This data class wraps all the data needed for the AnchoredDesign movers. More...

#include <AnchorMoversData.hh>

Inheritance diagram for protocols::anchored_design::AnchorMoversData:

Collaboration diagram for protocols::anchored_design::AnchorMoversData:

Public Types
typedef utility::keys::Key3Tuple < protocols::loops::Loop, core::kinematics::MoveMapOP, core::kinematics::MoveMapOP >	Loop_mm_tuple

typedef utility::vector1 < Loop_mm_tuple >	Loop_mm_tuples

Public Member Functions
	AnchorMoversData ()
	empty constructor is empty - don't use it unless you intend to set alllllllll the data manually... More...

	AnchorMoversData (protocols::anchored_design::AnchorCOP anchor, protocols::loops::Loops const &loops, bool const options=false)
	constructor takes an anchor and loop object and sets up internals reasonably; options boolean is optionally optional. If you use this constructor, you will need to later manually give fragments to the AnchorMoversData object or use one of its fragments functions to determine what type of fragments to use. More...

	AnchorMoversData (core::pose::Pose const &pose)
	constructor takes a pose to generate its own internals (also using the option system) More...

virtual	~AnchorMoversData ()
	virtual dtors make c++ happy More...

	AnchorMoversData (AnchorMoversData const &rhs)
	copy ctor More...

AnchorMoversData &	operator= (AnchorMoversData const &rhs)
	assignment operator More...

AnchorMoversDataOP	clone () const

void	pick_new_cutpoints (bool reset_always)
	randomly reset loop cutpoints. Useful only when starting structure is well-closed. Best for MPI-style runs More...

void	anchor_noise_constraints_setup (core::pose::Pose &pose)
	set up constraints for anchor_noise_constraints_mode More...

void	set_frags (core::fragment::FragSetOP)
	set fragments object More...

core::fragment::FragSetCOP	autogenerate_design_frags ()
	brew its own design frags (LLLLL secondary structure) More...

core::fragment::FragSetCOP	autogenerate_constseq_frags (std::string const &seq)
	brew its own sequence-specific frags More...

void	autogenerate_frags (core::pose::Pose const &pose)
	figure out what type of fragments to use, and use them; pose needed to make packertask to detect if design is occuring More...

void	set_task_factory (core::pack::task::TaskFactoryOP)
	set packertask factory More...

void	set_fullatom_scorefunction (core::scoring::ScoreFunctionOP)
	set fullatom scorefunction More...

void	set_centroid_scorefunction (core::scoring::ScoreFunctionOP)
	set centroid scorefunction More...

void	set_loops_and_anchor (protocols::anchored_design::AnchorCOP anchor, protocols::loops::Loops loops)
	set up kinematics' loops and anchors More...

protocols::loops::Loop const &	anchored_loop () const
	access anchored loop More...

core::kinematics::MoveMapOP	movemap_fa_all () const
	access for movemap that covers all loops; fullatom More...

core::kinematics::MoveMapOP	movemap_cen_all () const
	access for movemap that covers all loops; centroid More...

core::Size	num_loops () const
	number of loops/mms More...

protocols::loops::Loop const &	loop (core::Size i) const
	accessor for a loop More...

core::kinematics::MoveMapOP	movemap_fa (core::Size i) const
	accessor for omega-variable movemap (most movers); fullatom phase (may allow anchor movement w/constraints) More...

core::kinematics::MoveMapOP	movemap_fa_omegafixed (core::Size i) const
	accessor for omega-fixed movemap (appropriate for CCD movers); fullatom phase (may allow anchor movement w/constraints) More...

core::kinematics::MoveMapOP	movemap_cen (core::Size i) const
	accessor for omega-variable movemap (most movers); centroid phase (no anchor movement) More...

core::kinematics::MoveMapOP	movemap_cen_omegafixed (core::Size i) const
	accessor for omega-fixed movemap (appropriate for CCD movers); centroid phase More...

protocols::loops::Loops const &	loops () const
	accessor for loops object More...

core::Size	anchor_start () const
	access for anchor start More...

core::Size	anchor_end () const
	access for anchor end More...

core::fragment::FragSetCOP	get_frags () const
	access fragments object More...

core::pack::task::TaskFactoryCOP	get_task_factory () const
	access packertask factory More...

core::pack::task::TaskFactoryCOP	get_late_factory () const
	access packertask factory More...

core::scoring::ScoreFunctionOP	get_fullatom_scorefunction () const
	access fullatom scorefunction More...

core::scoring::ScoreFunctionOP	get_centroid_scorefunction () const
	access centroid scorefunction More...

core::scoring::ScoreFunctionOP	get_centroid_scorefunction_min () const
	access centroid scorefunction for minimization More...

core::pack::task::PackerTaskOP	get_task (core::pose::Pose const &pose) const
	return packertask from factory More...

void	set_akash_dyepos (core::Size const akash_dyepos)
	dye position used in dye modeling publication More...

