CHNOSZ: Chemical Thermodynamics and Activity Diagrams

Tools for thermodynamic calculations in compositional biology and low-temperature geochemistry. Thermodynamic properties are taken from a database including aqueous species, minerals, and 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 functions calculate activity coefficients for aqueous species or optimize multiple thermodynamic variables using an objective function for chemical activities.

AuthorJeffrey Dick
Date of publication2017-03-20 12:46:58
MaintainerJeffrey Dick <j3ffdick@gmail.com>
LicenseGPL (>= 2)
Version1.0.8-75
http://www.chnosz.net/
http://chnosz.r-forge.r-project.org/

View on R-Forge

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: Equilibrium 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

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

sideeffects: Side effects of functions in CHNOSZ

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.program: Functions for Various Programming Tasks

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

aasum Man page
add.obigt Man page
add.protein Man page
affinity Man page
allparents Man page
aminoacids Man page
anim Man page
anim.carboxylase Man page
anim.TCA Man page
apc Man page
as.chemical.formula Man page
axis.label Man page
basis Man page
basis.elements Man page
basis.logact Man page
buffer Man page
buffers Man page
cgl Man page
checkEOS Man page
checkGHS Man page
check.obigt Man page
CHNOSZ-package Man page
convert Man page
count.aa Man page
count.elements Man page
Cp_s_var Man page
CV Man page
CVRMSD Man page
DDGmix Man page
def2gi Man page
demos Man page
describe.basis Man page
describe.property Man page
describe.reaction Man page
DGinf Man page
DGmix Man page
DGtr Man page
diagram Man page
dimSums Man page
dPdTtr Man page
draw.transfer Man page
element Man page
element.mu Man page
element.potentials Man page
entropy Man page
EOScalc Man page
EOScoeffs Man page
EOSlab Man page
EOSplot Man page
EOSregress Man page
EOSvar Man page
eqdata Man page
equil.boltzmann Man page
equilibrate Man page
equil.potentials Man page
equil.reaction Man page
E.units Man page
examples Man page
expr.property Man page
expr.species Man page
expr.units Man page
extdata Man page
feldspar Man page
findit Man page
find.tp Man page
getnames Man page
getnodes Man page
getrank Man page
GHS Man page
GHS_Tr Man page
group.formulas Man page
groups Man page
guess Man page
hkf Man page
i2A Man page
IAPWS95 Man page
ibasis Man page
id.blast Man page
info Man page
invertible.combs Man page
ionize.aa Man page
is.near.equil Man page
label.figure Man page
label.plot Man page
list2array Man page
logact Man page
makeup Man page
mass Man page
mod.buffer Man page
mod.obigt Man page
more.aa Man page
mosaic Man page
MP90.cp Man page
mtitle Man page
nonideal Man page
nucleic.complement Man page
nucleic.formula Man page
OBIGT Man page
objective Man page
opt Man page
palply Man page
parent Man page
pearson Man page
pinfo Man page
plot_findit Man page
protein Man page
protein.basis Man page
protein.equil Man page
protein.formula Man page
protein.info Man page
protein.length Man page
protein.obigt Man page
P.units Man page
qqr Man page
ratlab Man page
read.blast Man page
read.expr Man page
read.fasta Man page
refs Man page
revisit Man page
RH2obigt Man page
rho.IAPWS95 Man page
richness Man page
RMSD Man page
run.guess Man page
run.wjd Man page
sciname Man page
SD Man page
seq2aa Man page
shannon Man page
sideeffects Man page
slice Man page
slice.affinity Man page
spearman Man page
species Man page
strip Man page
subcrt Man page
swap.basis Man page
syslab Man page
taxonomy Man page
thermo Man page
thermo.plot.new Man page
thermo.refs Man page
today Man page
transfer Man page
Ttr Man page
T.units Man page
uniprot.aa Man page
unitize Man page
usrfig Man page
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.program Man page
util.seq Man page
util.units Man page
util.water Man page
V_s_var Man page
water Man page
water.AW90 Man page
water.IAPWS95 Man page
water.lines Man page
water.props Man page
water.SUPCRT92 Man page
which.pmax Man page
wjd Man page
WP02.auxiliary Man page
write.blast Man page
yeastgfp Man page
ZC Man page
ZC.col Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.