yxhelper: Yx's Personal R packages

# TestTube <- R6Class(
#     classname = 'TestTube',
#     public = list(
#         temp = NULL,
#         # K
#         chemicals = list(),
#         concs = list(),
#         solvent = NULL,
#         pH = 7.0,
#         vol = NULL,
#         # m^3
#         chemicals.pairings = 0,
#         chemicals.moles = 0,
#         water.size = k.water.size,
#         initialize = function() {
#             self$temp = 298.15
#             self$vol = 0
#         },
#         get.system.properties = function() {
#             return(
#                 list(
#                     chemicals = sapply(chemicals, function(x)
#                         x$name),
#                     polymer.num = sapply(chemicals, function(x)
#                         x$degree.of.polym),
#                     sigma = sapply(chemicals, function(x)
#                         x$frac.of.charged),
#                     size.ratio = sapply(chemicals, function(x)
#                         x$size / self$water.size, ),
#                     molar.ratio = charge.ratio2molar.ratio(charge.ratio = c(1, 1, 1, 1, 0)),
#                     water.size = self$k.water.size,
#                     vol = self$vol,
#                     pH = self$pH,
#                     temp = self$temp
#                 )
#             )
#         },
#         init.solvent = function(solvent, volume, pH) {
#             self$solvent <- solvent$name
#             self$pH <- solvent$pH
#             self$vol <- solvent$volume
#             self$set.chemicals(solvent,)
#         },
#         set.chemicals = function(chemicals, concs, vols) {
#             self$chemicals <- append(self$chemicals, chemicals)
#             self$concs <- append(self$concs, concs)
#             self$vol <- self$vol + sum(vols)
#         },
#         get.water = function(vol, temp = 298.15) {
#             water.molecule <-
#                 Molecule$new(
#                     name = 'water',
#                     MW = 18,
#                     diameter = k.water.size,
#                     charge = 0,
#                     degree.of.polym = 1,
#                     frac.of.charge = 0
#                 )
#
#             water <- Matter$new(
#                 water.molecule,
#                 vol = vol,
#                 density = 1e3,
#                 pH = 7,
#                 temp = temp
#             )
#
#             self$solvent <- water
#         }
#     )
# )
#
# Molecule <- R6Class(
#     classname = 'Molecule',
#     private = list(),
#     public = list(
#         name = 'water',
#         MW = 18,
#         diameter = 3.1e-10,
#         charge = 0,
#         degree.of.polym = 1,
#         frac.of.charge = 0,
#         initialize = function(name,
#                               MW,
#                               diameter,
#                               charge,
#                               degree.of.polym,
#                               frac.of.charge) {
#             self$name = name
#             self$diameter = diameter
#             self$charge = charge
#             self$degree.of.polym = degree.of.polym
#             self$frac.of.charge = frac.of.charge
#         }
#     )
# )
#
# Matter <- R6Class(
#     'material',
#     public = list(
#         vol = 0,
#         temp = 0,
#         pH = 0,
#         density = 0,
#         molecule = NULL,
#         initialize = function(molecule, vol, density, pH, temp) {
#             self$molecule = molecule
#             self$vol = vol
#             self$density = density
#             self$pH = pH
#             self$temp = temp
#         }
#     )
# )
#
#
# testtube <- TestTube$new()
# testtube$get.water(1e-3)
# testtube$set.chemicals(
#     chemicals = list(
#         protein = Molecule$new(
#             name = 'proteinA',
#             MW = 22000,
#             diameter = k.water.size,
#             charge = 11,
#             degree.of.polym = 207,
#             frac.of.charge = 11 / 207
#         )
#     ),
#     concs = list(20e-3),
#     vols = 1
# )