Chemical Thermodynamics and Activity Diagrams


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Documentation for package ‘CHNOSZ’ version 1.0.0

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

CHNOSZ-package Chemical Thermodynamics and Activity Diagrams

-- A --

A.ionization Functions to Work With Chemical Affinities
aa2eos Amino Acid Compositions of Proteins
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.plasma 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 --

balance Equilibrium Chemical Activities of Species
basis Define Basis Species
basis.logact Swap Basis Species
basis.matrix Swap Basis Species
browse.refs Functions to Work with the Thermodynamic Database
buffer Calculating Buffered Chemical Activities
buffers Thermodynamic Database and System Definition

-- C --

c2s Functions to Manipulate Character Objects
caller.name Functions for Various Programming Tasks
can.be.numeric Functions to Manipulate Character Objects
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.charge Parse Chemical Formulas
count.elements Parse Chemical Formulas
count.formulas Parse Chemical Formulas
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 Equilibrium 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
energy Functions to Work With Chemical Affinities
energy.args Functions to Work With Chemical Affinities
entropy Functions to Work with Chemical Formulas
envert Functions to Convert Units
eos.args Functions for Processing Argument Lists
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
extremes Plots and Optima of Objective Functions

-- F --

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

-- G --

get.formula Functions to Work with Chemical Formulas
get.objfun Objective Functions
getnames Extract Data from NCBI Taxonomy Files
getnodes Extract Data from NCBI Taxonomy Files
getrank Extract Data from NCBI Taxonomy Files
gfun Equations of State
GHS Functions to Work with Chemical Formulas
grep.file Functions for Reading FASTA Files and Downloading from UniProt
group.formulas Summaries of Thermodynamic Properties of Proteins
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
IAPWS95.idealgas Properties of Water from IAPWS-95
IAPWS95.residual Properties of Water from IAPWS-95
id.blast Functions to Work with BLAST Output Files
info Search the Thermodynamic Database
info.approx Search the Thermodynamic Database
info.character Search the Thermodynamic Database
info.numeric Search the Thermodynamic Database
info.text Search the Thermodynamic Database
invertible.combs Functions for Various Matrix Operations
ionize.aa Properties of Ionization of Proteins
ip2aa Amino Acid Compositions of Proteins
iprotein Amino Acid Compositions of Proteins
is.near.equil Gibbs Energy Minimization by Steepest Descent

-- L --

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

-- M --

makeup Parse Chemical Formulas
mass Functions to Work with Chemical Formulas
mod.basis Define Basis Species
mod.buffer Calculating Buffered Chemical Activities
mod.obigt Functions to Work with the Thermodynamic Database
more.aa Proteins from Model Organisms
MP90.cp Summaries of Thermodynamic Properties of Proteins
msgout Functions for Various Programming Tasks
mtitle Functions to Create and Modify Plots

-- N --

nonideal Functions for Miscellaneous Tasks
nucleicacids Functions to Work with Sequence Data

-- O --

OBIGT Thermodynamic Database and System Definition
obigt2eos Functions to Work with the Thermodynamic Database
objective Objective Functions
opt Thermodynamic Database and System Definition
optimal.index Plots and Optima of Objective Functions
outvert Functions to Convert Units

-- P --

P.units Functions to Convert Units
palply Functions for Various Programming Tasks
parent Extract Data from NCBI Taxonomy Files
pearson Objective Functions
plot.findit Gridded Search to Optimize Objective Functions
pprod Functions to Work with Lists
preset.basis Define Basis Species
preset.logact Define Basis Species
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
put.basis Define Basis Species

-- Q --

qqr Objective Functions

-- R --

read.aa Amino Acid Compositions of Proteins
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
residualsplot Functions to Create and Modify Plots
revisit Plots and Optima of Objective Functions
RH2obigt Functions to Work with the Thermodynamic Database
rho.IAPWS95 Properties of Water
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 --

s2c Functions to Manipulate Character Objects
sciname Extract Data from NCBI Taxonomy Files
SD Objective Functions
seq2aa Amino Acid Compositions of Proteins
shannon Objective Functions
sideeffects Side effects of functions in CHNOSZ
slice Functions to Work with Multidimensional Arrays
slice.affinity Functions to Work with Multidimensional Arrays
spearman Objective Functions
species Species of Interest
species.basis Species of Interest
state.args Functions for Processing Argument Lists
stress Experimental Data for Protein Abundances and Localizations
strip Equilibrium Chemical Activity Diagrams
subcrt Properties of Species and Reactions
swap.basis Swap Basis Species

-- T --

T.units Functions to Convert Units
taxonomy Extract Data from NCBI Taxonomy Files
thermo Thermodynamic Database and System Definition
thermo.axis Functions to Create and Modify Plots
thermo.plot.new Functions to Create and Modify Plots
today Functions to Work with the Thermodynamic Database
TP.args Functions for Processing Argument Lists
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
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 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.program Functions for Various Programming Tasks
util.seq Functions to Work with Sequence Data
util.units Functions to Convert Units

-- W --

water Properties of Water
water.AW90 Properties of Water
water.IAPWS95 Properties of Water
water.lines Functions to Create and Modify Plots
water.props Properties of Water
water.SUPCRT92 Properties of Water
which.balance Functions for Miscellaneous Tasks
which.pmax Functions to Work with Lists
wjd Gibbs Energy Minimization by Steepest Descent
WP02.auxiliary Properties of Water from IAPWS-95
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