protocols::abinitio::abscript Namespace Reference

Classes
class	AbscriptLoopCloserCM
class	AbscriptLoopCloserCMCreator
class	AbscriptMover
class	AbscriptMoverCreator
class	AbscriptStageMover
class	ConstraintPreparer
class	ConstraintPreparerCreator
class	FragmentCM
class	FragmentCMCreator
class	FragmentJumpCM
class	FragmentJumpCMCreator
class	JumpSampleData
class	JumpSampleDataCreator
class	ResidueChunkSelection
class	AtomPack
class	RigidChunkCM
class	RigidChunkCMCreator
class	StagePreparer
class	StructPerturberCM
class	StructPerturberCMCreator

Typedefs
typedef utility::pointer::shared_ptr< AbscriptLoopCloserCM >	AbscriptLoopCloserCMOP
typedef utility::pointer::shared_ptr< AbscriptLoopCloserCM const >	AbscriptLoopCloserCMCOP
typedef utility::pointer::shared_ptr< AbscriptMover >	AbscriptMoverOP
typedef utility::pointer::shared_ptr< AbscriptMover const >	AbscriptMoverCOP
typedef utility::pointer::shared_ptr< AbscriptStageMover >	AbscriptStageMoverOP
typedef utility::pointer::shared_ptr< AbscriptStageMover const >	AbscriptStageMoverCOP
typedef utility::pointer::shared_ptr< ConstraintPreparer >	ConstraintPreparerOP
typedef utility::pointer::shared_ptr< ConstraintPreparer const >	ConstraintPreparerCOP
typedef utility::pointer::shared_ptr< FragmentCM >	FragmentCMOP
typedef utility::pointer::shared_ptr< FragmentCM const >	FragmentCMCOP
typedef utility::pointer::shared_ptr< FragmentJumpCM >	FragmentJumpCMOP
typedef utility::pointer::shared_ptr< FragmentJumpCM const >	FragmentJumpCMCOP
typedef utility::pointer::shared_ptr< JumpSampleData >	JumpSampleDataOP
typedef utility::pointer::shared_ptr< JumpSampleData const >	JumpSampleDataCOP
typedef utility::pointer::shared_ptr< RigidChunkCM >	RigidChunkCMOP
typedef utility::pointer::shared_ptr< RigidChunkCM const >	RigidChunkCMCOP
typedef utility::vector1< StageID >	StageIDs
typedef utility::pointer::shared_ptr< StagePreparer >	StagePreparerOP
typedef utility::pointer::shared_ptr< StagePreparer const >	StagePreparerCOP
typedef utility::pointer::shared_ptr< StructPerturberCM >	StructPerturberCMOP
typedef utility::pointer::shared_ptr< StructPerturberCM const >	StructPerturberCMCOP

Enumerations
enum	StageID {   I = 1 , II , IIIa , IIIb ,   IVa , IVb , END }

Functions
core::Real	angle_diff (core::Real const &a, core::Real const &b)
bool	angle_cpy (core::pose::Pose &target, core::pose::Pose const &source, core::id::TorsionID t_id)
StageID &	increment_stageid (StageID &id)
core::scoring::ScoreFunctionOP	setup_score (std::string const &scorename, basic::options::FileVectorOptionKey optkey)
void	verify_stage_ID (std::map< std::string, StageID > const &id_map, std::string const &id)
core::Real	score_cst (core::pose::Pose &pose, core::scoring::ScoreFunction const &scfxn)
bool	loop_stop_comp (loops::Loop const &lhs, loops::Loop const &rhs)
core::Size	determine_frag_size (std::string const &file)
loops::Loops	read_rigid_core (std::string const &file)
core::Size	find_disulfide_partner (core::pose::Pose const &pose, core::Size const resid)
void	fix_internal_coords_of_siblings (core::pose::Pose &pose, core::pose::Pose const &ref_pose, core::id::AtomID atom, core::id::AtomID ref_atom)
void	fix_mainchain_connect (core::pose::Pose &pose, core::Size global_upper, core::pose::Pose const &ref_pose, core::Size local_upper)

Variables
core::Real const	DEFAULT_TEMP = 2.0

Typedef Documentation

AbscriptLoopCloserCMCOP

typedef utility::pointer::shared_ptr< AbscriptLoopCloserCM const > protocols::abinitio::abscript::AbscriptLoopCloserCMCOP

AbscriptLoopCloserCMOP

typedef utility::pointer::shared_ptr< AbscriptLoopCloserCM > protocols::abinitio::abscript::AbscriptLoopCloserCMOP

AbscriptMoverCOP

typedef utility::pointer::shared_ptr< AbscriptMover const > protocols::abinitio::abscript::AbscriptMoverCOP

