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IMP Reference Guide
develop.7400db2aee,2024/11/23
The Integrative Modeling Platform
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Store info for a chain of a protein. More...
#include <IMP/atom/Chain.h>
Inheritance diagram for IMP::atom::Chain: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 (author-provided) chain id. More... | |
| std::string | get_label_asym_id () const |
| Return the mmCIF asym 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 (author-provided) chain id. More... | |
| void | set_label_asym_id (std::string c) |
| Set the mmCIF asym 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 > | |
| 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 DecoratorTraits & | get_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... | |
| Model * | get_model () const |
| Returns the Model containing the particle. More... | |
| Particle * | get_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 | |
| Particle * | operator-> () 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 author-provided chain ID. More... | |
| static bool | get_is_setup (const IMP::ParticleAdaptor &p) |
| static bool | get_is_setup (Model *m, ParticleIndex pi) |
| static SparseStringKey | get_label_asym_id_key () |
| The key used to store the mmCIF asym ID. More... | |
| 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 (IMP::ParticleAdaptor pa, std::string id) |
| static Chain | setup_particle (Model *m, ParticleIndex pi, 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 (IMP::ParticleAdaptor pa, Chain other) |
| static Chain | setup_particle (Model *m, ParticleIndex pi, 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 DecoratorTraits & | get_default_decorator_traits () |
| static const HierarchyTraits & | get_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) | |
| Related Functions inherited from IMP::atom::Hierarchy | |
| Hierarchy | create_clone (Hierarchy d) |
| Clone the Hierarchy. More... | |
| Hierarchy | create_clone_one (Hierarchy d) |
| Clone the node in the Hierarchy. More... | |
| Hierarchy | create_fragment (const Hierarchies &ps) |
| Create a fragment containing the specified nodes. More... | |
| void | destroy (Hierarchy d) |
| Delete the Hierarchy. More... | |
| algebra::BoundingBoxD< 3 > | get_bounding_box (const Hierarchy &h) |
| Get a bounding box for the Hierarchy. More... | |
| algebra::Sphere3D | get_bounding_sphere (const Hierarchy &h) |
| Hierarchies | get_by_type (Hierarchy mhd, GetByType t) |
| Gather all the molecular particles of a certain level in the hierarchy. More... | |
| Bonds | get_internal_bonds (Hierarchy mhd) |
| Get the bonds internal to this tree. More... | |
| bool | get_is_heterogen (Hierarchy h) |
| Return true if the piece of hierarchy should be classified as a heterogen. More... | |
| Hierarchies | get_leaves (Hierarchy h) |
| Hierarchies | get_leaves (const Hierarchies &h) |
| Hierarchy | get_residue (Hierarchy mhd, unsigned int index) |
| Get the residue with the specified index. More... | |
| Hierarchy | get_root (Hierarchy h) |
| Return the root of the hierarchy. More... | |
| void | show (Hierarchy h, std::ostream &out=std::cout) |
| Print out a molecular hierarchy. More... | |
| ChainType IMP::atom::Chain::get_chain_type | ( | ) | const |
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The key used to store the polymer type.
| std::string IMP::atom::Chain::get_id | ( | ) | const |
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The key used to store the author-provided chain ID.
| std::string IMP::atom::Chain::get_label_asym_id | ( | ) | const |
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The key used to store the mmCIF asym ID.
| std::string IMP::atom::Chain::get_sequence | ( | ) | const |
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The key used to store the primary sequence.
| int IMP::atom::Chain::get_sequence_offset | ( | ) | const |
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The key used to store the sequence offset.
| std::string IMP::atom::Chain::get_uniprot_accession | ( | ) | const |
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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.
Definition at line 185 of file Chain.h.
Here is the call graph for this function:| void IMP::atom::Chain::set_id | ( | std::string | c | ) |
| void IMP::atom::Chain::set_label_asym_id | ( | std::string | c | ) |
| 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).
Definition at line 134 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 152 of file Chain.h.
Here is the call graph for this function:| void IMP::atom::Chain::set_uniprot_accession | ( | std::string | accession | ) |
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