[CHNOSZ-commits] r752 - in pkg/CHNOSZ: . R man

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

Author: jedick
Date: 2022-10-18 11:49:47 +0200 (Tue, 18 Oct 2022)
New Revision: 752

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/util.character.R
   pkg/CHNOSZ/man/protein.info.Rd
   pkg/CHNOSZ/man/util.formula.Rd
Log:
Minor formatting changes


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2022-10-16 00:14:48 UTC (rev 751)
+++ pkg/CHNOSZ/DESCRIPTION	2022-10-18 09:49:47 UTC (rev 752)
@@ -1,6 +1,6 @@
-Date: 2022-10-15
+Date: 2022-10-16
 Package: CHNOSZ
-Version: 1.9.9-43
+Version: 1.9.9-44
 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/util.character.R
===================================================================
--- pkg/CHNOSZ/R/util.character.R	2022-10-16 00:14:48 UTC (rev 751)
+++ pkg/CHNOSZ/R/util.character.R	2022-10-18 09:49:47 UTC (rev 752)
@@ -35,7 +35,7 @@
           xtail <- paste("",xtail,sep=sep)
         } 
         # a match at the end ... grep here causes problems
-        # when sep contains control characters (e.g. protein.refseq)
+        # when sep contains control characters
         #if(length(grep(paste(sep,"$",sep=""),x[[i]]) > 0)) xtail <- c(xtail,sep)
         # use substr instead
         nx <- nchar(x[[i]])

Modified: pkg/CHNOSZ/man/protein.info.Rd
===================================================================
--- pkg/CHNOSZ/man/protein.info.Rd	2022-10-16 00:14:48 UTC (rev 751)
+++ pkg/CHNOSZ/man/protein.info.Rd	2022-10-18 09:49:47 UTC (rev 752)
@@ -69,32 +69,32 @@
 }
 
 \examples{\dontshow{reset()}
-# search by name in thermo()$protein
-# these are the same: ip1 == ip2
+# Search by name in thermo()$protein
+# These are the same: ip1 == ip2
 ip1 <- pinfo("LYSC_CHICK")
 ip2 <- pinfo("LYSC", "CHICK")
-# two organisms with the same protein name
+# Two organisms with the same protein name
 ip3 <- pinfo("MYG", c("HORSE", "PHYCA"))
-# their amino acid compositions
+# Their amino acid compositions
 pinfo(ip3)
-# their thermodynamic properties by group additivity
+# Their thermodynamic properties by group additivity
 protein.OBIGT(ip3)
 
-# an unknown protein name gives NA
+# An unknown protein name gives NA
 ip4 <- pinfo("MYGPHYCA")
 
-## example for chicken lysozyme C
-# index in thermo()$protein
+## Example for chicken lysozyme C
+# Index in thermo()$protein
 ip <- pinfo("LYSC_CHICK")
-# amino acid composition
+# Amino acid composition
 pinfo(ip)
-# length and chemical formula
+# Protein length and chemical formula
 protein.length(ip)
 protein.formula(ip)
-# group additivity for thermodynamic properties and HKF equation-of-state
+# Group additivity for thermodynamic properties and HKF equation-of-state
 # parameters of non-ionized protein
 protein.OBIGT(ip)
-# calculation of standard thermodynamic properties
+# Calculation of standard thermodynamic properties
 # (subcrt uses the species name, not ip)
 subcrt("LYSC_CHICK")
 # NOTE: subcrt() only shows the properties of the non-ionized
@@ -101,7 +101,7 @@
 # protein, but affinity() uses the properties of the ionized
 # protein if the basis species have H+
 
-## these are all the same
+## These are all the same
 protein.formula("P53_PIG")
 protein.formula(pinfo("P53_PIG"))
 protein.formula(pinfo(pinfo("P53_PIG")))

Modified: pkg/CHNOSZ/man/util.formula.Rd
===================================================================
--- pkg/CHNOSZ/man/util.formula.Rd	2022-10-16 00:14:48 UTC (rev 751)
+++ pkg/CHNOSZ/man/util.formula.Rd	2022-10-18 09:49:47 UTC (rev 752)
@@ -72,7 +72,6 @@
 
 \seealso{
 \code{\link{makeup}}, used by \code{mass} and \code{entropy}, and \code{ZC} and \code{i2A} for counting the elements in a formula (the latter two make use of the \code{count.zero} argument).
-\code{\link{protein.formula}} has an example of computing ZC for proteins compiled from the RefSeq database.
 }
 
 \examples{\dontshow{reset()}