AbscriptMoverOP

typedef utility::pointer::shared_ptr< AbscriptMover > protocols::abinitio::abscript::AbscriptMoverOP

AbscriptStageMoverCOP

typedef utility::pointer::shared_ptr< AbscriptStageMover const > protocols::abinitio::abscript::AbscriptStageMoverCOP

AbscriptStageMoverOP

typedef utility::pointer::shared_ptr< AbscriptStageMover > protocols::abinitio::abscript::AbscriptStageMoverOP

ConstraintPreparerCOP

typedef utility::pointer::shared_ptr< ConstraintPreparer const > protocols::abinitio::abscript::ConstraintPreparerCOP

ConstraintPreparerOP

typedef utility::pointer::shared_ptr< ConstraintPreparer > protocols::abinitio::abscript::ConstraintPreparerOP

FragmentCMCOP

typedef utility::pointer::shared_ptr< FragmentCM const > protocols::abinitio::abscript::FragmentCMCOP

FragmentCMOP

typedef utility::pointer::shared_ptr< FragmentCM > protocols::abinitio::abscript::FragmentCMOP

FragmentJumpCMCOP

typedef utility::pointer::shared_ptr< FragmentJumpCM const > protocols::abinitio::abscript::FragmentJumpCMCOP

FragmentJumpCMOP

typedef utility::pointer::shared_ptr< FragmentJumpCM > protocols::abinitio::abscript::FragmentJumpCMOP

JumpSampleDataCOP

typedef utility::pointer::shared_ptr< JumpSampleData const > protocols::abinitio::abscript::JumpSampleDataCOP

JumpSampleDataOP

typedef utility::pointer::shared_ptr< JumpSampleData > protocols::abinitio::abscript::JumpSampleDataOP

RigidChunkCMCOP

typedef utility::pointer::shared_ptr< RigidChunkCM const > protocols::abinitio::abscript::RigidChunkCMCOP

RigidChunkCMOP

typedef utility::pointer::shared_ptr< RigidChunkCM > protocols::abinitio::abscript::RigidChunkCMOP

StageIDs

typedef utility::vector1< StageID > protocols::abinitio::abscript::StageIDs

StagePreparerCOP

typedef utility::pointer::shared_ptr< StagePreparer const > protocols::abinitio::abscript::StagePreparerCOP

StagePreparerOP

typedef utility::pointer::shared_ptr< StagePreparer > protocols::abinitio::abscript::StagePreparerOP

StructPerturberCMCOP

typedef utility::pointer::shared_ptr< StructPerturberCM const > protocols::abinitio::abscript::StructPerturberCMCOP

StructPerturberCMOP

typedef utility::pointer::shared_ptr< StructPerturberCM > protocols::abinitio::abscript::StructPerturberCMOP

Enumeration Type Documentation

StageID

enum protocols::abinitio::abscript::StageID

Enumerator
I
II
IIIa
IIIb
IVa
IVb
END

Function Documentation

angle_cpy()

bool protocols::abinitio::abscript::angle_cpy	(	core::pose::Pose &	target,
		core::pose::Pose const &	source,
		core::id::TorsionID	t_id
	)

References angle_diff(), core::id::omega_torsion(), core::id::phi_torsion(), core::id::psi_torsion(), core::id::TorsionID::rsd(), core::pose::Pose::set_torsion(), protocols::environment::TOLERANCE, core::id::TorsionID::torsion(), core::pose::Pose::torsion(), and tr().

Referenced by protocols::abinitio::abscript::AbscriptLoopCloserCM::apply().

angle_diff()

core::Real protocols::abinitio::abscript::angle_diff	(	core::Real const &	a,
		core::Real const &	b
	)

References core::pose::motif::a(), and protocols::match::upstream::b.

Referenced by core::scoring::dna::DNATorsionPotential::add_dna_base_distance_constraints(), angle_cpy(), core::pack::dunbrack::DunbrackRotamerSampleData::chi_probability(), core::scoring::mm::MMBondAngleScore::dscore(), and core::scoring::mm::MMBondAngleScore::score().

determine_frag_size()

core::Size protocols::abinitio::abscript::determine_frag_size

(

std::string const &

file

)

References core::fragment::FragmentIO::read_data().

Referenced by protocols::abinitio::abscript::FragmentCM::parse_my_tag().

find_disulfide_partner()

core::Size protocols::abinitio::abscript::find_disulfide_partner	(	core::pose::Pose const &	pose,
		core::Size const	resid
	)

References core::conformation::Residue::atom_index(), core::chemical::ResidueConnection::atomno(), core::conformation::Residue::connect_map(), core::chemical::DISULFIDE, core::conformation::Residue::has(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueType::n_possible_residue_connections(), core::chemical::ResConnID::resid(), core::pose::Pose::residue(), core::chemical::ResidueType::residue_connection(), and core::conformation::Residue::type().

