Mercurial > repos > workflow4metabolomics > ms2snoop

changeset 7:2a1f120a6874 draft default tip

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planemo upload commit d9b3849751af6f74e3371db0c3525dcd08728723
author workflow4metabolomics
date Tue, 10 Jan 2023 11:07:48 +0000
parents 77abacd33c31
children
files MS2snoop.R MS2snoop.xml README.md macros.xml test-data/smol/out-smol-base.tsv test-data/smol/out-smol-delta-0.05mz.tsv test-data/smol/out-smol-delta-8.542.tsv
diffstat 7 files changed, 55 insertions(+), 44 deletions(-) [+]
line wrap: on
line diff
--- a/MS2snoop.R	Fri Sep 30 16:18:56 2022 +0000
+++ b/MS2snoop.R	Tue Jan 10 11:07:48 2023 +0000
@@ -54,7 +54,8 @@
   mzref,
   spectra,
   processing_parameters,
-  background = !TRUE
+  background = !TRUE,
+  show_sirius_outputs = !TRUE
 ) {
   if (is.vector(mzref) && length(mzref) > 1) {
     return(lapply(
@@ -89,13 +90,16 @@
       "-i='%s'",
       "-o='%s'",
       "tree",
-      ## loglevel is not working taken into account during
-      ## sirius startup, so we filter outputs...
-      "2>&1 | grep '^(WARNING|SEVERE)'"
+      "2>&1"
     ),
     input,
     output
   )
+  if (!show_sirius_outputs) {
+    ## loglevel is not taken into account during
+    ## sirius startup, so we filter outputs...
+    command <- paste(command, "| grep '^(WARNING|SEVERE)'")
+  }
   verbose_catf(
     ">> Sirius is running %swith the command: %s\n",
     if (background) "in the background " else "",
@@ -189,7 +193,8 @@
     return(rep(NA, length(mz_list)))
   }
   if (!is.null(trees_filename)) {
-    sirius_results <- cbind(sirius_results, extract_sirius_ppm(trees_filename))
+    extracted_ppm <- extract_sirius_ppm(trees_filename)
+    sirius_results <- cbind(sirius_results, extracted_ppm)
   } else {
     return(rep(NA, length(mz_list)))
   }
@@ -210,7 +215,7 @@
 
   for (index in seq_len(nrow(sirius_results))) {
     result <- sirius_results[index, ]
-    filter <- which(order(abs(fragment_matchings$mz - result$mz)) == 1)
+    filter <- order(abs(fragment_matchings$mz - result$mz))[1]
     fragment_matchings[filter, "formula"] <- result$formula
     fragment_matchings[filter, "ppm"] <- result$ppm
     catf(
@@ -1124,7 +1129,7 @@
 
 zip_pdfs <- function(processing_parameters) {
   if (processing_parameters$do_pdf) {
-    if (zip <- Sys.getenv("R_ZIPCMD", "zip") == "") {
+    if ((zip <- Sys.getenv("R_ZIPCMD", "zip")) == "") {
       catf("R could not fin the zip executable. Trying luck: zip = \"zip\"")
       zip <- "zip"
     } else {
--- a/MS2snoop.xml	Fri Sep 30 16:18:56 2022 +0000
+++ b/MS2snoop.xml	Tue Jan 10 11:07:48 2023 +0000
@@ -48,9 +48,15 @@
     --ionization '$sirius.ionization'
     --fragment_match_delta '$sirius.fragment_match_delta'
     --fragment_match_delta_unit '$sirius.fragment_match_delta_unit'
-    $advenced.pdf
+    #if $advenced.pdf:
+        --pdf_path './out.zip'
+    #end if
     $advenced.debug
     $advenced.verbose
+#if $advenced.pdf:
+&& cat ./out.zip > '$pdf_output'
+#end if
+
 ]]>
     </command>
     <inputs>
@@ -128,7 +134,7 @@
         </section>
 
