aa.index                AAindex: Amino Acid Index Database
aa.table                Table of Relevant Amino Acids
aa123                   Convert Between 1-letter and 3-letter Aminoacid
                        Codes
aa2index                Convert an Aminoacid Sequence to AAIndex Values
aa2mass                 Amino Acid Residues to Mass Converter
aanma                   All Atom Normal Mode Analysis
aanma.pdbs              Ensemble Normal Mode Analysis with All-Atom ENM
aln2html                Create a HTML Page For a Given Alignment
angle.xyz               Calculate the Angle Between Three Atoms
as.fasta                Alignment to FASTA object
as.pdb                  Convert to PDB format
as.select               Convert Atomic Indices to a Select Object
atom.index              Atom Names/Types
atom.select             Atom Selection from PDB and PRMTOP Structure
                        Objects
atom2ele                Atom Names/Types to Atomic Symbols Converter
atom2mass               Atom Names/Types to Mass Converter
atom2xyz                Convert Between Atom and xyz Indices
basename.pdb            Manipulate PDB File Names
bhattacharyya           Bhattacharyya Coefficient
binding.site            Binding Site Residues
bio3d-package           Biological Structure Analysis
biounit                 Biological Units Construction
blast.pdb               NCBI BLAST Sequence Search and Summary Plot of
                        Hit Statistics
bounds                  Bounds of a Numeric Vector
bounds.sse              Obtain A SSE Object From An SSE Sequence Vector
bwr.colors              Color Palettes
cat.pdb                 Concatenate Multiple PDB Objects
chain.pdb               Find Possible PDB Chain Breaks
check.utility           Check on Missing Utility Programs
clean.pdb               Inspect And Clean Up A PDB Object
cmap                    Contact Map
cna                     Protein Dynamic Correlation Network
                        Construction and Community Analysis.
cnapath                 Suboptimal Path Analysis for Correlation
                        Networks
com                     Center of Mass
combine.select          Combine Atom Selections From PDB Structure
community.aln           Align communities from two or more networks
community.tree          Reconstruction of the Girvan-Newman Community
                        Tree for a CNA Class Object.
consensus               Sequence Consensus for an Alignment
conserv                 Score Residue Conservation At Each Position in
                        an Alignment
convert.pdb             Renumber and Convert Between Various PDB
                        formats
core.find               Identification of Invariant Core Positions
cov.nma                 Calculate Covariance Matrix from Normal Modes
covsoverlap             Covariance Overlap
dccm                    DCCM: Dynamical Cross-Correlation Matrix
dccm.enma               Cross-Correlation for Ensemble NMA (eNMA)
dccm.gnm                Dynamic Cross-Correlation from Gaussian Network
                        Model
dccm.nma                Dynamic Cross-Correlation from Normal Modes
                        Analysis
dccm.pca                Dynamic Cross-Correlation from Principal
                        Component Analysis
dccm.xyz                DCCM: Dynamical Cross-Correlation Matrix
deformation.nma         Deformation Analysis
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
dssp                    Secondary Structure Analysis with DSSP or
                        STRIDE
elements                Periodic Table of the Elements
entropy                 Shannon Entropy Score
example.data            Bio3d Example Data
filter.cmap             Contact Map Consensus Filtering
filter.dccm             Filter for Cross-correlation Matrices (Cij)
filter.identity         Percent Identity Filter
filter.rmsd             RMSD Filter
fit.xyz                 Coordinate Superposition
fluct.nma               NMA Fluctuations
formula2mass            Chemical Formula to Mass Converter
gap.inspect             Alignment Gap Summary
geostas                 GeoStaS Domain Finder
get.pdb                 Download PDB Coordinate Files
get.seq                 Download FASTA Sequence Files
gnm                     Gaussian Network Model
hclustplot              Dendrogram with Clustering Annotation
hmmer                   HMMER Sequence Search
identify.cna            Identify Points in a CNA Protein Structure
                        Network Plot
inner.prod              Mass-weighted Inner Product
inspect.connectivity    Check the Connectivity of Protein Structures
is.gap                  Gap Characters
is.mol2                 Is an Object of Class 'mol2'?
is.pdb                  Is an Object of Class 'pdb(s)'?
is.select               Is an Object of Class 'select'?
is.xyz                  Is an Object of Class 'xyz'?
layout.cna              Protein Structure Network Layout
lbio3d                  List all Functions in the bio3d Package
lmi                     LMI: Linear Mutual Information Matrix
load.enmff              ENM Force Field Loader
mask                    Mask a Subset of Atoms in a DCCM Object.
mktrj                   PCA / NMA Atomic Displacement Trajectory
motif.find              Find Sequence Motifs.
