Biological Structure Analysis

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Documentation for package ‘bio3d’ version 1.1-3

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bio3d-package Biological Structure Analysis
aa.index AAindex: Amino Acid Index Database
aa123 Convert Between 1-letter and 3-letter Aminoacid Codes
aa2index Convert an Aminoacid Sequence to AAIndex Values
aa321 Convert Between 1-letter and 3-letter Aminoacid Codes
aln Bio3d Example Data
aln2html Create a HTML Page For a Given Alignment
angle.xyz Calculate the Angle Between Three Atoms
atom.select Atom Selection From PDB Structure
atom2xyz Convert Between Atom and xyz Indices
bio3d Biological Structure Analysis
blast.pdb NCBI BLAST Sequence Search
bounds Bounds of a Numeric Vector
bwr.colors Color Palettes
chain.pdb Find Possible PDB Chain Breaks
cmap Contact Map
consensus Sequence Consensus for an Alignment
conserv Score Residue Conservation At Each Position in an Alignment
convert.pdb Convert Between Various PDB formats
core Bio3d Example Data
core.find Identification of Invariant Core Positions
dccm DCCM: Dynamical Cross-Correlation Matrix
diag.ind Diagonal Indices of a Matrix
dist.xyz Calculate the Distances Between the Rows of Two Matrices
dm Distance Matrix Analysis
dm.xyz Distance Matrix Analysis
dssp Secondary Structure Analysis with DSSP
entropy Shannon Entropy Score
fit.xyz Coordinate Superposition
gap.inspect Alignment Gap Summary
get.pdb Download PDB Coordinate Files
get.seq Download FASTA Sequence Files
ide.filter Percent Identity Filter
identity Percent Identity
is.gap Gap Characters
kinesin Bio3d Example Data
lbio3d List all Functions in the bio3d Package
mktrj.pca PCA Atomic Displacement Trajectory
mono.colors Color Palettes
motif.find Find Sequence Motifs.
orient.pdb Orient a PDB Structure
pairwise Pair Indices
pc.xray Bio3d Example Data
pca.project Project Data onto Principal Components
pca.tor Principal Component Analysis
pca.xyz Principal Component Analysis
pca.xyz2z Project Data onto Principal Components
pca.z2xyz Project Data onto Principal Components
pdb.summary Atom Selection From PDB Structure
pdbaln Sequence Alignment of PDB Files
pdbs Bio3d Example Data
plot.bio3d Plots with marginal SSE annotation
plot.blast Plot a Summary of BLAST Hit Statistics.
plot.core Plot Core Fitting Progress
plot.dccm DCCM Plot
plot.dmat Plot Distance Matrix
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
print.core Printing Core Positions and Returning Indices
read.all Read Aligned Structure Data
read.crd 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.ncdf Read AMBER Binary netCDF files
read.pdb Read PDB File
read.pdcBD Read PQR output from pdcBD File
read.pqr Read PQR File
rmsd Root Mean Square Deviation
rmsd.filter RMSD Filter
rmsf Atomic RMS Fluctuations
rot.lsq Coordinate Superposition
seq.pdb Extract The Aminoacid Sequence From A PDB Object
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
split.pdb Split a PDB File Into Separate Files, One For Each Chain.
sse Bio3d Example Data
store.atom Store all-atom data from a PDB object
stride Secondary Structure Analysis with STRIDE
torsion.pdb Calculate Mainchain and Sidechain Torsion/Dihedral Angles
torsion.xyz Calculate Torsion/Dihedral Angles
trim.pdb Trim a PDB Object To A Subset of Atoms.
unbound Sequence Generation from a Bounds Vector
vec2resno Replicate Per-residue Vector Values
wiki.tbl Wiki Table
wrap.tor Wrap Torsion Angle Data
write.crd Write CRD File
write.fasta Write FASTA Formated Sequences
write.ncdf Write AMBER Binary netCDF files
write.pdb Write PDB Format Coordinate File
write.pqr Write PQR Format Coordinate File
xyz Bio3d Example Data