void	set_unbound_mode (bool unbound_mode)
	used for unbound mode More...

void	set_anchor_via_constraints (bool anchor_via_constraints)
	used to test anchoring via constraints More...

void	set_VDW_weight (core::Real VDW_weight)
	VDW weight in centroid scorefunction. More...

void	set_chainbreak_weight (core::Real chainbreak_weight)
	chainbreak weight in fullatom scorefunction More...

void	set_allow_anchor_repack (bool allow_anchor_repack)
	allow anchor to repack More...

void	set_resfile_1 (std::string const &resfile_1)
	resfile for design More...

void	set_resfile_2 (std::string const &resfile_2)
	later-stage resfile if desired More...

void	set_frag3 (std::string const &frag3)
	copy of cmdline option loop_file More...

void	set_no_frags (bool no_frags)
	do not use fragments? More...

void	set_anchor_noise_constraints_mode (bool anchor_noise_constraints_mode)
	special anchor_noise_constraints_mode More...

void	set_super_secret_fixed_interface_mode (bool super_secret_fixed_interface_mode)
	special super_secret_fixed_interface_mode More...

core::Size	get_akash_dyepos () const
	dye position used in dye modeling publication More...

bool	get_unbound_mode () const
	used for unbound mode More...

bool	get_anchor_via_constraints () const
	used to test anchoring via constraints More...

core::Real	get_VDW_weight () const
	VDW weight in centroid scorefunction. More...

core::Real	get_chainbreak_weight () const
	chainbreak weight in fullatom scorefunction More...

bool	get_allow_anchor_repack () const
	allow anchor to repack More...

std::string const &	get_resfile_1 () const
	resfile for design More...

std::string const &	get_resfile_2 () const
	later-stage resfile if desired More...

std::string const &	get_loop_file () const
	copy of cmdline option loop_file More...

std::string const &	get_frag3 () const
	copy of cmdline option frag3 More...

bool	get_no_frags () const
	do not use fragments? More...

bool	get_anchor_noise_constraints_mode () const
	special anchor_noise_constraints_mode More...

bool	get_super_secret_fixed_interface_mode () const
	special super_secret_fixed_interface_mode More...

void	read_options ()
	read options from the option system More...

std::string const &	interface_calc () const
	get string name for interface_calc_ More...

std::string const &	neighborhood_calc () const
	get string name for neighborhood_calc_ More...

Private Member Functions
void	setup_movemaps ()
	constructor subunit; generates movemaps from loops, including master movemap_all_ More...

void	set_movemap (core::kinematics::MoveMapOP movemap, core::Size seqpos, bool omega=false)
	setup_movemaps subunit More...

void	fix_anchor (core::kinematics::MoveMapOP movemap, bool const centroid)
	setup_movemaps subunit; boolean controls fullatom ignoring of fixing movemap if constraints exist More...

void	locate_anchor_loop ()
	constructor subunit, determines which loop is anchor's loop More...

void	input_loops_into_tuples (protocols::loops::Loops const &loops)
	constructor subunit, rearranges multiple-loops input structure into internal data structure More...

void	set_unset_defaults ()
	determined which pointers are unset, and sets them if possible More...

void	set_unset_scorefunctions ()
	set_unset_defaults subunit, sets default scorefunctions as necessary More...

void	set_unset_packertask_factory ()
	set_unset_defaults subunit, sets default packertask factory as necessary More...

core::Size	pick_new_cutpoint (core::Size const loopstart, core::Size const loopend)
	randomly reset just one cutpoint; used by pick_new_cutpoints More...

Private Attributes
protocols::anchored_design::AnchorCOP	anchor_
	the anchor itself More...

core::Size	anchor_loop_index_
	location of the anchored loop within loop_mm_tuples vector More...

core::kinematics::MoveMapOP	movemap_fa_all_
	movemap allowing all loops to move; fullatom phase More...

core::kinematics::MoveMapOP	movemap_cen_all_
	movemap allowing all loops to move; centroid phase More...

Loop_mm_tuples	loops_and_fa_mms_
	pairs of loops and movemaps to move those loops for loop closure/smallmover; fullatom versions More...

Loop_mm_tuples	loops_and_cen_mms_
	pairs of loops and movemaps to move those loops for loop closure/smallmover; centroid versions More...

protocols::loops::Loops	loops_
	a copy of the input loops object, in case a Loops type is needed More...

core::fragment::FragSetOP	fragset_
	fragments if we've got them More...

core::pack::task::TaskFactoryOP	task_factory_
	PackerTask factory. More...

core::pack::task::TaskFactoryOP	late_factory_
	second TaskFactory for more rotamers late in refinement More...

core::scoring::ScoreFunctionOP	fullatom_scorefunction_
	fullatom scorefunction More...

core::scoring::ScoreFunctionOP	centroid_scorefunction_
	centroid scorefunction More...

