IMP logo
IMP Reference Guide  develop.ba5ef9f91e,2024/02/26
The Integrative Modeling Platform
IMP::atom::Chain Class Reference

Store info for a chain of a protein. More...

#include <IMP/atom/Chain.h>

+ Inheritance diagram for IMP::atom::Chain:

Detailed Description

Store info for a chain of a protein.

See Also
Hierarchy
Examples:
atom/dope_and_excluded_volume.cpp.

Definition at line 61 of file Chain.h.

Public Member Functions

 Chain (::IMP::Model *m,::IMP::ParticleIndex id)
 
 Chain (const IMP::ParticleAdaptor &d)
 
ChainType get_chain_type () const
 Return the chain type. More...
 
std::string get_id () const
 Return the chain id. More...
 
std::string get_sequence () const
 Return the primary sequence (or any empty string) More...
 
int get_sequence_offset () const
 Return the offset from the sequence numbering to residue indexes. More...
 
std::string get_uniprot_accession () const
 Return the UniProt accession for the chain's sequence. More...
 
void set_chain_type (ChainType t)
 Set the chain type, using IMP::atom::ChainType. More...
 
void set_id (std::string c)
 Set the chain id. More...
 
void set_sequence (std::string sequence)
 Set the primary sequence, as a string. More...
 
void set_sequence_offset (int offset)
 Set the offset from the sequence numbering to residue indexes. More...
 
void set_uniprot_accession (std::string accession)
 Set the UniProt accession for the chain's sequence. More...
 
void show (std::ostream &out=std::cout) const
 
- Public Member Functions inherited from IMP::atom::Hierarchy
 Hierarchy (Model *m, ParticleIndex pi)
 
 Hierarchy (ParticleAdaptor pi)
 
 Hierarchy ()
 Null constructor. More...
 
 Hierarchy (IMP::core::Hierarchy h)
 The traits must match. More...
 
void add_child (Hierarchy o)
 Add a child and check that the types are appropriate. More...
 
Hierarchy get_child (unsigned int i) const
 Get the ith child based on the order they were added. More...
 
Hierarchies get_children () const
 Return the children in the order they were added. More...
 
template<class C >
get_children () const
 Get the children in a container of your choosing, eg ParticlesTemp. More...
 
bool get_is_valid (bool print_info=false) const
 Return true if the hierarchy is valid. More...
 
Hierarchy get_parent () const
 Get the parent particle. More...
 
void show (std::ostream &out=std::cout) const
 
- Public Member Functions inherited from IMP::core::Hierarchy
 Hierarchy (const IMP::ParticleAdaptor &d, const HierarchyTraits &tr=get_default_traits())
 
 Hierarchy (::IMP::Model *m,::IMP::ParticleIndex id, const HierarchyTraits &tr=get_default_traits())
 
void add_child (Hierarchy h) const
 
void add_child_at (Hierarchy h, unsigned int pos)
 
void clear_children ()
 
Hierarchy get_child (unsigned int i) const
 
ParticleIndex get_child_index (unsigned int i) const
 
int get_child_index () const
 Return i such that get_parent().get_child(i) == this More...
 
GenericHierarchies get_children () const
 
ParticleIndexes get_children_indexes () const
 
const DecoratorTraitsget_decorator_traits () const
 
unsigned int get_number_of_children () const
 
Hierarchy get_parent () const
 
HierarchyTraits get_traits ()
 
void remove_child (unsigned int i)
 
void remove_child (Hierarchy h)
 
void show (std::ostream &out=std::cout) const
 
- Public Member Functions inherited from IMP::Decorator
bool get_is_valid () const
 Returns true if constructed with a non-default constructor. More...
 
Modelget_model () const
 Returns the Model containing the particle. More...
 
Particleget_particle () const
 Returns the particle decorated by this decorator. More...
 
