protocols::helical_bundle Namespace Reference

Namespaces
	parameters

Classes
class	BackboneGridSampler
class	BackboneGridSamplerCreator
class	BackboneGridSamplerHelper
	BackboneGridSamplerHelper class, which stores options for the PerturbBundle mover. More...
class	BundleGridSampler
class	BundleGridSamplerCreator
class	BundleGridSamplerHelper
	BundleGridSamplerHelper class, which stores options for the PerturbBundle mover. More...
class	BundleParametrizationCalculator
	BundleParametrizationCalculator class, used for parametric helical bundle backbone generation. More...
class	BundleReporterFilter
class	BundleReporterFilterCreator
class	FitSimpleHelix
class	FitSimpleHelixCreator
class	FitSimpleHelixMultiFunc
	Multifunction class for fitting a simple (straight) helix to the Crick parameters. More...
class	MakeBundle
class	MakeBundleCreator
class	MakeBundleHelix
class	MakeBundleHelixCreator
class	PerturbBundle
class	PerturbBundleCreator
class	PerturbBundleHelix
class	PerturbBundleHelixCreator

Typedefs
typedef utility::pointer::shared_ptr< BackboneGridSampler >	BackboneGridSamplerOP
typedef utility::pointer::shared_ptr< BackboneGridSampler const >	BackboneGridSamplerCOP
typedef utility::vector1< BackboneGridSamplerOP >	BackboneGridSamplerOPs
typedef utility::vector1< BackboneGridSamplerCOP >	BackboneGridSamplerCOPs
typedef utility::pointer::weak_ptr< BackboneGridSamplerHelper >	BackboneGridSamplerHelperAP
typedef utility::pointer::weak_ptr< BackboneGridSamplerHelper const >	BackboneGridSamplerHelperCAP
typedef utility::pointer::shared_ptr< BackboneGridSamplerHelper >	BackboneGridSamplerHelperOP
typedef utility::pointer::shared_ptr< BackboneGridSamplerHelper const >	BackboneGridSamplerHelperCOP
typedef utility::vector1< BackboneGridSamplerHelperOP >	BackboneGridSamplerHelperOPs
typedef utility::vector1< BackboneGridSamplerHelperCOP >	BackboneGridSamplerHelperCOPs
typedef utility::vector1< BackboneGridSamplerHelperCAP >	BackboneGridSamplerHelperCAPs
typedef utility::pointer::shared_ptr< BundleGridSampler >	BundleGridSamplerOP
typedef utility::pointer::shared_ptr< BundleGridSampler const >	BundleGridSamplerCOP
typedef utility::vector1< BundleGridSamplerOP >	BundleGridSamplerOPs
typedef utility::vector1< BundleGridSamplerCOP >	BundleGridSamplerCOPs
typedef utility::pointer::weak_ptr< BundleGridSamplerHelper >	BundleGridSamplerHelperAP
typedef utility::pointer::weak_ptr< BundleGridSamplerHelper const >	BundleGridSamplerHelperCAP
typedef utility::pointer::shared_ptr< BundleGridSamplerHelper >	BundleGridSamplerHelperOP
typedef utility::pointer::shared_ptr< BundleGridSamplerHelper const >	BundleGridSamplerHelperCOP
typedef utility::vector1< BundleGridSamplerHelperOP >	BundleGridSamplerHelperOPs
typedef utility::vector1< BundleGridSamplerHelperCOP >	BundleGridSamplerHelperCOPs
typedef utility::vector1< BundleGridSamplerHelperCAP >	BundleGridSamplerHelperCAPs
typedef utility::pointer::weak_ptr< BundleParametrizationCalculator >	BundleParametrizationCalculatorAP
typedef utility::pointer::weak_ptr< BundleParametrizationCalculator const >	BundleParametrizationCalculatorCAP
typedef utility::pointer::shared_ptr< BundleParametrizationCalculator >	BundleParametrizationCalculatorOP
typedef utility::pointer::shared_ptr< BundleParametrizationCalculator const >	BundleParametrizationCalculatorCOP
typedef utility::vector1< BundleParametrizationCalculatorOP >	BundleParametrizationCalculatorOPs
typedef utility::vector1< BundleParametrizationCalculatorCOP >	BundleParametrizationCalculatorCOPs
typedef utility::vector1< BundleParametrizationCalculatorCAP >	BundleParametrizationCalculatorCAPs
typedef utility::pointer::shared_ptr< FitSimpleHelix >	FitSimpleHelixOP
typedef utility::pointer::shared_ptr< FitSimpleHelix const >	FitSimpleHelixCOP
typedef utility::vector1< FitSimpleHelixOP >	FitSimpleHelixOPs
typedef utility::vector1< FitSimpleHelixCOP >	FitSimpleHelixCOPs
typedef utility::pointer::shared_ptr< MakeBundle >	MakeBundleOP
typedef utility::pointer::shared_ptr< MakeBundle const >	MakeBundleCOP
typedef utility::vector1< MakeBundleOP >	MakeBundleOPs
typedef utility::vector1< MakeBundleCOP >	MakeBundleCOPs
typedef utility::pointer::shared_ptr< MakeBundleHelix >	MakeBundleHelixOP
typedef utility::pointer::shared_ptr< MakeBundleHelix const >	MakeBundleHelixCOP
typedef utility::vector1< MakeBundleHelixOP >	MakeBundleHelixOPs
typedef utility::vector1< MakeBundleHelixCOP >	MakeBundleHelixCOPs
typedef utility::pointer::shared_ptr< PerturbBundle >	PerturbBundleOP
typedef utility::pointer::shared_ptr< PerturbBundle const >	PerturbBundleCOP
typedef utility::vector1< PerturbBundleOP >	PerturbBundleOPs
typedef utility::vector1< PerturbBundleCOP >	PerturbBundleCOPs
typedef utility::pointer::shared_ptr< PerturbBundleHelix >	PerturbBundleHelixOP
typedef utility::pointer::shared_ptr< PerturbBundleHelix const >	PerturbBundleHelixCOP
typedef utility::vector1< PerturbBundleHelixOP >	PerturbBundleHelixOPs
typedef utility::vector1< PerturbBundleHelixCOP >	PerturbBundleHelixCOPs

