RMF Categories

Categories are divided up by the arity of the entity they are used for (eg whether they are for single nodes, pairs of nodes etc.). The same category name can be used for different arities.

Categories

The following are pre-defined Categories for data stored in single nodes.

Physics

Identifying string: "physics"

Keys:

name	type	description	invariants
cartesian x	Float	the x coordinate in angstrom
cartesian y	Float	the y coordinate in angstrom	required if other cartesian coordinates are included
cartesian z	Float	the z coordinate in angstrom	required if other cartesian coordinates are included
radius	Float	the radius of the volume occupied by the entity in angstrom	positive; requires coordinates
mass	Float	the mass of the node in Daltons	positive; requires coordinates
diffusion coefficient	Float	the diffusion coefficient for the node in angstroms per squared femtosecond	positive
orientation r	Float	the real component or the orientation quaterion	required if there are any orientation components
orientation i	Float	the i component or the orientation quaterion	required if there are any orientation components
orientation j	Float	the j component or the orientation quaterion	required if there are any orientation components
orientation k	Float	the k component or the orientation quaterion	required if there are any orientation components

Related decorators: RMF::Particle, RMF::RigidParticle.

Sequence

Identifying string: "sequence"

Keys:

name	type	description	invariants
first residue index	Int	the first residue index included in this node	any descendent that has an index must be in the specified range
last residue index	Int	the last residue index included in this node	must be greater than begin residue index
element	Index	the atomic number of the element	nodes with elements cannot have children
secondary structure	Index	0 for unstructured; 1 for helix; 2 for strand	node must have a residue type
sequence	Strings	store the sequence as a list of three letter codes	if the index range is specified then the lengths must match; children with residue types must match
residue type	String	the three letter code for the residue type	this must match any sequence information higher in the tree and no descendent must have a residue type
chain id	Index	stores an integer for the chain identifier. When translating from pdb files the position in the alphabet of the chain should probably be used (eg chain 'A' is 0)
copy index	Index	stores an integer identifying which copy of a moleule this is

Related decorators: RMF::Residue.

Shape

Identifying string: "shape"

Keys:

name	type	description	invariants
cartesian x	Float	the x coordinate	must have y and z or no coordinates fields
cartesian y	Float	the y coordinate	must have x and z or no coordinates fields
cartesian z	Float	the z coordinate	must have x and y or no coordinates fields
cartesian xs	Floats	the x coordinates	the number must match that of the y and z coordinates
cartesian ys	Floats	the y coordinates	the number must match that of the x and z coordinates
cartesian zs	Floats	the z coordinates	the number must match that of the x and y coordinates
radius	Float	the radius	positive
rgb color red	Float	the red channel for the color	between 0 and 1; must have green and blue
rgb color green	Float	the green channel for the color	between 0 and 1; must have red and blue
rgb color blue	Float	the blue channel for the color	between 0 and 1; must have red and green {triangle vertex 0s Indexes, indexes into the coordinates fields to define triangular faces, indexes must be less than the coordinates length; triangle vertex 1s and triangle vertex 2s must be there}
triangle vertex 1s	Indexes	indexes into the coordinates fields to define triangular faces	indexes must be less than the coordinates length; triangles vertex 1 and triangles vertex 2 must be there
triangle vertex 2s	Indexes	indexes into the coordinates fields to define triangular faces	indexes must be less than the coordinates length; triangles vertex 1 and triangles vertex 2 must be there
type	Index	0 for sphere(s); 1 for cylinder(s); 2 for surface	appropriate attributes must be there; if cylinders or spheres there must be a radius; if cylinder and the coordinates fields are used the size must be divisible by 2

Related decorators: RMF::Ball, RMF::Cylinder.

Feature

Identifying string: "feature"

Keys:

name	type	description	invariants
score	Float	the score
representation	NodeIDs	the nodes involved in the feature

Related decorators: RMF::Score.

Publication

Identifying string: "publication"

Keys:

name	type	description	invariants
title	String	article title
book title	String	the book title
chapter	String	the book chapter	must have book title
journal	String	the name of the journal
url	String	a url for the publication
pubmed id	Int	the pubmed id
year	Int	the year of publication
first page	Index	the first page number
last page	Index	the last page number
author	Strings	the author names as a list for "Firstname Lastname"

Related decorators: RMF::JournalArticle.

Pair Categories

The following are categories for storing data on pairs of nodes.

Bond

Identifying string: "bond"

Keys:

name	type	description	invariants
length	Float	the length in angstroms	positive
type	Index	the bond type (0 covalent; 1 ionic; 2 hydrogen...)

Decorators

The library provides decorators to aid using the standard types of data. Each decorator comes in a const and a non-const version (as does everything else) and is constructued by an associated factory. It is simpler than this description sounds. See the RMF decorator example.