Decorators and Attributes

Table of Contents

• Static and Frame Attributes
• Path attributes
• Physics
  • Attributes
  • Decorators
• Sequence
  • Attributes
  • Decorators
• Uncertainty
  • Attributes
• Feature
  • Attributes
  • Decorators
• Shape
  • Attributes
  • Decorators
• Alternatives
  • Attributes
  • Decorators
• Alias
  • Attributes
  • Decorators
• External
  • Attributes
  • Decorators
• Publication
  • Attributes
  • Decorators
• Provenance
  • Attributes
  • Decorators

Overview

The attributes and decorators are divided into several categories, each associated with a different RMF::Category. Each decorator has three associated types eg RMF::decorator::Particle, RMF::decorator::ParticleConst and RMF::decorator::ParticleFactory. The non-const decorator inherits from the const one. The factory is used to test whether a given node has the needed attributes and to create decorators decorating a given node. Note, that if passed an RMF::NodeConstHandle, the node already having the required attributes is a precondition for the factory get() method.

Static and Frame Attributes

Each get_ method and set_ method has three variants. For get they are

• get_foo get a value for the attribute
• get_frame_foo get a value for the attribute as stored in the current frame
• get_static_foo get a value for the attribute as stored for the whole file

All have the precondition that the appropriate value exists. For set

• set_frame_foo: set a value that is stored once per frame
• set_static_foo: set a value that is stored once for the whole file
• set_foo: if there is no static value, set it, otherwise, if the passed value differs from the static value, set it as a frame value.

Path attributes

String attributes can be used either to store arbitrary text, or paths to files. Paths are stored internally as relative paths, relative to the directory containing the RMF file. (This ensures that if the entire directory structure containing the RMF file is archived, the paths are still correct.) However, the set_* methods will accept both absolute and relative paths, and the get_* methods will always return absolute paths.

Physics

The category name is physics. It includes information about the physical structure of molecules.

Attributes

Name	Type	Description
coordinates	RMF::Vector3	The cartesian coordinates in angstroms
orientation	RMF::Vector4	The orientation quaternion
mass	float	The mass in Daltons
radius	float	The radius in angstroms
rotation	RMF::Vector4	The rotation quaternion
translation	RMF::Vector3	The translation vector in angstroms
bonded {0,1}	int	The RMF::NodeID of the bond endpoints
element	int	The atomic number of the element
diffusion coefficient	float	A diffusion coefficient in A^2/fs

Decorators

Name	Node Type	Attributes
RMF::decorator::Particle	RMF::REPRESENTATION	coordinates, mass, radius
RMF::decorator::ReferenceFrame	any	rotation, translation
RMF::decorator::Bond	RMF::BOND	bonded {0,1}
RMF::decorator::Atom	RMF::REPRESENTATION	coordinates, mass, radius, element
RMF::decorator::Diffuser	RMF::REPRESENTATION	diffusion coefficient, coordinates

Sequence

The category name is sequence and it includes information about the types and indexes of residues.

Attributes

Name	Type	Description
residue type	string	Three letter residue type
residue index	int	The index of a residue
chain id	string	The chain ID
sequence	string	Primary sequence of a chain
sequence offset	int	Offset from sequence index to residue index
chain type	string	Type of chain sequence (e.g. Protein, DNA, RNA)
label asym id	string	mmCIF asym ID for a chain
uniprot accession	string	UniProt accession code for the sequence
first residue index	int	The index of the first residue (in a domain)
last residue index	int	The index of the last residue (in a domain)
residue indexes	ints	The list of indexes in a fragment
copy index	int	The index of this particular copy of a protein (when there are multiple copies of the same protein)
type name	string	An arbitrary type name for a particle. It could be the protein type or ligand type.
state index	int	An arbitrary integer to label different states of a hierarchy.
explicit resolution	float	Explicitly-specified resolution for a hierarchy.
reference	int	The RMF::NodeID of the reference node

Decorators

Name	Node Type	Attributes
RMF::decorator::Residue	RMF::REPRESENTATION	index, residue type
RMF::decorator::Chain	RMF::REPRESENTATION	chain id, sequence
RMF::decorator::Domain	RMF::REPRESENTATION	first residue index, last residue index
RMF::decorator::Fragment	RMF::REPRESENTATION	residue indexes
RMF::decorator::Copy	RMF::REPRESENTATION	copy index
RMF::decorator::Typed	RMF::REPRESENTATION	type name
RMF::decorator::State	RMF::REPRESENTATION	state index
RMF::decorator::ExplicitResolution	RMF::REPRESENTATION	explicit resolution
RMF::decorator::Reference	RMF::REPRESENTATION	pointer to reference node

Uncertainty

The category name is uncertainty and it expresses data or theory uncertainty in the model.