Enumerations
enum	BPC_Parameters {   BPC_r0 = 1 , BPC_omega0 , BPC_delta_omega0 , BPC_delta_omega1 ,   BPC_delta_t , BPC_z0_offset , BPC_z1_offset , BPC_epsilon ,   BPC_last_parameter_to_be_sampled = BPC_epsilon , BPC_residues_per_repeat , BPC_repeating_unit_offset , BPC_atoms_per_residue ,   BPC_r1_peratom , BPC_omega1 , BPC_z1 , BPC_delta_omega1_peratom ,   BPC_delta_z1_peratom , BPC_invert_helix , BPC_set_dihedrals , BPC_set_bondangles ,   BPC_set_bondlengths , BPC_unknown_parameter , BPC_end_of_list = BPC_unknown_parameter }
	Enum for relevant parameters. More...
enum	BundleReporterFilterBehaviour { brf_always_true = 1 , brf_always_false , brf_filter_by_energy , brf_undefined }
	The behaviour of this filter. More...

Functions
static basic::Tracer	TR ("protocols.helical_bundle.BackboneGridSampler")
static basic::Tracer	TR_Results ("protocols.helical_bundle.BackboneGridSampler.Results")
std::string	subtag_for_bbgrid (std::string const &tag_name)
static basic::Tracer	TR ("protocols.helical_bundle.BackboneGridSamplerHelper")
static basic::Tracer	TR ("protocols.helical_bundle.BundleGridSampler")
std::string	subtag_for_bundgrid (std::string const &subtag)
static basic::Tracer	TR ("protocols.helical_bundle.BundleGridSamplerHelper")
static basic::Tracer	TR ("protocols.helical_bundle.BundleParametrizationCalculator")
static basic::Tracer	TR ("protocols.helical_bundle.BundleReporterFilter")
static basic::Tracer	TRReport ("protocols.helical_bundle.BundleReporterFilter.REPORT")
static basic::Tracer	TR ("protocols.helical_bundle.FitSimpleHelix")
static basic::Tracer	TR ("protocols.helical_bundle.MakeBundle")
static basic::Tracer	TR ("protocols.helical_bundle.MakeBundleHelix")
static basic::Tracer	TR ("protocols.helical_bundle.PerturbBundle")
static basic::Tracer	TR ("protocols.helical_bundle.PerturbBundleHelix")
static basic::Tracer	TR ("protocols.helical_bundle.util")
void	add_attributes_for_make_bundle_symmetry (AttributeList &attlist)
void	add_attributes_for_make_bundle_minorhelix_defaults (AttributeList &attlist)
void	add_attributes_for_make_bundle_other_defaults (AttributeList &attlist)
void	add_attributes_for_helix_params (AttributeList &attlist)
void	add_attributes_for_minor_helix_params (AttributeList &attlist)
void	add_attributes_for_other_helix_params (AttributeList &attlist)
void	write_crick_params_file_data (utility::io::ozstream &outfile, utility::vector1< core::Real > const &r1, core::Real const &omega1, core::Real const &z1, utility::vector1< core::Real > const &delta_omega1, utility::vector1< core::Real > const &delta_z1)
	Actual write of the crick_params file data. More...
void	write_minor_helix_params (std::string const &filename, utility::vector1< core::Real > const &r1, core::Real const &omega1, core::Real const &z1, utility::vector1< core::Real > const &delta_omega1, utility::vector1< core::Real > const &delta_z1)
	Write out a crick_params file. More...
void	write_minor_helix_params (std::string const &filename, core::Size const &residues_per_repeat, utility::vector1< core::Size > const &atoms_per_residue, utility::vector1< core::Real > const &r1, core::Real const &omega1, core::Real const &z1, utility::vector1< core::Real > const &delta_omega1, utility::vector1< core::Real > const &delta_z1)
	Write out a crick_params file. More...
std::string	get_crick_params_filename_formatted (std::string const &basename)
	Given a Crick params filename stub (e.g. "alpha_helix_100"), get the string with the full path and extension (e.g. "protocol_data/crick_parameters/alpha_helix_100.crick_params"). More...
void	read_minor_helix_params (std::string const &filename, utility::vector1< core::Real > &r1, core::Real &omega1, core::Real &z1, utility::vector1< core::Real > &delta_omega1, utility::vector1< core::Real > &delta_z1, core::Size &residues_per_repeat, utility::vector1< core::Size > &atoms_per_residue)
	Read minor helix parameters from a crick_params file. More...
