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CHNOSZ (version 1.0.5)

Chemical Thermodynamics and Activity Diagrams

Description

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.

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Version

Install

install.packages('CHNOSZ')

Monthly Downloads

1,117

Version

1.0.5

License

GPL (>= 2)

Maintainer

Jeffrey Dick

Last Published

May 19th, 2015

Functions in CHNOSZ (1.0.5)

IAPWS95

Properties of Water from IAPWS-95
CHNOSZ-package

Chemical Thermodynamics and Activity Diagrams
basis

Define Basis Species
anim.TCA

Functions to Make Animations
eos

Equations of State
sideeffects

Side effects of functions in CHNOSZ
makeup

Parse Chemical Formulas
objective

Objective Functions
util.matrix

Functions for Various Matrix Operations
EOSregress

Regress Equations-of-State Parameters for Aqueous Species
read.expr

Experimental Data for Protein Abundances and Localizations
examples

Run Examples from the Documentation
util.fasta

Functions for Reading FASTA Files and Downloading from UniProt
util.blast

Functions to Work with BLAST Output Files
more.aa

Proteins from Model Organisms
util.expression

Functions to Express Chemical Formulas and Properties
species

Species of Interest
mosaic

Chemical Affinities with Changing Basis Species
util.units

Functions to Convert Units
util.args

Functions for Processing Argument Lists
ionize.aa

Properties of Ionization of Proteins
info

Search the Thermodynamic Database
util.data

Functions to Work with the Thermodynamic Database
eqdata

Read data from an EQ6 output file
equilibrate

Equilibrium Chemical Activities of Species
util.program

Functions for Various Programming Tasks
util.array

Functions to Work with Multidimensional Arrays
extdata

Extra Data
transfer

Mass Transfer Calculations
util.list

Functions to Work with Lists
util.formula

Functions to Work with Chemical Formulas
affinity

Chemical Affinities of Formation Reactions
util.affinity

Functions to Work With Chemical Affinities
subcrt

Properties of Species and Reactions
protein.info

Summaries of Thermodynamic Properties of Proteins
util.seq

Functions to Work with Sequence Data
util.character

Functions to Manipulate Character Objects
swap.basis

Swap Basis Species
diagram

Equilibrium Chemical Activity Diagrams
revisit

Plots and Optima of Objective Functions
taxonomy

Extract Data from NCBI Taxonomy Files
buffer

Calculating Buffered Chemical Activities
protein

Examples of Calculations for Proteins
thermo

Thermodynamic Database and System Definition
wjd

Gibbs Energy Minimization by Steepest Descent
util.misc

Functions for Miscellaneous Tasks
findit

Gridded Search to Optimize Objective Functions
util.plot

Functions to Create and Modify Plots
iprotein

Amino Acid Compositions of Proteins
water

Properties of Water