core::scoring::ScoreFunctionOP	centroid_scorefunction_min_
	centroid scorefunction with no-derivative functions off (for minimizing) More...

std::string const	interface_calc_
	calculator name More...

std::string const	neighborhood_calc_
	calculator name More...

core::Size	akash_dyepos_
	dye position used in dye modeling publication More...

bool	unbound_mode_
	used for unbound mode More...

bool	anchor_via_constraints_
	used to test anchoring via constraints More...

core::Real	VDW_weight_
	VDW weight in centroid scorefunction. More...

core::Real	chainbreak_weight_
	chainbreak weight in fullatom scorefunction More...

bool	allow_anchor_repack_
	allow anchor to repack More...

std::string	resfile_1_
	resfile for design More...

std::string	resfile_2_
	later-stage resfile if desired More...

std::string	loop_file_
	copy of loop_file cmdline option More...

std::string	frag3_
	copy of frag3 cmdline option More...

bool	no_frags_
	use no fragments More...

bool	anchor_noise_constraints_mode_
	special anchor_noise_constraints_mode More...

bool	super_secret_fixed_interface_mode_
	special super_secret_fixed_interface_mode More...

Detailed Description

This data class wraps all the data needed for the AnchoredDesign movers.

This data class keeps the anchor, mobile loops, and movemaps associated with the loops all together. It generates its own movemaps.

Definition at line 50 of file AnchorMoversData.hh.

Member Typedef Documentation

typedef utility::keys::Key3Tuple< protocols::loops::Loop, core::kinematics::MoveMapOP, core::kinematics::MoveMapOP> protocols::anchored_design::AnchorMoversData::Loop_mm_tuple

Definition at line 55 of file AnchorMoversData.hh.

typedef utility::vector1< Loop_mm_tuple > protocols::anchored_design::AnchorMoversData::Loop_mm_tuples

Definition at line 56 of file AnchorMoversData.hh.

Constructor & Destructor Documentation

protocols::anchored_design::AnchorMoversData::AnchorMoversData ( )

empty constructor is empty - don't use it unless you intend to set alllllllll the data manually...

empty, useless ctor. You'll need to manually set all the data later. Why did you make me waste my time writing this ctor?

mechanicals (ctor, dtor, etc)/////////////////////////////////////

Definition at line 100 of file AnchorMoversData.cc.

protocols::anchored_design::AnchorMoversData::AnchorMoversData	(	protocols::anchored_design::AnchorCOP	anchor,
		protocols::loops::Loops const &	loops,
		bool const	options = `false`
	)

constructor takes an anchor and loop object and sets up internals reasonably; options boolean is optionally optional. If you use this constructor, you will need to later manually give fragments to the AnchorMoversData object or use one of its fragments functions to determine what type of fragments to use.

Definition at line 133 of file AnchorMoversData.cc.

References read_options(), set_loops_and_anchor(), and set_unset_defaults().

protocols::anchored_design::AnchorMoversData::AnchorMoversData ( core::pose::Pose const & pose)

constructor takes a pose to generate its own internals (also using the option system)

use pose and option system to set up loops and create anchor, then call set_loops_and_anchor and set_unset_defaults to set up internal data to reasonable defaults, with or without option system help

Definition at line 181 of file AnchorMoversData.cc.

References anchor_, autogenerate_frags(), loop_file_, loops_, read_options(), set_loops_and_anchor(), and set_unset_defaults().

protocols::anchored_design::AnchorMoversData::~AnchorMoversData ( )

virtual

virtual dtors make c++ happy

Definition at line 238 of file AnchorMoversData.cc.

protocols::anchored_design::AnchorMoversData::AnchorMoversData ( AnchorMoversData const & rhs)

copy ctor

Definition at line 241 of file AnchorMoversData.cc.

Member Function Documentation

core::Size protocols::anchored_design::AnchorMoversData::anchor_end ( ) const

access for anchor end

Definition at line 392 of file AnchorMoversData.cc.

void protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup ( core::pose::Pose & pose)

set up constraints for anchor_noise_constraints_mode

This function automatically generates constraints for an anchor from and for the given pose. It is intended for use only with single-residue anchors. The constraints are between the residue CA and the four closest cross-chain CA. They are parabolic constraints with scores of 0.5 units at 1 Angstrom deviation.

Definition at line 892 of file AnchorMoversData.cc.

References core::pose::Pose::add_constraint(), core::chemical::ResidueType::atom_index(), core::scoring::atom_pair_constraint, protocols::frag_picker::CA, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::sequence::end, core::conformation::Conformation::num_chains(), core::pose::Pose::residue_type(), protocols::TR(), and core::pose::Pose::xyz().

core::Size protocols::anchored_design::AnchorMoversData::anchor_start ( ) const

access for anchor start

anchor functions//////////////////////////////////////////////

access for anchor start

Definition at line 389 of file AnchorMoversData.cc.

protocols::loops::Loop const & protocols::anchored_design::AnchorMoversData::anchored_loop ( ) const

access anchored loop

loops and movemap functions//////////////////////////////////////////////

Definition at line 353 of file AnchorMoversData.cc.

core::fragment::FragSetCOP protocols::anchored_design::AnchorMoversData::autogenerate_constseq_frags ( std::string const & seq)

brew its own sequence-specific frags

autogenerate_constseq_frags will use Andrew Ban's fragment picker to read the Vall and find fragments. It looks for fragments of loop secondary structure and known, fixed sequence. The string argument is the whole pose sequence.

