# Biological Structure Analysis

## Documentation for package ‘bio3d’ version 1.1-5

- DESCRIPTION file.

## Help Pages

A B C D E F G I K L M O P R S T U V W X

bio3d-package | Biological Structure Analysis

## -- A --

aa.index | AAindex: Amino Acid Index Database
aa123 | Convert Between 1-letter and 3-letter Aminoacid Codes
aa2index | Convert an Aminoacid Sequence to AAIndex Values
aa321 | Convert Between 1-letter and 3-letter Aminoacid Codes
aln | Bio3d Example Data
aln2html | Create a HTML Page For a Given Alignment
angle.xyz | Calculate the Angle Between Three Atoms
atom.select | Atom Selection From PDB Structure
atom2xyz | Convert Between Atom and xyz Indices

## -- B --

bio3d | Biological Structure Analysis
blast.pdb | NCBI BLAST Sequence Search
bounds | Bounds of a Numeric Vector
bwr.colors | Color Palettes

## -- C --

chain.pdb | Find Possible PDB Chain Breaks
cmap | Contact Map
consensus | Sequence Consensus for an Alignment
conserv | Score Residue Conservation At Each Position in an Alignment
convert.pdb | Convert Between Various PDB formats
core | Bio3d Example Data
core.find | Identification of Invariant Core Positions

## -- D --

dccm | DCCM: Dynamical Cross-Correlation Matrix
diag.ind | Diagonal Indices of a Matrix
difference.vector | Difference Vector
dist.xyz | Calculate the Distances Between the Rows of Two Matrices
dm | Distance Matrix Analysis
dm.xyz | Distance Matrix Analysis
dssp | Secondary Structure Analysis with DSSP

## -- E --

entropy | Shannon Entropy Score

## -- F --

fit.xyz | Coordinate Superposition

## -- G --

gap.inspect | Alignment Gap Summary
get.pdb | Download PDB Coordinate Files
get.seq | Download FASTA Sequence Files

## -- I --

ide.filter | Percent Identity Filter
identity | Percent Identity
is.gap | Gap Characters

## -- K --

kinesin | Bio3d Example Data

## -- L --

lbio3d | List all Functions in the bio3d Package

## -- M --

mktrj.pca | PCA Atomic Displacement Trajectory
mono.colors | Color Palettes
motif.find | Find Sequence Motifs.

## -- O --

orient.pdb | Orient a PDB Structure
overlap | Overlap analysis

## -- P --

pairwise | Pair Indices
pc.xray | Bio3d Example Data
pca.project | Project Data onto Principal Components
pca.tor | Principal Component Analysis
pca.xyz | Principal Component Analysis
pca.xyz2z | Project Data onto Principal Components
pca.z2xyz | Project Data onto Principal Components
pdb.summary | Atom Selection From PDB Structure
pdbaln | Sequence Alignment of PDB Files
pdbs | Bio3d Example Data
plot.bio3d | Plots with marginal SSE annotation
plot.blast | Plot a Summary of BLAST Hit Statistics.
plot.core | Plot Core Fitting Progress
plot.dccm | DCCM Plot
plot.dmat | Plot Distance Matrix
plot.pca | Plot PCA Results
plot.pca.loadings | Plot Residue Loadings along PC1 to PC3
plot.pca.score | Plot PCA Results
plot.pca.scree | Plot PCA Results
print.core | Printing Core Positions and Returning Indices
print.pdb | Read PDB File
print.rle2 | Run Length Encoding with Indices

## -- R --

read.all | Read Aligned Structure Data
read.crd | Read CRD File
read.dcd | Read CHARMM/X-PLOR/NAMD Binary DCD files
read.fasta | Read FASTA formated Sequences
read.fasta.pdb | Read Aligned Structure Data
read.ncdf | Read AMBER Binary netCDF files
read.pdb | Read PDB File
read.pdcBD | Read PQR output from pdcBD File
read.pqr | Read PQR File
rle2 | Run Length Encoding with Indices
rmsd | Root Mean Square Deviation
rmsd.filter | RMSD Filter
rmsf | Atomic RMS Fluctuations
rmsip | Root Mean Square Inner Product
rot.lsq | Coordinate Superposition

## -- S --

seq.pdb | Extract The Aminoacid Sequence From A PDB Object
seq2aln | Add a Sequence to an Existing Alignmnet
seqaln | Sequence Alignment with MUSCLE
seqaln.pair | Sequence Alignment of Identical Protein Sequences
seqbind | Combine Sequences by Rows Without Recycling
split.pdb | Split a PDB File Into Separate Files, One For Each Chain.
sse | Bio3d Example Data
store.atom | Store all-atom data from a PDB object
stride | Secondary Structure Analysis with STRIDE

## -- T --

torsion.pdb | Calculate Mainchain and Sidechain Torsion/Dihedral Angles
torsion.xyz | Calculate Torsion/Dihedral Angles
trim.pdb | Trim a PDB Object To A Subset of Atoms.

## -- U --

unbound | Sequence Generation from a Bounds Vector

## -- V --

vec2resno | Replicate Per-residue Vector Values

## -- W --

wiki.tbl | Wiki Table
wrap.tor | Wrap Torsion Angle Data
write.crd | Write CRD File
write.fasta | Write FASTA Formated Sequences
write.ncdf | Write AMBER Binary netCDF files
write.pdb | Write PDB Format Coordinate File
write.pqr | Write PQR Format Coordinate File

## -- X --

xyz | Bio3d Example Data