CHNOSZ: Chemical Thermodynamics and Activity Diagrams
Version 1.1.0

An integrated set of tools for thermodynamic calculations in compositional biology and geochemistry. Thermodynamic properties are taken from a database for minerals and inorganic and organic aqueous species including biomolecules, or from amino acid group additivity for proteins. High-temperature properties are calculated using the revised Helgeson-Kirkham-Flowers equations of state for aqueous species. Functions are provided to define a system using basis species, automatically balance reactions, calculate the chemical affinities of reactions for selected species, and plot the results on potential diagrams or equilibrium activity diagrams. Experimental features are available to calculate activity coefficients for aqueous species or for multidimensional optimization of thermodynamic variables using an objective function.

Browse man pages Browse package API and functions Browse package files

AuthorJeffrey Dick
Date of publication2017-05-04 17:48:31 UTC
MaintainerJeffrey Dick <j3ffdick@gmail.com>
LicenseGPL (>= 2)
Version1.1.0
URL http://www.chnosz.net/ http://chnosz.r-forge.r-project.org/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("CHNOSZ")

Man pages

add.protein: Amino Acid Compositions of Proteins
affinity: Chemical Affinities of Formation Reactions
anim: Functions to Make Animations
basis: Define Basis Species
buffer: Calculating Buffered Chemical Activities
CHNOSZ-package: Chemical Thermodynamics and Activity Diagrams
data: Thermodynamic Database and System Definition
diagram: Chemical Activity Diagrams
eos: Equations of State
EOSregress: Regress Equations-of-State Parameters for Aqueous Species
eqdata: Read data from an EQ6 output file
equilibrate: Equilibrium Chemical Activities of Species
examples: Run Examples from the Documentation
extdata: Extra Data
findit: Gridded Search to Optimize Objective Functions
IAPWS95: Properties of Water from IAPWS-95
info: Search the Thermodynamic Database
ionize.aa: Properties of Ionization of Proteins
makeup: Parse Chemical Formulas
more.aa: Proteins from Model Organisms
mosaic: Chemical Affinities with Changing Basis Species
nonideal: Activity coefficients of aqueous species
objective: Objective Functions
palply: Conditional Parallel Processing
protein: Examples of Calculations for Proteins
protein.info: Summaries of Thermodynamic Properties of Proteins
read.expr: Experimental Data for Protein Abundances and Localizations
revisit: Plots and Optima of Objective Functions
species: Species of Interest
subcrt: Properties of Species and Reactions
swap.basis: Swap Basis Species
taxonomy: Extract Data from NCBI Taxonomy Files
transfer: Mass Transfer Calculations
util.array: Functions to Work with Multidimensional Arrays
util.blast: Functions to Work with BLAST Output Files
util.data: Functions to Work with the Thermodynamic Database
util.expression: Functions to Express Chemical Formulas and Properties
util.fasta: Functions for Reading FASTA Files and Downloading from...
util.formula: Functions to Work with Chemical Formulas
util.list: Functions to Work with Lists
util.matrix: Functions for Various Matrix Operations
util.misc: Functions for Miscellaneous Tasks
util.plot: Functions to Create and Modify Plots
util.protein: Functions for Proteins (Other Calculations)
util.seq: Functions to Work with Sequence Data
util.units: Functions to Convert Units
util.water: Functions for Properties of Water and Steam
water: Properties of Water
wjd: Gibbs Energy Minimization by Steepest Descent

