# Biological Structure Analysis

## Documentation for package ‘bio3d’ version 2.3-4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

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

bio3d-package | Biological Structure Analysis

## -- A --

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
aa321 | Convert Between 1-letter and 3-letter Aminoacid Codes
aanma | All Atom Normal Mode Analysis
aanma.pdb | All Atom Normal Mode Analysis
aanma.pdbs | Ensemble Normal Mode Analysis with All-Atom ENM
aln2html | Create a HTML Page For a Given Alignment
amsm.xyz | GeoStaS Domain Finder
angle.xyz | Calculate the Angle Between Three Atoms
annotation | Bio3d Example Data
as.fasta | Alignment to FASTA object
as.pdb | Convert to PDB format
as.pdb.default | Convert to PDB format
as.pdb.mol2 | Convert to PDB format
as.pdb.prmtop | Convert to PDB format
as.select | Convert Atomic Indices to a Select Object
as.xyz | Is an Object of Class 'xyz'?
atom.index | Atom Names/Types
atom.select | Atom Selection from PDB and PRMTOP Structure Objects
atom.select.mol2 | Atom Selection from PDB and PRMTOP Structure Objects
atom.select.pdb | Atom Selection from PDB and PRMTOP Structure Objects
atom.select.prmtop | Atom Selection from PDB and PRMTOP Structure Objects
atom2ele | Atom Names/Types to Atomic Symbols Converter
atom2ele.default | Atom Names/Types to Atomic Symbols Converter
atom2ele.pdb | Atom Names/Types to Atomic Symbols Converter
atom2mass | Atom Names/Types to Mass Converter
atom2mass.default | Atom Names/Types to Mass Converter
atom2mass.pdb | Atom Names/Types to Mass Converter
atom2xyz | Convert Between Atom and xyz Indices

## -- B --

basename.pdb | Manipulate PDB File Names
bhattacharyya | Bhattacharyya Coefficient
bhattacharyya.array | Bhattacharyya Coefficient
bhattacharyya.enma | Bhattacharyya Coefficient
bhattacharyya.matrix | Bhattacharyya Coefficient
bhattacharyya.nma | Bhattacharyya Coefficient
bhattacharyya.pca | Bhattacharyya Coefficient
binding.site | Binding Site Residues
bio3d | 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
build.hessian | Normal Mode Analysis
bwr.colors | Color Palettes

## -- C --

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
cmap.default | Contact Map
cmap.pdb | Contact Map
cmap.xyz | Contact Map
cna | Protein Dynamic Correlation Network Construction and Community Analysis.
cna.dccm | Protein Dynamic Correlation Network Construction and Community Analysis.
cna.ensmb | Protein Dynamic Correlation Network Construction and Community Analysis.
cnapath | Suboptimal Path Analysis for Correlation Networks
com | Center of Mass
com.pdb | Center of Mass
com.xyz | 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 | Bio3d Example Data
core.find | Identification of Invariant Core Positions
core.find.default | Identification of Invariant Core Positions
core.find.pdb | Identification of Invariant Core Positions
core.find.pdbs | Identification of Invariant Core Positions
cov.enma | Calculate Covariance Matrix from Normal Modes
cov.nma | Calculate Covariance Matrix from Normal Modes
cov2dccm | DCCM: Dynamical Cross-Correlation Matrix
covsoverlap | Covariance Overlap
covsoverlap.enma | Covariance Overlap
covsoverlap.nma | Covariance Overlap

## -- D --

dccm | DCCM: Dynamical Cross-Correlation Matrix
dccm.egnm | Dynamic Cross-Correlation from Gaussian Network Model
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
dm.pdb | Distance Matrix Analysis
dm.pdbs | Distance Matrix Analysis
dm.xyz | Distance Matrix Analysis
dssp | Secondary Structure Analysis with DSSP or STRIDE
dssp.pdb | Secondary Structure Analysis with DSSP or STRIDE
dssp.pdbs | Secondary Structure Analysis with DSSP or STRIDE
dssp.xyz | Secondary Structure Analysis with DSSP or STRIDE

## -- E --

elements | Periodic Table of the Elements
entropy | Shannon Entropy Score
example.data | Bio3d Example Data

## -- F --

ff.aaenm | ENM Force Field Loader
ff.aaenm2 | ENM Force Field Loader
ff.anm | ENM Force Field Loader
ff.calpha | ENM Force Field Loader
ff.pfanm | ENM Force Field Loader
ff.reach | ENM Force Field Loader
ff.sdenm | ENM Force Field Loader
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

## -- G --

gap.inspect | Alignment Gap Summary
geostas | GeoStaS Domain Finder
geostas.default | GeoStaS Domain Finder
geostas.enma | GeoStaS Domain Finder
geostas.nma | GeoStaS Domain Finder
geostas.pdb | GeoStaS Domain Finder
geostas.pdbs | GeoStaS Domain Finder
geostas.xyz | GeoStaS Domain Finder
get.blast | NCBI BLAST Sequence Search and Summary Plot of Hit Statistics
get.pdb | Download PDB Coordinate Files
get.seq | Download FASTA Sequence Files
gnm | Gaussian Network Model
gnm.pdb | Gaussian Network Model
gnm.pdbs | Gaussian Network Model

## -- H --

hclustplot | Dendrogram with Clustering Annotation
hivp | Bio3d Example Data
hmmer | HMMER Sequence Search

## -- I --

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.pdbs | Is an Object of Class 'pdb(s)'?
is.select | Is an Object of Class 'select'?
is.xyz | Is an Object of Class 'xyz'?

