Rosetta 3.4
Public Types | Public Member Functions
protocols::simple_moves::sidechain_moves::SidechainMoverBase Class Reference

class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions More...

#include <SidechainMoverBase.hh>

Inheritance diagram for protocols::simple_moves::sidechain_moves::SidechainMoverBase:
Inheritance graph
[legend]
Collaboration diagram for protocols::simple_moves::sidechain_moves::SidechainMoverBase:
Collaboration graph
[legend]

List of all members.

Public Types

typedef utility::vector1
< core::Real
ChiVector

Public Member Functions

 SidechainMoverBase ()
 default constructor
 SidechainMoverBase (core::pack::dunbrack::RotamerLibrary const &rotamer_library)
 constructor with user provided rotamer library
 SidechainMoverBase (SidechainMoverBase const &mover)
 ~SidechainMoverBase ()
virtual void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.
void init_task (core::pose::Pose const &pose)
 initialize the packer task if necessary
virtual void initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle)
 callback executed before any Monte Carlo trials
virtual
core::conformation::ResidueOP 
make_move (core::conformation::ResidueOP res)
virtual void make_chi_move (core::conformation::Residue const &residue, ChiVector const &old_chi, ChiVector &new_chi)=0
virtual core::Size suggest_residue_number (core::pose::Pose const &) const
virtual void apply (core::pose::Pose &pose)
 apply a sidechain move to a Pose object
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
virtual core::Real compute_proposal_density (core::conformation::Residue const &new_residue, core::Size const resnum, core::chemical::ResidueType const &old_res_type, ChiVector const &old_chi) const =0
 all angles in degree
void idealize_sidechains (core::pose::Pose &pose)
 idealize sidechains that might be altered
core::pack::dunbrack::RotamerLibrary
const & 
rotamer_library () const
 get the rotamer library
core::pack::task::TaskFactoryCOP task_factory () const
 get the task factory
void set_task_factory (core::pack::task::TaskFactoryCOP task_factory)
 set the task factory
core::pack::task::PackerTaskCOP task () const
 get the packer task
void set_task (core::pack::task::PackerTaskCOP task)
 set the task
bool preserve_detailed_balance () const
 get whether detailed balance is preserved (i.e. proposal density ratio calculated)
void set_preserve_detailed_balance (bool setting)
 set whether detailed balance is preserved (i.e. proposal density ratio calculated)
bool change_chi_without_replacing_residue () const
 perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain.
void set_change_chi_without_replacing_residue (bool setting)
 perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain.
virtual bool have_mutated_residue () const
 return true if your last move has mutated residue --- make sure the residue is replaced entirely
virtual utility::vector1
< core::id::TorsionID_Range
torsion_id_ranges (core::pose::Pose &pose)
 get the TorsionIDs perturbed by the mover during moves, along with their ranges
virtual utility::vector1
< core::id::DOF_ID_Range
dof_id_ranges (core::pose::Pose &pose)
 get the DOF_IDs perturbed by the mover during moves, along with their ranges
utility::vector1< core::Size >
const & 
packed_residues () const
 get the residues that can be changed by this mover
utility::vector1< bool > const & residue_packed () const
 get a vector indicating whether each residue can be packed
virtual core::Real last_proposal_density_ratio ()
 get the ratio of proposal densities for the last move

Detailed Description

class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions


Member Typedef Documentation


Constructor & Destructor Documentation

protocols::simple_moves::sidechain_moves::SidechainMoverBase::SidechainMoverBase ( )

default constructor

protocols::simple_moves::sidechain_moves::SidechainMoverBase::SidechainMoverBase ( core::pack::dunbrack::RotamerLibrary const &  rotamer_library)

constructor with user provided rotamer library

protocols::simple_moves::sidechain_moves::SidechainMoverBase::SidechainMoverBase ( SidechainMoverBase const &  mover)
protocols::simple_moves::sidechain_moves::SidechainMoverBase::~SidechainMoverBase ( )

Member Function Documentation

void protocols::simple_moves::sidechain_moves::SidechainMoverBase::apply ( core::pose::Pose pose) [virtual]
bool protocols::simple_moves::sidechain_moves::SidechainMoverBase::change_chi_without_replacing_residue ( ) const

perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain.

Referenced by apply(), parse_my_tag(), and set_change_chi_without_replacing_residue().

