IMP Reference Guide
2.14.0
The Integrative Modeling Platform
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Track creation of a system fragment from a PDB file. More...
#include <IMP/core/provenance.h>
Track creation of a system fragment from a PDB file.
This tracks the filename of the PDB file, and the chain ID, that was used to populate an IMP Model (if multiple chains are read, IMP::atom::read_pdb() assigns a StructureProvenance to each chain). The offset between the residue indexes in the PDB file and the Model is also recorded. Normally this is zero, but can be used to indicate that residues were renumbered, e.g. to match canonical numbering. The convention is PDB residue # - offset = Model residue #.
Definition at line 86 of file provenance.h.
Public Member Functions | |
StructureProvenance (::IMP::Model *m,::IMP::ParticleIndex id) | |
StructureProvenance (const IMP::ParticleAdaptor &d) | |
std::string | get_chain_id () const |
std::string | get_filename () const |
int | get_residue_offset () const |
void | set_chain_id (std::string chain_id) const |
Set the chain ID. More... | |
void | set_filename (std::string filename) const |
Set the filename. More... | |
void | set_residue_offset (int residue_offset) const |
Set the offset between PDB and internal numbering (defaults to 0) More... | |
void | show (std::ostream &out=std::cout) const |
Public Member Functions inherited from IMP::core::Provenance | |
Provenance (::IMP::Model *m,::IMP::ParticleIndex id) | |
Provenance (const IMP::ParticleAdaptor &d) | |
Provenance | get_previous () const |
void | set_previous (Provenance p) |
Set the previous provenance. More... | |
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 bool | get_is_setup (Model *m, ParticleIndex pi) |
static bool | get_is_setup (const IMP::ParticleAdaptor &p) |
static StructureProvenance | setup_particle (IMP::ParticleAdaptor decorator, std::string filename, std::string chain_id, int residue_offset) |
static StructureProvenance | setup_particle (Model *m, ParticleIndex pi, std::string filename, std::string chain_id, int residue_offset) |
static StructureProvenance | setup_particle (Model *m, ParticleIndex pi, std::string filename, std::string chain_id) |
static StructureProvenance | setup_particle (IMP::ParticleAdaptor decorator, std::string filename, std::string chain_id) |
static StructureProvenance | setup_particle (IMP::ParticleAdaptor decorator, StructureProvenance o) |
static StructureProvenance | setup_particle (Model *m, ParticleIndex pi, StructureProvenance o) |
Static Public Member Functions inherited from IMP::core::Provenance | |
static bool | get_is_setup (Model *m, ParticleIndex pi) |
static bool | get_is_setup (const IMP::ParticleAdaptor &p) |
static Provenance | setup_particle (Model *m, ParticleIndex pi) |
static Provenance | setup_particle (IMP::ParticleAdaptor decorator) |
Additional Inherited Members | |
Protected Member Functions inherited from IMP::Decorator | |
Decorator (Model *m, ParticleIndex pi) | |
Decorator (ParticleAdaptor p) | |
std::string IMP::core::StructureProvenance::get_chain_id | ( | ) | const |
Definition at line 138 of file provenance.h.
std::string IMP::core::StructureProvenance::get_filename | ( | ) | const |
Definition at line 127 of file provenance.h.
int IMP::core::StructureProvenance::get_residue_offset | ( | ) | const |
Definition at line 150 of file provenance.h.
void IMP::core::StructureProvenance::set_chain_id | ( | std::string | chain_id | ) | const |
Set the chain ID.
Definition at line 132 of file provenance.h.
void IMP::core::StructureProvenance::set_filename | ( | std::string | filename | ) | const |
Set the filename.
The path can be relative or absolute. Internally, an absolute path will be stored (although generally it will be converted to a relative path when storing in a file, such as RMF).
Definition at line 120 of file provenance.h.
void IMP::core::StructureProvenance::set_residue_offset | ( | int | residue_offset | ) | const |
Set the offset between PDB and internal numbering (defaults to 0)
Definition at line 143 of file provenance.h.
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Setup the particle so it can be used with this decorator.
Definition at line 157 of file provenance.h.
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Setup the particle so it can be used with this decorator.
Definition at line 159 of file provenance.h.
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Setup the particle so that it can be used with this decorator
Definition at line 160 of file provenance.h.
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Definition at line 160 of file provenance.h.