adding gibson_calculator function

R/gibson_calculator.R

@@ -0,0 +1,73 @@
+#' gibson_calculator
+#' This function is useful for calculating how to set up the Gibson reaction given user input lists of parts,concentrations, and lengths.
+#'
+#' @param names a vector of the names of each of the parts. Make sure the vector is first, followed by the inserts.
+#' @param concentrations a vector of concentrations. Make sure that they are in the same order as names
+#' @param lengths a vector of lengths. Make sure these are in the same order as the names
+#'
+#' @return
+#' a tibble containing all the ingredients at the max molarity according to the NEB protocol that is possible given the constraints imposed by the concentration of the parts. .
+#'
+#' @examples
+#' concentrations = c(100,10,10,10)
+#' lengths = c(5000,1000,1000,1000)
+#' names = c("pUC19","insert_1","insert_2","insert_3")
+#'
+#' gibson_calculator(concentrations,lengths,names)
+#'
+#'
+concentrations = c(100,10,10,10)
+lengths = c(5000,1000,1000,1000)
+names = c("pUC19","CB001","CB002","CB003")
+gibson_calculator = function(concentrations,lengths,names){
+
+ num_of_pieces = length(lengths)
+  #determining what ratio to use
+  if(num_of_pieces <= 3){
+    ratio = 0.5
+    max_vector_pmol = (0.2 / num_of_pieces) * ratio
+    max_insert_pmol =   (0.2 - max_vector_pmol)/ (num_of_pieces-1)
+
+  }else{
+    ratio = 1
+    max_vector_pmol = 0.5/num_of_pieces
+    max_insert_pmol  = 0.5/num_of_pieces
+  }
+
+ #determining mass of DNA needed to get the max molarity
+ #moles of dsDNA (mol) x ((length of dsDNA (bp) x 617.96 g/mol/bp) + 36.04 g/mol)
+  vector_mass_for_max_molarity = max_vector_pmol * 1E-12 * (lengths[1] * 617.96 + 36.04) /1E-9
+  insert_masses_for_max_molarity = max_insert_pmol * 1E-12 * (lengths[2:num_of_pieces] * 617.96 + 36.04) / 1E-9
+
+  #can we achieve the max given volume constraints?
+  uL_vector = vector_mass_for_max_molarity / concentrations[1]
+  uL_insert = insert_masses_for_max_molarity / concentrations[2:num_of_pieces]
+
+  total_uL = uL_vector + sum(uL_insert)
+
+  #Adjusting the total volume to be 10 if it is not.
+  if(total_uL > 10){
+    adjustment = total_uL/10
+    uL_vector = uL_vector / adjustment
+    uL_insert = uL_insert / adjustment
+    vector_pmol = max_vector_pmol / adjustment
+    insert_pmol = max_insert_pmol / adjustment
+  }else{
+    vector_pmol = max_vector_pmol
+    insert_pmol = max_insert_pmol
+  }
+
+  pmol = c(vector_pmol,rep(insert_pmol,num_of_pieces-1))
+  uL = c(uL_vector,uL_insert)
+
+  df = tibble::tibble(names,pmol,uL)
+
+  #adding other components
+  water_uL = 10-  sum(df$uL)
+  water = list(names = "water",pmol = NA_real_,uL = water_uL)
+  MM = list(names = "2x MM", pmol = NA_real_, uL = 10)
+
+  df2 = dplyr::bind_rows(df,water,MM)
+
+  return(df2)
+}