Attributes

Name	Type	Description
scale	float	Bayesian nuisance parameter bounded to be positive
scale lower	float	Lower bound of scale value
scale upper	float	Upper bound of scale value

Feature

The category name is feature and the data stored relates to scoring functions, scores and which part of the structure they apply to.

Attributes

Name	Type	Description
score	float	Some sort of score
representation	RMF::Ints	The NodeIDs of the nodes involved in this score

Decorators

Name	Node Type	Attributes
RMF::decorator::Score	RMF::FEATURE	score
RMF::decorator::Representation	RMF::FEATURE	representation

Shape

The category name is shape and the information relates to geometric markup of the structure.

Attributes

Name	Type	Description
rgb color	RMF::Vector3	The red, green, and blue color components; each component is in the range from 0 to 1.
coordinates list	RMF::Vector3s	A list of coordinates.
coordinates	RMF::Vector3	The coordinates in angstroms.
radius	float	The radius in angstroms.
axis lengths	RMF::Vector3	The length along each coordinate axis.
orientation	RMF::Vector4	The orientation quaternion.

Decorators

Name	Node Type	Attributes
RMF::decorator::Colored	any	color
RMF::decorator::Ball	RMF::GEOMETRY	coordinates, radius
RMF::decorator::Segment	RMF::GEOMETRY	coordinates list
RMF::decorator::Cylinder	RMF::GEOMETRY	coordinates list, radius
RMF::decorator::Ellipsoid	RMF::GEOMETRY	coordinates, axis lengths, orientation

Alternatives

The alternatives family is used to store alternative representation schemes for a given subhierarchy. For example, there can be representations at multiple resolutions or using a surface instead of particles. Since, in general, one wants to interact with one representation at a time, the alternative ones are hidden away until explicitly requested.

Each alternative should be viewed as an alternative version of the tree rooted at the alternative node.

Attributes

Name	Type	Description
types	RMF::Ints	The RMF::decorator::RepresentationType entries for the alternative representations.
roots	RMF::Ints	The RMF::NodeID for each alternative hierarchy root.

Decorators

Name	Node Type	Attributes
RMF::decorator::Alternatives	any	You can use RMF::decorator::Alternatives::add_alternative() to add an alternative representation and RMF::decorator::Alternatives::get_alternatives() or RMF::decorator::Alternatives::get_alternative() to get them.

Alias

The category name is alias and it stores information for nodes that provide a reference to another node, for example to provide an alternative organizational scheme.

Attributes

Name	Type	Description
alias	int	NodeID of the node being aliased

Decorators

Name	Node Type	Attributes
RMF::decorator::Alias	RMF::ALIAS	alias

External

The category name is external and it stores references to all or part of external files, for example, a path to a PDB file that should be loaded as a child of the current node.

Attributes

Name	Type	Description
path	string	Relative path to the external file

Decorators

Name	Node Type	Attributes
RMF::decorator::External	RMF::REPRESENTATION	path

Publication

Attributes

Name	Type	Description
title	string	Title of the article
journal	string	Title of the journal
pubmed id	string	The pubmed ID
year	int	The year
authors	RMF::Strings	The author names as "First Last"

Decorators

Name	Node Type	Attributes
RMF::decorator::JournalArticle	RMF::ORGANIZATIONAL	title, journal, pubmed id, year, authors

Provenance

The category name is provenance. It includes information about how the structure was generated.

Attributes

Name	Type	Description
structure filename	string	File from which the structure was read
structure chain	string	Chain ID of the structure that was read
structure residue offset	int	Model residue # = Structure residue # + offset
sampling method	string	Sampling method utilized
sampling frames	int	Number of frames in the sample ensemble
sampling iterations	int	Number of sampling iterations used
sampling replicas	int	Number of sampling replicas used
combined runs	int	Number of sampling runs utilized
combined frames	int	Total number of frames combined
filter method	string	Filtering method utilized
filter threshold	float	Score threshold to discard bad models
filter frames	float	Number of frames after filtering
cluster members	int	Number of members in a cluster
script filename	string	Path of a script used to generate the model
software name	string	Name of the software used to make the model
software version	string	Version of the software used to make the model
software location	string	URI where the software can be found

Decorators

Name	Node Type	Attributes
RMF::decorator::StructureProvenance	RMF::PROVENANCE	structure filename, structure chain, structure residue offset
RMF::decorator::SampleProvenance	RMF::PROVENANCE	sampling method, sampling frames, sampling iterations, sampling replicas
RMF::decorator::CombineProvenance	RMF::PROVENANCE	combined runs, combined frames
RMF::decorator::FilterProvenance	RMF::PROVENANCE	filter threshold, filter frames
RMF::decorator::ClusterProvenance	RMF::PROVENANCE	cluster members, cluster precision, cluster density
RMF::decorator::ScriptProvenance	RMF::PROVENANCE	script filename
RMF::decorator::SoftwareProvenance	RMF::PROVENANCE	software name, software version, software location