag for when init function has run.

Referenced by apply(), HECTAllMover::init_on_new_input(), and HECTUBQMover::init_on_new_input().

◆ movemap_

core::kinematics::MoveMapOP HECTMover::movemap_
protected

Referenced by HECTAllMover::add_frag_mover(), apply(), HECTAllMover::init_on_new_input(), and HECTUBQMover::init_on_new_input().

◆ task_factory_

core::pack::task::TaskFactoryOP HECTMover::task_factory_
protected

Referenced by apply(), and set_up_taskfactory().

◆ ubqchain_

char HECTMover::ubqchain_
protected

Referenced by parse_options(), and ubq_constraints().

◆ ubqchain_end_

core::Size HECTMover::ubqchain_end_
protected

Referenced by build_AtomID_vec(), HECTAllMover::init_on_new_input(), HECTUBQMover::init_on_new_input(), parse_options(), set_up_foldtree(), and set_up_taskfactory().

◆ ubqchain_num_

core::Size HECTMover::ubqchain_num_
protected

Referenced by parse_options().

◆ ubqchain_start_

core::Size HECTMover::ubqchain_start_
protected

Referenced by parse_options(), set_up_foldtree(), and set_up_taskfactory().

◆ utail_start_

core::Size HECTMover::utail_start_
protected

Referenced by HECTAllMover::init_on_new_input(), HECTUBQMover::init_on_new_input(), parse_options(), and set_up_taskfactory().

◆ utail_stop_

core::Size HECTMover::utail_stop_
protected

Referenced by parse_options().

◆ xtal_pose_

core::pose::PoseCOP HECTMover::xtal_pose_
protected

Referenced by create_extra_output(), and HECTMover().

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