Functions

A.ionization Source code
CHNOSZ-package Man page
CV Man page
CVRMSD Man page
Cp_s_var Man page Source code
DDGmix Man page
DGinf Man page
DGmix Man page
DGtr Man page
E.units Man page Source code
EOScalc Man page Source code
EOScoeffs Man page Source code
EOSlab Man page Source code
EOSplot Man page Source code
EOSregress Man page Source code
EOSvar Man page Source code
GHS Man page Source code
GHS_Tr Man page Source code
IAPWS95 Man page Source code
IAPWS95.idealgas Source code
IAPWS95.residual Source code
MP90.cp Man page Source code
OBIGT Man page
P.units Man page Source code
RH2obigt Man page Source code
RMSD Man page
SD Man page
T.units Man page
TP.args Source code
Ttr Man page Source code
V_s_var Man page Source code
WP02.auxiliary Man page Source code
ZC Man page Source code
ZC.col Man page Source code
aasum Man page Source code
add.obigt Man page Source code
add.protein Man page Source code
affinity Man page Source code
allparents Man page Source code
aminoacids Man page Source code
anim Man page
anim.TCA Man page Source code
anim.carboxylase Man page Source code
apc Man page Source code
as.chemical.formula Man page Source code
as.integer.nowarn Source code
as.numeric.nowarn Source code
axis.label Man page Source code
balance Source code
basis Man page Source code
basis.elements Man page Source code
basis.logact Man page Source code
buffer Man page Source code
buffers Man page
c2s Source code
caller.name Source code
can.be.numeric Source code
cgl Man page Source code
check.obigt Man page Source code
checkEOS Man page Source code
checkGHS Man page Source code
convert Man page Source code
count.aa Man page Source code
count.charge Source code
count.elements Man page Source code
count.formulas Source code
dPdTtr Man page Source code
def2gi Man page Source code
demos Man page Source code
describe.basis Man page Source code
describe.property Man page Source code
describe.reaction Man page Source code
diagram Man page Source code
dimSums Man page Source code
draw.transfer Man page Source code
element Man page
element.mu Man page Source code
element.potentials Man page Source code
energy Source code
energy.args Source code
entropy Man page Source code
envert Source code
eos.args Source code
eqdata Man page Source code
equil.boltzmann Man page Source code
equil.potentials Man page Source code
equil.reaction Man page Source code
equilibrate Man page Source code
examples Man page Source code
expr.property Man page Source code
expr.species Man page Source code
expr.units Man page Source code
extdata Man page
extremes Source code
feldspar Man page Source code
find.tp Man page Source code
findit Man page Source code
get.formula Source code
get.objfun Source code
getnames Man page Source code
getnodes Man page Source code
getrank Man page Source code
gfun Source code
group.formulas Man page Source code
groups Man page
guess Man page Source code
hkf Man page Source code
i2A Man page Source code
ibasis Man page Source code
id.blast Man page Source code
info Man page Source code
info.approx Source code
info.character Source code
info.numeric Source code
info.text Source code
invertible.combs Man page Source code
ionize.aa Man page Source code
is.near.equil Man page Source code
label.figure Man page Source code
label.plot Man page Source code
list2array Man page Source code
logact Man page
lsub Source code
lsum Source code
makeup Man page Source code
mass Man page Source code
mod.basis Source code
mod.buffer Man page Source code
mod.obigt Man page Source code
more.aa Man page Source code
mosaic Man page Source code
mtitle Man page Source code
nonideal Man page Source code
nucleic.complement Man page Source code
nucleic.formula Man page Source code
obigt2eos Source code
objective Man page
onAttach Source code
opt Man page
optimal.index Source code
outvert Source code
palply Man page Source code
parent Man page Source code
pearson Man page
pinfo Man page Source code
plot_findit Man page Source code
pprod Source code
preset.basis Source code
preset.logact Source code
protein Man page
protein.basis Man page Source code
protein.equil Man page Source code
protein.formula Man page Source code
protein.info Man page
protein.length Man page Source code
protein.obigt Man page Source code
put.basis Source code
qqr Man page
ratlab Man page Source code
read.blast Man page Source code
read.expr Man page Source code
read.fasta Man page Source code
refs Man page
revisit Man page Source code
rho.IAPWS95 Man page Source code
richness Man page
run.guess Man page Source code
run.wjd Man page Source code
s2c Source code
sciname Man page Source code
seq2aa Man page Source code
shannon Man page
slice Man page Source code
slice.affinity Man page Source code
spearman Man page
species Man page Source code
species.basis Source code
state.args Source code
strip Man page Source code
subcrt Man page Source code
swap.basis Man page Source code
syslab Man page Source code
taxonomy Man page
thermo Man page
thermo.axis Source code
thermo.plot.new Man page Source code
thermo.refs Man page Source code
today Man page Source code
transfer Man page Source code
uniprot.aa Man page Source code
unitize Man page Source code
units Source code
usrfig Man page Source code
util.array Man page
util.blast Man page
util.data Man page
util.expression Man page
util.fasta Man page
util.formula Man page
util.list Man page
util.matrix Man page
util.misc Man page
util.plot Man page
util.seq Man page
util.units Man page
util.water Man page
water Man page Source code
water.AW90 Man page Source code
water.IAPWS95 Man page Source code
water.SUPCRT92 Man page Source code
water.lines Man page Source code
water.props Man page Source code
which.balance Source code
which.pmax Man page Source code
wjd Man page Source code
write.blast Man page Source code
yeastgfp Man page Source code