void	generate_atom_positions (utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > &outvector, core::pose::Pose const &helixpose, core::Size const helix_start, core::Size const helix_end, core::Real const &r0, core::Real const &omega0, core::Real const &delta_omega0, core::Real const &delta_t, core::Real const &z1_offset, core::Real const &z0_offset, core::Real const &epsilon, bool const invert_helix, utility::vector1< core::Real > const &r1, core::Real const &omega1, core::Real const &z1, utility::vector1< core::Real > const &delta_omega1, core::Real const &delta_omega1_all, utility::vector1< core::Real > const &delta_z1, core::Size const residues_per_repeat, utility::vector1< core::Size > const &atoms_per_residue, core::Size const repeating_unit_offset, bool &failed)
	Generate the x,y,z coordinates of the mainchain atoms using the Crick equations. More...
void	place_atom_positions (core::pose::Pose &pose, utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > const &atom_positions, core::Size const helix_start, core::Size const helix_end)
	Place the helix mainchain atoms based on the Crick equations. More...
void	copy_helix_bondlengths (core::pose::Pose &pose, core::pose::Pose const &ref_pose, core::Size const helix_start, core::Size const helix_end)
	Copy backbone bond length values from one pose, where helix mainchain atom coordinates have been set with the Crick equations, to another with ideal geometry. More...
void	copy_helix_bondangles (core::pose::Pose &pose, core::pose::Pose const &ref_pose, core::Size const helix_start, core::Size const helix_end)
	Copy backbone bond angle values from one pose, where helix mainchain atom coordinates have been set with the Crick equations, to another with ideal geometry. More...
void	copy_helix_dihedrals (core::pose::Pose &pose, core::pose::Pose const &ref_pose, core::Size const helix_start, core::Size const helix_end)
	Copy backbone dihedral values from one pose, where helix mainchain atom coordinates have been set with the Crick equations, to another with ideal geometry. More...
void	align_mainchain_atoms (core::pose::Pose &pose, core::pose::Pose const &ref_pose, core::Size const helix_start, core::Size const helix_end)
	Align mainchain atoms of pose to ref_pose mainchain atoms. More...
void	align_mainchain_atoms_of_residue_range (core::pose::Pose &pose, core::pose::Pose const &ref_pose, core::Size const helix_start, core::Size const helix_end)
	Align mainchain atoms of pose to ref_pose mainchain atoms, moving ONLY the residues involved in the alignment. More...
void	parse_resnames (std::string const &string_in, utility::vector1< std::string > &vect_out)
	Given a comma-separated list of residue names, separate these out into a vector of residue names. More...
void	add_attributes_for_make_bundle_symmetry (utility::tag::AttributeList &attlist)
void	add_attributes_for_make_bundle_other_defaults (utility::tag::AttributeList &attlist)
void	add_attributes_for_make_bundle_minorhelix_defaults (utility::tag::AttributeList &attlist)
void	add_attributes_for_helix_params (utility::tag::AttributeList &subtag_attributes)
void	add_attributes_for_minor_helix_params (utility::tag::AttributeList &subtag_attributes)
void	add_attributes_for_other_helix_params (utility::tag::AttributeList &subtag_attributes)

Typedef Documentation

BackboneGridSamplerCOP

typedef utility::pointer::shared_ptr< BackboneGridSampler const > protocols::helical_bundle::BackboneGridSamplerCOP

BackboneGridSamplerCOPs

typedef utility::vector1<BackboneGridSamplerCOP> protocols::helical_bundle::BackboneGridSamplerCOPs

BackboneGridSamplerHelperAP

typedef utility::pointer::weak_ptr< BackboneGridSamplerHelper > protocols::helical_bundle::BackboneGridSamplerHelperAP

BackboneGridSamplerHelperCAP

typedef utility::pointer::weak_ptr< BackboneGridSamplerHelper const > protocols::helical_bundle::BackboneGridSamplerHelperCAP

BackboneGridSamplerHelperCAPs

typedef utility::vector1< BackboneGridSamplerHelperCAP > protocols::helical_bundle::BackboneGridSamplerHelperCAPs

