Detailed Description

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 pa, 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 pa, std::string filename, std::string chain_id)

static StructureProvenance	setup_particle (IMP::ParticleAdaptor pa, 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 pa)

Additional Inherited Members
Protected Member Functions inherited from IMP::Decorator
	Decorator (Model *m, ParticleIndex pi)

	Decorator (ParticleAdaptor p)