         <section title="Advenced Options" name="advenced">
-            <param argument="--pdf" type="boolean" truevalue="--pdf_path '$pdf_output'" falsevalue="" value="" optional="true"
+            <param argument="--pdf" type="boolean" value="" optional="true"
                 label="Output PDF"
                 help="The tool will output some pdf in a zip file"
             />
@@ -143,14 +149,14 @@
         </section>
     </inputs>
     <outputs>
-        <data name="frag_result_txt" format="tsv" label="${tool.name} on ${peaklist_frag_tsv.name}" />
-        <data name="pdf_output" format="zip" label="${tool.name} PDFs for ${peaklist_frag_tsv.name}">
+        <data name="frag_result_txt" format="tsv" label="${tool.name}_on_${peaklist_frag_tsv.name}" />
+        <data name="pdf_output" format="zip" label="${tool.name}_PDFs_for_${peaklist_frag_tsv.name}">
             <filter>advenced['pdf']</filter>
         </data>
     </outputs>
     <tests>
         <test>
-            <!-- Regular test with no option -->
+            <!-- #1 Regular test with no option -->
             <param name="compound_txt" value="compounds_pos.txt" />
             <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
             <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
@@ -163,7 +169,7 @@
         </test>
 
         <test>
-            <!-- Regular files with verbose output -->
+            <!-- #2 Regular files with verbose output -->
             <param name="compound_txt" value="compounds_pos.txt" />
             <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
             <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
@@ -177,7 +183,7 @@
         </test>
 
         <test>
-            <!-- Regular test with debug outputs -->
+            <!-- #3 Regular test with debug outputs -->
             <param name="compound_txt" value="compounds_pos.txt" />
             <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
             <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
@@ -191,7 +197,7 @@
         </test>
 
         <test>
-            <!-- Regular test with both verbose and debug outputs -->
+            <!-- #4 Regular test with both verbose and debug outputs -->
             <param name="compound_txt" value="compounds_pos.txt" />
             <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
             <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
@@ -207,7 +213,7 @@
 
         <test>
             <!--
-            This test mixes tsv, csv, and so, and ms2snoop is expected
+            #5 This test mixes tsv, csv, and so, and ms2snoop is expected
             handle them like usual.
             -->
             <param name="compound_txt" value="compounds_pos.csv" />
@@ -224,7 +230,7 @@
 
         <test>
             <!--
-            This test contains smaller datasets. This is the "regular"
+            #6 This test contains smaller datasets. This is the "regular"
             smol test, to prepare further smolah tests.
             -->
             <param name="ionization" value="[M+?]+" />
@@ -237,7 +243,7 @@
 
         <test>
             <!--
-            Test for pdf generation
+            #7 Test for pdf generation
             -->
             <param name="pdf" value="True" />
             <param name="ionization" value="[M+?]+" />
@@ -250,7 +256,7 @@
 
         <test>
             <!--
-                test for delta in ppm
+               #8  test for delta in ppm
             -->
             <param name="ionization" value="[M+?]+" />
             <param name="mzdecimal" value="3" />
@@ -263,7 +269,7 @@
 
         <test>
             <!--
-                test for delta in m/z
+                #9 test for delta in m/z
             -->
             <param name="ionization" value="[M+?]+" />
             <param name="mzdecimal" value="3" />
@@ -278,7 +284,7 @@
         <!--  === expected to fail tests === -->
         <test expect_exit_code="2" expect_failure="true">
             <!--
-            This test uses old format for molecules file.
+            #10 This test uses old format for molecules file.
             Is is expected to fail
             -->
             <param name="compound_txt" value="compounds_pos_old_format.txt" />
--- a/README.md	Fri Sep 30 16:18:56 2022 +0000
+++ b/README.md	Tue Jan 10 11:07:48 2023 +0000
@@ -5,7 +5,7 @@
 -----------
 