Definition at line 706 of file AnchorMoversData.cc.

References core::fragment::picking_old::FragmentLibraryManager::clear_Vall(), core::sequence::end, core::fragment::picking_old::FragmentLibraryManager::get_instance(), core::fragment::picking_old::vall::pick_fragments_by_ss_plus_aa(), protocols::loops::start, protocols::loops::stop, and protocols::TR().

core::fragment::FragSetCOP protocols::anchored_design::AnchorMoversData::autogenerate_design_frags ( )

brew its own design frags (LLLLL secondary structure)

autogenerate_design_frags will use Andrew Ban's fragment picker to read the Vall and find fragments. It looks for fragments of loop secondary structure (for now, just 3mers.). This function is used in a design context and thus uses only secondary structure to define the fragments.

Definition at line 674 of file AnchorMoversData.cc.

References core::fragment::picking_old::FragmentLibraryManager::clear_Vall(), core::sequence::end, core::fragment::picking_old::FragmentLibraryManager::get_instance(), core::fragment::picking_old::vall::pick_fragments_by_ss(), protocols::loops::start, protocols::loops::stop, and protocols::TR().

void protocols::anchored_design::AnchorMoversData::autogenerate_frags ( core::pose::Pose const & pose)

figure out what type of fragments to use, and use them; pose needed to make packertask to detect if design is occuring

autogenerate_frags will determine from this object's state what fragments to use, and generate fragments as needed. The logic was originally at the executeable level, src/apps/pilot/smlewis/AnchoredDesign.cc:116-136 SVN 40529

Definition at line 741 of file AnchorMoversData.cc.

References protocols::anchored_design::EMPTY_STRING(), core::pose::Pose::sequence(), and protocols::TR().

Referenced by AnchorMoversData().

protocols::anchored_design::AnchorMoversDataOP protocols::anchored_design::AnchorMoversData::clone ( ) const

Definition at line 289 of file AnchorMoversData.cc.

void protocols::anchored_design::AnchorMoversData::fix_anchor	(	core::kinematics::MoveMapOP	movemap,
		bool const	centroid
	)

private

setup_movemaps subunit; boolean controls fullatom ignoring of fixing movemap if constraints exist

Definition at line 520 of file AnchorMoversData.cc.

References core::id::BB, core::scoring::omega, core::id::omega_torsion(), core::id::phi_torsion(), and core::id::psi_torsion().

core::Size protocols::anchored_design::AnchorMoversData::get_akash_dyepos ( ) const

dye position used in dye modeling publication

Definition at line 796 of file AnchorMoversData.cc.

Referenced by operator=().

bool protocols::anchored_design::AnchorMoversData::get_allow_anchor_repack ( ) const

allow anchor to repack

Definition at line 806 of file AnchorMoversData.cc.

Referenced by operator=().

bool protocols::anchored_design::AnchorMoversData::get_anchor_noise_constraints_mode ( ) const

special anchor_noise_constraints_mode

Definition at line 818 of file AnchorMoversData.cc.

Referenced by operator=().

bool protocols::anchored_design::AnchorMoversData::get_anchor_via_constraints ( ) const

used to test anchoring via constraints

Definition at line 800 of file AnchorMoversData.cc.

Referenced by operator=().

core::scoring::ScoreFunctionOP protocols::anchored_design::AnchorMoversData::get_centroid_scorefunction ( ) const

access centroid scorefunction

Definition at line 408 of file AnchorMoversData.cc.

Referenced by operator=().

core::scoring::ScoreFunctionOP protocols::anchored_design::AnchorMoversData::get_centroid_scorefunction_min ( ) const

access centroid scorefunction for minimization

Definition at line 411 of file AnchorMoversData.cc.

Referenced by operator=().

core::Real protocols::anchored_design::AnchorMoversData::get_chainbreak_weight ( ) const

chainbreak weight in fullatom scorefunction

Definition at line 804 of file AnchorMoversData.cc.

Referenced by operator=().

std::string const & protocols::anchored_design::AnchorMoversData::get_frag3 ( ) const

copy of cmdline option frag3

frag3 file

Definition at line 814 of file AnchorMoversData.cc.

Referenced by operator=().

core::fragment::FragSetCOP protocols::anchored_design::AnchorMoversData::get_frags ( ) const

access fragments object

scfxn, packertask, fragments accessors//////////////////////////////

Definition at line 396 of file AnchorMoversData.cc.