Real protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::compute_proposal_density ( core::conformation::Residue const &  new_residue,
core::Size const  resnum,
core::chemical::ResidueType const &  old_res_type,
ChiVector const &  old_chi 
) const [pure virtual]
utility::vector1< id::DOF_ID_Range > protocols::simple_moves::sidechain_moves::SidechainMoverBase::dof_id_ranges ( core::pose::Pose pose) [virtual]
std::string protocols::simple_moves::sidechain_moves::SidechainMoverBase::get_name ( ) const [virtual]
virtual bool protocols::simple_moves::sidechain_moves::SidechainMoverBase::have_mutated_residue ( ) const [inline, virtual]

return true if your last move has mutated residue --- make sure the residue is replaced entirely

Referenced by apply().

void protocols::simple_moves::sidechain_moves::SidechainMoverBase::idealize_sidechains ( core::pose::Pose pose)

idealize sidechains that might be altered

Detailed:
all sidechains that might be changed are replaced with ideal coordinates that have the original chi angles

References core::chemical::aa_pro, core::pose::Pose::chi(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), init_task(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::pose::Pose::set_chi().

Referenced by initialize_simulation().

void protocols::simple_moves::sidechain_moves::SidechainMoverBase::init_task ( core::pose::Pose const &  pose)

initialize the packer task if necessary

Detailed:
Check to make sure that a packer task exists and matches the numer of residues in the given pose. If that isn't the case, create a new one with the task factory. Exits with an error if no task factory exists.

References set_task(), and core::pose::Pose::total_residue().

Referenced by apply(), dof_id_ranges(), idealize_sidechains(), and initialize_simulation().

void protocols::simple_moves::sidechain_moves::SidechainMoverBase::initialize_simulation ( core::pose::Pose pose,
protocols::canonical_sampling::MetropolisHastingsMover const &  metropolis_hastings_mover,
core::Size  cycle 
) [virtual]

callback executed before any Monte Carlo trials

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

References idealize_sidechains(), and init_task().

Real protocols::simple_moves::sidechain_moves::SidechainMoverBase::last_proposal_density_ratio ( ) [virtual]

get the ratio of proposal densities for the last move

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

virtual void protocols::simple_moves::sidechain_moves::SidechainMoverBase::make_chi_move ( core::conformation::Residue const &  residue,
ChiVector const &  old_chi,
ChiVector new_chi 
) [pure virtual]
conformation::ResidueOP protocols::simple_moves::sidechain_moves::SidechainMoverBase::make_move ( core::conformation::ResidueOP  res) [virtual]
utility::vector1< Size > const & protocols::simple_moves::sidechain_moves::SidechainMoverBase::packed_residues ( ) const

get the residues that can be changed by this mover

void protocols::simple_moves::sidechain_moves::SidechainMoverBase::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 
) [virtual]

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover, protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover, and protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover.

References change_chi_without_replacing_residue(), core::sequence::end, protocols::moves::DataMap::get(), protocols::moves::DataMap::has(), preserve_detailed_balance(), set_change_chi_without_replacing_residue(), and set_preserve_detailed_balance().

bool protocols::simple_moves::sidechain_moves::SidechainMoverBase::preserve_detailed_balance ( ) const [virtual]

get whether detailed balance is preserved (i.e. proposal density ratio calculated)

Implements protocols::canonical_sampling::ThermodynamicMover.

Referenced by parse_my_tag(), and set_preserve_detailed_balance().

utility::vector1< bool > const & protocols::simple_moves::sidechain_moves::SidechainMoverBase::residue_packed ( ) const

get a vector indicating whether each residue can be packed

pack::dunbrack::RotamerLibrary const & protocols::simple_moves::sidechain_moves::SidechainMoverBase::rotamer_library ( ) const
void protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_change_chi_without_replacing_residue ( bool  setting)

perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain.

References change_chi_without_replacing_residue().

Referenced by parse_my_tag().

void protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_preserve_detailed_balance ( bool  setting) [virtual]

set whether detailed balance is preserved (i.e. proposal density ratio calculated)

Implements protocols::canonical_sampling::ThermodynamicMover.

References preserve_detailed_balance().

Referenced by parse_my_tag().

void protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_task ( core::pack::task::PackerTaskCOP  task)

set the task

References core::chemical::aa_pro, and task().

Referenced by init_task().

void protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_task_factory ( core::pack::task::TaskFactoryCOP  task_factory)

set the task factory

References task_factory().

core::Size protocols::simple_moves::sidechain_moves::SidechainMoverBase::suggest_residue_number ( core::pose::Pose const &  pose) const [virtual]
pack::task::PackerTaskCOP protocols::simple_moves::sidechain_moves::SidechainMoverBase::task ( ) const

get the packer task

Referenced by set_task().

pack::task::TaskFactoryCOP protocols::simple_moves::sidechain_moves::SidechainMoverBase::task_factory ( ) const

get the task factory

Referenced by set_task_factory().

utility::vector1< id::TorsionID_Range > protocols::simple_moves::sidechain_moves::SidechainMoverBase::torsion_id_ranges ( core::pose::Pose pose) [virtual]

get the TorsionIDs perturbed by the mover during moves, along with their ranges

Implements protocols::canonical_sampling::ThermodynamicMover.


The documentation for this class was generated from the following files:
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines