Biological Structure Analysis

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Documentation for package ‘bio3d’ version 2.4-4

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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.pdbs 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.pdbs 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.cmap Identification of Contact Map Core Positions
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
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 Dynamical Cross-Correlation Matrix from Principal Component Analysis
dccm.xyz Dynamical Cross-Correlation Matrix from Cartesian Coordinates
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
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.cnapath Suboptimal Path Analysis for Correlation Networks
plot.core Plot Core Fitting Progress
plot.dccm DCCM Plot
plot.dmat Plot Distance Matrix
plot.ecna Protein Structure Network Plots in 2D and 3D.
plot.ecnapath Suboptimal Path Analysis for Correlation Networks
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.ecna View CNA Protein Structure Network Community Output in VMD
vmd.ecnapath 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