  * **@name**: MS2 Snoop
- * **@version**: 2.2.0
+ * **@version**: 2.2.1
  * **@authors**: Jean François Martin (INRAE), Kevin Wagner (INRAE)
  * **@maintainers**: Lain Pavot (PFEM - INRAE - MetaboHUB)
  * **@init date**: 2022, April
--- a/macros.xml	Fri Sep 30 16:18:56 2022 +0000
+++ b/macros.xml	Tue Jan 10 11:07:48 2023 +0000
@@ -138,7 +138,7 @@
 ]]>
     </token>
 
-    <token name="@TOOL_VERSION@">2.2.0</token>
+    <token name="@TOOL_VERSION@">2.2.1</token>
     <token name="@VERSION_SUFFIX@">0</token>
 
     <xml name="has_smol_stdout">
--- a/test-data/smol/out-smol-base.tsv	Fri Sep 30 16:18:56 2022 +0000
+++ b/test-data/smol/out-smol-base.tsv	Tue Jan 10 11:07:48 2023 +0000
@@ -1,18 +1,18 @@
 "compoundName"	"inchikey"	"elemcomposition"	"fragment"	"fragment_mz"	"ppm"	"fileid"	"CorWithPrecursor"	"AbsoluteIntensity"	"relativeIntensity"	"corValid"
 "Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	"C13H8O4"	229.05	2.02930325023702	"1"	NA	203723.75	0.932156767504374	NA
 "Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	NA	312.059	NA	"1"	NA	3981.51538085938	0.0182177900573243	NA
-"Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	NA	313.068	NA	"1"	NA	7264.93603515625	0.0332413834452649	NA
-"Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	"C17H12O6"	367.081	-8.51110969664126	"1"	NA	218550.953125	1	NA
-"Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	"C20H14O7"	451.115	-0.624494567969591	"1"	NA	135964.078125	0.622116152690652	NA
+"Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	"C17H12O6"	313.068	-8.51110969664126	"1"	NA	7264.93603515625	0.0332413834452649	NA
+"Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	"C20H14O7"	367.081	-0.624494567969591	"1"	NA	218550.953125	1	NA
+"Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	NA	451.115	NA	"1"	NA	135964.078125	0.622116152690652	NA
 "Caffeic acid"	"QAIPRVGONGVQAS-DUXPYHPUSA-N"	"C9H8O4"	NA	109.101	NA	"1"	NA	1663.78308105469	1	NA
 "Caffeic acid"	"QAIPRVGONGVQAS-DUXPYHPUSA-N"	"C9H8O4"	NA	140.951	NA	"1"	NA	1119.27758789062	0.672730478291135	NA
 "Berberine"	"YBHILYKTIRIUTE-UHFFFAOYSA-N"	"C20H18NO4+"	NA	55.575	NA	"1"	NA	959.281677246094	0.00801122428782145	NA
-"Berberine"	"YBHILYKTIRIUTE-UHFFFAOYSA-N"	"C20H18NO4+"	NA	278.081	NA	"1"	NA	49810.07421875	0.415977585963074	NA
-"Berberine"	"YBHILYKTIRIUTE-UHFFFAOYSA-N"	"C20H18NO4+"	"C17H11NO3"	323.106	-0.610124713635454	"1"	1	119742.20703125	1	TRUE
+"Berberine"	"YBHILYKTIRIUTE-UHFFFAOYSA-N"	"C20H18NO4+"	"C17H11NO3"	278.081	-0.610124713635454	"1"	NA	49810.07421875	0.415977585963074	NA
