separated individual mass related tests into individual functions

CDK-R · Nov 13, 2018 · 68ddb0b89674b1a7e3fefd82b5ee2a1476ed374b · 68ddb0b · schymane · Nov 29, 2018
1 parent 7df8c6d
commit 68ddb0b89674b1a7e3fefd82b5ee2a1476ed374b
Unified Split

Showing with 23 additions and 22 deletions.

+23 −22 rcdk/inst/unitTests/runit.mass.R
diff --git a/rcdk/inst/unitTests/runit.mass.R b/rcdk/inst/unitTests/runit.mass.R
@@ -1,14 +1,7 @@
-test.get.mass <- function() {
-  smiles <- c("CCNC1=NC(NC(C)C)=NC(Cl)=N1", # normal atrazine, DTXSID9020112
-              "[2H]N(CC)C1=NC(=NC(Cl)=N1)N([2H])C(C)C", #2H on implicit locations, DTXSID40892885
-              "[2H]C([2H])([2H])C([2H])([2H])NC1=NC(Cl)=NC(NC(C)C)=N1", #d5, DTXSID20486781
-              "CC[15NH]C1=NC(NC(C)C)=NC(Cl)=N1", #15N DTXSID40583908
-              "OC1=C(Br)C(Br)=C(Br)C(Br)=C1Br", #pentabromophenol, DTXSID9022079
-              "C[Se]CC[C@H](N)C(O)=O" # Selenium-L-methionine, DTXSID8046824
-  ) 
-  #atrzine
-  m <- parse.smiles(smiles[1])[[1]]
+test.get.mass.atrazine <- function() {
+  m <- parse.smiles("CCNC1=NC(NC(C)C)=NC(Cl)=N1")[[1]] # normal atrazine, DTXSID9020112
  f <- get.mol2formula(m)
+  
  # Dashboard ref mass: 215.093773, 215.69
  #checkEquals(get.mass(m,type="total.exact"),215.0938, tolerance=1e-6) #currently NPE
  #checkEquals(get.mass(m,type="natural.exact"),215.6835, tolerance=1e-6) #currently NPE
@@ -18,15 +11,18 @@ test.get.mass <- function() {
  #fails with NPE right now
  #checkEquals(get.exact.mass(m),get.mass(m,type="total.exact"), tolerance=1e-6)
  #checkEquals(get.natural.mass(m),get.mass(m,type="natural.exact"), tolerance=1e-6)
+  
  ###formula testing
  checkEquals(get.mass(f,type="total.exact"),215.0938, tolerance=1e-6) 
  #checkEquals(get.mass(f,type="natural.exact"),215.6835, tolerance=1e-6) #currently returns wrong mass
  checkEquals(get.mass(f,type="mass.number"),215, tolerance=1e-6) #215
  checkEquals(get.mass(f,type="major.isotope"),215.0938, tolerance=1e-6) #215.0938 
  #checkEquals(get.mass(f,type="molecular.weight"),215.6835, tolerance=1e-6) #215.6835 # NPE
-  
+}
+
+test.get.mass.deuterium.xchg <- function() {
+  m <- parse.smiles("[2H]N(CC)C1=NC(=NC(Cl)=N1)N([2H])C(C)C")[[1]] #2H on implicit locations, DTXSID40892885
  #deuterium on exchangeable locations
-  m <- parse.smiles(smiles[2])[[1]]
  # do.aromaticity(m)
  # do.typing(m)
  # do.isotopes(m)
@@ -42,9 +38,11 @@ test.get.mass <- function() {
  #checkEquals(get.natural.mass(m),get.mass(m,type="natural.exact"), tolerance=1e-6)
  #checkEquals(get.exact.mass(m),217.1063, tolerance=1e-6)
  #checkEquals(get.natural.mass(m),215.6835) #this is wrong! It should be 217.7something
-  
+}
+
+test.get.mass.deuterium.fixed <- function() {
+  m <- parse.smiles("[2H]C([2H])([2H])C([2H])([2H])NC1=NC(Cl)=NC(NC(C)C)=N1")[[1]] # #d5, DTXSID20486781