BackboneGridSamplerHelperCOP

typedef utility::pointer::shared_ptr< BackboneGridSamplerHelper const > protocols::helical_bundle::BackboneGridSamplerHelperCOP

BackboneGridSamplerHelperCOPs

typedef utility::vector1< BackboneGridSamplerHelperCOP > protocols::helical_bundle::BackboneGridSamplerHelperCOPs

BackboneGridSamplerHelperOP

typedef utility::pointer::shared_ptr< BackboneGridSamplerHelper > protocols::helical_bundle::BackboneGridSamplerHelperOP

BackboneGridSamplerHelperOPs

typedef utility::vector1< BackboneGridSamplerHelperOP > protocols::helical_bundle::BackboneGridSamplerHelperOPs

BackboneGridSamplerOP

typedef utility::pointer::shared_ptr< BackboneGridSampler > protocols::helical_bundle::BackboneGridSamplerOP

BackboneGridSamplerOPs

typedef utility::vector1<BackboneGridSamplerOP> protocols::helical_bundle::BackboneGridSamplerOPs

BundleGridSamplerCOP

typedef utility::pointer::shared_ptr< BundleGridSampler const > protocols::helical_bundle::BundleGridSamplerCOP

BundleGridSamplerCOPs

typedef utility::vector1<BundleGridSamplerCOP> protocols::helical_bundle::BundleGridSamplerCOPs

BundleGridSamplerHelperAP

typedef utility::pointer::weak_ptr< BundleGridSamplerHelper > protocols::helical_bundle::BundleGridSamplerHelperAP

BundleGridSamplerHelperCAP

typedef utility::pointer::weak_ptr< BundleGridSamplerHelper const > protocols::helical_bundle::BundleGridSamplerHelperCAP

BundleGridSamplerHelperCAPs

typedef utility::vector1< BundleGridSamplerHelperCAP > protocols::helical_bundle::BundleGridSamplerHelperCAPs

BundleGridSamplerHelperCOP

typedef utility::pointer::shared_ptr< BundleGridSamplerHelper const > protocols::helical_bundle::BundleGridSamplerHelperCOP

BundleGridSamplerHelperCOPs

typedef utility::vector1< BundleGridSamplerHelperCOP > protocols::helical_bundle::BundleGridSamplerHelperCOPs

BundleGridSamplerHelperOP

typedef utility::pointer::shared_ptr< BundleGridSamplerHelper > protocols::helical_bundle::BundleGridSamplerHelperOP

BundleGridSamplerHelperOPs

typedef utility::vector1< BundleGridSamplerHelperOP > protocols::helical_bundle::BundleGridSamplerHelperOPs

BundleGridSamplerOP

typedef utility::pointer::shared_ptr< BundleGridSampler > protocols::helical_bundle::BundleGridSamplerOP

BundleGridSamplerOPs

typedef utility::vector1<BundleGridSamplerOP> protocols::helical_bundle::BundleGridSamplerOPs

BundleParametrizationCalculatorAP

typedef utility::pointer::weak_ptr< BundleParametrizationCalculator > protocols::helical_bundle::BundleParametrizationCalculatorAP

BundleParametrizationCalculatorCAP

typedef utility::pointer::weak_ptr< BundleParametrizationCalculator const > protocols::helical_bundle::BundleParametrizationCalculatorCAP

BundleParametrizationCalculatorCAPs

typedef utility::vector1< BundleParametrizationCalculatorCAP > protocols::helical_bundle::BundleParametrizationCalculatorCAPs

BundleParametrizationCalculatorCOP

typedef utility::pointer::shared_ptr< BundleParametrizationCalculator const > protocols::helical_bundle::BundleParametrizationCalculatorCOP

BundleParametrizationCalculatorCOPs

typedef utility::vector1< BundleParametrizationCalculatorCOP > protocols::helical_bundle::BundleParametrizationCalculatorCOPs

BundleParametrizationCalculatorOP

typedef utility::pointer::shared_ptr< BundleParametrizationCalculator > protocols::helical_bundle::BundleParametrizationCalculatorOP

BundleParametrizationCalculatorOPs

typedef utility::vector1< BundleParametrizationCalculatorOP > protocols::helical_bundle::BundleParametrizationCalculatorOPs

FitSimpleHelixCOP

typedef utility::pointer::shared_ptr< FitSimpleHelix const > protocols::helical_bundle::FitSimpleHelixCOP

FitSimpleHelixCOPs

typedef utility::vector1<FitSimpleHelixCOP> protocols::helical_bundle::FitSimpleHelixCOPs

FitSimpleHelixOP

typedef utility::pointer::shared_ptr< FitSimpleHelix > protocols::helical_bundle::FitSimpleHelixOP

FitSimpleHelixOPs

typedef utility::vector1<FitSimpleHelixOP> protocols::helical_bundle::FitSimpleHelixOPs

MakeBundleCOP

typedef utility::pointer::shared_ptr< MakeBundle const > protocols::helical_bundle::MakeBundleCOP