+"Berberine"	"YBHILYKTIRIUTE-UHFFFAOYSA-N"	"C20H18NO4+"	NA	323.106	NA	"1"	1	119742.20703125	1	TRUE
 "Theobromine "	"YAPQBXQYLJRXSA-UHFFFAOYSA-N"	"C7H8N4O2"	NA	51.94	NA	"1"	NA	1706.40014648438	0.0178528316194543	NA
 "Theobromine "	"YAPQBXQYLJRXSA-UHFFFAOYSA-N"	"C7H8N4O2"	"C5H6"	67.054	-3.38002342189334	"1"	NA	1413.32275390625	0.0147865746503924	NA
-"Theobromine "	"YAPQBXQYLJRXSA-UHFFFAOYSA-N"	"C7H8N4O2"	NA	122.059	NA	"1"	NA	40171.04296875	0.420280593374599	NA
-"Theobromine "	"YAPQBXQYLJRXSA-UHFFFAOYSA-N"	"C7H8N4O2"	"C7H7NO"	135.117	-8.52289540743972	"1"	NA	95581.484375	1	NA
+"Theobromine "	"YAPQBXQYLJRXSA-UHFFFAOYSA-N"	"C7H8N4O2"	"C7H7NO"	122.059	-8.52289540743972	"1"	NA	40171.04296875	0.420280593374599	NA
+"Theobromine "	"YAPQBXQYLJRXSA-UHFFFAOYSA-N"	"C7H8N4O2"	NA	135.117	NA	"1"	NA	95581.484375	1	NA
 "Theobromine "	"YAPQBXQYLJRXSA-UHFFFAOYSA-N"	"C7H8N4O2"	NA	232.845	NA	"1"	NA	17855.763671875	0.186811952007572	NA
 "Bergapten "	"BGEBZHIAGXMEMV-UHFFFAOYSA-N"	"C12H8O4"	NA	135.071	NA	"1"	NA	1388.24841308594	0.0111932237930481	NA
 "Bergapten "	"BGEBZHIAGXMEMV-UHFFFAOYSA-N"	"C12H8O4"	NA	177.092	NA	"1"	NA	1346.46130371094	0.0108563010474573	NA
--- a/test-data/smol/out-smol-delta-0.05mz.tsv	Fri Sep 30 16:18:56 2022 +0000
+++ b/test-data/smol/out-smol-delta-0.05mz.tsv	Tue Jan 10 11:07:48 2023 +0000
@@ -1,18 +1,18 @@
 "compoundName"	"inchikey"	"elemcomposition"	"fragment"	"fragment_mz"	"ppm"	"fileid"	"CorWithPrecursor"	"AbsoluteIntensity"	"relativeIntensity"	"corValid"
 "Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	"C13H8O4"	229.05	2.02930325023702	"1"	NA	203723.75	0.932156767504374	NA
 "Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	NA	312.059	NA	"1"	NA	3981.51538085938	0.0182177900573243	NA
-"Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	NA	313.068	NA	"1"	NA	7264.93603515625	0.0332413834452649	NA
-"Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	"C17H12O6"	367.081	-8.51110969664126	"1"	NA	218550.953125	1	NA
-"Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	"C20H14O7"	451.115	-0.624494567969591	"1"	NA	135964.078125	0.622116152690652	NA
+"Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	"C17H12O6"	313.068	-8.51110969664126	"1"	NA	7264.93603515625	0.0332413834452649	NA
+"Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	"C20H14O7"	367.081	-0.624494567969591	"1"	NA	218550.953125	1	NA
+"Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	NA	451.115	NA	"1"	NA	135964.078125	0.622116152690652	NA
