CHNOSZ: Chemical Thermodynamics and Activity Diagrams

Functions and data sets to support chemical thermodynamic modeling in biochemistry and low-temperature geochemistry. The features include calculation of the standard molal thermodynamic properties and chemical affinities of reactions involving minerals and/or biomolecules; a database of thermodynamic properties of aqueous, crystalline and gaseous species; amino acid group additivity for the standard molal thermodynamic properties of neutral and ionized proteins; use of the revised Helgeson-Kirkham-Flowers equations of state for aqueous species; construction of equilibrium activity diagrams as a function of temperature, pressure, and chemical activities or fugacities of basis species.

AuthorJeffrey Dick
Date of publication2017-01-22 10:27:31
MaintainerJeffrey Dick <j3ffdick@gmail.com>
LicenseGPL (>= 2)
Version1.0.8-11
http://www.chnosz.net/
http://chnosz.r-forge.r-project.org/

View on R-Forge

Man pages

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

iprotein: Amino Acid Compositions 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.affinity: Functions to Work With Chemical Affinities

util.args: Functions for Processing Argument Lists

util.array: Functions to Work with Multidimensional Arrays

util.blast: Functions to Work with BLAST Output Files

util.character: Functions to Manipulate Character Objects

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.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

Files in this package

CHNOSZ/.Rinstignore
CHNOSZ/DESCRIPTION
CHNOSZ/NAMESPACE
CHNOSZ/R
CHNOSZ/R/EOSregress.R CHNOSZ/R/IAPWS95.R CHNOSZ/R/affinity.R CHNOSZ/R/anim.R CHNOSZ/R/basis.R CHNOSZ/R/buffer.R CHNOSZ/R/cgl.R CHNOSZ/R/diagram.R CHNOSZ/R/eqdata.R CHNOSZ/R/equilibrate.R CHNOSZ/R/examples.R CHNOSZ/R/findit.R CHNOSZ/R/hkf.R CHNOSZ/R/info.R CHNOSZ/R/ionize.aa.R CHNOSZ/R/iprotein.R CHNOSZ/R/makeup.R CHNOSZ/R/more.aa.R CHNOSZ/R/mosaic.R CHNOSZ/R/msgout.R CHNOSZ/R/nonideal.R CHNOSZ/R/objective.R CHNOSZ/R/protein.info.R CHNOSZ/R/read.expr.R CHNOSZ/R/revisit.R CHNOSZ/R/species.R CHNOSZ/R/subcrt.R CHNOSZ/R/swap.basis.R CHNOSZ/R/taxonomy.R CHNOSZ/R/transfer.R CHNOSZ/R/util.affinity.R CHNOSZ/R/util.args.R CHNOSZ/R/util.array.R CHNOSZ/R/util.blast.R CHNOSZ/R/util.character.R CHNOSZ/R/util.data.R CHNOSZ/R/util.expression.R CHNOSZ/R/util.fasta.R CHNOSZ/R/util.formula.R CHNOSZ/R/util.list.R CHNOSZ/R/util.matrix.R CHNOSZ/R/util.misc.R CHNOSZ/R/util.plot.R CHNOSZ/R/util.program.R CHNOSZ/R/util.seq.R CHNOSZ/R/util.units.R CHNOSZ/R/util.water.R CHNOSZ/R/water.R CHNOSZ/R/wjd.R CHNOSZ/R/zzz.R
CHNOSZ/build
CHNOSZ/build/vignette.rds
CHNOSZ/data
CHNOSZ/data/OBIGT.csv
CHNOSZ/data/buffer.csv
CHNOSZ/data/element.csv
CHNOSZ/data/groups.csv
CHNOSZ/data/opt.csv
CHNOSZ/data/protein.csv
CHNOSZ/data/refs.csv
CHNOSZ/data/thermo.R
CHNOSZ/demo
CHNOSZ/demo/00Index
CHNOSZ/demo/NaCl.R
CHNOSZ/demo/ORP.R
