API for bio3d
Biological Structure Analysis

Global functions
.arg.filter	Source code
.calcAlnModes	Source code
.calcRMSIP	Source code
.check.residue.ambiguity	Source code
.check.sse	Source code
.cij.cutoff.guess	Source code
.close.pb	Source code
.cnapath.core	Source code
.cov2dccm	Source code
.diag.rtb	Source code
.dm.xyz1	Source code
.ebi_msa	Source code
.fetchmodes	Source code
.format.log	Source code
.format_tbl	Source code
.get.exepath	Source code
.inds2ids	Source code
.init.pb	Source code
.map_terms	Source code
.match.chain	Source code
.match.elena	Source code
.match.eleno	Source code
.match.elety	Source code
.match.insert	Source code
.match.resid	Source code
.match.resno	Source code
.match.segid	Source code
.match.statbit	Source code
.match.type	Source code
.nma.trim.hessian.rtb	Source code
.parse.pdb.remark350	Source code
.print.fasta.ali	Man page Source code
.read_cif	Source code
.read_crd	Source code
.read_pdb	Source code
.read_prmtop	Source code
.resno2str	Source code
.string2json	Source code
.test.exefile	Source code
.tr	Source code
.update.chain	Source code
.update.log	Source code
.update.pb	Source code
`aln2html`	Source code
`blast.pdb`	Source code
`chain.pdb`	Source code
`cna`	Source code
`conserv`	Source code
`dccm.xyz`	Source code
`dccm`	Source code
`dist.xyz`	Source code
`get.seq`	Source code
`is.gap`	Source code
`motif.find`	Source code
`pdbseq`	Source code
`pdbsplit`	Source code
`plot.blast`	Source code
`plot.core`	Source code
`plot.hmmer`	Source code
`plot.pca.scree`	Source code
`plot.pca`	Source code
`read.ncdf`	Source code
`seqaln.pair`	Source code
`vec2resno`	Source code
`write.ncdf`	Source code
aa.index	Man page
aa.table	Man page
aa123	Man page
aa2index	Man page
aa2mass	Man page
aa321	Man page
aanma	Man page
aanma.pdb	Man page
aanma.pdbs	Man page Source code
aln2html	Man page
amsm.xyz	Man page
angle.xyz	Man page
annotation	Man page
as.fasta	Man page
as.pdb	Man page Source code
as.pdb.default	Man page Source code
as.pdb.mol2	Man page Source code
as.pdb.prmtop	Man page Source code
as.select	Man page
as.xyz	Man page
atom.index	Man page
atom.select	Man page
atom.select.mol2	Man page Source code
atom.select.pdb	Man page Source code
atom.select.pdbs	Man page Source code
atom.select.prmtop	Man page
atom2ele	Man page Source code
atom2ele.default	Man page Source code
atom2ele.pdb	Man page Source code
atom2mass	Man page Source code
atom2mass.default	Man page Source code
atom2mass.pdb	Man page Source code
atom2xyz	Man page
basename.pdb	Man page Source code
bhattacharyya	Man page Source code
bhattacharyya.array	Man page Source code
bhattacharyya.enma	Man page Source code
bhattacharyya.matrix	Man page Source code
bhattacharyya.nma	Man page Source code
bhattacharyya.pca	Man page Source code
binding.site	Man page
bio3d	Man page
bio3d-package	Man page
biounit	Man page Source code
blast.pdb	Man page
bounds	Man page
bounds.sse	Man page Source code
build.hessian	Man page
bwr.colors	Man page
cat.pdb	Man page Source code
chain.pdb	Man page
check.utility	Man page Source code
clean.pdb	Man page
cmap	Man page Source code
cmap.default	Man page Source code
cmap.pdb	Man page Source code
cmap.pdbs	Man page Source code
cmap.xyz	Man page Source code
cna	Man page
cna.dccm	Man page Source code
cna.ensmb	Man page Source code
cnapath	Man page Source code
com	Man page
com.pdb	Man page
com.xyz	Man page
combine.select	Man page Source code
community.aln	Man page Source code
community.tree	Man page Source code
consensus	Man page
conserv	Man page
convert.pdb	Man page
core	Man page
core.cmap	Man page
core.find	Man page Source code
core.find.default	Man page Source code
core.find.pdb	Man page Source code
core.find.pdbs	Man page
cov.enma	Man page Source code
cov.nma	Man page Source code
covsoverlap	Man page Source code
covsoverlap.enma	Man page Source code
covsoverlap.nma	Man page Source code
dccm	Man page
dccm.egnm	Man page
dccm.enma	Man page
dccm.gnm	Man page
dccm.nma	Man page
dccm.pca	Man page
dccm.xyz	Man page
deformation.nma	Man page
diag.ind	Man page
difference.vector	Man page
dist.xyz	Man page
dm	Man page
dm.pdb	Man page
dm.pdbs	Man page
dm.xyz	Man page Source code
dssp	Man page
dssp.pdb	Man page
dssp.pdbs	Man page
dssp.xyz	Man page Source code
elements	Man page
entropy	Man page
example.data	Man page
ff.aaenm	Man page
ff.aaenm2	Man page Source code
ff.anm	Man page
ff.calpha	Man page
ff.pfanm	Man page
ff.reach	Man page
ff.sdenm	Man page
filter.cmap	Man page Source code
filter.dccm	Man page Source code
filter.identity	Man page Source code
filter.rmsd	Man page Source code
fit.xyz	Man page
fluct.nma	Man page
