core::pose::MiniPose Class Reference

lightweight version of the pose with stuff I need. More...

#include <MiniPose.hh>

Inheritance diagram for core::pose::MiniPose:

Public Member Functions
	MiniPose (core::pose::Pose const &pose)
	MiniPose (utility::vector1< utility::vector1< PointPosition > > const &coords, core::kinematics::FoldTree const &fold_tree, std::string const &sequence)
	~MiniPose () override
core::kinematics::FoldTree const &	fold_tree () const
utility::vector1< utility::vector1< PointPosition > > const &	coords () const
utility::vector1< utility::vector1< std::string > > const &	atom_names_list () const
utility::vector1< utility::vector1< std::string > > const &	variant_types_list () const
Size	size () const
std::string const &	sequence () const
PointPosition const &	xyz (core::id::AtomID atom_id) const
std::string const &	atom_name (core::id::AtomID atom_id) const
utility::vector1< std::string > const &	variant_types (Size const seq_num) const

Private Attributes
utility::vector1< utility::vector1< PointPosition > >	coords_
core::kinematics::FoldTree	fold_tree_
std::string	sequence_
utility::vector1< utility::vector1< std::string > >	atom_names_list_
utility::vector1< utility::vector1< std::string > >	variant_types_list_

Detailed Description

lightweight version of the pose with stuff I need.

not quite (silent_structs don't necessarily have xyz). Kind of like a Conformation but without the overtree of an atom_tree.

Remarks

Should save memory compared to keeping the full pose (which includes atom_tree, energies etc.) This is a bit like the SilentStruct – although that class has gotten a bit complicated – easier to start from scratch.

Constructor & Destructor Documentation

MiniPose() [1/2]

core::pose::MiniPose::MiniPose

(

core::pose::Pose const &

pose

)

References core::pose::Pose::aa(), core::chemical::aa_unk, core::chemical::aa_unp, atom_name(), core::chemical::ResidueType::atom_name(), atom_names_list_, core::chemical::ResidueTypeBase::base_name(), coords_, core::pose::Pose::fold_tree(), fold_tree_, core::chemical::ResidueProperties::get_list_of_variants(), core::chemical::ResidueTypeBase::name(), core::conformation::Residue::natoms(), core::chemical::ResidueTypeBase::properties(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::sequence(), sequence_, core::pose::Pose::size(), variant_types_list_, xyz(), and core::conformation::Residue::xyz().

MiniPose() [2/2]

core::pose::MiniPose::MiniPose	(	utility::vector1< utility::vector1< PointPosition > > const &	coords,
		core::kinematics::FoldTree const &	fold_tree,
		std::string const &	sequence
	)

~MiniPose()

core::pose::MiniPose::~MiniPose ( )

overridedefault

Member Function Documentation

atom_name()

std::string const & core::pose::MiniPose::atom_name

(

core::id::AtomID

atom_id

)

const

References atom_names_list_, core::id::AtomID::atomno(), and core::id::AtomID::rsd().

Referenced by MiniPose().

atom_names_list()

utility::vector1< utility::vector1< std::string > > const & core::pose::MiniPose::atom_names_list

(

)

const

References atom_names_list_.

Referenced by core::pose::copydofs::setup_atom_id_map_match_atom_names().

coords()

utility::vector1< utility::vector1< PointPosition > > const & core::pose::MiniPose::coords

(

)

const

References coords_.

fold_tree()

core::kinematics::FoldTree const & core::pose::MiniPose::fold_tree

(

)

const

References fold_tree_.

sequence()

std::string const & core::pose::MiniPose::sequence

(

)

const

References sequence_.

Referenced by core::import_pose::libraries::ChunkSet::filter_poses_have_same_sequence_and_variants(), and core::import_pose::libraries::ChunkSet::insert_protein_chunk_into_pose().

size()

Size core::pose::MiniPose::size

(

)

const

References coords_.

Referenced by core::import_pose::libraries::ChunkSet::filter_poses_have_same_sequence_and_variants().

variant_types()

utility::vector1< std::string > const & core::pose::MiniPose::variant_types

(

Size const

seq_num

)

const

References variant_types_list_.

Referenced by core::import_pose::libraries::ChunkSet::filter_poses_have_same_sequence_and_variants().

variant_types_list()

utility::vector1< utility::vector1< std::string > > const & core::pose::MiniPose::variant_types_list

(

)

const

References variant_types_list_.

xyz()

PointPosition const & core::pose::MiniPose::xyz

(

core::id::AtomID

atom_id

)

const

References core::id::AtomID::atomno(), coords_, and core::id::AtomID::rsd().

Referenced by core::pose::copydofs::CopyDofs::figure_out_dofs(), MiniPose(), and core::scoring::superimpose_pose().

Member Data Documentation

atom_names_list_

utility::vector1< utility::vector1< std::string > > core::pose::MiniPose::atom_names_list_

private

Referenced by atom_name(), atom_names_list(), and MiniPose().

coords_

utility::vector1< utility::vector1< PointPosition > > core::pose::MiniPose::coords_

private

Referenced by coords(), MiniPose(), size(), and xyz().

fold_tree_

core::kinematics::FoldTree core::pose::MiniPose::fold_tree_

private

Referenced by fold_tree(), and MiniPose().

sequence_

std::string core::pose::MiniPose::sequence_

private

Referenced by MiniPose(), and sequence().

variant_types_list_

utility::vector1< utility::vector1< std::string > > core::pose::MiniPose::variant_types_list_

private

Referenced by MiniPose(), variant_types(), and variant_types_list().

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

• src/core/pose/MiniPose.hh
• src/core/pose/MiniPose.cc