MakeBundleCOPs

typedef utility::vector1<MakeBundleCOP> protocols::helical_bundle::MakeBundleCOPs

MakeBundleHelixCOP

typedef utility::pointer::shared_ptr< MakeBundleHelix const > protocols::helical_bundle::MakeBundleHelixCOP

MakeBundleHelixCOPs

typedef utility::vector1<MakeBundleHelixCOP> protocols::helical_bundle::MakeBundleHelixCOPs

MakeBundleHelixOP

typedef utility::pointer::shared_ptr< MakeBundleHelix > protocols::helical_bundle::MakeBundleHelixOP

MakeBundleHelixOPs

typedef utility::vector1<MakeBundleHelixOP> protocols::helical_bundle::MakeBundleHelixOPs

MakeBundleOP

typedef utility::pointer::shared_ptr< MakeBundle > protocols::helical_bundle::MakeBundleOP

MakeBundleOPs

typedef utility::vector1<MakeBundleOP> protocols::helical_bundle::MakeBundleOPs

PerturbBundleCOP

typedef utility::pointer::shared_ptr< PerturbBundle const > protocols::helical_bundle::PerturbBundleCOP

PerturbBundleCOPs

typedef utility::vector1<PerturbBundleCOP> protocols::helical_bundle::PerturbBundleCOPs

PerturbBundleHelixCOP

typedef utility::pointer::shared_ptr< PerturbBundleHelix const > protocols::helical_bundle::PerturbBundleHelixCOP

PerturbBundleHelixCOPs

typedef utility::vector1<PerturbBundleHelixCOP> protocols::helical_bundle::PerturbBundleHelixCOPs

PerturbBundleHelixOP

typedef utility::pointer::shared_ptr< PerturbBundleHelix > protocols::helical_bundle::PerturbBundleHelixOP

PerturbBundleHelixOPs

typedef utility::vector1<PerturbBundleHelixOP> protocols::helical_bundle::PerturbBundleHelixOPs

PerturbBundleOP

typedef utility::pointer::shared_ptr< PerturbBundle > protocols::helical_bundle::PerturbBundleOP

PerturbBundleOPs

typedef utility::vector1<PerturbBundleOP> protocols::helical_bundle::PerturbBundleOPs

Enumeration Type Documentation

BPC_Parameters

enum protocols::helical_bundle::BPC_Parameters

Enum for relevant parameters.

If you add to this list, update the parameter_name_from_enum() function, the short_parameter_description_from_enum() function, the parameter_units_from_enum() function, the parameter_type_from_enum() function, the parameter_properties_from_enum() function, and the parameter_description_from_enum() function.

Enumerator
BPC_r0
BPC_omega0
BPC_delta_omega0
BPC_delta_omega1
BPC_delta_t
BPC_z0_offset
BPC_z1_offset
BPC_epsilon
BPC_last_parameter_to_be_sampled
BPC_residues_per_repeat
BPC_repeating_unit_offset
BPC_atoms_per_residue
BPC_r1_peratom
BPC_omega1
BPC_z1
BPC_delta_omega1_peratom
BPC_delta_z1_peratom
BPC_invert_helix
BPC_set_dihedrals
BPC_set_bondangles
BPC_set_bondlengths
BPC_unknown_parameter
BPC_end_of_list

BundleReporterFilterBehaviour

enum protocols::helical_bundle::BundleReporterFilterBehaviour

The behaviour of this filter.

The filter can return true always, false always, or can filter by energy. If you update this enum, add new behaviours to the two set_filter_behaviour() functions (setting by string and by enum).

Enumerator
brf_always_true
brf_always_false
brf_filter_by_energy
brf_undefined

Function Documentation

add_attributes_for_helix_params() [1/2]

void protocols::helical_bundle::add_attributes_for_helix_params

(

AttributeList &

attlist

)

Referenced by protocols::helical_bundle::BundleGridSampler::provide_xml_schema(), and protocols::helical_bundle::MakeBundle::provide_xml_schema().

add_attributes_for_helix_params() [2/2]

void protocols::helical_bundle::add_attributes_for_helix_params

(

utility::tag::AttributeList &

subtag_attributes

)

add_attributes_for_make_bundle_minorhelix_defaults() [1/2]

void protocols::helical_bundle::add_attributes_for_make_bundle_minorhelix_defaults

(

AttributeList &

attlist

)

Referenced by protocols::helical_bundle::BundleGridSampler::provide_xml_schema(), and protocols::helical_bundle::MakeBundle::provide_xml_schema().

add_attributes_for_make_bundle_minorhelix_defaults() [2/2]

void protocols::helical_bundle::add_attributes_for_make_bundle_minorhelix_defaults

(

utility::tag::AttributeList &

attlist

)

add_attributes_for_make_bundle_other_defaults() [1/2]

void protocols::helical_bundle::add_attributes_for_make_bundle_other_defaults

(

AttributeList &

attlist

)

Referenced by protocols::helical_bundle::BundleGridSampler::provide_xml_schema().