formula2mass	Man page
gap.inspect	Man page
geostas	Man page Source code
geostas.default	Man page Source code
geostas.enma	Man page Source code
geostas.nma	Man page Source code
geostas.pdb	Man page Source code
geostas.pdbs	Man page Source code
geostas.xyz	Man page Source code
get.blast	Man page Source code
get.pdb	Man page
get.seq	Man page
gnm	Man page Source code
gnm.pdb	Man page Source code
gnm.pdbs	Man page Source code
hclustplot	Man page
hivp	Man page
hmmer	Man page
identify.cna	Man page Source code
inner.prod	Man page
inspect.connectivity	Man page
is.gap	Man page
is.mol2	Man page Source code
is.pdb	Man page Source code
is.pdbs	Man page Source code
is.select	Man page Source code
is.xyz	Man page Source code
kinesin	Man page
layout.cna	Man page Source code
lbio3d	Man page
load.enmff	Man page
mask	Man page Source code
mask.dccm	Man page Source code
mktrj	Man page
mktrj.enma	Man page
mktrj.nma	Man page
mktrj.pca	Man page
mono.colors	Man page
motif.find	Man page
mustang	Man page
network.amendment	Man page Source code
nma	Man page
nma.pdb	Man page
nma.pdbs	Man page
normalize.vector	Man page
orient.pdb	Man page
overlap	Man page
pairwise	Man page
pca	Man page
pca.array	Man page
pca.pdbs	Man page
pca.tor	Man page
pca.xyz	Man page
pdb.annotate	Man page
pdb.pfam	Man page Source code
pdb2aln	Man page
pdb2aln.ind	Man page
pdb2sse	Man page Source code
pdbaln	Man page Source code
pdbfit	Man page Source code
pdbfit.pdb	Man page Source code
pdbfit.pdbs	Man page Source code
pdbs	Man page
pdbs2pdb	Man page
pdbs2sse	Man page
pdbseq	Man page
pdbsplit	Man page
pfam	Man page
plot.bio3d	Man page Source code
plot.blast	Man page
plot.cmap	Man page Source code
plot.cna	Man page Source code
plot.cnapath	Man page Source code
plot.core	Man page
plot.dccm	Man page Source code
plot.dmat	Man page
plot.ecna	Man page Source code
plot.ecnapath	Man page Source code
plot.enma	Man page
plot.fasta	Man page
plot.fluct	Man page
plot.geostas	Man page Source code
plot.hmmer	Man page
plot.matrix.loadings	Man page Source code
plot.nma	Man page
plot.pca	Man page
plot.pca.loadings	Man page
plot.pca.score	Man page
plot.pca.scree	Man page
plot.rmsip	Man page
plotb3	Man page Source code
print.cna	Man page Source code
print.cnapath	Man page Source code
print.core	Man page Source code
print.enma	Man page
print.fasta	Man page Source code
print.geostas	Man page
print.mol2	Man page Source code
print.nma	Man page
print.pca	Man page
print.pdb	Man page Source code
print.prmtop	Man page Source code
print.rle2	Man page Source code
print.select	Man page Source code
print.sse	Man page
print.xyz	Man page Source code
project.pca	Man page
prune.cna	Man page Source code
pymol	Man page Source code
pymol.dccm	Man page Source code
pymol.modes	Man page Source code
pymol.nma	Man page Source code
pymol.pca	Man page Source code
pymol.pdbs	Man page Source code
read.all	Man page
read.cif	Man page Source code
read.crd	Man page
read.crd.amber	Man page Source code
read.crd.charmm	Man page
read.dcd	Man page
read.fasta	Man page
read.fasta.pdb	Man page
read.mol2	Man page
read.ncdf	Man page
read.pdb	Man page Source code
read.pdb2	Man page
read.pdcBD	Man page
read.pqr	Man page
read.prmtop	Man page Source code
rgyr	Man page Source code
rle2	Man page
rmsd	Man page
rmsf	Man page
rmsip	Man page Source code
rmsip.default	Man page Source code
rmsip.enma	Man page Source code
rot.lsq	Man page
rtb	Man page Source code
sdENM	Man page
seq2aln	Man page Source code
seqaln	Man page
seqaln.pair	Man page
seqbind	Man page Source code
seqidentity	Man page
setup.ncore	Man page Source code
sip	Man page Source code
sip.default	Man page Source code
sip.enma	Man page Source code
sip.nma	Man page Source code
sse.bridges	Man page
store.atom	Man page
stride	Man page
struct.aln	Man page
summary.cna	Man page Source code
summary.cnapath	Man page Source code
summary.pdb	Man page Source code
torsion.pdb	Man page
torsion.xyz	Man page
transducin	Man page
trim	Man page Source code
trim.mol2	Man page Source code
trim.pdb	Man page
trim.pdbs	Man page Source code
trim.xyz	Man page
unbound	Man page
uniprot	Man page Source code
var.pdbs	Man page
var.xyz	Man page
vec2resno	Man page
vmd	Man page Source code
vmd.cna	Man page Source code
vmd.cnapath	Man page Source code
vmd.ecna	Man page Source code
vmd.ecnapath	Man page Source code
vmd_colors	Man page Source code
wrap.tor	Man page
write.crd	Man page
write.fasta	Man page
write.mol2	Man page Source code
write.ncdf	Man page
write.pdb	Man page
write.pir	Man page
write.pqr	Man page
xyz2atom	Man page Source code
xyz2z.pca	Man page Source code
z2xyz.pca	Man page Source code