Structure of the S4 class

Structure of the S4 class "Organism"

Slots

cellDiameter: Numeric for the initial Diameter of cell spheres in \(\mu\)m
cellMassInit: Numeric for the initial cell mass in pg
cellMassAtDivision: Limit of a cell's mass before it divided into two daughter cells. Unit: pg
cellShape: Character for the cell shape type. Currently, only coccus/sphere shapes are supported.
vmax: Numeric for the maximum speed a cell can move in \(\mu\)m/s
scavengeDist: Numeric indicating the maximum distance (from cell surface) a cell can scavenge nutrients from its surrounding. Unit: \(\mu\)m
chemotaxisCompound: Character vector with the compound IDs that influence the cells chemotaxis behavior.
chemotaxisStrength: Numeric vector that indicates the strength of chemotaxis. Positive value for attraction; Negative for repelling effect. A value of 1 indicates that in case of a maximum gradient (concentration-weighted center in cell's scavenge area is at the edge of the area) the cell moves with its maximum speed (vmax) in the direction of the gradient.
chemotaxisHillKA: Numeric vector for K_A value in Hill equation in chemotactic metabolite sensing. Unit: mM
chemotaxisHillCoef: Numeric vector for the Hill coefficient. Unitless
mod: Object of S4-class modelorg for the organisms metabolic network model.
exoenzymes: Character vector of IDs of the organism's exoenzymes
exoenzymes.prod: Numeric vector of the production rates of exoenzymes. Unit: nmol / gDW / hr (nmol Enzyme per gDW cells per hr)
color: Color of organism in visualizations.