[CHNOSZ-commits] r943 - in pkg/CHNOSZ: . R inst

[noreply at r-forge.r-project.org]

Author: jedick
Date: 2025-12-08 08:05:24 +0100 (Mon, 08 Dec 2025)
New Revision: 943

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/phosphorylate.R
   pkg/CHNOSZ/inst/NEWS.Rd
Log:
Add check for speciating H3PO4 in phosphorylate()


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2025-12-08 03:39:36 UTC (rev 942)
+++ pkg/CHNOSZ/DESCRIPTION	2025-12-08 07:05:24 UTC (rev 943)
@@ -1,6 +1,6 @@
 Date: 2025-12-08
 Package: CHNOSZ
-Version: 2.2.0-9
+Version: 2.2.0-10
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors at R: c(
     person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),

Modified: pkg/CHNOSZ/R/phosphorylate.R
===================================================================
--- pkg/CHNOSZ/R/phosphorylate.R	2025-12-08 03:39:36 UTC (rev 942)
+++ pkg/CHNOSZ/R/phosphorylate.R	2025-12-08 07:05:24 UTC (rev 943)
@@ -35,11 +35,11 @@
     # Basic reaction: acetic acid + P = acetylphosphate + H2O
     # Load initial species for mosaic reaction (uncharged species)
     basis(c("acetic acid", "H3PO4", "acetylphosphate0", "O2", "H+"))
-    # The basis species we will swap through for mosaic
+    # The basis species we will speciate using mosaic()
     bases <- list(
       c("H3PO4", "H2PO4-", "HPO4-2", "PO4-3"),
-      c("acetylphosphate0", "acetylphosphate-1", "acetylphosphate-2", "acetylphosphate-3"),
-      c("acetic acid", "acetate")
+      c("acetic acid", "acetate"),
+      c("acetylphosphate0", "acetylphosphate-1", "acetylphosphate-2", "acetylphosphate-3")
     )
   } else if(reactant == "glycerol") {
     # Basic reaction: glycerol + P = 1-glycerolphosphate + H2O
@@ -90,6 +90,7 @@
     # Basic reaction: AMP + P = ADP + H2O
     basis(c("H2AMP", "H3PO4", "H3ADP", "N2", "O2", "H+"))
     bases <- list(
+      c("H3PO4", "H2PO4-", "HPO4-2", "PO4-3"),
       c("H2AMP", "HAMP-", "AMP-2"),
       c("H3ADP", "H2ADP-", "HADP-2", "ADP-3")
     )
@@ -97,6 +98,7 @@
     # Basic reaction: ADP + P = ATP + H2O
     basis(c("H3ADP", "H3PO4", "H4ATP", "N2", "O2", "H+"))
     bases <- list(
+      c("H3PO4", "H2PO4-", "HPO4-2", "PO4-3"),
       c("H3ADP", "H2ADP-", "HADP-2", "ADP-3"),
       c("H4ATP", "H3ATP-", "H2ATP-2", "HATP-3", "ATP-4")
     )
@@ -112,13 +114,16 @@
     basis(c("pyruvic acid", "H3PO4", "phosphoenolpyruvate", "O2", "H+"))
     bases <- list(
       c("H3PO4", "H2PO4-", "HPO4-2", "PO4-3"),
-      c("phosphoenolpyruvate", "phosphoenolpyruvate-1", "phosphoenolpyruvate-2", "phosphoenolpyruvate-3"),
-      c("pyruvic acid", "pyruvate")
+      c("pyruvic acid", "pyruvate"),
+      c("phosphoenolpyruvate", "phosphoenolpyruvate-1", "phosphoenolpyruvate-2", "phosphoenolpyruvate-3")
     )
   } else {
     stop(paste("unrecognized reactant:", reactant))
   }
 
+  # Make sure we are speciating H3PO4 (in addition to the other reactants)
+  stopifnot(bases[[1]][1] == "H3PO4")
+
   # Set activity of H3PO4
   # Basic reaction: H3PO4 is the P_source
   if(P_source == "P") basis("H3PO4", loga_P_source)

Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd	2025-12-08 03:39:36 UTC (rev 942)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2025-12-08 07:05:24 UTC (rev 943)
@@ -15,7 +15,7 @@
 \newcommand{\Cp}{\ifelse{latex}{\eqn{C_P}}{\ifelse{html}{\out{<I>C<sub>P</sub></I>}}{Cp}}}
 \newcommand{\DG0}{\ifelse{latex}{\eqn{{\Delta}G^{\circ}}}{\ifelse{html}{\out{Δ<I>G</I>°}}{ΔG°}}}
 
-\section{Changes in CHNOSZ version 2.2.0-7 (2025-12-07)}{
+\section{Changes in CHNOSZ version 2.2.0-9 (2025-12-08)}{
 
     \itemize{
 
@@ -34,6 +34,9 @@
       \item Add \code{phosphorylate()} to calculate affinity of phosphorylation
       reactions with pH-dependent speciation.
 
+      \item Add \code{hyphen.in.pdf()} for replacing minus signs with
+      hyphens in text added to PDF plots.
+
     }
 
 }