  #deuterium on fixed locations
-  m <- parse.smiles(smiles[3])[[1]]
  # Dashboard ref mass: 220.125157, 220.72
  #checkEquals(get.mass(m,type="total.exact"),220.1252, tolerance=1e-6) #currently NPE
  #checkEquals(get.mass(m,type="natural.exact"),215.6835, tolerance=1e-6) #currently NPE - have to check mass
@@ -56,9 +54,11 @@ test.get.mass <- function() {
  #checkEquals(get.natural.mass(m),get.mass(m,type="natural.exact"), tolerance=1e-6)
  #checkEquals(get.exact.mass(m),220.1252, tolerance=1e-6)
  #checkEquals(get.natural.mass(m),215.6835) #this is wrong! It should be 220.7something
-  
+}  
+
+test.get.mass.atrazine15N <- function() {
+  m <- parse.smiles("CC[15NH]C1=NC(NC(C)C)=NC(Cl)=N1")[[1]] #15N DTXSID40583908
  #15N-atrazine
-  m <- parse.smiles(smiles[4])[[1]]
  # Dashboard ref mass: 216.090808, 216.68
  #checkEquals(get.mass(m,type="total.exact"),216.0908, tolerance=1e-6) #currently NPE
  #checkEquals(get.mass(m,type="natural.exact"),215.6835, tolerance=1e-6) #currently NPE - have to check mass
@@ -70,9 +70,11 @@ test.get.mass <- function() {
  #checkEquals(get.natural.mass(m),get.mass(m,type="natural.exact"), tolerance=1e-6)
  #checkEqualsNumeric(get.exact.mass(m),216.0908, tolerance=1e-6)
  #checkEquals(get.natural.mass(m),215.6835) #this is wrong! It should be 216.68something
-  
+}
+
+test.get.mass.pentabromophenol<- function() {
+  m <- parse.smiles("OC1=C(Br)C(Br)=C(Br)C(Br)=C1Br")[[1]] #pentabromophenol, DTXSID9022079
  #pentabromophenol, DTXSID9022079 - tricky as lots of Br shifts pattern
-  m <- parse.smiles(smiles[5])[[1]]
  # Dashboard ref mass: 483.59443, 488.593
  #checkEquals(get.mass(m,type="total.exact"),483.5944, tolerance=1e-6) #currently NPE
  #checkEquals(get.mass(m,type="natural.exact"),488.5894, tolerance=1e-6) #currently NPE - have to check mass
@@ -85,8 +87,9 @@ test.get.mass <- function() {
  #checkEquals(get.exact.mass(m),483.5944, tolerance=1e-6)
  #checkEquals(get.natural.mass(m),488.5894, tolerance=1e-6) 
  
-  # Selenium-L-methionine, DTXSID8046824 - tricky as Se primary isotope not lowest mass
-  m <- parse.smiles(smiles[6])[[1]]
+}
+test.get.mass.selenium <- function() {
+  m <- parse.smiles("C[Se]CC[C@H](N)C(O)=O")[[1]] # Selenium-L-methionine, DTXSID8046824
  # Dashboard ref mass: 196.995501, 196.119
  #checkEquals(get.mass(m,type="total.exact"),196.9955, tolerance=1e-6) #currently NPE
  #checkEquals(get.mass(m,type="natural.exact"),196.1059, tolerance=1e-6) #currently NPE - have to check mass
@@ -106,6 +109,4 @@ test.get.mass <- function() {
  #checkEquals(get.mass(get.formula("C6H6"),type="molecular.weight"),78.114, tolerance=1e-6) #NPE
  checkEquals(get.mass(get.formula("C6H6"),type="mass.number"),78, tolerance=1e-6) 
  checkEquals(get.mass(get.formula("C6H6"),type="major.isotope"),78.04695, tolerance=1e-6) 
-  
-  
 }