Chemical Thermodynamics and Activity Diagrams


Documentation for package ‘CHNOSZ’ version 1.1.0 (2017-05-04)

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A B C D E F G H I L M N O P Q R S T U V W Y Z

CHNOSZ-package Chemical Thermodynamics and Activity Diagrams

-- A --

aasum Amino Acid Compositions of Proteins
add.obigt Functions to Work with the Thermodynamic Database
add.protein Amino Acid Compositions of Proteins
affinity Chemical Affinities of Formation Reactions
allparents Extract Data from NCBI Taxonomy Files
aminoacids Functions to Work with Sequence Data
anim Functions to Make Animations
anim.carboxylase Functions to Make Animations
anim.TCA Functions to Make Animations
apc Mass Transfer Calculations
as.chemical.formula Functions to Work with Chemical Formulas
axis.label Functions to Express Chemical Formulas and Properties

-- B --

basis Define Basis Species
basis.elements Swap Basis Species
basis.logact Swap Basis Species
buffer Calculating Buffered Chemical Activities
buffers Thermodynamic Database and System Definition

-- C --

cgl Equations of State
check.obigt Functions to Work with the Thermodynamic Database
checkEOS Functions to Work with the Thermodynamic Database
checkGHS Functions to Work with the Thermodynamic Database
convert Functions to Convert Units
count.aa Functions for Reading FASTA Files and Downloading from UniProt
count.elements Parse Chemical Formulas
Cp_s_var Regress Equations-of-State Parameters for Aqueous Species
CV Objective Functions
CVRMSD Objective Functions

-- D --

DDGmix Objective Functions
def2gi Functions to Work with BLAST Output Files
demos Run Examples from the Documentation
describe.basis Functions to Express Chemical Formulas and Properties
describe.property Functions to Express Chemical Formulas and Properties
describe.reaction Functions to Express Chemical Formulas and Properties
DGinf Objective Functions
DGmix Objective Functions
DGtr Objective Functions
diagram Chemical Activity Diagrams
dimSums Functions to Work with Multidimensional Arrays
dPdTtr Functions for Miscellaneous Tasks
draw.transfer Mass Transfer Calculations

-- E --

E.units Functions to Convert Units
element Thermodynamic Database and System Definition
element.mu Swap Basis Species
element.potentials Gibbs Energy Minimization by Steepest Descent
entropy Functions to Work with Chemical Formulas
EOScalc Regress Equations-of-State Parameters for Aqueous Species
EOScoeffs Regress Equations-of-State Parameters for Aqueous Species
EOSlab Regress Equations-of-State Parameters for Aqueous Species
EOSplot Regress Equations-of-State Parameters for Aqueous Species
EOSregress Regress Equations-of-State Parameters for Aqueous Species
EOSvar Regress Equations-of-State Parameters for Aqueous Species
eqdata Read data from an EQ6 output file
equil.boltzmann Equilibrium Chemical Activities of Species
equil.potentials Gibbs Energy Minimization by Steepest Descent
equil.reaction Equilibrium Chemical Activities of Species
equilibrate Equilibrium Chemical Activities of Species
examples Run Examples from the Documentation
expr.property Functions to Express Chemical Formulas and Properties
expr.species Functions to Express Chemical Formulas and Properties
expr.units Functions to Express Chemical Formulas and Properties
extdata Extra Data

-- F --

feldspar Mass Transfer Calculations
find.tp Chemical Activity Diagrams
findit Gridded Search to Optimize Objective Functions

-- G --

getnames Extract Data from NCBI Taxonomy Files
getnodes Extract Data from NCBI Taxonomy Files
getrank Extract Data from NCBI Taxonomy Files
GHS Functions to Work with Chemical Formulas
GHS_Tr Functions for Miscellaneous Tasks
group.formulas Functions for Proteins (Other Calculations)
groups Thermodynamic Database and System Definition
guess Gibbs Energy Minimization by Steepest Descent

-- H --

hkf Equations of State

-- I --

i2A Functions to Work with Chemical Formulas
IAPWS95 Properties of Water from IAPWS-95
ibasis Swap Basis Species
id.blast Functions to Work with BLAST Output Files
info Search the Thermodynamic Database
invertible.combs Functions for Various Matrix Operations
ionize.aa Properties of Ionization of Proteins
is.near.equil Gibbs Energy Minimization by Steepest Descent