Referenced by operator=().

core::scoring::ScoreFunctionOP protocols::anchored_design::AnchorMoversData::get_fullatom_scorefunction ( ) const

access fullatom scorefunction

Definition at line 405 of file AnchorMoversData.cc.

Referenced by operator=().

core::pack::task::TaskFactoryCOP protocols::anchored_design::AnchorMoversData::get_late_factory ( ) const

access packertask factory

Definition at line 402 of file AnchorMoversData.cc.

Referenced by operator=().

std::string const & protocols::anchored_design::AnchorMoversData::get_loop_file ( ) const

copy of cmdline option loop_file

loop file

Definition at line 812 of file AnchorMoversData.cc.

Referenced by operator=().

bool protocols::anchored_design::AnchorMoversData::get_no_frags ( ) const

do not use fragments?

Definition at line 816 of file AnchorMoversData.cc.

Referenced by operator=().

std::string const & protocols::anchored_design::AnchorMoversData::get_resfile_1 ( ) const

resfile for design

Definition at line 808 of file AnchorMoversData.cc.

Referenced by operator=().

std::string const & protocols::anchored_design::AnchorMoversData::get_resfile_2 ( ) const

later-stage resfile if desired

Definition at line 810 of file AnchorMoversData.cc.

Referenced by operator=().

bool protocols::anchored_design::AnchorMoversData::get_super_secret_fixed_interface_mode ( ) const

special super_secret_fixed_interface_mode

Definition at line 820 of file AnchorMoversData.cc.

Referenced by operator=().

core::pack::task::PackerTaskOP protocols::anchored_design::AnchorMoversData::get_task ( core::pose::Pose const & pose) const

return packertask from factory

runs the member factory to create a task

Definition at line 414 of file AnchorMoversData.cc.

core::pack::task::TaskFactoryCOP protocols::anchored_design::AnchorMoversData::get_task_factory ( ) const

access packertask factory

Definition at line 399 of file AnchorMoversData.cc.

Referenced by operator=().

bool protocols::anchored_design::AnchorMoversData::get_unbound_mode ( ) const

used for unbound mode

Definition at line 798 of file AnchorMoversData.cc.

Referenced by operator=().

core::Real protocols::anchored_design::AnchorMoversData::get_VDW_weight ( ) const

VDW weight in centroid scorefunction.

Definition at line 802 of file AnchorMoversData.cc.

Referenced by operator=().

void protocols::anchored_design::AnchorMoversData::input_loops_into_tuples ( protocols::loops::Loops const & loops)

private

constructor subunit, rearranges multiple-loops input structure into internal data structure

private functions generate internal data from input and defaults///////////////

rearranges input loops data structure into the class's internal data structure

Definition at line 420 of file AnchorMoversData.cc.

References protocols::loops::Loops::begin(), and protocols::loops::Loops::end().

std::string const & protocols::anchored_design::AnchorMoversData::interface_calc ( ) const

get string name for interface_calc_

Definition at line 889 of file AnchorMoversData.cc.

void protocols::anchored_design::AnchorMoversData::locate_anchor_loop ( )

private

constructor subunit, determines which loop is anchor's loop

determines which loop contains the anchor (this loop may be treated differently)

Definition at line 441 of file AnchorMoversData.cc.

References protocols::loops::start, protocols::loops::stop, and protocols::TR().

protocols::loops::Loop const & protocols::anchored_design::AnchorMoversData::loop ( core::Size i) const

accessor for a loop

Definition at line 363 of file AnchorMoversData.cc.

protocols::loops::Loops const & protocols::anchored_design::AnchorMoversData::loops ( ) const

accessor for loops object

Definition at line 383 of file AnchorMoversData.cc.

Referenced by operator=().

core::kinematics::MoveMapOP protocols::anchored_design::AnchorMoversData::movemap_cen ( core::Size i) const

accessor for omega-variable movemap (most movers); centroid phase (no anchor movement)

Definition at line 375 of file AnchorMoversData.cc.

core::kinematics::MoveMapOP protocols::anchored_design::AnchorMoversData::movemap_cen_all ( ) const

access for movemap that covers all loops; centroid

Definition at line 357 of file AnchorMoversData.cc.

core::kinematics::MoveMapOP protocols::anchored_design::AnchorMoversData::movemap_cen_omegafixed ( core::Size i) const

accessor for omega-fixed movemap (appropriate for CCD movers); centroid phase

Definition at line 379 of file AnchorMoversData.cc.

core::kinematics::MoveMapOP protocols::anchored_design::AnchorMoversData::movemap_fa ( core::Size i) const

accessor for omega-variable movemap (most movers); fullatom phase (may allow anchor movement w/constraints)

Definition at line 367 of file AnchorMoversData.cc.

core::kinematics::MoveMapOP protocols::anchored_design::AnchorMoversData::movemap_fa_all ( ) const

access for movemap that covers all loops; fullatom

Definition at line 360 of file AnchorMoversData.cc.

