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CHNOSZ (version 1.0.8)

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

770

Version

1.0.8

License

GPL (>= 2)

Maintainer

Jeffrey Dick

Last Published

May 28th, 2016

Functions in CHNOSZ (1.0.8)

eqdata

Read data from an EQ6 output file
basis

Define Basis Species
diagram

Equilibrium Chemical Activity Diagrams
thermo

Thermodynamic Database and System Definition
CHNOSZ-package

Chemical Thermodynamics and Activity Diagrams
buffer

Calculating Buffered Chemical Activities
anim.TCA

Functions to Make Animations
eos

Equations of State
EOSregress

Regress Equations-of-State Parameters for Aqueous Species
affinity

Chemical Affinities of Formation Reactions
info

Search the Thermodynamic Database
ionize.aa

Properties of Ionization of Proteins
examples

Run Examples from the Documentation
equilibrate

Equilibrium Chemical Activities of Species
more.aa

Proteins from Model Organisms
IAPWS95

Properties of Water from IAPWS-95
iprotein

Amino Acid Compositions of Proteins
makeup

Parse Chemical Formulas
extdata

Extra Data
findit

Gridded Search to Optimize Objective Functions
protein.info

Summaries of Thermodynamic Properties of Proteins
protein

Examples of Calculations for Proteins
subcrt

Properties of Species and Reactions
mosaic

Chemical Affinities with Changing Basis Species
sideeffects

Side effects of functions in CHNOSZ
revisit

Plots and Optima of Objective Functions
species

Species of Interest
nonideal

Activity coefficients of aqueous species
read.expr

Experimental Data for Protein Abundances and Localizations
objective

Objective Functions
util.args

Functions for Processing Argument Lists
taxonomy

Extract Data from NCBI Taxonomy Files
util.character

Functions to Manipulate Character Objects
util.affinity

Functions to Work With Chemical Affinities
util.data

Functions to Work with the Thermodynamic Database
util.blast

Functions to Work with BLAST Output Files
util.array

Functions to Work with Multidimensional Arrays
util.expression

Functions to Express Chemical Formulas and Properties
transfer

Mass Transfer Calculations
swap.basis

Swap Basis Species
util.matrix

Functions for Various Matrix Operations
util.misc

Functions for Miscellaneous Tasks
util.fasta

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

Functions to Create and Modify Plots
util.formula

Functions to Work with Chemical Formulas
util.program

Functions for Various Programming Tasks
util.water

Functions for Properties of Water and Steam
util.seq

Functions to Work with Sequence Data
util.units

Functions to Convert Units
wjd

Gibbs Energy Minimization by Steepest Descent
util.list

Functions to Work with Lists
water

Properties of Water