-- L --

label.figure Functions to Create and Modify Plots
label.plot Functions to Create and Modify Plots
list2array Functions to Work with Multidimensional Arrays
logact Objective Functions

-- M --

makeup Parse Chemical Formulas
mass Functions to Work with Chemical Formulas
mod.buffer Calculating Buffered Chemical Activities
mod.obigt Functions to Work with the Thermodynamic Database
more.aa Proteins from Model Organisms
mosaic Chemical Affinities with Changing Basis Species
MP90.cp Functions for Proteins (Other Calculations)
mtitle Functions to Create and Modify Plots

-- N --

nonideal Activity coefficients of aqueous species
nucleic.complement Functions to Work with Sequence Data
nucleic.formula Functions to Work with Sequence Data

-- O --

OBIGT Thermodynamic Database and System Definition
objective Objective Functions
opt Thermodynamic Database and System Definition

-- P --

P.units Functions to Convert Units
palply Conditional Parallel Processing
parent Extract Data from NCBI Taxonomy Files
pearson Objective Functions
pinfo Summaries of Thermodynamic Properties of Proteins
plot_findit Gridded Search to Optimize Objective Functions
protein Examples of Calculations for Proteins
protein.basis Summaries of Thermodynamic Properties of Proteins
protein.equil Summaries of Thermodynamic Properties of Proteins
protein.formula Summaries of Thermodynamic Properties of Proteins
protein.info Summaries of Thermodynamic Properties of Proteins
protein.length Summaries of Thermodynamic Properties of Proteins
protein.obigt Summaries of Thermodynamic Properties of Proteins

-- Q --

qqr Objective Functions

-- R --

ratlab Functions to Express Chemical Formulas and Properties
read.blast Functions to Work with BLAST Output Files
read.expr Experimental Data for Protein Abundances and Localizations
read.fasta Functions for Reading FASTA Files and Downloading from UniProt
refs Thermodynamic Database and System Definition
revisit Plots and Optima of Objective Functions
RH2obigt Functions to Work with the Thermodynamic Database
rho.IAPWS95 Functions for Properties of Water and Steam
richness Plots and Optima of Objective Functions
RMSD Objective Functions
run.guess Gibbs Energy Minimization by Steepest Descent
run.wjd Gibbs Energy Minimization by Steepest Descent

-- S --

sciname Extract Data from NCBI Taxonomy Files
SD Objective Functions
seq2aa Amino Acid Compositions of Proteins
shannon Objective Functions
slice Functions to Work with Multidimensional Arrays
slice.affinity Functions to Work with Multidimensional Arrays
spearman Objective Functions
species Species of Interest
strip Chemical Activity Diagrams
subcrt Properties of Species and Reactions
swap.basis Swap Basis Species
syslab Functions to Express Chemical Formulas and Properties

-- T --

T.units Functions to Convert Units
taxonomy Extract Data from NCBI Taxonomy Files
thermo Thermodynamic Database and System Definition
thermo.plot.new Functions to Create and Modify Plots
thermo.refs Functions to Work with the Thermodynamic Database
today Functions to Work with the Thermodynamic Database
transfer Mass Transfer Calculations
Ttr Functions for Miscellaneous Tasks

-- U --

uniprot.aa Functions for Reading FASTA Files and Downloading from UniProt
unitize Functions for Miscellaneous Tasks
usrfig Functions to Create and Modify Plots
util.array Functions to Work with Multidimensional Arrays
util.blast Functions to Work with BLAST Output Files
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 UniProt
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.seq Functions to Work with Sequence Data
util.units Functions to Convert Units
util.water Functions for Properties of Water and Steam

-- V --

V_s_var Regress Equations-of-State Parameters for Aqueous Species

-- W --

water Properties of Water
water.AW90 Functions for Properties of Water and Steam
water.IAPWS95 Properties of Water
water.lines Functions to Create and Modify Plots
water.props Properties of Water
water.SUPCRT92 Properties of Water
which.pmax Functions to Work with Lists
wjd Gibbs Energy Minimization by Steepest Descent
WP02.auxiliary Functions for Properties of Water and Steam
write.blast Functions to Work with BLAST Output Files

-- Y --

yeastgfp Experimental Data for Protein Abundances and Localizations

-- Z --

ZC Functions to Work with Chemical Formulas
ZC.col Functions to Create and Modify Plots