CHNOSZ/demo/buffer.R
CHNOSZ/demo/bugstab.R
CHNOSZ/demo/copper.R
CHNOSZ/demo/dehydration.R
CHNOSZ/demo/density.R
CHNOSZ/demo/findit.R
CHNOSZ/demo/ionize.R
CHNOSZ/demo/mosaic.R
CHNOSZ/demo/nucleobase.R
CHNOSZ/demo/revisit.R
CHNOSZ/demo/solubility.R
CHNOSZ/demo/sources.R
CHNOSZ/demo/wjd.R
CHNOSZ/demo/yeastgfp.R
CHNOSZ/inst
CHNOSZ/inst/CHECKLIST
CHNOSZ/inst/CITATION
CHNOSZ/inst/NEWS
CHNOSZ/inst/ONEWS
CHNOSZ/inst/doc
CHNOSZ/inst/doc/EOSregress.Rmd
CHNOSZ/inst/doc/EOSregress.html
CHNOSZ/inst/doc/anintro.R
CHNOSZ/inst/doc/anintro.Rnw
CHNOSZ/inst/doc/anintro.pdf
CHNOSZ/inst/doc/equilibrium.Rnw
CHNOSZ/inst/doc/equilibrium.pdf
CHNOSZ/inst/doc/hotspring.Rnw
CHNOSZ/inst/doc/hotspring.pdf
CHNOSZ/inst/doc/wjd.R
CHNOSZ/inst/doc/wjd.Rnw
CHNOSZ/inst/doc/wjd.pdf
CHNOSZ/inst/extdata
CHNOSZ/inst/extdata/abundance
CHNOSZ/inst/extdata/abundance/AA03.csv
CHNOSZ/inst/extdata/abundance/ISR+08.csv.xz
CHNOSZ/inst/extdata/abundance/microbes.csv
CHNOSZ/inst/extdata/abundance/stress.csv
CHNOSZ/inst/extdata/abundance/yeastgfp.csv.xz
CHNOSZ/inst/extdata/bison
CHNOSZ/inst/extdata/bison/bisonN_vs_refseq57.blastp.xz
CHNOSZ/inst/extdata/bison/bisonP_vs_refseq57.blastp.xz
CHNOSZ/inst/extdata/bison/bisonQ_vs_refseq57.blastp.xz
CHNOSZ/inst/extdata/bison/bisonR_vs_refseq57.blastp.xz
CHNOSZ/inst/extdata/bison/bisonS_vs_refseq57.blastp.xz
CHNOSZ/inst/extdata/bison/gi.taxid.txt.xz
CHNOSZ/inst/extdata/cpetc
CHNOSZ/inst/extdata/cpetc/BKM60_Fig7.csv
CHNOSZ/inst/extdata/cpetc/Cp.CH4.HW97.csv
CHNOSZ/inst/extdata/cpetc/PM90.csv
CHNOSZ/inst/extdata/cpetc/RH95.csv
CHNOSZ/inst/extdata/cpetc/RT71.csv
CHNOSZ/inst/extdata/cpetc/SC10_Rainbow.csv
CHNOSZ/inst/extdata/cpetc/SOJSH.csv
CHNOSZ/inst/extdata/cpetc/V.CH4.HWM96.csv
CHNOSZ/inst/extdata/fasta
CHNOSZ/inst/extdata/fasta/EF-Tu.aln
CHNOSZ/inst/extdata/fasta/HTCC1062.faa.xz
CHNOSZ/inst/extdata/js
CHNOSZ/inst/extdata/js/sorttable.js
CHNOSZ/inst/extdata/protein
CHNOSZ/inst/extdata/protein/DS11.csv
CHNOSZ/inst/extdata/protein/DS13.csv
CHNOSZ/inst/extdata/protein/Eco.csv.xz
CHNOSZ/inst/extdata/protein/Sce.csv.xz
CHNOSZ/inst/extdata/protein/microbial.aa.csv
CHNOSZ/inst/extdata/refseq
CHNOSZ/inst/extdata/refseq/README.txt
CHNOSZ/inst/extdata/refseq/gencat.sh
CHNOSZ/inst/extdata/refseq/mkfaa.sh
CHNOSZ/inst/extdata/refseq/protein.refseq.R
CHNOSZ/inst/extdata/refseq/protein_refseq.csv.xz
CHNOSZ/inst/extdata/refseq/taxid.names.R
CHNOSZ/inst/extdata/refseq/taxid_names.csv.xz
CHNOSZ/inst/extdata/refseq/trim_refseq.R
CHNOSZ/inst/extdata/taxonomy
CHNOSZ/inst/extdata/taxonomy/names.dmp
CHNOSZ/inst/extdata/taxonomy/nodes.dmp
CHNOSZ/inst/extdata/thermo
CHNOSZ/inst/extdata/thermo/DLEN67.csv
CHNOSZ/inst/extdata/thermo/OBIGT-2.csv
CHNOSZ/inst/extdata/thermo/RH98_Table15.csv
CHNOSZ/inst/extdata/thermo/groups_big.csv
CHNOSZ/inst/extdata/thermo/groups_small.csv
CHNOSZ/inst/extdata/thermo/obigt_check.csv
CHNOSZ/man
