Man pages for bio3d
Biological Structure Analysis

aa123Convert Between 1-letter and 3-letter Aminoacid Codes
aa2indexConvert an Aminoacid Sequence to AAIndex Values
aa2massAmino Acid Residues to Mass Converter
aa.indexAAindex: Amino Acid Index Database
aanma.pdbAll Atom Normal Mode Analysis
aanma.pdbsEnsemble Normal Mode Analysis with All-Atom ENM
aa.tableTable of Relevant Amino Acids
aln2htmlCreate a HTML Page For a Given Alignment
angle.xyzCalculate the Angle Between Three Atoms
as.fastaAlignment to FASTA object
as.pdbConvert to PDB format
as.selectConvert Atomic Indices to a Select Object
atom2eleAtom Names/Types to Atomic Symbols Converter
atom2massAtom Names/Types to Mass Converter
atom2xyzConvert Between Atom and xyz Indices
atom.indexAtom Names/Types
atom.selectAtom Selection from PDB and PRMTOP Structure Objects
basename.pdbManipulate PDB File Names
bhattacharyyaBhattacharyya Coefficient
binding.siteBinding Site Residues
bio3d.packageBiological Structure Analysis
biounitBiological Units Construction
blast.pdbNCBI BLAST Sequence Search and Summary Plot of Hit Statistics
boundsBounds of a Numeric Vector
bounds.sseObtain A SSE Object From An SSE Sequence Vector
bwr.colorsColor Palettes
cat.pdbConcatenate Multiple PDB Objects
chain.pdbFind Possible PDB Chain Breaks
check.utilityCheck on Missing Utility Programs
clean.pdbInspect And Clean Up A PDB Object
cmapContact Map
cnaProtein Dynamic Correlation Network Construction and...
cnapathSuboptimal Path Analysis for Correlation Networks
comCenter of Mass
combine.selectCombine Atom Selections From PDB Structure
community.alnAlign communities from two or more networks
community.treeReconstruction of the Girvan-Newman Community Tree for a CNA...
consensusSequence Consensus for an Alignment
conservScore Residue Conservation At Each Position in an Alignment
convert.pdbRenumber and Convert Between Various PDB formats
core.findIdentification of Invariant Core Positions
cov.nmaCalculate Covariance Matrix from Normal Modes
covsoverlapCovariance Overlap
dccmDCCM: Dynamical Cross-Correlation Matrix
dccm.enmaCross-Correlation for Ensemble NMA (eNMA)
dccm.gnmDynamic Cross-Correlation from Gaussian Network Model
dccm.nmaDynamic Cross-Correlation from Normal Modes Analysis
dccm.pcaDynamic Cross-Correlation from Principal Component Analysis
dccm.xyzDCCM: Dynamical Cross-Correlation Matrix
deformation.nmaDeformation Analysis
diag.indDiagonal Indices of a Matrix
difference.vectorDifference Vector
dist.xyzCalculate the Distances Between the Rows of Two Matrices
dmDistance Matrix Analysis
dsspSecondary Structure Analysis with DSSP or STRIDE
elementsPeriodic Table of the Elements
entropyShannon Entropy Score
example.dataBio3d Example Data
filter.cmapContact Map Consensus Filtering
filter.dccmFilter for Cross-correlation Matrices (Cij)
filter.identityPercent Identity Filter
filter.rmsdRMSD Filter
fit.xyzCoordinate Superposition
fluct.nmaNMA Fluctuations
formula2massChemical Formula to Mass Converter
gap.inspectAlignment Gap Summary
geostasGeoStaS Domain Finder
get.pdbDownload PDB Coordinate Files
get.seqDownload FASTA Sequence Files
gnmGaussian Network Model
hclustplotDendrogram with Clustering Annotation
hmmerHMMER Sequence Search
identify.cnaIdentify Points in a CNA Protein Structure Network Plot
inner.prodMass-weighted Inner Product
inspect.connectivityCheck the Connectivity of Protein Structures
is.gapGap Characters
is.mol2Is an Object of Class 'mol2'?
is.pdbIs an Object of Class 'pdb(s)'?
is.selectIs an Object of Class 'select'?
is.xyzIs an Object of Class 'xyz'?
layout.cnaProtein Structure Network Layout
lbio3dList all Functions in the bio3d Package
lmiLMI: Linear Mutual Information Matrix
load.enmffENM Force Field Loader
mask.dccmMask a Subset of Atoms in a DCCM Object.
mktrjPCA / NMA Atomic Displacement Trajectory
motif.findFind Sequence Motifs.
mustangStructure-based Sequence Alignment with MUSTANG
network.amendmentAmendment of a CNA Network According To A Input Community...