Files

inst
inst/CITATION
inst/CHECKLIST
inst/NEWS
inst/extdata
inst/extdata/OBIGT
inst/extdata/OBIGT/organic_aq.csv.xz
inst/extdata/OBIGT/inorganic_cr.csv.xz
inst/extdata/OBIGT/organic_liq.csv.xz
inst/extdata/OBIGT/H2O_aq.csv.xz
inst/extdata/OBIGT/inorganic_aq.csv.xz
inst/extdata/OBIGT/organic_cr.csv.xz
inst/extdata/OBIGT/organic_gas.csv.xz
inst/extdata/OBIGT/CHNOSZ_aq.csv.xz
inst/extdata/OBIGT/inorganic_gas.csv.xz
inst/extdata/OBIGT/biotic_aq.csv.xz
inst/extdata/thermo
inst/extdata/thermo/obigt_check.csv
inst/extdata/thermo/BZA10.csv
inst/extdata/thermo/DLEN67.csv
inst/extdata/thermo/RH98_Table15.csv
inst/extdata/thermo/Ste01.csv
inst/extdata/taxonomy
inst/extdata/taxonomy/nodes.dmp
inst/extdata/taxonomy/names.dmp
inst/extdata/protein
inst/extdata/protein/Eco.csv.xz
inst/extdata/protein/DS11.csv
inst/extdata/protein/microbial.aa.csv
inst/extdata/protein/DS13.csv
inst/extdata/protein/Sce.csv.xz
inst/extdata/refseq
inst/extdata/refseq/protein.refseq.R
inst/extdata/refseq/gencat.sh
inst/extdata/refseq/taxid.names.R
inst/extdata/refseq/taxid_names.csv.xz
inst/extdata/refseq/protein_refseq.csv.xz
inst/extdata/refseq/README.txt
inst/extdata/refseq/mkfaa.sh
inst/extdata/refseq/trim_refseq.R
inst/extdata/fasta
inst/extdata/fasta/rubisco.fasta
inst/extdata/fasta/EF-Tu.aln
inst/extdata/bison
inst/extdata/bison/gi.taxid.txt.xz
inst/extdata/bison/bisonN_vs_refseq57.blastp.xz
inst/extdata/bison/bisonQ_vs_refseq57.blastp.xz
inst/extdata/bison/bisonS_vs_refseq57.blastp.xz
inst/extdata/bison/bisonR_vs_refseq57.blastp.xz
inst/extdata/bison/bisonP_vs_refseq57.blastp.xz
inst/extdata/supcrt
inst/extdata/supcrt/newnames.csv
inst/extdata/supcrt/read.supcrt.R
inst/extdata/supcrt/compare.R
inst/extdata/cpetc
inst/extdata/cpetc/SS98_Fig5a.csv
inst/extdata/cpetc/V.CH4.HWM96.csv
inst/extdata/cpetc/rubisco.csv
inst/extdata/cpetc/RH95.csv
inst/extdata/cpetc/RT71.csv
inst/extdata/cpetc/SS98_Fig5b.csv
inst/extdata/cpetc/Cp.CH4.HW97.csv
inst/extdata/cpetc/SOJSH.csv
inst/extdata/cpetc/SC10_Rainbow.csv
inst/extdata/cpetc/PM90.csv
inst/extdata/abundance
inst/extdata/abundance/TBD+05.csv
inst/extdata/abundance/microbes.csv
inst/extdata/abundance/ISR+08.csv.xz
inst/extdata/abundance/yeastgfp.csv.xz
inst/doc
inst/doc/hotspring.Rnw
inst/doc/wjd.pdf
inst/doc/eos-regress.R
inst/doc/hotspring.pdf
inst/doc/wjd.R
inst/doc/obigt.Rmd
inst/doc/anintro.html
inst/doc/obigt.html
inst/doc/equilibrium.Rnw
inst/doc/equilibrium.R
inst/doc/anintro.Rmd
inst/doc/wjd.Rnw
inst/doc/obigt.R
inst/doc/eos-regress.Rmd
inst/doc/equilibrium.pdf
inst/doc/anintro.R
inst/doc/eos-regress.html
inst/doc/hotspring.R
inst/ONEWS
tests
tests/testthat.R
tests/testthat
tests/testthat/test-eos.R
tests/testthat/test-yeastgfp.R
tests/testthat/test-util.list.R
tests/testthat/test-IAPWS95.R
tests/testthat/test-EOSregress.R
tests/testthat/test-mosaic.R
tests/testthat/test-protein.info.R
tests/testthat/test-ionize.aa_pK.R
tests/testthat/test-ionize.aa.R
tests/testthat/test-equilibrate.R
tests/testthat/test-diagram.R
tests/testthat/test-util.affinity.R