CHNOSZ/man/CHNOSZ-package.Rd CHNOSZ/man/EOSregress.Rd CHNOSZ/man/IAPWS95.Rd CHNOSZ/man/affinity.Rd CHNOSZ/man/anim.Rd CHNOSZ/man/basis.Rd CHNOSZ/man/buffer.Rd CHNOSZ/man/data.Rd CHNOSZ/man/diagram.Rd CHNOSZ/man/eos.Rd CHNOSZ/man/eqdata.Rd CHNOSZ/man/equilibrate.Rd CHNOSZ/man/examples.Rd CHNOSZ/man/extdata.Rd CHNOSZ/man/findit.Rd CHNOSZ/man/info.Rd CHNOSZ/man/ionize.aa.Rd CHNOSZ/man/iprotein.Rd CHNOSZ/man/makeup.Rd CHNOSZ/man/more.aa.Rd CHNOSZ/man/mosaic.Rd CHNOSZ/man/nonideal.Rd CHNOSZ/man/objective.Rd CHNOSZ/man/protein.Rd CHNOSZ/man/protein.info.Rd CHNOSZ/man/read.expr.Rd CHNOSZ/man/revisit.Rd CHNOSZ/man/sideeffects.Rd CHNOSZ/man/species.Rd CHNOSZ/man/subcrt.Rd CHNOSZ/man/swap.basis.Rd CHNOSZ/man/taxonomy.Rd CHNOSZ/man/transfer.Rd CHNOSZ/man/util.affinity.Rd CHNOSZ/man/util.args.Rd CHNOSZ/man/util.array.Rd CHNOSZ/man/util.blast.Rd CHNOSZ/man/util.character.Rd CHNOSZ/man/util.data.Rd CHNOSZ/man/util.expression.Rd CHNOSZ/man/util.fasta.Rd CHNOSZ/man/util.formula.Rd CHNOSZ/man/util.list.Rd CHNOSZ/man/util.matrix.Rd CHNOSZ/man/util.misc.Rd CHNOSZ/man/util.plot.Rd CHNOSZ/man/util.program.Rd CHNOSZ/man/util.seq.Rd CHNOSZ/man/util.units.Rd CHNOSZ/man/util.water.Rd CHNOSZ/man/water.Rd CHNOSZ/man/wjd.Rd
CHNOSZ/src
CHNOSZ/src/H2O92D.f
CHNOSZ/tests
CHNOSZ/tests/testthat
CHNOSZ/tests/testthat.R
CHNOSZ/tests/testthat/test-EOSregress.R
CHNOSZ/tests/testthat/test-IAPWS95.R
CHNOSZ/tests/testthat/test-affinity.R
CHNOSZ/tests/testthat/test-basis.R
CHNOSZ/tests/testthat/test-diagram.R
CHNOSZ/tests/testthat/test-eos.R
CHNOSZ/tests/testthat/test-equilibrate.R
CHNOSZ/tests/testthat/test-findit.R
CHNOSZ/tests/testthat/test-info.R
CHNOSZ/tests/testthat/test-ionize.aa.R
CHNOSZ/tests/testthat/test-ionize.aa_pK.R
CHNOSZ/tests/testthat/test-iprotein.R
CHNOSZ/tests/testthat/test-makeup.R
CHNOSZ/tests/testthat/test-more.aa.R
CHNOSZ/tests/testthat/test-mosaic.R
CHNOSZ/tests/testthat/test-nonideal.R
CHNOSZ/tests/testthat/test-protein.info.R
CHNOSZ/tests/testthat/test-revisit.R
CHNOSZ/tests/testthat/test-species.R
CHNOSZ/tests/testthat/test-subcrt.R
CHNOSZ/tests/testthat/test-swap.basis.R
CHNOSZ/tests/testthat/test-thermo.R
CHNOSZ/tests/testthat/test-util.R
CHNOSZ/tests/testthat/test-util.affinity.R
CHNOSZ/tests/testthat/test-util.data.R
CHNOSZ/tests/testthat/test-util.list.R
CHNOSZ/tests/testthat/test-util.program.R
CHNOSZ/tests/testthat/test-util.seq.R
CHNOSZ/tests/testthat/test-water.R
CHNOSZ/tests/testthat/test-wjd.R
CHNOSZ/tests/testthat/test-yeastgfp.R
CHNOSZ/vignettes
CHNOSZ/vignettes/EOSregress.Rmd
CHNOSZ/vignettes/EOSregress.bib
CHNOSZ/vignettes/anintro.Rnw
CHNOSZ/vignettes/anintro.lyx
CHNOSZ/vignettes/equilibrium.Rnw
CHNOSZ/vignettes/equilibrium.lyx
CHNOSZ/vignettes/flowchart.dia
CHNOSZ/vignettes/flowchart.pdf
CHNOSZ/vignettes/hotspring.Rnw
CHNOSZ/vignettes/hotspring.lyx
CHNOSZ/vignettes/vig.bib
CHNOSZ/vignettes/wjd.Rnw
CHNOSZ/vignettes/wjd.lyx

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