add_attributes_for_make_bundle_other_defaults() [2/2]

void protocols::helical_bundle::add_attributes_for_make_bundle_other_defaults

(

utility::tag::AttributeList &

attlist

)

add_attributes_for_make_bundle_symmetry() [1/2]

void protocols::helical_bundle::add_attributes_for_make_bundle_symmetry

(

AttributeList &

attlist

)

Referenced by protocols::helical_bundle::BundleGridSampler::provide_xml_schema(), and protocols::helical_bundle::MakeBundle::provide_xml_schema().

add_attributes_for_make_bundle_symmetry() [2/2]

void protocols::helical_bundle::add_attributes_for_make_bundle_symmetry

(

utility::tag::AttributeList &

attlist

)

add_attributes_for_minor_helix_params() [1/2]

void protocols::helical_bundle::add_attributes_for_minor_helix_params

(

AttributeList &

attlist

)

Referenced by protocols::helical_bundle::BundleGridSampler::provide_xml_schema(), and protocols::helical_bundle::MakeBundle::provide_xml_schema().

add_attributes_for_minor_helix_params() [2/2]

void protocols::helical_bundle::add_attributes_for_minor_helix_params

(

utility::tag::AttributeList &

subtag_attributes

)

add_attributes_for_other_helix_params() [1/2]

void protocols::helical_bundle::add_attributes_for_other_helix_params

(

AttributeList &

attlist

)

Referenced by protocols::helical_bundle::BundleGridSampler::provide_xml_schema(), and protocols::helical_bundle::MakeBundle::provide_xml_schema().

add_attributes_for_other_helix_params() [2/2]

void protocols::helical_bundle::add_attributes_for_other_helix_params

(

utility::tag::AttributeList &

subtag_attributes

)

align_mainchain_atoms()

void protocols::helical_bundle::align_mainchain_atoms	(	core::pose::Pose &	pose,
		core::pose::Pose const &	ref_pose,
		core::Size const	helix_start,
		core::Size const	helix_end
	)

Align mainchain atoms of pose to ref_pose mainchain atoms.

References core::id::AtomID::BOGUS_ATOM_ID(), core::pose::initialize_atomid_map(), core::chemical::ResidueType::mainchain_atom(), core::chemical::ResidueType::mainchain_atoms(), core::pose::Pose::residue_type(), and core::scoring::superimpose_pose().

align_mainchain_atoms_of_residue_range()

void protocols::helical_bundle::align_mainchain_atoms_of_residue_range	(	core::pose::Pose &	pose,
		core::pose::Pose const &	ref_pose,
		core::Size const	helix_start,
		core::Size const	helix_end
	)

Align mainchain atoms of pose to ref_pose mainchain atoms, moving ONLY the residues involved in the alignment.

References core::id::AtomID::BOGUS_ATOM_ID(), core::pose::initialize_atomid_map(), core::chemical::ResidueType::mainchain_atom(), core::conformation::Residue::n_mainchain_atoms(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::scoring::superimpose_pose(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::helical_bundle::BundleParametrizationCalculator::build_helix().

copy_helix_bondangles()

void protocols::helical_bundle::copy_helix_bondangles	(	core::pose::Pose &	pose,
		core::pose::Pose const &	ref_pose,
		core::Size const	helix_start,
		core::Size const	helix_end
	)

Copy backbone bond angle values from one pose, where helix mainchain atom coordinates have been set with the Crick equations, to another with ideal geometry.

References core::pose::Pose::conformation(), core::chemical::ResidueType::mainchain_atom(), core::chemical::ResidueType::mainchain_atoms(), core::conformation::Residue::n_mainchain_atoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::Conformation::set_bond_angle(), core::pose::Pose::update_residue_neighbors(), and core::pose::Pose::xyz().

Referenced by protocols::helical_bundle::BundleParametrizationCalculator::build_helix().

copy_helix_bondlengths()

void protocols::helical_bundle::copy_helix_bondlengths	(	core::pose::Pose &	pose,
		core::pose::Pose const &	ref_pose,
		core::Size const	helix_start,
		core::Size const	helix_end
	)

Copy backbone bond length values from one pose, where helix mainchain atom coordinates have been set with the Crick equations, to another with ideal geometry.

References core::pose::Pose::conformation(), core::chemical::ResidueType::mainchain_atom(), core::chemical::ResidueType::mainchain_atoms(), core::conformation::Residue::n_mainchain_atoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::Conformation::set_bond_length(), core::pose::Pose::update_residue_neighbors(), and core::pose::Pose::xyz().

Referenced by protocols::helical_bundle::BundleParametrizationCalculator::build_helix().

copy_helix_dihedrals()

void protocols::helical_bundle::copy_helix_dihedrals	(	core::pose::Pose &	pose,
		core::pose::Pose const &	ref_pose,
		core::Size const	helix_start,
		core::Size const	helix_end
	)

Copy backbone dihedral values from one pose, where helix mainchain atom coordinates have been set with the Crick equations, to another with ideal geometry.