mustang                 Structure-based Sequence Alignment with MUSTANG
network.amendment       Amendment of a CNA Network According To A Input
                        Community Membership Vector.
nma                     Normal Mode Analysis
nma.pdb                 Normal Mode Analysis
nma.pdbs                Ensemble Normal Mode Analysis
normalize.vector        Mass-Weighted Normalized Vector
orient.pdb              Orient a PDB Structure
overlap                 Overlap analysis
pairwise                Pair Indices
pca                     Principal Component Analysis
pca.array               Principal Component Analysis of an array of
                        matrices
pca.pdbs                Principal Component Analysis
pca.tor                 Principal Component Analysis
pca.xyz                 Principal Component Analysis
pdb.annotate            Get Customizable Annotations From PDB Or PFAM
                        Databases
pdb2aln                 Align a PDB structure to an existing alignment
pdb2aln.ind             Mapping from alignment positions to PDB atomic
                        indices
pdb2sse                 Obtain An SSE Sequence Vector From A PDB Object
pdbaln                  Sequence Alignment of PDB Files
pdbfit                  PDB File Coordinate Superposition
pdbs2pdb                PDBs to PDB Converter
pdbs2sse                SSE annotation for a PDBs Object
pdbseq                  Extract The Aminoacid Sequence From A PDB
                        Object
pdbsplit                Split a PDB File Into Separate Files, One For
                        Each Chain.
pfam                    Download Pfam FASTA Sequence Alignment
plot.bio3d              Plots with marginal SSE annotation
plot.cmap               Plot Contact Matrix
plot.cna                Protein Structure Network Plots in 2D and 3D.
plot.core               Plot Core Fitting Progress
plot.dccm               DCCM Plot
plot.dmat               Plot Distance Matrix
plot.enma               Plot eNMA Results
plot.fasta              Plot a Multiple Sequence Alignment
plot.fluct              Plot Fluctuations
plot.geostas            Plot Geostas Results
plot.hmmer              Plot a Summary of HMMER Hit Statistics.
plot.matrix.loadings    Plot Residue-Residue Matrix Loadings
plot.nma                Plot NMA Results
plot.pca                Plot PCA Results
plot.pca.loadings       Plot Residue Loadings along PC1 to PC3
plot.rmsip              Plot RMSIP Results
print.cna               Summarize and Print Features of a cna Network
                        Graph
print.core              Printing Core Positions and Returning Indices
print.fasta             Printing Sequence Alignments
print.xyz               Printing XYZ coordinates
project.pca             Project Data onto Principal Components
prune.cna               Prune A cna Network Object
pymol                   Biomolecular Visualization with PyMOL
read.all                Read Aligned Structure Data
read.cif                Read mmCIF File
read.crd                Read Coordinate Data from Amber or Charmm
read.crd.amber          Read AMBER Coordinate files
read.crd.charmm         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.mol2               Read MOL2 File
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
read.prmtop             Read AMBER Parameter/Topology files
rgyr                    Radius of Gyration
rle2                    Run Length Encoding with Indices
rmsd                    Root Mean Square Deviation
rmsf                    Atomic RMS Fluctuations
rmsip                   Root Mean Square Inner Product
sdENM                   Index for the sdENM ff
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
seqidentity             Percent Identity
setup.ncore             Setup for Running Bio3D Functions using
                        Multiple CPU Cores
sip                     Square Inner Product
sse.bridges             SSE Backbone Hydrogen Bonding
store.atom              Store all-atom data from a PDB object
struct.aln              Structure Alignment Of Two PDB Files
torsion.pdb             Calculate Mainchain and Sidechain
                        Torsion/Dihedral Angles
torsion.xyz             Calculate Torsion/Dihedral Angles
trim                    Trim a PDB Object To A Subset of Atoms.
trim.mol2               Trim a MOL2 Object To A Subset of Atoms.
trim.pdbs               Filter or Trim a PDBs Object
trim.xyz                Trim a XYZ Object of Cartesian Coordinates.
unbound                 Sequence Generation from a Bounds Vector
uniprot                 Fetch UniProt Entry Data.
var.xyz                 Pairwise Distance Variance in Cartesian
                        Coordinates
vec2resno               Replicate Per-residue Vector Values
vmd                     View CNA Protein Structure Network Community
                        Output in VMD
vmd_colors              VMD Color Palette
wrap.tor                Wrap Torsion Angle Data
write.crd               Write CRD File
write.fasta             Write FASTA Formated Sequences
write.mol2              Write MOL2 Format Coordinate File
write.ncdf              Write AMBER Binary netCDF files
write.pdb               Write PDB Format Coordinate File
write.pir               Write PIR Formated Sequences
write.pqr               Write PQR Format Coordinate File
