variant_util.cc File Reference

Pose class utilities. More...

#include <core/pose/variant_util.hh>
#include <core/pose/util.hh>
#include <core/pose/Pose.hh>
#include <core/pose/full_model_info/FullModelInfo.hh>
#include <core/pose/full_model_info/util.hh>
#include <core/pose/rna/util.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/VariantType.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/util.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/conformation/Residue.fwd.hh>
#include <basic/Tracer.hh>
#include <utility/exit.hh>
#include <utility/vector1.hh>
#include <iostream>
#include <algorithm>
#include <numeric/conversions.hh>

Namespaces
	core
	A class for reading in the atom type properties.
	core::pose

Functions
static basic::Tracer	core::pose::TR ("core.pose.variant_util")
core::conformation::ResidueOP	core::pose::remove_variant_type_from_residue (conformation::Residue const &old_rsd, core::chemical::VariantType const variant_type, pose::Pose const &pose)
	Remove variant from an existing residue. More...
conformation::ResidueOP	core::pose::add_variant_type_to_residue (conformation::Residue const &old_rsd, core::chemical::VariantType const variant_type, pose::Pose const &pose)
	Construct a variant of an existing residue. More...
void	core::pose::add_variant_type_to_pose_residue (pose::Pose &pose, chemical::VariantType const variant_type, Size const seqpos)
	Construct a variant of an existing pose residue. More...
void	core::pose::add_variant_type_to_pose_residue (pose::Pose &pose, std::string const &variant_type, Size const seqpos)
void	core::pose::add_custom_variant_type_to_pose_residue (pose::Pose &pose, std::string const &variant_type, Size const seqpos)
void	core::pose::remove_variant_type_from_pose_residue (pose::Pose &pose, chemical::VariantType const variant_type, Size const seqpos)
	Construct a non-variant of an existing pose residue. More...
void	core::pose::add_lower_terminus_type_to_pose_residue (pose::Pose &pose, Size const seqpos)
void	core::pose::add_upper_terminus_type_to_pose_residue (pose::Pose &pose, Size const seqpos)
void	core::pose::remove_lower_terminus_type_from_pose_residue (pose::Pose &pose, Size const seqpos)
void	core::pose::remove_upper_terminus_type_from_pose_residue (pose::Pose &pose, Size const seqpos)
void	core::pose::correctly_add_cutpoint_variants (core::pose::Pose &pose)
	Add cutpoint variants to all residues annotated as cutpoints in the FoldTree in the Pose. More...
void	core::pose::correctly_add_2prime_connection_variants (pose::Pose &pose, Size const twoprime_res, Size const next_res)
void	core::pose::correctly_add_cutpoint_variants (core::pose::Pose &pose, Size const cutpoint_res, bool const check_fold_tree, Size const next_res_in)
	Add CUTPOINT_LOWER and CUTPOINT_UPPER types to two residues, remove incompatible types, and declare a chemical bond between them. More...
void	core::pose::correctly_remove_variants_incompatible_with_lower_cutpoint_variant (core::pose::Pose &pose, Size const res_index)
	Remove variant types incompatible with CUTPOINT_LOWER from a position in a pose. More...
void	core::pose::correctly_remove_variants_incompatible_with_upper_cutpoint_variant (core::pose::Pose &pose, Size const res_index)
	Remove variant types incompatible with CUTPOINT_UPPER from a position in a pose. More...
bool	core::pose::pose_residue_is_terminal (Pose const &pose, Size const resid)
	returns true if the given residue in the pose is a chain ending or has upper/lower terminal variants More...
bool	core::pose::is_lower_terminus (pose::Pose const &pose, Size const resid)
	checks to see if this is a lower chain ending more intelligently than just checking residue variants More...
bool	core::pose::is_upper_terminus (pose::Pose const &pose, Size const resid)
	checks to see if this is a lower chain ending more intelligently than just checking residue variants More...
void	core::pose::show_adjacent_nt_connections (pose::Pose const &pose, Size const res)
void	core::pose::fix_up_residue_type_variants_at_strand_end (pose::Pose &pose, Size const res)
void	core::pose::fix_up_residue_type_variants_at_strand_beginning (pose::Pose &pose, Size const res)
void	core::pose::fix_up_residue_type_variants_at_floating_base (pose::Pose &pose, Size const res)
void	core::pose::update_block_stack_variants (pose::Pose &pose, Size const n)
void	core::pose::fix_up_residue_type_variants (pose::Pose &pose)

Detailed Description

Pose class utilities.

Author

Phil Bradley

Modified by Sergey Lyskov, Rhiju Das, Steven Lewis, Vikram K. Mulligan