References core::id::BB, core::pose::Pose::conformation(), core::conformation::Residue::mainchain_torsions(), core::pose::Pose::residue(), core::conformation::Conformation::set_torsion(), core::conformation::Conformation::torsion(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::helical_bundle::BundleParametrizationCalculator::build_helix().

generate_atom_positions()

void protocols::helical_bundle::generate_atom_positions	(	utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > &	outvector,
		core::pose::Pose const &	helixpose,
		core::Size const	helix_start,
		core::Size const	helix_end,
		core::Real const &	r0,
		core::Real const &	omega0,
		core::Real const &	delta_omega0,
		core::Real const &	delta_t,
		core::Real const &	z1_offset,
		core::Real const &	z0_offset,
		core::Real const &	epsilon,
		bool const	invert_helix,
		utility::vector1< core::Real > const &	r1,
		core::Real const &	omega1,
		core::Real const &	z1,
		utility::vector1< core::Real > const &	delta_omega1,
		core::Real const &	delta_omega1_all,
		utility::vector1< core::Real > const &	delta_z1,
		core::Size const	residues_per_repeat,
		utility::vector1< core::Size > const &	atoms_per_residue,
		core::Size const	repeating_unit_offset,
		bool &	failed
	)

Generate the x,y,z coordinates of the mainchain atoms using the Crick equations.

Coordinates will be returned as a vector of vectors of xyzVectors. The outer index will refer to residue number, and the inner index will refer to atom number. Returns failed=true if coordinates could not be generated, false otherwise.

Note

The pose is just used to look up mainchain atom counts in residues.

References core::conformation::Residue::n_mainchain_atoms(), protocols::hybridization::r1, core::pose::Pose::residue(), and protocols::hybridization::t.

Referenced by protocols::helical_bundle::BundleParametrizationCalculator::build_helix(), and protocols::helical_bundle_predict::HBPHelix::get_torsions_for_helix().

get_crick_params_filename_formatted()

std::string protocols::helical_bundle::get_crick_params_filename_formatted

(

std::string const &

basename

)

Given a Crick params filename stub (e.g. "alpha_helix_100"), get the string with the full path and extension (e.g. "protocol_data/crick_parameters/alpha_helix_100.crick_params").

Checks a few locations (current path, database path), so this necessarily involves a read from disk!

Referenced by read_minor_helix_params().

parse_resnames()

void protocols::helical_bundle::parse_resnames	(	std::string const &	string_in,
		utility::vector1< std::string > &	vect_out
	)

Given a comma-separated list of residue names, separate these out into a vector of residue names.

The string_in string is the input; the vect_out vector is the output (which will be reset by this operation).

Referenced by protocols::helical_bundle::BundleGridSampler::parse_my_tag(), and protocols::helical_bundle::MakeBundle::parse_my_tag().

place_atom_positions()

void protocols::helical_bundle::place_atom_positions	(	core::pose::Pose &	pose,
		utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > const &	atom_positions,
		core::Size const	helix_start,
		core::Size const	helix_end
	)

Place the helix mainchain atoms based on the Crick equations.

References core::chemical::ResidueType::mainchain_atom(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::helical_bundle::BundleParametrizationCalculator::build_helix().

read_minor_helix_params()

void protocols::helical_bundle::read_minor_helix_params	(	std::string const &	filename,
		utility::vector1< core::Real > &	r1,
		core::Real &	omega1,
		core::Real &	z1,
		utility::vector1< core::Real > &	delta_omega1,
		utility::vector1< core::Real > &	delta_z1,
		core::Size &	residues_per_repeat,
		utility::vector1< core::Size > &	atoms_per_residue
	)

Read minor helix parameters from a crick_params file.

References protocols::abinitio::filename(), get_crick_params_filename_formatted(), protocols::hybridization::r1, and TR().

Referenced by protocols::helical_bundle::BundleParametrizationCalculator::init_from_file().

subtag_for_bbgrid()

std::string protocols::helical_bundle::subtag_for_bbgrid

(

std::string const &

tag_name

)

Referenced by protocols::helical_bundle::BackboneGridSampler::provide_xml_schema().

subtag_for_bundgrid()

std::string protocols::helical_bundle::subtag_for_bundgrid

(

std::string const &

subtag

)

Referenced by protocols::helical_bundle::BundleGridSampler::provide_xml_schema().

