# Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences

## Documentation for package ‘Peptides’ version 2.4.6

- DESCRIPTION file.

## Help Pages

aaComp | Compute the amino acid composition of a protein sequence
AAdata | Properties, scales and indices for the 20 naturally occurring amino acids from various sources
aaDescriptors | Compute 66 descriptors for each amino acid of a protein sequence.
aaList | Return a vector with the 20 standard amino acids in upper case
aaSMILES | Create Smiles String from aminoacid sequences
aIndex | Compute the aliphatic index of a protein sequence
autoCorrelation | Compute the auto-correlation index of a protein sequence
autoCovariance | Compute the auto-covariance index of a protein sequence
blosumIndices | Compute the BLOSUM62 derived indices of a protein sequence
boman | Compute the Boman (Potential Protein Interaction) index
charge | Compute the theoretical net charge of a protein sequence
crossCovariance | Compute the cross-covariance index of a protein sequence
crucianiProperties | Compute the Cruciani properties of a protein sequence
fasgaiVectors | Compute the FASGAI vectors of a protein sequence
hmoment | Compute the hydrophobic moment of a protein sequence
hydrophobicity | Compute the hydrophobicity index of a protein sequence
instaIndex | Compute the instability index of a protein sequence
kideraFactors | Compute the Kidera factors of a protein sequence
lengthpep | Compute the amino acid length of a protein sequence
massShift | Calculate the mass difference of modified peptides.
membpos | Compute theoretically the class of a protein sequence
mswhimScores | Compute the MS-WHIM scores of a protein sequence
mw | Compute the molecular weight of a protein sequence
mz | Calculate the m/z for peptides.
pepdata | Physicochemical properties and indices from 100 amino acid sequences
pI | Compute the isoelectic point (pI) of a protein sequence
plotXVG | Plot time series from GROMACS XVG files
protFP | Compute the protFP descriptors of a protein sequence
readXVG | Read output data from a XVG format file.
stScales | Compute the ST-scales of a protein sequence
tScales | Compute the T-scales of a protein sequence
vhseScales | Compute the VHSE-scales of a protein sequence
zScales | Compute the Z-scales of a protein sequence