Detailed Description

This module provides RMF I/O for IMP.

This modules provides support for RMF file format for storing hierarchical molecular data (such as atomic or coarse grained representations of proteins), along with markup, including geometry and score data.

IMP.rmf supports I/O of IMP::atom::Hierarchy and associated types as well as output of IMP::display::Geometry, IMP::Restraint and arbitrary IMP::Particles. For each of these there are methods like:

IMP::rmf::add_hierarchies() to add them to an RMF file
IMP::rmf::create_hierarchies() to create hierarchies from an RMF file
IMP::rmf::link_hierarchies() to link existing hierarchies to a corresponding ones in the rmf file

Once objects are linked/added/created, they are attached to the RMF file. IMP::rmf::load_frame() can be used to change the state of the linked objects to that of an arbitrary frame and IMP::rmf::save_frame() can be used to save the current state of the objects into a frame in the RMF file.

See the RMF library page for more information.

Examples:

Author(s): Daniel Russel

Version: SVN.r14091

License: LGPL. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Publications:

Daniel Russel, Keren Lasker, Ben Webb, Dina Schneidman, Javier Velázquez-Muriel, Andrej Sali, “Putting the pieces together: integrative structure determination of macromolecular assemblies”, PLoS Biology, 2012. This paper provides an overview of the key concepts in IMP and how to apply them to biological problems.
Frank Alber, Friedrich Foerster, Dmitry Korkin, Maya Topf, Andrej Sali, “Integrating diverse data for structure determination of macromolecular assemblies”, Annual Review of Biochemistry, 2008. This paper provides a review of the integrative structure determination methodology and various data sources that can be used.

Classes
class	LoadLink
class	RMFRestraint
class	SaveLink
class	SaveOptimizerState

Hierarchy I/O
Hierarchy I/O writes IMP::atom::Hierarchy information along with the information contained in the following decorators IMP::atom::Atom IMP::atom::Residue IMP::core::XYZR IMP::atom::Mass IMP::atom::Diffusion IMP::core::Typed IMP::display::Colored IMP::atom::Domain IMP::atom::Molecule IMP::atom::Copy IMP::core::RigidBody Note: The handling of rigid bodies is not entirely straight forward and might have some side effects. When loading them, the orientation of the rigid body is read from the file as well as the coordinates of the members. The internal coordinats of the members are then updated that so their coordinates, the pose of the rigid body and the internal coordinates are all in sync. This is to avoid issues with rigid bodies not always being created consistently by `IMP` (since the principal axes of the body may be numerically unstable).
IMPRMFEXPORT void	add_hierarchies (RMF::FileHandle fh, const atom::Hierarchies &hs)
IMPRMFEXPORT void	add_hierarchy (RMF::FileHandle fh, atom::Hierarchy hs)
IMPRMFEXPORT atom::Hierarchies	create_hierarchies (RMF::FileConstHandle fh, Model *m)
IMPRMFEXPORT void	link_hierarchies (RMF::FileConstHandle fh, const atom::Hierarchies &hs)

Geometry I/O
The geometry I/O support currently handles geometry composed of IMP::display::SegmentGeometry IMP::display::CylinderGeometry IMP::display::SphereGeometry Other types can be supported when requested. Be aware, many more complex geometry types are automatically decomposed into the above types and so, more or less, supported.
void	add_geometries (RMF::FileHandle parent, const display::GeometriesTemp &r)
void	add_static_geometries (RMF::FileHandle parent, const display::GeometriesTemp &r)
display::Geometries	create_geometries (RMF::FileConstHandle parent)
void	link_geometries (RMF::FileConstHandle parent, const display::GeometriesTemp &r)

Particle I/O
Arbitrary (non IMP::atom::Hierarchy) particles can be written to the file and read back from them. All non-IMP::Object attributes are supported. Note that currently particles must be added so that any particles that are store in a given particles attributes are added to the file first. The data is stored in a category named IMP.
IMPRMFEXPORT void	add_particles (RMF::FileHandle fh, const ParticlesTemp &hs)
IMPRMFEXPORT void	add_particle (RMF::FileHandle fh, Particle *hs)
IMPRMFEXPORT ParticlesTemp	create_particles (RMF::FileConstHandle fh, Model *m)
IMPRMFEXPORT void	link_particles (RMF::FileConstHandle fh, const ParticlesTemp &hs)

Restraint I/O
Restraints are written as am RMF::FEATURE node with subnodes for the decomposed restraints (Restraint::create_current_decompositon()). The Restraints::get_last_score() value is what is saved to the file, so make sure that the restraints have been evaluated before saving a frame.
IMPRMFEXPORT void	add_restraints (RMF::FileHandle fh, const RestraintsTemp &hs)
IMPRMFEXPORT void	add_restraint (RMF::FileHandle fh, Restraint *hs)
IMPRMFEXPORT RMFRestraints	create_restraints (RMF::FileConstHandle fh, Model *m)
IMPRMFEXPORT void	link_restraints (RMF::FileConstHandle fh, const RMFRestraints &hs)

Typedefs
typedef base::Object *	AssociationType
typedef base::Pointer< LoadLink >	LoadLinkAssociationType
typedef base::Pointer< SaveLink >	SaveLinkAssociationType

Functions
template<class T >
T *	get_association (RMF::NodeConstHandle nh)
bool	get_has_linker (RMF::FileConstHandle nh, unsigned int id)
LoadLinkAssociationType	get_load_linker (RMF::FileConstHandle nh, unsigned int id)
RMF::NodeConstHandle	get_node_from_association (RMF::FileConstHandle nh, base::Object *oi)
RMF::NodeHandle	get_node_from_association (RMF::FileHandle nh, base::Object *oi)
SaveLinkAssociationType	get_save_linker (RMF::FileConstHandle nh, unsigned int id)
void	load_frame (RMF::FileConstHandle file, unsigned int frame)
void	save_frame (RMF::FileHandle file, unsigned int frame)
void	set_association (RMF::NodeConstHandle nh, base::Object *o, bool overwrite=false)
void	set_linker (RMF::FileConstHandle nh, unsigned int id, SaveLinkAssociationType l)

Function Documentation

void IMP::rmf::add_geometries	(	RMF::FileHandle	parent,
		const display::GeometriesTemp &	r
	)

Add the geometry to the file

IMP::rmf::add_hierarchy	(	RMF::FileHandle	fh,
		atom::Hierarchy	hs
	)

Examples: restraint cache, adding data, simulation, sample 0

void IMP::rmf::add_static_geometries	(	RMF::FileHandle	parent,
		const display::GeometriesTemp &	r
	)

Add the following geometry, assuming they do not move between frames. This can be space saving compared to resaving the constant position each frame.

IMP::rmf::create_hierarchies	(	RMF::FileConstHandle	fh,
		Model *	m
	)

Examples: pdb

void IMP::rmf::load_frame	(	RMF::FileConstHandle	file,
		unsigned int	frame
	)

Load the specified frame into the state of the associated IMP::base::Objects with the RMF file

void IMP::rmf::save_frame	(	RMF::FileHandle	file,
		unsigned int	frame
	)

Save the current state of the objects linked to the RMF file as the frameth frame.

Detailed Description

Classes

Hierarchy I/O

Geometry I/O

Particle I/O

Restraint I/O

Typedefs

Functions

Function Documentation