Structure of the S4 class "growthEnvironment"

Structure of the S4 class "growthEnvironment"

Slots

field.pts

Object of class 'XYZ'. Coordinates of rhombic dodecahedron centroids.

compounds

Character vector with compound IDs

compound.names

Character vector with compound names

compound.D

Numeric vector of the diffusion coefficient values for each compound. Unit: \(\mu\)m^2/s

concentrations

(n x m) numeric matrix with n columns representing compounds and m grid field (field.pts). Units of matrix entries: mM

conc.isConstant

Logical vector indicating if the respective compound is fixed (i.e. buffered) in its concentration.

fieldLayers

Integer specifying how many layers (z-dimension) of rhomic dodecahedra fields are in the environment representation.

nfields

Integer indicating the number of fields in the environment representation.

fieldSize

Size of each rhomic dodecahedron in \(\mu\)m as the distance between opposite faces.

fieldVol

Volume of each field. Unit: \(\mu\)m^3

mat.in

A two column numeric matrix as a representation of the grid environment as a directed graph. First column (From) and second column (To) are denoting field's indices in `field.pts`

mat.out

A two column matrix. First column: indices of each field in `field.pts`; second column: Number of neighboring fields

exoenzymes

A list with the Exoenzyme S4 objects.

exoenzymes.conc

Same as `concentrations`, but for the exoenzymes and in nM.