ParticleIndex get_particle_index () const
 Returns the particle index decorated by this decorator. More...
 
 operator Particle * () const
 
 operator ParticleIndex () const
 
Particleoperator-> () const
 

Static Public Member Functions

static SparseIntKey get_chain_type_key ()
 The key used to store the polymer type. More...
 
static SparseStringKey get_id_key ()
 The key used to store the chain. More...
 
static bool get_is_setup (const IMP::ParticleAdaptor &p)
 
static bool get_is_setup (Model *m, ParticleIndex pi)
 
static SparseStringKey get_sequence_key ()
 The key used to store the primary sequence. More...
 
static SparseIntKey get_sequence_offset_key ()
 The key used to store the sequence offset. More...
 
static SparseStringKey get_uniprot_accession_key ()
 The key used to store the UniProt accession. More...
 
static Chain setup_particle (Model *m, ParticleIndex pi, std::string id)
 
static Chain setup_particle (IMP::ParticleAdaptor pa, std::string id)
 
static Chain setup_particle (IMP::ParticleAdaptor pa, char id)
 
static Chain setup_particle (Model *m, ParticleIndex pi, char id)
 
static Chain setup_particle (Model *m, ParticleIndex pi, Chain other)
 
static Chain setup_particle (IMP::ParticleAdaptor pa, Chain other)
 
- Static Public Member Functions inherited from IMP::atom::Hierarchy
static bool get_is_setup (Model *m, ParticleIndex p)
 Check if the particle has the needed attributes for a cast to succeed. More...
 
static const
IMP::core::HierarchyTraits
get_traits ()
 Get the molecular hierarchy HierarchyTraits. More...
 
static Hierarchy setup_particle (Model *m, ParticleIndex pi, ParticleIndexesAdaptor children=ParticleIndexesAdaptor())
 Create a Hierarchy of level t by adding the needed attributes. More...
 
- Static Public Member Functions inherited from IMP::core::Hierarchy
static TriggerKey get_changed_key ()
 The key used to signal to the Model that the Hierarchy has changed. More...
 
static const DecoratorTraitsget_default_decorator_traits ()
 
static const HierarchyTraitsget_default_traits ()
 Get the default hierarchy traits. More...
 
static bool get_is_setup (const IMP::ParticleAdaptor &p, const HierarchyTraits &tr=get_default_traits())
 
static bool get_is_setup (Model *, ParticleIndex, HierarchyTraits=Hierarchy::get_default_traits())
 
static Hierarchy setup_particle (IMP::ParticleAdaptor d, DecoratorTraits tr=get_default_decorator_traits())
 
static Hierarchy setup_particle (Model *m, ParticleIndex pi, DecoratorTraits tr=get_default_decorator_traits())
 
static Hierarchy setup_particle (Model *m, ParticleIndex pi, ParticleIndexes children, DecoratorTraits tr=get_default_decorator_traits())
 
static Hierarchy setup_particle (IMP::ParticleAdaptor d, ParticleIndexes children, DecoratorTraits tr=get_default_decorator_traits())
 
static Hierarchy setup_particle (IMP::ParticleAdaptor d, ParticlesTemp children, DecoratorTraits tr=get_default_decorator_traits())
 
static Hierarchy setup_particle (Model *m, ParticleIndex pi, ParticlesTemp children, DecoratorTraits tr=get_default_decorator_traits())
 

Additional Inherited Members

- Public Types inherited from IMP::core::Hierarchy
typedef HierarchyTraits DecoratorTraits
 
- Protected Member Functions inherited from IMP::Decorator
 Decorator (Model *m, ParticleIndex pi)
 
 Decorator (ParticleAdaptor p)
 

Member Function Documentation

ChainType IMP::atom::Chain::get_chain_type ( ) const

Return the chain type.

Definition at line 156 of file Chain.h.

+ Here is the call graph for this function:

static SparseIntKey IMP::atom::Chain::get_chain_type_key ( )
static

The key used to store the polymer type.

std::string IMP::atom::Chain::get_id ( ) const

Return the chain id.

Definition at line 97 of file Chain.h.

+ Here is the call graph for this function:

static SparseStringKey IMP::atom::Chain::get_id_key ( )
static

The key used to store the chain.

std::string IMP::atom::Chain::get_sequence ( ) const

Return the primary sequence (or any empty string)

Definition at line 107 of file Chain.h.