core::kinematics::MoveMapOP protocols::anchored_design::AnchorMoversData::movemap_fa_omegafixed ( core::Size i) const

accessor for omega-fixed movemap (appropriate for CCD movers); fullatom phase (may allow anchor movement w/constraints)

Definition at line 371 of file AnchorMoversData.cc.

std::string const & protocols::anchored_design::AnchorMoversData::neighborhood_calc ( ) const

get string name for neighborhood_calc_

Definition at line 887 of file AnchorMoversData.cc.

core::Size protocols::anchored_design::AnchorMoversData::num_loops ( ) const

inline

number of loops/mms

Definition at line 117 of file AnchorMoversData.hh.

References loops_and_fa_mms_.

AnchorMoversData & protocols::anchored_design::AnchorMoversData::operator= ( AnchorMoversData const & rhs)

assignment operator

Definition at line 250 of file AnchorMoversData.cc.

References akash_dyepos_, allow_anchor_repack_, anchor_, anchor_noise_constraints_mode_, anchor_via_constraints_, centroid_scorefunction_, centroid_scorefunction_min_, chainbreak_weight_, frag3_, fragset_, fullatom_scorefunction_, get_akash_dyepos(), get_allow_anchor_repack(), get_anchor_noise_constraints_mode(), get_anchor_via_constraints(), get_centroid_scorefunction(), get_centroid_scorefunction_min(), get_chainbreak_weight(), get_frag3(), get_frags(), get_fullatom_scorefunction(), get_late_factory(), get_loop_file(), get_no_frags(), get_resfile_1(), get_resfile_2(), get_super_secret_fixed_interface_mode(), get_task_factory(), get_unbound_mode(), get_VDW_weight(), late_factory_, loop_file_, loops(), no_frags_, resfile_1_, resfile_2_, set_loops_and_anchor(), super_secret_fixed_interface_mode_, task_factory_, unbound_mode_, and VDW_weight_.

core::Size protocols::anchored_design::AnchorMoversData::pick_new_cutpoint	(	core::Size const	loopstart,
		core::Size const	loopend
	)

private

randomly reset just one cutpoint; used by pick_new_cutpoints

Definition at line 312 of file AnchorMoversData.cc.

References protocols::RG().

void protocols::anchored_design::AnchorMoversData::pick_new_cutpoints ( bool reset_always)

randomly reset loop cutpoints. Useful only when starting structure is well-closed. Best for MPI-style runs

Definition at line 294 of file AnchorMoversData.cc.

References protocols::loops::start, protocols::loops::stop, and protocols::TR().

void protocols::anchored_design::AnchorMoversData::read_options ( )

read options from the option system

Definition at line 822 of file AnchorMoversData.cc.

References protocols::anchored_design::EMPTY_STRING(), core::io::serialization::size(), and protocols::TR().

Referenced by AnchorMoversData().

void protocols::anchored_design::AnchorMoversData::set_akash_dyepos ( core::Size const akash_dyepos)

dye position used in dye modeling publication

option system replacement/////////////////////////////

Definition at line 769 of file AnchorMoversData.cc.

void protocols::anchored_design::AnchorMoversData::set_allow_anchor_repack ( bool allow_anchor_repack)

allow anchor to repack

Definition at line 779 of file AnchorMoversData.cc.

void protocols::anchored_design::AnchorMoversData::set_anchor_noise_constraints_mode ( bool anchor_noise_constraints_mode)

special anchor_noise_constraints_mode

Definition at line 791 of file AnchorMoversData.cc.

void protocols::anchored_design::AnchorMoversData::set_anchor_via_constraints ( bool anchor_via_constraints)

used to test anchoring via constraints

Definition at line 773 of file AnchorMoversData.cc.

void protocols::anchored_design::AnchorMoversData::set_centroid_scorefunction ( core::scoring::ScoreFunctionOP in)

set centroid scorefunction

Definition at line 332 of file AnchorMoversData.cc.

void protocols::anchored_design::AnchorMoversData::set_chainbreak_weight ( core::Real chainbreak_weight)

chainbreak weight in fullatom scorefunction

Definition at line 777 of file AnchorMoversData.cc.

void protocols::anchored_design::AnchorMoversData::set_frag3 ( std::string const & frag3)

copy of cmdline option loop_file

copy of cmdline option frag3

loop file

Definition at line 787 of file AnchorMoversData.cc.

void protocols::anchored_design::AnchorMoversData::set_frags ( core::fragment::FragSetOP in)

set fragments object

set functions/////////////////////////////////////////////////////////

Definition at line 322 of file AnchorMoversData.cc.

void protocols::anchored_design::AnchorMoversData::set_fullatom_scorefunction ( core::scoring::ScoreFunctionOP in)

set fullatom scorefunction

Definition at line 328 of file AnchorMoversData.cc.

void protocols::anchored_design::AnchorMoversData::set_loops_and_anchor	(	protocols::anchored_design::AnchorCOP	anchor,
		protocols::loops::Loops	loops
	)

set up kinematics' loops and anchors

set up kinematics' loops and anchors; these are combined because loop setup depends on anchor

Definition at line 336 of file AnchorMoversData.cc.