nmaNormal Mode Analysis
nma.pdbNormal Mode Analysis
nma.pdbsEnsemble Normal Mode Analysis
normalize.vectorMass-Weighted Normalized Vector
orient.pdbOrient a PDB Structure
overlapOverlap analysis
pairwisePair Indices
pcaPrincipal Component Analysis
pca.arrayPrincipal Component Analysis of an array of matrices
pca.pdbsPrincipal Component Analysis
pca.torPrincipal Component Analysis
pca.xyzPrincipal Component Analysis
pdb2alnAlign a PDB structure to an existing alignment
pdb2aln.indMapping from alignment positions to PDB atomic indices
pdb2sseObtain An SSE Sequence Vector From A PDB Object
pdbalnSequence Alignment of PDB Files
pdb.annotateGet Customizable Annotations From PDB Or PFAM Databases
pdbfitPDB File Coordinate Superposition
pdbs2pdbPDBs to PDB Converter
pdbs2sseSSE annotation for a PDBs Object
pdbseqExtract The Aminoacid Sequence From A PDB Object
pdbsplitSplit a PDB File Into Separate Files, One For Each Chain.
pfamDownload Pfam FASTA Sequence Alignment
plot.bio3dPlots with marginal SSE annotation
plot.cmapPlot Contact Matrix
plot.cnaProtein Structure Network Plots in 2D and 3D.
plot.corePlot Core Fitting Progress
plot.dccmDCCM Plot
plot.dmatPlot Distance Matrix
plot.enmaPlot eNMA Results
plot.fastaPlot a Multiple Sequence Alignment
plot.fluctPlot Fluctuations
plot.geostasPlot Geostas Results
plot.hmmerPlot a Summary of HMMER Hit Statistics.
plot.matrix.loadingsPlot Residue-Residue Matrix Loadings
plot.nmaPlot NMA Results
plot.pcaPlot PCA Results
plot.pca.loadingsPlot Residue Loadings along PC1 to PC3
plot.rmsipPlot RMSIP Results
print.cnaSummarize and Print Features of a cna Network Graph
print.corePrinting Core Positions and Returning Indices
print.fastaPrinting Sequence Alignments
print.xyzPrinting XYZ coordinates
project.pcaProject Data onto Principal Components
prune.cnaPrune A cna Network Object
pymolBiomolecular Visualization with PyMOL
read.allRead Aligned Structure Data
read.cifRead mmCIF File
read.crdRead Coordinate Data from Amber or Charmm
read.crd.amberRead AMBER Coordinate files
read.crd.charmmRead CRD File
read.dcdRead CHARMM/X-PLOR/NAMD Binary DCD files
read.fastaRead FASTA formated Sequences
read.fasta.pdbRead Aligned Structure Data
read.mol2Read MOL2 File
read.ncdfRead AMBER Binary netCDF files
read.pdbRead PDB File
read.pdcBDRead PQR output from pdcBD File
read.pqrRead PQR File
read.prmtopRead AMBER Parameter/Topology files
rgyrRadius of Gyration
rle2Run Length Encoding with Indices
rmsdRoot Mean Square Deviation
rmsfAtomic RMS Fluctuations
rmsipRoot Mean Square Inner Product
sdENMIndex for the sdENM ff
seq2alnAdd a Sequence to an Existing Alignmnet
seqalnSequence Alignment with MUSCLE
seqaln.pairSequence Alignment of Identical Protein Sequences
seqbindCombine Sequences by Rows Without Recycling
seqidentityPercent Identity
setup.ncoreSetup for Running Bio3D Functions using Multiple CPU Cores
sipSquare Inner Product
sse.bridgesSSE Backbone Hydrogen Bonding
store.atomStore all-atom data from a PDB object
struct.alnStructure Alignment Of Two PDB Files
torsion.pdbCalculate Mainchain and Sidechain Torsion/Dihedral Angles
torsion.xyzCalculate Torsion/Dihedral Angles
trim.mol2Trim a MOL2 Object To A Subset of Atoms.
trim.pdbTrim a PDB Object To A Subset of Atoms.
trim.pdbsFilter or Trim a PDBs Object
trim.xyzTrim a XYZ Object of Cartesian Coordinates.
unboundSequence Generation from a Bounds Vector
uniprotFetch UniProt Entry Data.
var.xyzPairwise Distance Variance in Cartesian Coordinates
vec2resnoReplicate Per-residue Vector Values
vmd.cnaView CNA Protein Structure Network Community Output in VMD
vmd_colorsVMD Color Palette
wrap.torWrap Torsion Angle Data
write.crdWrite CRD File
write.fastaWrite FASTA Formated Sequences
write.mol2Write MOL2 Format Coordinate File
write.ncdfWrite AMBER Binary netCDF files
write.pdbWrite PDB Format Coordinate File
write.pirWrite PIR Formated Sequences
write.pqrWrite PQR Format Coordinate File
bio3d documentation built on April 3, 2018, 9:05 a.m.