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variant_util.cc File Reference

Pose class utilities. More...

#include <core/pose/variant_util.hh>
#include <core/pose/extra_pose_info_util.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/Pose.hh>
#include <core/pose/MiniPose.hh>
#include <core/pose/full_model_info/FullModelInfo.hh>
#include <core/pose/full_model_info/util.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <core/pose/datacache/PositionConservedResiduesStore.hh>
#include <core/pose/rna/util.hh>
#include <core/pose/carbohydrates/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/Patch.hh>
#include <core/chemical/PatchOperation.hh>
#include <core/chemical/util.hh>
#include <core/chemical/AtomICoor.hh>
#include <core/chemical/ResidueConnection.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/util.hh>
#include <core/id/DOF_ID_Map.hh>
#include <core/id/Exceptions.hh>
#include <core/id/NamedStubID.hh>
#include <core/id/NamedAtomID.hh>
#include <core/id/TorsionID.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/io/StructFileRep.hh>
#include <core/io/raw_data/DisulfideFile.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/func/CircularHarmonicFunc.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/id/SequenceMapping.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/util.hh>
#include <basic/Tracer.hh>
#include <basic/datacache/DataCache.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <basic/datacache/CacheableString.hh>
#include <basic/datacache/CacheableStringFloatMap.hh>
#include <basic/datacache/CacheableStringMap.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <numeric/constants.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyzVector.string.hh>
#include <utility/io/izstream.hh>
#include <utility/exit.hh>
#include <utility/string_constants.hh>
#include <utility/string_util.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/vector1.hh>
#include <utility/vector1.functions.hh>
#include <cmath>
#include <iostream>
#include <algorithm>
#include <numeric>
#include <ObjexxFCL/string.functions.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