+ Here is the call graph for this function:

static SparseStringKey IMP::atom::Chain::get_sequence_key ( )
static

The key used to store the primary sequence.

int IMP::atom::Chain::get_sequence_offset ( ) const

Return the offset from the sequence numbering to residue indexes.

Definition at line 126 of file Chain.h.

+ Here is the call graph for this function:

static SparseIntKey IMP::atom::Chain::get_sequence_offset_key ( )
static

The key used to store the sequence offset.

std::string IMP::atom::Chain::get_uniprot_accession ( ) const

Return the UniProt accession for the chain's sequence.

Definition at line 144 of file Chain.h.

+ Here is the call graph for this function:

static SparseStringKey IMP::atom::Chain::get_uniprot_accession_key ( )
static

The key used to store the UniProt accession.

void IMP::atom::Chain::set_chain_type ( ChainType  t)

Set the chain type, using IMP::atom::ChainType.

Usually the chain type can be uniquely deduced by iterating over all child Residue decorators and querying their type. However, this may not be possible in all cases.

Note
The type set here should be consistent with that of any children of this Chain. This is not currently enforced. One can use IMP::atom::Residue::get_is_protein() on the leaves.

Definition at line 171 of file Chain.h.

+ Here is the call graph for this function:

void IMP::atom::Chain::set_id ( std::string  c)

Set the chain id.

Definition at line 102 of file Chain.h.

+ Here is the call graph for this function:

void IMP::atom::Chain::set_sequence ( std::string  sequence)

Set the primary sequence, as a string.

Usually the primary sequence of a chain can be uniquely deduced by iterating over all child Residue decorators and querying their type. However, this may not be possible in all cases (e.g. if there are gaps in the sequence or parts that are not explicitly represented).

Note
The sequence set here should be consistent with that of any children of this Chain. This is not currently enforced.

Definition at line 120 of file Chain.h.

+ Here is the call graph for this function:

void IMP::atom::Chain::set_sequence_offset ( int  offset)

Set the offset from the sequence numbering to residue indexes.

This offset is added to 1-based indexes into the chain primary sequence (see set_sequence()) to get corresponding residue indexes. By default, the offset is zero, corresponding to residues being numbered from 1. For example, if residues were instead numbered starting from 0, the offset would be -1.

Definition at line 138 of file Chain.h.

+ Here is the call graph for this function:

void IMP::atom::Chain::set_uniprot_accession ( std::string  accession)

Set the UniProt accession for the chain's sequence.

Definition at line 150 of file Chain.h.

+ Here is the call graph for this function:

static Chain IMP::atom::Chain::setup_particle ( Model m,
ParticleIndex  pi,
std::string  id 
)
static
Returns
a Chain object that decorates particle pi
Examples:
atom/dope_and_excluded_volume.cpp.

Definition at line 83 of file Chain.h.

static Chain IMP::atom::Chain::setup_particle ( IMP::ParticleAdaptor  pa,
std::string  id 
)
static
Returns
a Chain object that decorates the particle specified by pa
See Also
setup_particle(m, pi, id )

Definition at line 83 of file Chain.h.

static Chain IMP::atom::Chain::setup_particle ( Model m,
ParticleIndex  pi,
char  id 
)
static
Returns
a Chain object that decorates particle pi

Definition at line 84 of file Chain.h.

static Chain IMP::atom::Chain::setup_particle ( IMP::ParticleAdaptor  pa,
char  id 
)
static
Returns
a Chain object that decorates the particle specified by pa
See Also
setup_particle(m, pi, id )

Definition at line 84 of file Chain.h.

static Chain IMP::atom::Chain::setup_particle ( Model m,
ParticleIndex  pi,
Chain  other 
)
static
Returns
a Chain object that decorates particle pi

Definition at line 85 of file Chain.h.

static Chain IMP::atom::Chain::setup_particle ( IMP::ParticleAdaptor  pa,
Chain  other 
)
static
Returns
a Chain object that decorates the particle specified by pa
See Also
setup_particle(m, pi, other )

Definition at line 85 of file Chain.h.


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