Learn R Programming

⚠️There's a newer version (2.1.0) of this package.Take me there.

CHNOSZ (version 0.9-1)

Chemical Thermodynamics and Activity Diagrams

Description

Calculation of the standard molal thermodynamic properties and chemical affinities of reactions between and among minerals, inorganic, organic, and/or biomolecular aqueous and crystalline species. Incorporation of an extensive database of thermodynamic properties of species and algorithms for computing the standard thermodynamic properties of neutral and ionized proteins from amino acid group contributions. Generation of chemical speciation and predominance diagrams for stable and metastable equilibrium in open systems as a function of temperature, pressure, and chemical activities or fugacities of basis species.

Copy Link

Version

Install

install.packages('CHNOSZ')

Monthly Downloads

702

Version

0.9-1

License

GPL (>= 2)

Maintainer

Jeffrey Dick

Last Published

July 24th, 2010

Functions in CHNOSZ (0.9-1)

transfer

Mass Transfer Calculations
ionize

Ionization Properties of Proteins
eos

Equations of State
info

Search the Thermodynamic Database
taxonomy

Extract Data from NCBI Taxonomy Files
util.character

Functions to Manipulate Character Objects
affinity

Chemical Affinities of Formation Reactions
CHNOSZ

Chemical Thermodynamics and Activity Diagrams
thermo

Thermodynamic Properties and Compositional Data
util.args

Functions for Processing Argument Lists
protein

Properties of Proteins
util.data

Functions to Modify the Thermodynamic Database
util.seq

Functions to Work with Sequence Data
util.plot

Functions to Create and Modify Plots
makeup

Chemical Formulas and Compositions
species

Species of Interest
util.blast

Functions to Work with BLAST Output Files
eqdata

Read data from an EQ6 output file
util.fasta

Functions for Accessing FASTA Files
revisit

Diversity Calculations for Chemical Species
basis

Basis Species
subcrt

Properties of Species and Reactions
util.list

Functions to Work with Lists
buffer

Chemical Potential Buffers
util.array

Functions to Work with Multidimensional Arrays
util.units

Functions to Convert Units
util.misc

Miscellaneous Utility Functions
examples

Run examples from the documentation
util.formula

Functions to Work with Chemical Formulas
diagram

Calculate and Plot Relative Abundances of Species
get.protein

Proteins from Model Organisms
water

Properties of Water
findit

Multidimensionally Optimize Chemical Activities
logact

Calculate Logarithms of Activity of Species
CHNOSZ-package

Chemical Thermodynamics and Activity Diagrams
anim.TCA

Functions to Make Animations
more.aa

Proteins from Model Organisms
EOSregress

Regress equations-of-state parameters for aqueous species
iprotein

Amino Acid Compositions of Proteins
get.expr

Protein Expression Data
ionize.aa

Properties of Ionization of Proteins
extdata

Extra Data
util.program

Functions for Various Programming Tasks
util.affinity

Functions to Work With Chemical Affinities
util.stat

Functions for Various Statistical Operations
equilibrate

Equilibrium Chemical Activities of Species
equil

Calculate Logarithms of Activity of Species
protein.info

Summaries of Thermodynamic Properties of Proteins
objective

Objective Functions
util.matrix

Functions for Various Matrix Operations
swap.basis

Swap Basis Species
wjd

Gibbs Energy Minimization by Steepest Descent
nuts

Unit Conversions
utilities

Utility and Miscellaneous Functions
util.expression

Functions to Express Chemical Formulas and Properties
sideeffects

Side effects of functions in CHNOSZ
read.expr

Experimental Data for Protein Abundances and Localizations