 "Caffeic acid"	"QAIPRVGONGVQAS-DUXPYHPUSA-N"	"C9H8O4"	NA	109.101	NA	"1"	NA	1663.78308105469	1	NA
 "Caffeic acid"	"QAIPRVGONGVQAS-DUXPYHPUSA-N"	"C9H8O4"	NA	140.951	NA	"1"	NA	1119.27758789062	0.672730478291135	NA
 "Berberine"	"YBHILYKTIRIUTE-UHFFFAOYSA-N"	"C20H18NO4+"	NA	55.575	NA	"1"	NA	959.281677246094	0.00801122428782145	NA
-"Berberine"	"YBHILYKTIRIUTE-UHFFFAOYSA-N"	"C20H18NO4+"	NA	278.081	NA	"1"	NA	49810.07421875	0.415977585963074	NA
-"Berberine"	"YBHILYKTIRIUTE-UHFFFAOYSA-N"	"C20H18NO4+"	"C17H11NO3"	323.106	-0.610124713635454	"1"	1	119742.20703125	1	TRUE
+"Berberine"	"YBHILYKTIRIUTE-UHFFFAOYSA-N"	"C20H18NO4+"	"C17H11NO3"	278.081	-0.610124713635454	"1"	NA	49810.07421875	0.415977585963074	NA
+"Berberine"	"YBHILYKTIRIUTE-UHFFFAOYSA-N"	"C20H18NO4+"	NA	323.106	NA	"1"	1	119742.20703125	1	TRUE
 "Theobromine "	"YAPQBXQYLJRXSA-UHFFFAOYSA-N"	"C7H8N4O2"	NA	51.94	NA	"1"	NA	1706.40014648438	0.0178528316194543	NA
 "Theobromine "	"YAPQBXQYLJRXSA-UHFFFAOYSA-N"	"C7H8N4O2"	"C5H6"	67.054	-3.38002342189334	"1"	NA	1413.32275390625	0.0147865746503924	NA
-"Theobromine "	"YAPQBXQYLJRXSA-UHFFFAOYSA-N"	"C7H8N4O2"	NA	122.059	NA	"1"	NA	40171.04296875	0.420280593374599	NA
-"Theobromine "	"YAPQBXQYLJRXSA-UHFFFAOYSA-N"	"C7H8N4O2"	"C7H7NO"	135.117	-8.52289540743972	"1"	NA	95581.484375	1	NA
+"Theobromine "	"YAPQBXQYLJRXSA-UHFFFAOYSA-N"	"C7H8N4O2"	"C7H7NO"	122.059	-8.52289540743972	"1"	NA	40171.04296875	0.420280593374599	NA
+"Theobromine "	"YAPQBXQYLJRXSA-UHFFFAOYSA-N"	"C7H8N4O2"	NA	135.117	NA	"1"	NA	95581.484375	1	NA
 "Theobromine "	"YAPQBXQYLJRXSA-UHFFFAOYSA-N"	"C7H8N4O2"	NA	232.845	NA	"1"	NA	17855.763671875	0.186811952007572	NA
 "Bergapten "	"BGEBZHIAGXMEMV-UHFFFAOYSA-N"	"C12H8O4"	NA	135.071	NA	"1"	NA	1388.24841308594	0.0111932237930481	NA
 "Bergapten "	"BGEBZHIAGXMEMV-UHFFFAOYSA-N"	"C12H8O4"	NA	177.092	NA	"1"	NA	1346.46130371094	0.0108563010474573	NA
--- a/test-data/smol/out-smol-delta-8.542.tsv	Fri Sep 30 16:18:56 2022 +0000
+++ b/test-data/smol/out-smol-delta-8.542.tsv	Tue Jan 10 11:07:48 2023 +0000
@@ -1,18 +1,18 @@
 "compoundName"	"inchikey"	"elemcomposition"	"fragment"	"fragment_mz"	"ppm"	"fileid"	"CorWithPrecursor"	"AbsoluteIntensity"	"relativeIntensity"	"corValid"
 "Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	"C13H8O4"	229.05	2.02930325023702	"1"	NA	203723.75	0.932156767504374	NA
 "Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	NA	312.059	NA	"1"	NA	3981.51538085938	0.0182177900573243	NA
-"Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	NA	313.068	NA	"1"	NA	7264.93603515625	0.0332413834452649	NA
