/usr/lib/R/site-library/bio3d/INDEX is in r-other-bio3d 1.1-5-1build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 | 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
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-package 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.find Identification of Invariant Core Positions
dccm DCCM: Dynamical Cross-Correlation Matrix
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
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
motif.find Find Sequence Motifs.
orient.pdb Orient a PDB Structure
overlap Overlap analysis
pairwise Pair Indices
pca.project Project Data onto Principal Components
pca.tor Principal Component Analysis
pca.xyz Principal Component Analysis
pdbaln Sequence Alignment of PDB Files
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
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
rle2 Run Length Encoding with Indices
rmsd Root Mean Square Deviation
rmsd.filter RMSD Filter
rmsf Atomic RMS Fluctuations
rmsip Root Mean Square Inner Product
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.
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
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