#include <ExtendedPoseBuilder.hh>
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
◆ Resids
| typedef utility::vector1< core::Size > protocols::denovo_design::components::ExtendedPoseBuilder::Resids |
Constructor & Destructor Documentation
◆ ExtendedPoseBuilder()
| protocols::denovo_design::components::ExtendedPoseBuilder::ExtendedPoseBuilder | ( | ) |
◆ ~ExtendedPoseBuilder()
|
overridedefault |
Member Function Documentation
◆ apply()
|
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().
◆ calc_chain_endings()
|
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().
◆ clone()
|
overridevirtual |
◆ create_template_pose()
|
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().
◆ extend_pose()
|
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().
◆ find_template_segments()
|
private |
Finds the segments that have template conformations.
References 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().
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