## -- K --

kinesin | Bio3d Example Data

## -- L --

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

## -- M --

mask | Mask a Subset of Atoms in a DCCM Object.
mask.dccm | Mask a Subset of Atoms in a DCCM Object.
mktrj | PCA / NMA Atomic Displacement Trajectory
mktrj.enma | PCA / NMA Atomic Displacement Trajectory
mktrj.nma | PCA / NMA Atomic Displacement Trajectory
mktrj.pca | PCA / NMA Atomic Displacement Trajectory
mono.colors | Color Palettes
motif.find | Find Sequence Motifs.
mustang | Structure-based Sequence Alignment with MUSTANG

## -- N --

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

## -- O --

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

## -- P --

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
pdb.pfam | 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
pdbfit.pdb | PDB File Coordinate Superposition
pdbfit.pdbs | PDB File Coordinate Superposition
pdbs | Bio3d Example Data
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.blast | NCBI BLAST Sequence Search and Summary Plot of Hit Statistics
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.pca.score | Plot PCA Results
plot.pca.scree | Plot PCA Results
plot.rmsip | Plot RMSIP Results
plotb3 | Plots with marginal SSE annotation
print.cna | Summarize and Print Features of a cna Network Graph
print.cnapath | Suboptimal Path Analysis for Correlation Networks
print.core | Printing Core Positions and Returning Indices
print.enma | Ensemble Normal Mode Analysis
print.fasta | Printing Sequence Alignments
print.geostas | GeoStaS Domain Finder
print.mol2 | Read MOL2 File
print.nma | Normal Mode Analysis
print.pca | Principal Component Analysis
print.pdb | Read PDB File
print.prmtop | Read AMBER Parameter/Topology files
print.rle2 | Run Length Encoding with Indices
print.select | Atom Selection from PDB and PRMTOP Structure Objects
print.sse | Secondary Structure Analysis with DSSP or STRIDE
print.xyz | Printing XYZ coordinates
project.pca | Project Data onto Principal Components
prune.cna | Prune A cna Network Object
pymol | Biomolecular Visualization with PyMOL
pymol.dccm | Biomolecular Visualization with PyMOL
pymol.modes | Biomolecular Visualization with PyMOL
pymol.nma | Biomolecular Visualization with PyMOL
pymol.pca | Biomolecular Visualization with PyMOL
pymol.pdbs | Biomolecular Visualization with PyMOL

## -- R --

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.pdb2 | 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
rmsip.default | Root Mean Square Inner Product
rmsip.enma | Root Mean Square Inner Product
rot.lsq | Coordinate Superposition
rtb | All Atom Normal Mode Analysis

## -- S --

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
sip.default | Square Inner Product
sip.enma | Square Inner Product
sip.nma | Square Inner Product
sse.bridges | SSE Backbone Hydrogen Bonding
store.atom | Store all-atom data from a PDB object
stride | Secondary Structure Analysis with DSSP or STRIDE
struct.aln | Structure Alignment Of Two PDB Files
summary.cna | Summarize and Print Features of a cna Network Graph
summary.cnapath | Suboptimal Path Analysis for Correlation Networks
summary.pdb | Read PDB File

## -- T --

torsion.pdb | Calculate Mainchain and Sidechain Torsion/Dihedral Angles
torsion.xyz | Calculate Torsion/Dihedral Angles
transducin | Bio3d Example Data
trim | Trim a PDB Object To A Subset of Atoms.
trim.mol2 | Trim a MOL2 Object To A Subset of Atoms.
trim.pdb | Trim a PDB Object To A Subset of Atoms.
trim.pdbs | Filter or Trim a PDBs Object
trim.xyz | Trim a XYZ Object of Cartesian Coordinates.

## -- U --

unbound | Sequence Generation from a Bounds Vector
uniprot | Fetch UniProt Entry Data.

## -- V --

var.pdbs | Pairwise Distance Variance in Cartesian Coordinates
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.cna | View CNA Protein Structure Network Community Output in VMD
vmd.cnapath | View CNA Protein Structure Network Community Output in VMD
vmd_colors | VMD Color Palette

## -- W --

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

## -- X --

xyz2atom | Convert Between Atom and xyz Indices
xyz2z.pca | Project Data onto Principal Components

## -- Z --

z2xyz.pca | Project Data onto Principal Components

## -- misc --

.print.fasta.ali | Printing Sequence Alignments