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protocols::anchored_design::AnchorMoversData Class Reference

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

#include <AnchorMoversData.hh>

Inheritance diagram for protocols::anchored_design::AnchorMoversData:
Inheritance graph
[legend]

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...
 
 ~AnchorMoversData () override
 virtual dtors make c++ happy More...
 
 AnchorMoversData (AnchorMoversData const &rhs)
 copy ctor More...
 
AnchorMoversDataoperator= (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.

Member Typedef Documentation

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)/////////////////////////////////////

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.

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.

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

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

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

virtual dtors make c++ happy

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

copy ctor

Member Function Documentation

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

access for anchor end

access for anchor end

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.

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//////////////////////////////////////////////

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

access for anchor start

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

access anchored loop

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

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.

References core::sequence::end, 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.

References core::sequence::end, 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

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
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

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

Referenced by operator=().

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

allow anchor to repack

Referenced by operator=().

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

special anchor_noise_constraints_mode

Referenced by operator=().

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

used to test anchoring via constraints

Referenced by operator=().

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

access centroid scorefunction

Referenced by operator=().

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

access centroid scorefunction for minimization

Referenced by operator=().

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

chainbreak weight in fullatom scorefunction

Referenced by operator=().

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

copy of cmdline option frag3

frag3 file

Referenced by operator=().

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

access fragments object

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

Referenced by operator=().

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

access fullatom scorefunction

Referenced by operator=().

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

access packertask factory

Referenced by operator=().

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

copy of cmdline option loop_file

loop file

Referenced by operator=().

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

do not use fragments?

Referenced by operator=().

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

resfile for design

Referenced by operator=().

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

later-stage resfile if desired

Referenced by operator=().

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

special super_secret_fixed_interface_mode

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

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

access packertask factory

Referenced by operator=().

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

used for unbound mode

Referenced by operator=().

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

VDW weight in centroid scorefunction.

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

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

get string name for interface_calc_

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)

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

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

accessor for loops object

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)

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

access for movemap that covers all loops; centroid

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

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)

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

access for movemap that covers all loops; fullatom

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)

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

get string name for neighborhood_calc_

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

number of loops/mms

References loops_and_fa_mms_.

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

References core::scoring::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

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

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

read options from the option system

References protocols::anchored_design::EMPTY_STRING(), 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/////////////////////////////

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

allow anchor to repack

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

special anchor_noise_constraints_mode

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

used to test anchoring via constraints

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

set centroid scorefunction

References core::conformation::membrane::in.

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

chainbreak weight in fullatom scorefunction

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

copy of cmdline option loop_file

copy of cmdline option frag3

loop file

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

set fragments object

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

References core::conformation::membrane::in.

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

set fullatom scorefunction

References core::conformation::membrane::in.

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

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

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

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

do not use fragments?

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

resfile for design

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

later-stage resfile if desired

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

special super_secret_fixed_interface_mode

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

set packertask factory

References core::conformation::membrane::in.

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

used for unbound mode

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

determined which pointers are unset, and sets them if possible

Referenced by AnchorMoversData().

void protocols::anchored_design::AnchorMoversData::set_unset_packertask_factory ( )
private
void protocols::anchored_design::AnchorMoversData::set_unset_scorefunctions ( )
private
void protocols::anchored_design::AnchorMoversData::set_VDW_weight ( core::Real  VDW_weight)

VDW weight in centroid scorefunction.

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_

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

Referenced by operator=().

bool protocols::anchored_design::AnchorMoversData::allow_anchor_repack_
private

allow anchor to repack

Referenced by operator=().

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

the anchor itself

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

bool protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_mode_
private

special anchor_noise_constraints_mode

Referenced by operator=().

bool protocols::anchored_design::AnchorMoversData::anchor_via_constraints_
private

used to test anchoring via constraints

Referenced by operator=().

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

centroid scorefunction

Referenced by operator=().

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

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

Referenced by operator=().

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

chainbreak weight in fullatom scorefunction

Referenced by operator=().

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

copy of frag3 cmdline option

Referenced by operator=().

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

fragments if we've got them

Referenced by operator=().

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

fullatom scorefunction

Referenced by operator=().

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

calculator name

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

second TaskFactory for more rotamers late in refinement

Referenced by operator=().

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

copy of loop_file cmdline option

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

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

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

Referenced by num_loops().

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

movemap allowing all loops to move; centroid phase

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

movemap allowing all loops to move; fullatom phase

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

calculator name

bool protocols::anchored_design::AnchorMoversData::no_frags_
private

use no fragments

Referenced by operator=().

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

resfile for design

Referenced by operator=().

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

later-stage resfile if desired

Referenced by operator=().

bool protocols::anchored_design::AnchorMoversData::super_secret_fixed_interface_mode_
private

special super_secret_fixed_interface_mode

Referenced by operator=().

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

PackerTask factory.

Referenced by operator=().

bool protocols::anchored_design::AnchorMoversData::unbound_mode_
private

used for unbound mode

Referenced by operator=().

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

VDW weight in centroid scorefunction.

Referenced by operator=().


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