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/usr/lib/R/site-library/bio3d/help/AnIndex 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.

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bio3d-package	bio3d.package
aa.index	aa.index
aa123	aa123
aa2index	aa2index
aa321	aa123
aln	kinesin
aln2html	aln2html
angle.xyz	angle.xyz
atom.select	atom.select
atom2xyz	atom2xyz
bio3d	bio3d.package
blast.pdb	blast.pdb
bounds	bounds
bwr.colors	bwr.colors
chain.pdb	chain.pdb
cmap	cmap
consensus	consensus
conserv	conserv
convert.pdb	convert.pdb
core	kinesin
core.find	core.find
dccm	dccm
diag.ind	diag.ind
difference.vector	difference.vector
dist.xyz	dist.xyz
dm	dm
dm.xyz	dm
dssp	dssp
entropy	entropy
fit.xyz	fit.xyz
gap.inspect	gap.inspect
get.pdb	get.pdb
get.seq	get.seq
ide.filter	ide.filter
identity	identity
is.gap	is.gap
kinesin	kinesin
lbio3d	lbio3d
mktrj.pca	mktrj.pca
mono.colors	bwr.colors
motif.find	motif.find
orient.pdb	orient.pdb
overlap	overlap
pairwise	pairwise
pc.xray	kinesin
pca.project	pca.project
pca.tor	pca.tor
pca.xyz	pca.xyz
pca.xyz2z	pca.project
pca.z2xyz	pca.project
pdb.summary	atom.select
pdbaln	pdbaln
pdbs	kinesin
plot.bio3d	plot.bio3d
plot.blast	plot.blast
plot.core	plot.core
plot.dccm	plot.dccm
plot.dmat	plot.dmat
plot.pca	plot.pca
plot.pca.loadings	plot.pca.loadings
plot.pca.score	plot.pca
plot.pca.scree	plot.pca
print.core	print.core
print.pdb	read.pdb
print.rle2	rle2
read.all	read.all
read.crd	read.crd
read.dcd	read.dcd
read.fasta	read.fasta
read.fasta.pdb	read.fasta.pdb
read.ncdf	read.ncdf
read.pdb	read.pdb
read.pdcBD	read.pdcBD
read.pqr	read.pqr
rle2	rle2
rmsd	rmsd
rmsd.filter	rmsd.filter
rmsf	rmsf
rmsip	rmsip
rot.lsq	fit.xyz
seq.pdb	seq.pdb
seq2aln	seq2aln
seqaln	seqaln
seqaln.pair	seqaln.pair
seqbind	seqbind
split.pdb	split.pdb
sse	kinesin
store.atom	store.atom
stride	stride
torsion.pdb	torsion.pdb
torsion.xyz	torsion.xyz
trim.pdb	trim.pdb
unbound	unbound
vec2resno	vec2resno
wiki.tbl	wiki.tbl
wrap.tor	wrap.tor
write.crd	write.crd
write.fasta	write.fasta
write.ncdf	write.ncdf
write.pdb	write.pdb
write.pqr	write.pqr
xyz	kinesin