-"Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	"C17H12O6"	367.081	-8.51110969664126	"1"	NA	218550.953125	1	NA
-"Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	"C20H14O7"	451.115	-0.624494567969591	"1"	NA	135964.078125	0.622116152690652	NA
+"Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	"C17H12O6"	313.068	-8.51110969664126	"1"	NA	7264.93603515625	0.0332413834452649	NA
+"Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	"C20H14O7"	367.081	-0.624494567969591	"1"	NA	218550.953125	1	NA
+"Orientin"	"PLAPMLGJVGLZOV-VPRICQMDSA-N"	"C21H20O11"	NA	451.115	NA	"1"	NA	135964.078125	0.622116152690652	NA
 "Caffeic acid"	"QAIPRVGONGVQAS-DUXPYHPUSA-N"	"C9H8O4"	NA	109.101	NA	"1"	NA	1663.78308105469	1	NA
 "Caffeic acid"	"QAIPRVGONGVQAS-DUXPYHPUSA-N"	"C9H8O4"	NA	140.951	NA	"1"	NA	1119.27758789062	0.672730478291135	NA
 "Berberine"	"YBHILYKTIRIUTE-UHFFFAOYSA-N"	"C20H18NO4+"	NA	55.575	NA	"1"	NA	959.281677246094	0.00801122428782145	NA
-"Berberine"	"YBHILYKTIRIUTE-UHFFFAOYSA-N"	"C20H18NO4+"	NA	278.081	NA	"1"	NA	49810.07421875	0.415977585963074	NA
-"Berberine"	"YBHILYKTIRIUTE-UHFFFAOYSA-N"	"C20H18NO4+"	"C17H11NO3"	323.106	-0.610124713635454	"1"	1	119742.20703125	1	TRUE
+"Berberine"	"YBHILYKTIRIUTE-UHFFFAOYSA-N"	"C20H18NO4+"	"C17H11NO3"	278.081	-0.610124713635454	"1"	NA	49810.07421875	0.415977585963074	NA
+"Berberine"	"YBHILYKTIRIUTE-UHFFFAOYSA-N"	"C20H18NO4+"	NA	323.106	NA	"1"	1	119742.20703125	1	TRUE
 "Theobromine "	"YAPQBXQYLJRXSA-UHFFFAOYSA-N"	"C7H8N4O2"	NA	51.94	NA	"1"	NA	1706.40014648438	0.0178528316194543	NA
 "Theobromine "	"YAPQBXQYLJRXSA-UHFFFAOYSA-N"	"C7H8N4O2"	"C5H6"	67.054	-3.38002342189334	"1"	NA	1413.32275390625	0.0147865746503924	NA
-"Theobromine "	"YAPQBXQYLJRXSA-UHFFFAOYSA-N"	"C7H8N4O2"	NA	122.059	NA	"1"	NA	40171.04296875	0.420280593374599	NA
-"Theobromine "	"YAPQBXQYLJRXSA-UHFFFAOYSA-N"	"C7H8N4O2"	"C7H7NO"	135.117	-8.52289540743972	"1"	NA	95581.484375	1	NA
+"Theobromine "	"YAPQBXQYLJRXSA-UHFFFAOYSA-N"	"C7H8N4O2"	"C7H7NO"	122.059	-8.52289540743972	"1"	NA	40171.04296875	0.420280593374599	NA
+"Theobromine "	"YAPQBXQYLJRXSA-UHFFFAOYSA-N"	"C7H8N4O2"	NA	135.117	NA	"1"	NA	95581.484375	1	NA
 "Theobromine "	"YAPQBXQYLJRXSA-UHFFFAOYSA-N"	"C7H8N4O2"	NA	232.845	NA	"1"	NA	17855.763671875	0.186811952007572	NA
 "Bergapten "	"BGEBZHIAGXMEMV-UHFFFAOYSA-N"	"C12H8O4"	NA	135.071	NA	"1"	NA	1388.24841308594	0.0111932237930481	NA
 "Bergapten "	"BGEBZHIAGXMEMV-UHFFFAOYSA-N"	"C12H8O4"	NA	177.092	NA	"1"	NA	1346.46130371094	0.0108563010474573	NA