Documentation


The bio3d package consists of input/output functions, conversion and manipulation functions, analysis functions, and graphics functions which are summarized below with links to further documentation.

Input/Output: Read and Write Common Data Types
read.pdb Read a PDB Format Coordinate File
read.dcd Read a CHARMM/X-PLOR/NAMD Binary DCD File
read.fasta Read FASTA formated Sequences
read.fasta.pdb Read Aligned Structure Data
read.crd Read a CHARMM CRD Format Coordinate File
write.fasta Write FASTA Formated Sequences
write.pdb Write a PDB Format Coordinate File
write.crd Write a CHARMM CRD Format Coordinate File
mktrj.pca Write a PCA Atomic Displacement Trajectory
aln2html Create a HTML Page For a Given Alignment

Analysis: Do Interesting Things
consensus Sequence Consensus for an Alignment
entropy Shannon Entropy Score Per Position in an Alignment
conserv Score Residue Conservation At Each Position in an Alignment
identity Percent Identity
rmsd Root Mean Square Deviation
core.find Identification of Invariant Core Positions
dm Distance Matrix Analysis
pca.xyz Principal Component Analysis
pca.tor Principal Component Analysis
mktrj.pca PCA Atomic Displacement Trajectory
pca.project Project Data onto Principal Components
fit.xyz Coordinate Superposition
rot.lsq Coordinate Superposition
dssp Secondary Structure Analysis with DSSP
stride Secondary Structure Analysis with STRIDE
rmsf Atomic RMS Fluctuations
seqaln Sequence Alignment
seqaln.pair Pairwise Alignment of Identical Protein Sequences
angle.xyz Angle Determination
torsion.pdb Calculate Mainchain and Sidechain Torsion/Dihedral Angles
torsion.xyz Calculate Torsion/Dihedral Angles
wrap.tor Wrap Torsion Angle Data

Graphics: Plotting and Graphic Display
mono.colors Color Palettes (black-gray-white)
bwr.colors Color Palettes (blue-white-red)
plot.bio3d Plots with marginal SSE annotation
plot.core Plot Core Fitting Progress
plot.dmat Plot Distance Matrix
plot.pca Plot a z-score Conformer Plot and an Eigen Spectrum Scree plot
plot.pca.loadings Plot Residue Loadings along PC1 to PC3
plot.pca.score Plot PCA Results
plot.pca.scree Plot PCA Results

Utilities: Convert and Manipulate Data
lbio3d List all Functions in the bio3d Package
pdb.summary PDB Structure Summary
atom.select Atom Selection From PDB Structure
aa123 Convert Between 1-letter and 3-letter Aminoacid Codes
aa321 Convert Between 3-letter and 1-letter Aminoacid Codes
orient.pdb Orient a PDB Structure
is.gap Test for the Presence of Gap Characters.
gap.inspect Alignment Gap Summary
bounds Bounds of a Numeric Vector
pairwise Pair Indices
ide.filter Percent Identity Filter
rmsd.filter RMSD Filter
seqbind Combine Sequences by Rows Without Recycling
unbound Sequence Generation from a Bounds Vector
convert.pdb Convert between CHARMM, Amber, Gromacs and Brookhaven PDB formats
atom2xyz Convert Between atom and xyz Indices
wiki.tbl WIKI Table
aln2html Create a HTML Page For a Given Alignment
aa.index AAindex: Amino Acid Index Database
aa2index Converts sequences to aminoacid indeces from the AAindex database
bio3d-package Overview of the Bio3d Package

Example Data:
kinesin Bio3d Example Data
pdbs Bio3d Example Data
aln Bio3d Example Data
core Bio3d Example Data
xyz Bio3d Example Data
pc.xray Bio3d Example Data

Remember that you can also get help on any particular function by using the command ?function or help(function) from within R itself.

There is also a package manual (in PDF format) that is a concatenation of all the above documentation.