References protocols::loops::Loops::sequential_order().

Referenced by AnchorMoversData(), and operator=().

void protocols::anchored_design::AnchorMoversData::set_movemap	(	core::kinematics::MoveMapOP	movemap,
		core::Size	seqpos,
		bool	omega = `false`
	)

private

setup_movemaps subunit

Definition at line 509 of file AnchorMoversData.cc.

References core::id::BB, and core::id::omega_torsion().

void protocols::anchored_design::AnchorMoversData::set_no_frags ( bool no_frags)

do not use fragments?

Definition at line 789 of file AnchorMoversData.cc.

void protocols::anchored_design::AnchorMoversData::set_resfile_1 ( std::string const & resfile_1)

resfile for design

Definition at line 781 of file AnchorMoversData.cc.

void protocols::anchored_design::AnchorMoversData::set_resfile_2 ( std::string const & resfile_2)

later-stage resfile if desired

Definition at line 783 of file AnchorMoversData.cc.

void protocols::anchored_design::AnchorMoversData::set_super_secret_fixed_interface_mode ( bool super_secret_fixed_interface_mode)

special super_secret_fixed_interface_mode

Definition at line 793 of file AnchorMoversData.cc.

void protocols::anchored_design::AnchorMoversData::set_task_factory ( core::pack::task::TaskFactoryOP in)

set packertask factory

Definition at line 325 of file AnchorMoversData.cc.

void protocols::anchored_design::AnchorMoversData::set_unbound_mode ( bool unbound_mode)

used for unbound mode

Definition at line 771 of file AnchorMoversData.cc.

void protocols::anchored_design::AnchorMoversData::set_unset_defaults ( )

private

determined which pointers are unset, and sets them if possible

Definition at line 544 of file AnchorMoversData.cc.

Referenced by AnchorMoversData().

void protocols::anchored_design::AnchorMoversData::set_unset_packertask_factory ( )

private

set_unset_defaults subunit, sets default packertask factory as necessary

Definition at line 587 of file AnchorMoversData.cc.

References protocols::anchored_design::EMPTY_STRING(), core::pose::metrics::CalculatorFactory::Instance(), core::pose::metrics::CalculatorFactory::register_calculator(), protocols::loops::start, protocols::loops::stop, and protocols::TR().

void protocols::anchored_design::AnchorMoversData::set_unset_scorefunctions ( )

private

set_unset_defaults subunit, sets default scorefunctions as necessary

Definition at line 550 of file AnchorMoversData.cc.

References core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn(), core::scoring::cbeta, core::scoring::cenpack, core::scoring::chainbreak, core::scoring::env, core::scoring::getScoreFunction(), core::scoring::hbond_lr_bb, core::scoring::hbond_sr_bb, core::scoring::pair, core::scoring::rama, core::scoring::ScoreFunction::set_weight(), protocols::TR(), and core::scoring::vdw.

void protocols::anchored_design::AnchorMoversData::set_VDW_weight ( core::Real VDW_weight)

VDW weight in centroid scorefunction.

Definition at line 775 of file AnchorMoversData.cc.

void protocols::anchored_design::AnchorMoversData::setup_movemaps ( )

private

constructor subunit; generates movemaps from loops, including master movemap_all_

private functions generate internal data from input and defaults/////////////////

sets all movemaps for the class - paired ones and single movemap_all_, also sets loop_or_notloop_

Definition at line 469 of file AnchorMoversData.cc.

References protocols::loops::start, and protocols::loops::stop.

Member Data Documentation

core::Size protocols::anchored_design::AnchorMoversData::akash_dyepos_

private

dye position used in dye modeling publication

Definition at line 279 of file AnchorMoversData.hh.

Referenced by operator=().

bool protocols::anchored_design::AnchorMoversData::allow_anchor_repack_

private

allow anchor to repack

Definition at line 289 of file AnchorMoversData.hh.

Referenced by operator=().

protocols::anchored_design::AnchorCOP protocols::anchored_design::AnchorMoversData::anchor_

private

the anchor itself

Definition at line 245 of file AnchorMoversData.hh.

Referenced by AnchorMoversData(), and operator=().

core::Size protocols::anchored_design::AnchorMoversData::anchor_loop_index_

private

location of the anchored loop within loop_mm_tuples vector

Definition at line 247 of file AnchorMoversData.hh.

bool protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_mode_

private

special anchor_noise_constraints_mode

Definition at line 303 of file AnchorMoversData.hh.

Referenced by operator=().

bool protocols::anchored_design::AnchorMoversData::anchor_via_constraints_

private

used to test anchoring via constraints

Definition at line 283 of file AnchorMoversData.hh.