Referenced by protocols::abinitio::abscript::RigidChunkCM::configure().

fix_internal_coords_of_siblings()

void protocols::abinitio::abscript::fix_internal_coords_of_siblings	(	core::pose::Pose &	pose,
		core::pose::Pose const &	ref_pose,
		core::id::AtomID	atom,
		core::id::AtomID	ref_atom
	)

References core::kinematics::AtomTree::atom(), core::conformation::Residue::atom_index(), core::conformation::Residue::atom_name(), core::conformation::Conformation::atom_tree(), core::id::AtomID::atomno(), core::pose::Pose::conformation(), core::kinematics::AtomTree::dof(), core::kinematics::AtomTree::has(), core::kinematics::tree::Atom::parent(), core::chemical::rings::PHI, core::pose::Pose::residue(), core::id::AtomID::rsd(), core::conformation::Conformation::set_bond_angle(), core::conformation::Conformation::set_dof(), core::pose::Pose::size(), tr(), and core::pose::Pose::xyz().

Referenced by fix_mainchain_connect().

fix_mainchain_connect()

void protocols::abinitio::abscript::fix_mainchain_connect	(	core::pose::Pose &	pose,
		core::Size	global_upper,
		core::pose::Pose const &	ref_pose,
		core::Size	local_upper
	)

References core::conformation::Residue::atom_index(), core::chemical::ResidueType::atom_index(), protocols::abinitio::abscript::AtomPack::bb0, protocols::abinitio::abscript::AtomPack::bb1, protocols::abinitio::abscript::AtomPack::bb2, protocols::abinitio::abscript::AtomPack::bb3, protocols::abinitio::abscript::AtomPack::bb4, protocols::abinitio::abscript::AtomPack::bbM1, core::conformation::Conformation::bond_angle(), core::conformation::Conformation::bond_length(), core::pose::Pose::conformation(), fix_internal_coords_of_siblings(), core::conformation::Residue::has(), core::pose::is_ideal_position(), core::conformation::Residue::mainchain_torsion(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::Conformation::set_bond_angle(), core::conformation::Conformation::set_bond_length(), core::conformation::Conformation::set_torsion_angle(), core::conformation::Conformation::torsion_angle(), and tr().

Referenced by protocols::abinitio::abscript::RigidChunkCM::initialize().

increment_stageid()

StageID& protocols::abinitio::abscript::increment_stageid

(

StageID &

id

)

References END.

Referenced by protocols::abinitio::abscript::AbscriptMover::add_frags(), protocols::abinitio::abscript::AbscriptMover::parse_my_tag(), and protocols::abinitio::abscript::AbscriptMover::parse_stage_id().

loop_stop_comp()

bool protocols::abinitio::abscript::loop_stop_comp	(	loops::Loop const &	lhs,
		loops::Loop const &	rhs
	)

References protocols::loops::Loop::stop().

Referenced by protocols::abinitio::abscript::ConstraintPreparer::combine_exclude_file().

read_rigid_core()

loops::Loops protocols::abinitio::abscript::read_rigid_core

(

std::string const &

file

)

References protocols::loops::PoseNumberedLoopFileReader::hijack_loop_reading_code_set_loop_line_begin_token(), protocols::loops::PoseNumberedLoopFileReader::read_pose_numbered_loops_file(), and tr().

Referenced by protocols::abinitio::abscript::RigidChunkCM::parse_my_tag().

score_cst()

core::Real protocols::abinitio::abscript::score_cst	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction const &	scfxn
	)

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, core::pose::Pose::energies(), and core::scoring::Energies::total_energies().

Referenced by protocols::rbsegment_relax::OptimizeThreadingMover::apply(), and protocols::abinitio::abscript::AbscriptStageMover::setup_stage().

setup_score()

core::scoring::ScoreFunctionOP protocols::abinitio::abscript::setup_score	(	std::string const &	scorename,
		basic::options::FileVectorOptionKey	optkey
	)

References core::scoring::atom_pair_constraint, and core::scoring::ScoreFunctionFactory::create_score_function().

Referenced by protocols::abinitio::abscript::AbscriptMover::AbscriptMover(), and protocols::mpi_refinement::WorkUnit_PartialAbinitio::run().

verify_stage_ID()

void protocols::abinitio::abscript::verify_stage_ID	(	std::map< std::string, StageID > const &	id_map,
		std::string const &	id
	)

Referenced by protocols::abinitio::abscript::AbscriptMover::parse_stage_id().

Variable Documentation

DEFAULT_TEMP

core::Real const protocols::abinitio::abscript::DEFAULT_TEMP = 2.0

Referenced by protocols::abinitio::abscript::AbscriptMover::AbscriptMover().