protocols::denovo_design::components::ExtendedPoseBuilder Class Reference

#include <ExtendedPoseBuilder.hh>

Inheritance diagram for protocols::denovo_design::components::ExtendedPoseBuilder:

Public Types
typedef utility::vector1 < core::Size >	Resids

Public Member Functions
	ExtendedPoseBuilder ()
	~ExtendedPoseBuilder () override
core::pose::PoseOP	apply (StructureData const &sd) const override
PoseBuilderOP	clone () const override
Public Member Functions inherited from protocols::denovo_design::components::PoseBuilder
	PoseBuilder ()
bool	debug () const
	Returns whether or not to output debugging PDBs will be outputted which could be useful for fixing problems (true=output extra PDBs; false=don't output extra PDBs) More...
void	set_debug (bool const debug)
	Sets whether or not to output debugging PDBs will be outputted which could be useful for fixing problems (true=output extra PDBs; false=don't output extra PDBs) More...
bool	write_debug_pdb (core::pose::Pose const &pose, std::string const &filename) const
	Writes a debugging pdb (as described above). Does nothing if "debug_" is false and only outputs a PDB if "debug_" is true. More...

Protected Member Functions
core::pose::PoseOP	create_template_pose (StructureData const &sd, SegmentNames const &template_segments) const
	Creates a pose that contains only the template segments. More...
void	extend_pose (core::pose::Pose &pose, StructureData const &sd, SegmentNames const &template_segments) const
	Extends a pose containing only template segments so that it also includes de novo segments. More...

Private Member Functions
SegmentNames	find_template_segments (StructureData const &sd) const
	Finds the segments that have template conformations. More...
Resids	calc_chain_endings (StructureData const &sd) const

Member Typedef Documentation

typedef utility::vector1< core::Size > protocols::denovo_design::components::ExtendedPoseBuilder::Resids

Constructor & Destructor Documentation

protocols::denovo_design::components::ExtendedPoseBuilder::ExtendedPoseBuilder

(

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protocols::denovo_design::components::ExtendedPoseBuilder::~ExtendedPoseBuilder ( )

overridedefault

Member Function Documentation

core::pose::PoseOP protocols::denovo_design::components::ExtendedPoseBuilder::apply ( StructureData const &  sd ) const

overridevirtual

Implements protocols::denovo_design::components::PoseBuilder.

References create_template_pose(), extend_pose(), find_template_segments(), protocols::denovo_design::components::FoldGraph::fold_tree(), protocols::denovo_design::components::StructureData::slice(), protocols::TR(), and protocols::denovo_design::components::PoseBuilder::write_debug_pdb().

ExtendedPoseBuilder::Resids protocols::denovo_design::components::ExtendedPoseBuilder::calc_chain_endings ( StructureData const &  sd ) const

private

References protocols::denovo_design::components::Segment::cterm_included(), protocols::denovo_design::components::StructureData::segment(), protocols::denovo_design::components::StructureData::segments_begin(), protocols::denovo_design::components::StructureData::segments_end(), and protocols::denovo_design::components::Segment::upper().

Referenced by extend_pose().

PoseBuilderOP protocols::denovo_design::components::ExtendedPoseBuilder::clone ( ) const

overridevirtual

Implements protocols::denovo_design::components::PoseBuilder.

core::pose::PoseOP protocols::denovo_design::components::ExtendedPoseBuilder::create_template_pose ( StructureData const &  sd, SegmentNames const &  template_segments  ) const

protected

Creates a pose that contains only the template segments.

References protocols::denovo_design::components::append_new_chain_from_template_segment(), protocols::denovo_design::components::append_residues_from_template_segment(), protocols::denovo_design::components::create_debug_filename(), protocols::denovo_design::components::Segment::lower_segment(), protocols::denovo_design::components::StructureData::segment(), protocols::TR(), and protocols::denovo_design::components::PoseBuilder::write_debug_pdb().

Referenced by apply().

void protocols::denovo_design::components::ExtendedPoseBuilder::extend_pose ( core::pose::Pose &  pose, StructureData const &  sd, SegmentNames const &  template_segments  ) const

protected

Extends a pose containing only template segments so that it also includes de novo segments.

References protocols::denovo_design::add_cutpoints(), protocols::denovo_design::components::add_terminus_variants(), protocols::denovo_design::components::append_new_residues(), calc_chain_endings(), core::conformation::Conformation::chains_from_termini(), core::pose::Pose::conformation(), protocols::denovo_design::components::create_debug_filename(), protocols::denovo_design::components::Segment::cutpoint(), protocols::denovo_design::components::Segment::elem_length(), protocols::denovo_design::components::Segment::has_free_upper_terminus(), protocols::denovo_design::components::Segment::length(), protocols::denovo_design::components::Segment::lower_dihedrals(), protocols::denovo_design::components::Segment::n_residues_after_cutpoint(), protocols::denovo_design::components::Segment::n_residues_before_cutpoint(), protocols::denovo_design::components::prepend_new_residues(), core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), protocols::denovo_design::components::StructureData::segment(), protocols::denovo_design::components::StructureData::segments_begin(), protocols::denovo_design::components::StructureData::segments_end(), core::pose::Pose::size(), protocols::TR(), protocols::denovo_design::components::Segment::upper_dihedrals(), and protocols::denovo_design::components::PoseBuilder::write_debug_pdb().

Referenced by apply().

SegmentNames protocols::denovo_design::components::ExtendedPoseBuilder::find_template_segments ( StructureData const &  sd ) const

private

Finds the segments that have template conformations.

References core::pack::dunbrack::c, protocols::denovo_design::components::StructureData::segment(), protocols::denovo_design::components::StructureData::segments_begin(), protocols::denovo_design::components::StructureData::segments_end(), and protocols::denovo_design::components::Segment::template_pose().

Referenced by apply().

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

• src/protocols/denovo_design/components/ExtendedPoseBuilder.hh
• src/protocols/denovo_design/components/ExtendedPoseBuilder.cc