TR() [1/12]

static basic::Tracer protocols::helical_bundle::TR ( "protocols.helical_bundle.BackboneGridSampler"  )

static

Referenced by protocols::helical_bundle::BackboneGridSampler::apply(), protocols::helical_bundle::BundleGridSampler::apply(), protocols::helical_bundle::FitSimpleHelix::apply(), protocols::helical_bundle::MakeBundle::apply(), protocols::helical_bundle::MakeBundleHelix::apply(), protocols::helical_bundle::PerturbBundle::apply(), protocols::helical_bundle::PerturbBundleHelix::apply(), protocols::helical_bundle::BundleReporterFilter::apply(), protocols::helical_bundle::BundleParametrizationCalculator::build_helix(), protocols::helical_bundle::FitSimpleHelixMultiFunc::dfunc(), protocols::helical_bundle::BackboneGridSamplerHelper::initialize_samples(), protocols::helical_bundle::BundleGridSamplerHelper::initialize_samples(), protocols::helical_bundle::FitSimpleHelixMultiFunc::operator()(), protocols::helical_bundle::BundleReporterFilter::parse_my_tag(), protocols::helical_bundle::BackboneGridSampler::parse_my_tag(), protocols::helical_bundle::BundleGridSampler::parse_my_tag(), protocols::helical_bundle::MakeBundle::parse_my_tag(), protocols::helical_bundle::PerturbBundle::parse_my_tag(), protocols::helical_bundle::PerturbBundle::perturb_values(), read_minor_helix_params(), protocols::helical_bundle::MakeBundle::set_symmetry_options_from_tag(), and protocols::helical_bundle::PerturbBundle::write_report().

TR() [2/12]

static basic::Tracer protocols::helical_bundle::TR ( "protocols.helical_bundle.BackboneGridSamplerHelper"  )

static

TR() [3/12]

static basic::Tracer protocols::helical_bundle::TR ( "protocols.helical_bundle.BundleGridSampler"  )

static

TR() [4/12]

static basic::Tracer protocols::helical_bundle::TR ( "protocols.helical_bundle.BundleGridSamplerHelper"  )

static

TR() [5/12]

static basic::Tracer protocols::helical_bundle::TR ( "protocols.helical_bundle.BundleParametrizationCalculator"  )

static

TR() [6/12]

static basic::Tracer protocols::helical_bundle::TR ( "protocols.helical_bundle.BundleReporterFilter"  )

static

TR() [7/12]

static basic::Tracer protocols::helical_bundle::TR ( "protocols.helical_bundle.FitSimpleHelix"  )

static

TR() [8/12]

static basic::Tracer protocols::helical_bundle::TR ( "protocols.helical_bundle.MakeBundle"  )

static

TR() [9/12]

static basic::Tracer protocols::helical_bundle::TR ( "protocols.helical_bundle.MakeBundleHelix"  )

static

TR() [10/12]

static basic::Tracer protocols::helical_bundle::TR ( "protocols.helical_bundle.PerturbBundle"  )

static

TR() [11/12]

static basic::Tracer protocols::helical_bundle::TR ( "protocols.helical_bundle.PerturbBundleHelix"  )

static

TR() [12/12]

static basic::Tracer protocols::helical_bundle::TR ( "protocols.helical_bundle.util"  )

static

TR_Results()

static basic::Tracer protocols::helical_bundle::TR_Results ( "protocols.helical_bundle.BackboneGridSampler.Results"  )

static

Referenced by protocols::helical_bundle::BackboneGridSampler::apply().

TRReport()

static basic::Tracer protocols::helical_bundle::TRReport ( "protocols.helical_bundle.BundleReporterFilter.REPORT"  )

static

Referenced by protocols::helical_bundle::BundleReporterFilter::apply().

write_crick_params_file_data()

void protocols::helical_bundle::write_crick_params_file_data	(	utility::io::ozstream &	outfile,
		utility::vector1< core::Real > const &	r1,
		core::Real const &	omega1,
		core::Real const &	z1,
		utility::vector1< core::Real > const &	delta_omega1,
		utility::vector1< core::Real > const &	delta_z1
	)

Actual write of the crick_params file data.

Called by both write_minor_helix_params variants. The outfile ozstream must already be opened, and will not be closed by this function.

References protocols::hybridization::r1.

Referenced by write_minor_helix_params().

write_minor_helix_params() [1/2]

void protocols::helical_bundle::write_minor_helix_params	(	std::string const &	filename,
		core::Size const &	residues_per_repeat,
		utility::vector1< core::Size > const &	atoms_per_residue,
		utility::vector1< core::Real > const &	r1,
		core::Real const &	omega1,
		core::Real const &	z1,
		utility::vector1< core::Real > const &	delta_omega1,
		utility::vector1< core::Real > const &	delta_z1
	)

Write out a crick_params file.

Variant for case of a multi-residue repeating unit.

References protocols::abinitio::filename(), protocols::hybridization::r1, and write_crick_params_file_data().

write_minor_helix_params() [2/2]

void protocols::helical_bundle::write_minor_helix_params	(	std::string const &	filename,
		utility::vector1< core::Real > const &	r1,
		core::Real const &	omega1,
		core::Real const &	z1,
		utility::vector1< core::Real > const &	delta_omega1,
		utility::vector1< core::Real > const &	delta_z1
	)

Write out a crick_params file.

Variant for case of a single-residue repeating unit.

References protocols::abinitio::filename(), protocols::hybridization::r1, and write_crick_params_file_data().