tests/testthat/test-affinity.R
tests/testthat/test-add.protein.R
tests/testthat/test-info.R
tests/testthat/test-revisit.R
tests/testthat/test-water.R
tests/testthat/test-wjd.R
tests/testthat/test-basis.R
tests/testthat/test-util.program.R
tests/testthat/test-findit.R
tests/testthat/test-util.seq.R
tests/testthat/test-thermo.R
tests/testthat/test-subcrt.R
tests/testthat/test-makeup.R
tests/testthat/test-more.aa.R
tests/testthat/test-util.data.R
tests/testthat/test-nonideal.R
tests/testthat/test-swap.basis.R
tests/testthat/test-util.R
tests/testthat/test-species.R
src
src/H2O92D.f
src/init.c
NAMESPACE
demo
demo/buffer.R
demo/revisit.R
demo/protbuff.R
demo/solubility.R
demo/copper.R
demo/NaCl.R
demo/dehydration.R
demo/wjd.R
demo/mosaic.R
demo/activity_ratios.R
demo/findit.R
demo/Shh.R
demo/density.R
demo/00Index
demo/yeastgfp.R
demo/ORP.R
demo/protein.equil.R
demo/sources.R
demo/ionize.R
demo/bugstab.R
demo/affinity.R
data
data/opt.csv
data/element.csv
data/groups.csv
data/refs.csv
data/thermo.R
data/buffer.csv
data/protein.csv
R
R/buffer.R
R/util.water.R
R/info.R
R/revisit.R
R/util.array.R
R/util.units.R
R/util.list.R
R/subcrt.R
R/EOSregress.R
R/water.R
R/eqdata.R
R/more.aa.R
R/util.fasta.R
R/makeup.R
R/IAPWS95.R
R/objective.R
R/equilibrate.R
R/util.protein.R
R/wjd.R
R/cgl.R
R/mosaic.R
R/anim.R
R/util.matrix.R
R/ionize.aa.R
R/util.formula.R
R/util.character.R
R/util.affinity.R
R/taxonomy.R
R/util.args.R
R/findit.R
R/diagram.R
R/util.misc.R
R/add.protein.R
R/hkf.R
R/swap.basis.R
R/util.data.R
R/util.plot.R
R/transfer.R
R/protein.info.R
R/examples.R
R/nonideal.R
R/palply.R
R/util.expression.R
R/read.expr.R
R/util.blast.R
R/zzz.R
R/affinity.R
R/basis.R
R/util.seq.R
R/species.R
vignettes
vignettes/hotspring.Rnw
vignettes/obigt.bib
vignettes/rubisco.svg
vignettes/dayhoff.pdf
vignettes/vig.bib
vignettes/vig.css
vignettes/equilibrium.lyx
vignettes/obigt.Rmd
vignettes/CHNOSZ.dia
vignettes/CHNOSZ.png
vignettes/wjd.lyx
vignettes/equilibrium.Rnw
vignettes/anintro.Rmd
vignettes/wjd.Rnw
vignettes/eos-regress.Rmd
vignettes/hotspring.lyx
vignettes/obigt.css
vignettes/elementa.csl
MD5
build
build/vignette.rds
DESCRIPTION
man
man/eqdata.Rd
man/eos.Rd
man/util.seq.Rd
man/affinity.Rd
man/water.Rd
man/more.aa.Rd
man/util.fasta.Rd
man/basis.Rd
man/util.formula.Rd
man/ionize.aa.Rd
man/subcrt.Rd
man/util.list.Rd
man/findit.Rd
man/wjd.Rd
man/util.plot.Rd
man/util.array.Rd
man/IAPWS95.Rd
man/util.misc.Rd
man/buffer.Rd
man/transfer.Rd
man/taxonomy.Rd
man/EOSregress.Rd
man/objective.Rd
man/protein.Rd
man/util.units.Rd
man/anim.Rd
man/diagram.Rd
man/util.blast.Rd
man/util.matrix.Rd
man/revisit.Rd
man/protein.info.Rd
man/nonideal.Rd
man/data.Rd
man/makeup.Rd
man/palply.Rd
man/util.water.Rd
man/swap.basis.Rd
man/CHNOSZ-package.Rd
man/species.Rd
man/info.Rd
man/mosaic.Rd
man/examples.Rd
man/macros
man/macros/macros.Rd
man/equilibrate.Rd
man/util.expression.Rd
man/util.protein.Rd
man/extdata.Rd
man/add.protein.Rd
man/read.expr.Rd
man/util.data.Rd
.Rinstignore
CHNOSZ documentation built on May 19, 2017, 11:17 a.m.