CHNOSZ: Chemical Thermodynamics and Activity Diagrams

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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.

Author
Jeffrey Dick
Date of publication
2016-11-29 02:50:22
Maintainer
Jeffrey Dick <j3ffdick@gmail.com>
License
GPL (>= 2)
Version
1.0.8-4
URLs

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/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/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/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-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