Referenced by operator=().

core::scoring::ScoreFunctionOP protocols::anchored_design::AnchorMoversData::centroid_scorefunction_

private

centroid scorefunction

Definition at line 268 of file AnchorMoversData.hh.

Referenced by operator=().

core::scoring::ScoreFunctionOP protocols::anchored_design::AnchorMoversData::centroid_scorefunction_min_

private

centroid scorefunction with no-derivative functions off (for minimizing)

Definition at line 270 of file AnchorMoversData.hh.

Referenced by operator=().

core::Real protocols::anchored_design::AnchorMoversData::chainbreak_weight_

private

chainbreak weight in fullatom scorefunction

Definition at line 287 of file AnchorMoversData.hh.

Referenced by operator=().

std::string protocols::anchored_design::AnchorMoversData::frag3_

private

copy of frag3 cmdline option

Definition at line 299 of file AnchorMoversData.hh.

Referenced by operator=().

core::fragment::FragSetOP protocols::anchored_design::AnchorMoversData::fragset_

private

fragments if we've got them

Definition at line 260 of file AnchorMoversData.hh.

Referenced by operator=().

core::scoring::ScoreFunctionOP protocols::anchored_design::AnchorMoversData::fullatom_scorefunction_

private

fullatom scorefunction

Definition at line 266 of file AnchorMoversData.hh.

Referenced by operator=().

std::string const protocols::anchored_design::AnchorMoversData::interface_calc_

private

calculator name

Definition at line 273 of file AnchorMoversData.hh.

core::pack::task::TaskFactoryOP protocols::anchored_design::AnchorMoversData::late_factory_

private

second TaskFactory for more rotamers late in refinement

Definition at line 264 of file AnchorMoversData.hh.

Referenced by operator=().

std::string protocols::anchored_design::AnchorMoversData::loop_file_

private

copy of loop_file cmdline option

Definition at line 297 of file AnchorMoversData.hh.

Referenced by AnchorMoversData(), and operator=().

protocols::loops::Loops protocols::anchored_design::AnchorMoversData::loops_

private

a copy of the input loops object, in case a Loops type is needed

Definition at line 257 of file AnchorMoversData.hh.

Referenced by AnchorMoversData().

Loop_mm_tuples protocols::anchored_design::AnchorMoversData::loops_and_cen_mms_

private

pairs of loops and movemaps to move those loops for loop closure/smallmover; centroid versions

Definition at line 255 of file AnchorMoversData.hh.

Loop_mm_tuples protocols::anchored_design::AnchorMoversData::loops_and_fa_mms_

private

pairs of loops and movemaps to move those loops for loop closure/smallmover; fullatom versions

Definition at line 253 of file AnchorMoversData.hh.

Referenced by num_loops().

core::kinematics::MoveMapOP protocols::anchored_design::AnchorMoversData::movemap_cen_all_

private

movemap allowing all loops to move; centroid phase

Definition at line 251 of file AnchorMoversData.hh.

core::kinematics::MoveMapOP protocols::anchored_design::AnchorMoversData::movemap_fa_all_

private

movemap allowing all loops to move; fullatom phase

Definition at line 249 of file AnchorMoversData.hh.

std::string const protocols::anchored_design::AnchorMoversData::neighborhood_calc_

private

calculator name

Definition at line 275 of file AnchorMoversData.hh.

bool protocols::anchored_design::AnchorMoversData::no_frags_

private

use no fragments

Definition at line 301 of file AnchorMoversData.hh.

Referenced by operator=().

std::string protocols::anchored_design::AnchorMoversData::resfile_1_

private

resfile for design

Definition at line 291 of file AnchorMoversData.hh.

Referenced by operator=().

std::string protocols::anchored_design::AnchorMoversData::resfile_2_

private

later-stage resfile if desired

Definition at line 293 of file AnchorMoversData.hh.

Referenced by operator=().

bool protocols::anchored_design::AnchorMoversData::super_secret_fixed_interface_mode_

private

special super_secret_fixed_interface_mode

Definition at line 305 of file AnchorMoversData.hh.

Referenced by operator=().

core::pack::task::TaskFactoryOP protocols::anchored_design::AnchorMoversData::task_factory_

private

PackerTask factory.

Definition at line 262 of file AnchorMoversData.hh.

Referenced by operator=().

bool protocols::anchored_design::AnchorMoversData::unbound_mode_

private

used for unbound mode

Definition at line 281 of file AnchorMoversData.hh.

Referenced by operator=().

core::Real protocols::anchored_design::AnchorMoversData::VDW_weight_

private

VDW weight in centroid scorefunction.

Definition at line 285 of file AnchorMoversData.hh.

Referenced by operator=().

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

src/protocols/anchored_design/AnchorMoversData.hh
src/protocols/anchored_design/AnchorMoversData.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation