bio3d: Biological Structure Analysis

Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.

AuthorBarry Grant [aut, cre], Xin-Qiu Yao [aut], Lars Skjaerven [aut], Julien Ide [aut]
Date of publication2016-11-12 00:26:53
MaintainerBarry Grant <bjgrant@umich.edu>
LicenseGPL (>= 2)
Version2.3-1
http://thegrantlab.org/bio3d/
http://bitbucket.org/Grantlab/bio3d

View on CRAN

Man pages

aa123: Convert Between 1-letter and 3-letter Aminoacid Codes

aa2index: Convert an Aminoacid Sequence to AAIndex Values

aa2mass: Amino Acid Residues to Mass Converter

aa.index: AAindex: Amino Acid Index Database

aanma.pdb: All Atom Normal Mode Analysis

aanma.pdbs: Ensemble Normal Mode Analysis with All-Atom ENM

aa.table: Table of Relevant Amino Acids

aln2html: Create a HTML Page For a Given Alignment

angle.xyz: Calculate the Angle Between Three Atoms

as.fasta: Alignment to FASTA object

as.pdb: Convert to PDB format

as.select: Convert Atomic Indices to a Select Object

atom2ele: Atom Names/Types to Atomic Symbols Converter

atom2mass: Atom Names/Types to Mass Converter

atom2xyz: Convert Between Atom and xyz Indices

atom.index: Atom Names/Types

atom.select: Atom Selection from PDB and PRMTOP Structure Objects

basename.pdb: Manipulate PDB File Names

bhattacharyya: Bhattacharyya Coefficient

binding.site: Binding Site Residues

bio3d.package: Biological Structure Analysis

biounit: Biological Units Construction

blast.pdb: NCBI BLAST Sequence Search and Summary Plot of Hit Statistics

bounds: Bounds of a Numeric Vector

bounds.sse: Obtain A SSE Object From An SSE Sequence Vector

bwr.colors: Color Palettes

cat.pdb: Concatenate Multiple PDB Objects

chain.pdb: Find Possible PDB Chain Breaks

check.utility: Check on Missing Utility Programs

clean.pdb: Inspect And Clean Up A PDB Object

cmap: Contact Map

cna: Protein Dynamic Correlation Network Construction and...

cnapath: Suboptimal Path Analysis for Correlation Networks

com: Center of Mass

combine.select: Combine Atom Selections From PDB Structure

community.aln: Align communities from two or more networks

community.tree: Reconstruction of the Girvan-Newman Community Tree for a CNA...

consensus: Sequence Consensus for an Alignment

conserv: Score Residue Conservation At Each Position in an Alignment

convert.pdb: Renumber and Convert Between Various PDB formats

core.find: Identification of Invariant Core Positions

cov.nma: Calculate Covariance Matrix from Normal Modes

covsoverlap: Covariance Overlap

dccm: DCCM: Dynamical Cross-Correlation Matrix

dccm.enma: Cross-Correlation for Ensemble NMA (eNMA)

dccm.gnm: Dynamic Cross-Correlation from Gaussian Network Model

dccm.nma: Dynamic Cross-Correlation from Normal Modes Analysis

dccm.pca: Dynamic Cross-Correlation from Principal Component Analysis

dccm.xyz: DCCM: Dynamical Cross-Correlation Matrix

deformation.nma: Deformation Analysis

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 or STRIDE

elements: Periodic Table of the Elements

entropy: Shannon Entropy Score

example.data: Bio3d Example Data

filter.cmap: Contact Map Consensus Filtering

filter.dccm: Filter for Cross-correlation Matrices (Cij)

filter.identity: Percent Identity Filter

filter.rmsd: RMSD Filter

fit.xyz: Coordinate Superposition

fluct.nma: NMA Fluctuations

formula2mass: Chemical Formula to Mass Converter

gap.inspect: Alignment Gap Summary

geostas: GeoStaS Domain Finder

get.pdb: Download PDB Coordinate Files

get.seq: Download FASTA Sequence Files

gnm: Gaussian Network Model

hclustplot: Dendrogram with Clustering Annotation

hmmer: HMMER Sequence Search

identify.cna: Identify Points in a CNA Protein Structure Network Plot

inner.prod: Mass-weighted Inner Product

inspect.connectivity: Check the Connectivity of Protein Structures

is.gap: Gap Characters

is.mol2: Is an Object of Class 'mol2'?

is.pdb: Is an Object of Class 'pdb(s)'?

is.select: Is an Object of Class 'select'?

is.xyz: Is an Object of Class 'xyz'?

layout.cna: Protein Structure Network Layout

lbio3d: List all Functions in the bio3d Package

lmi: LMI: Linear Mutual Information Matrix

load.enmff: ENM Force Field Loader

mask.dccm: Mask a Subset of Atoms in a DCCM Object.

mktrj: PCA / NMA Atomic Displacement Trajectory

motif.find: Find Sequence Motifs.

mustang: Structure-based Sequence Alignment with MUSTANG

network.amendment: Amendment of a CNA Network According To A Input Community...

nma: Normal Mode Analysis

nma.pdb: Normal Mode Analysis

nma.pdbs: Ensemble Normal Mode Analysis

normalize.vector: Mass-Weighted Normalized Vector

orient.pdb: Orient a PDB Structure

overlap: Overlap analysis

pairwise: Pair Indices

pca: Principal Component Analysis

pca.array: Principal Component Analysis of an array of matrices

pca.pdbs: Principal Component Analysis

pca.tor: Principal Component Analysis

pca.xyz: Principal Component Analysis

pdb2aln: Align a PDB structure to an existing alignment

pdb2aln.ind: Mapping from alignment positions to PDB atomic indices

pdb2sse: Obtain An SSE Sequence Vector From A PDB Object

pdbaln: Sequence Alignment of PDB Files

pdb.annotate: Get Customizable Annotations From PDB Or PFAM Databases

pdbfit: PDB File Coordinate Superposition

pdbs2pdb: PDBs to PDB Converter

pdbs2sse: SSE annotation for a PDBs Object

pdbseq: Extract The Aminoacid Sequence From A PDB Object

pdbsplit: Split a PDB File Into Separate Files, One For Each Chain.

pfam: Download Pfam FASTA Sequence Alignment

plot.bio3d: Plots with marginal SSE annotation

plot.cmap: Plot Contact Matrix

plot.cna: Protein Structure Network Plots in 2D and 3D.

plot.core: Plot Core Fitting Progress

plot.dccm: DCCM Plot

plot.dmat: Plot Distance Matrix

plot.enma: Plot eNMA Results

plot.fasta: Plot a Multiple Sequence Alignment

plot.fluct: Plot Fluctuations

plot.geostas: Plot Geostas Results

plot.hmmer: Plot a Summary of HMMER Hit Statistics.

plot.matrix.loadings: Plot Residue-Residue Matrix Loadings

plot.nma: Plot NMA Results

plot.pca: Plot PCA Results

plot.pca.loadings: Plot Residue Loadings along PC1 to PC3

plot.rmsip: Plot RMSIP Results

print.cna: Summarize and Print Features of a cna Network Graph

print.core: Printing Core Positions and Returning Indices

print.fasta: Printing Sequence Alignments

print.xyz: Printing XYZ coordinates

project.pca: Project Data onto Principal Components

prune.cna: Prune A cna Network Object

pymol: Biomolecular Visualization with PyMOL

read.all: Read Aligned Structure Data

read.cif: Read mmCIF File

read.crd: Read Coordinate Data from Amber or Charmm

read.crd.amber: Read AMBER Coordinate files

read.crd.charmm: 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.mol2: Read MOL2 File

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

read.prmtop: Read AMBER Parameter/Topology files

rgyr: Radius of Gyration

rle2: Run Length Encoding with Indices

rmsd: Root Mean Square Deviation

rmsf: Atomic RMS Fluctuations

rmsip: Root Mean Square Inner Product

sdENM: Index for the sdENM ff

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

seqidentity: Percent Identity

setup.ncore: Setup for Running Bio3D Functions using Multiple CPU Cores

sip: Square Inner Product

sse.bridges: SSE Backbone Hydrogen Bonding

store.atom: Store all-atom data from a PDB object

struct.aln: Structure Alignment Of Two PDB Files

torsion.pdb: Calculate Mainchain and Sidechain Torsion/Dihedral Angles

torsion.xyz: Calculate Torsion/Dihedral Angles

trim.mol2: Trim a MOL2 Object To A Subset of Atoms.

trim.pdb: Trim a PDB Object To A Subset of Atoms.

trim.pdbs: Filter or Trim a PDBs Object

trim.xyz: Trim a XYZ Object of Cartesian Coordinates.

unbound: Sequence Generation from a Bounds Vector

uniprot: Fetch UniProt Entry Data.

var.xyz: Pairwise Distance Variance in Cartesian Coordinates

vec2resno: Replicate Per-residue Vector Values

vmd.cna: View CNA Protein Structure Network Community Output in VMD

vmd_colors: VMD Color Palette

wrap.tor: Wrap Torsion Angle Data

write.crd: Write CRD File

write.fasta: Write FASTA Formated Sequences

write.mol2: Write MOL2 Format Coordinate File

write.ncdf: Write AMBER Binary netCDF files

write.pdb: Write PDB Format Coordinate File

write.pir: Write PIR Formated Sequences

write.pqr: Write PQR Format Coordinate File

Functions

aa123 Man page
aa2index Man page
aa2mass Man page
aa321 Man page
aa.index Man page
aanma Man page
aanma.pdb Man page
aanma.pdbs Man page
aa.table Man page
aln2html Man page
amsm.xyz Man page
angle.xyz Man page
annotation Man page
as.fasta Man page
as.pdb Man page
as.pdb.default Man page
as.pdb.mol2 Man page
as.pdb.prmtop Man page
as.select Man page
as.xyz Man page
atom2ele Man page
atom2ele.default Man page
atom2ele.pdb Man page
atom2mass Man page
atom2mass.default Man page
atom2mass.pdb Man page
atom2xyz Man page
atom.index Man page
atom.select Man page
atom.select.mol2 Man page
atom.select.pdb Man page
atom.select.prmtop Man page
basename.pdb Man page
bhattacharyya Man page
bhattacharyya.array Man page
bhattacharyya.enma Man page
bhattacharyya.matrix Man page
bhattacharyya.nma Man page
bhattacharyya.pca Man page
binding.site Man page
bio3d Man page
bio3d-package Man page
biounit Man page
blast.pdb Man page
bounds Man page
bounds.sse Man page
build.hessian Man page
bwr.colors Man page
cat.pdb Man page
chain.pdb Man page
check.utility Man page
clean.pdb Man page
cmap Man page
cmap.default Man page
cmap.pdb Man page
cmap.xyz Man page
cna Man page
cna.dccm Man page
cna.ensmb Man page
cnapath Man page
com Man page
combine.select Man page
community.aln Man page
community.tree Man page
com.pdb Man page
com.xyz Man page
consensus Man page
conserv Man page
convert.pdb Man page
core Man page
core.find Man page
core.find.default Man page
core.find.pdb Man page
core.find.pdbs Man page
cov2dccm Man page
cov.enma Man page
cov.nma Man page
covsoverlap Man page
covsoverlap.enma Man page
covsoverlap.nma Man page
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
dssp Man page
dssp.pdb Man page
dssp.pdbs Man page
dssp.xyz Man page
elements Man page
entropy Man page
example.data Man page
ff.aaenm Man page
ff.aaenm2 Man page
ff.anm Man page
ff.calpha Man page
ff.pfanm Man page
ff.reach Man page
ff.sdenm Man page
filter.cmap Man page
filter.dccm Man page
filter.identity Man page
filter.rmsd Man page
fit.xyz Man page
fluct.nma Man page
formula2mass Man page
gap.inspect Man page
geostas Man page
geostas.default Man page
geostas.enma Man page
geostas.nma Man page
geostas.pdb Man page
geostas.pdbs Man page
geostas.xyz Man page
get.blast Man page
get.pdb Man page
get.seq Man page
gnm Man page
gnm.pdb Man page
gnm.pdbs Man page
hclustplot Man page
hivp Man page
hmmer Man page
identify.cna Man page
inner.prod Man page
inspect.connectivity Man page
is.gap Man page
is.mol2 Man page
is.pdb Man page
is.pdbs Man page
is.select Man page
is.xyz Man page
kinesin Man page
layout.cna Man page
lbio3d Man page
lmi Man page
load.enmff Man page
mask Man page
mask.dccm Man page
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
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
pdb2aln Man page
pdb2aln.ind Man page
pdb2sse Man page
pdbaln Man page
pdb.annotate Man page
pdbfit Man page
pdbfit.pdb Man page
pdbfit.pdbs Man page
pdb.pfam Man page
pdbs Man page
pdbs2pdb Man page
pdbs2sse Man page
pdbseq Man page
pdbsplit Man page
pfam Man page
plotb3 Man page
plot.bio3d Man page
plot.blast Man page
plot.cmap Man page
plot.cna Man page
plot.core Man page
plot.dccm Man page
plot.dmat Man page
plot.enma Man page
plot.fasta Man page
plot.fluct Man page
plot.geostas Man page
plot.hmmer Man page
plot.matrix.loadings Man page
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
print.cna Man page
print.cnapath Man page
print.core Man page
print.enma Man page
print.fasta Man page
.print.fasta.ali Man page
print.geostas Man page
print.mol2 Man page
print.nma Man page
print.pca Man page
print.pdb Man page
print.prmtop Man page
print.rle2 Man page
print.select Man page
print.sse Man page
print.xyz Man page
project.pca Man page
prune.cna Man page
pymol Man page
pymol.dccm Man page
pymol.modes Man page
pymol.nma Man page
pymol.pca Man page
pymol.pdbs Man page
read.all Man page
read.cif Man page
read.crd Man page
read.crd.amber Man page
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
read.pdb2 Man page
read.pdcBD Man page
read.pqr Man page
read.prmtop Man page
rgyr Man page
rle2 Man page
rmsd Man page
rmsf Man page
rmsip Man page
rmsip.default Man page
rmsip.enma Man page
rot.lsq Man page
rtb Man page
sdENM Man page
seq2aln Man page
seqaln Man page
seqaln.pair Man page
seqbind Man page
seqidentity Man page
setup.ncore Man page
sip Man page
sip.default Man page
sip.enma Man page
sip.nma Man page
sse.bridges Man page
store.atom Man page
stride Man page
struct.aln Man page
summary.cna Man page
summary.cnapath Man page
summary.pdb Man page
torsion.pdb Man page
torsion.xyz Man page
transducin Man page
trim Man page
trim.mol2 Man page
trim.pdb Man page
trim.pdbs Man page
trim.xyz Man page
unbound Man page
uniprot Man page
var.pdbs Man page
var.xyz Man page
vec2resno Man page
vmd Man page
vmd.cna Man page
vmd.cnapath Man page
vmd_colors Man page
wrap.tor Man page
write.crd Man page
write.fasta Man page
write.mol2 Man page
write.ncdf Man page
write.pdb Man page
write.pir Man page
write.pqr Man page
xyz2atom Man page
xyz2z.pca Man page
z2xyz.pca Man page

Files

bio3d
bio3d/inst
bio3d/inst/examples
bio3d/inst/examples/hivp.pdb
bio3d/inst/examples/aspirin.mol2
bio3d/inst/examples/hivp_xray.fa
bio3d/inst/examples/1dpx.pdb
bio3d/inst/examples/hivp.dcd
bio3d/inst/examples/1hel.pdb
bio3d/inst/examples/test.pdb
bio3d/inst/examples/transducin.fa
bio3d/inst/examples/crambin.inpcrd
bio3d/inst/examples/kif1a.fa
bio3d/inst/examples/crambin.prmtop
bio3d/inst/staticdocs
bio3d/inst/staticdocs/index.r
bio3d/inst/CITATION
bio3d/inst/doc
bio3d/inst/doc/bio3d_vignettes.html
bio3d/inst/doc/bio3d_vignettes.Rmd
bio3d/inst/matrices
bio3d/inst/matrices/bio3d.mat
bio3d/inst/matrices/pam30.mat
bio3d/inst/matrices/blosum62.mat
bio3d/inst/matrices/custom.mat
bio3d/inst/matrices/similarity.mat
bio3d/inst/matrices/emboss_properties.mat
bio3d/inst/matrices/properties.mat
bio3d/tests
bio3d/tests/testthat.R
bio3d/tests/testthat
bio3d/tests/testthat/test-read.pdb.R
bio3d/tests/testthat/test-seqaln.R
bio3d/tests/testthat/test-clean.pdb.R
bio3d/tests/testthat/test-dssp.R
bio3d/tests/testthat/test-core.find.R
bio3d/tests/testthat/test-aa2mass.R
bio3d/tests/testthat/test-nma.pdbs.R
bio3d/tests/testthat/test-pdbsplit.R
bio3d/tests/testthat/test-mol2.R
bio3d/tests/testthat/test-cmap.R
bio3d/tests/testthat/test-aanma.pdbs.R
bio3d/tests/testthat/test-nma.R
bio3d/tests/testthat/test-atom2mass.R
bio3d/tests/testthat/test-gnm.R
bio3d/tests/testthat/test-read.ncdf.R
bio3d/tests/testthat/test-deformation.R
bio3d/tests/testthat/test-vector-funs.R
bio3d/tests/testthat/test-aanma.R
bio3d/tests/testthat/test-atom.select.R
bio3d/tests/testthat/test-pdb.annotate.R
bio3d/tests/testthat/test-get.pdb.R
bio3d/tests/testthat/test-dccm.R
bio3d/tests/testthat/test-pca.R
bio3d/tests/testthat/test-overlap.R
bio3d/tests/testthat/test-read.all.R
bio3d/tests/testthat/test-cna.R
bio3d/tests/testthat/test-rmsd.R
bio3d/tests/testthat/test-fitting.R
bio3d/src
bio3d/src/Makevars
bio3d/src/read_pdb.cpp
bio3d/src/read_crd.cpp
bio3d/src/utils.h
bio3d/src/utils.cpp
bio3d/src/convert.h
bio3d/src/gzstream.cpp
bio3d/src/gzstream.h
bio3d/src/read_cif.cpp
bio3d/src/RcppExports.cpp
bio3d/src/read_prmtop.cpp
bio3d/NAMESPACE
bio3d/demo
bio3d/demo/pca.R
bio3d/demo/00Index
bio3d/demo/md.R
bio3d/demo/pdb.R
bio3d/demo/nma.R
bio3d/NEWS
bio3d/data
bio3d/data/kinesin.RData
bio3d/data/elements.rda
bio3d/data/transducin.RData
bio3d/data/atom.index.rda
bio3d/data/sdENM.RData
bio3d/data/hivp.RData
bio3d/data/aa.index.rda
bio3d/data/aa.table.rda
bio3d/R
bio3d/R/pca.tor.R bio3d/R/is.select.R bio3d/R/rmsd.R bio3d/R/print.fasta.R bio3d/R/dssp.pdb.R bio3d/R/angle.xyz.R bio3d/R/pdbaln.R bio3d/R/entropy.R bio3d/R/normalize.vector.R bio3d/R/hclustplot.R bio3d/R/dm.xyz.R bio3d/R/as.select.R bio3d/R/pca.array.R bio3d/R/pdb2aln.R bio3d/R/gnm.R bio3d/R/print.prmtop.R bio3d/R/mktrj.nma.R bio3d/R/write.ncdf.R bio3d/R/is.gap.R bio3d/R/cnapath.R bio3d/R/plot.pca.score.R bio3d/R/dssp.xyz.R bio3d/R/pca.R bio3d/R/summary.cnapath.R bio3d/R/sse.bridges.R bio3d/R/print.core.R bio3d/R/atom2xyz.R bio3d/R/filter.identity.R bio3d/R/mktrj.R bio3d/R/mono.colors.R bio3d/R/vmd.cnapath.R bio3d/R/atom.select.mol2.R bio3d/R/as.xyz.R bio3d/R/plot.nma.R bio3d/R/community.aln.R bio3d/R/as.pdb.R bio3d/R/pairwise.R bio3d/R/read.all.R bio3d/R/read.pqr.R bio3d/R/pdbs2pdb.R bio3d/R/mktrj.pca.R bio3d/R/nma.pdb.R bio3d/R/print.geostas.R bio3d/R/prune.cna.R bio3d/R/write.pir.R bio3d/R/binding.site.R bio3d/R/read.crd.amber.R bio3d/R/get.blast.R bio3d/R/read.fasta.pdb.R bio3d/R/gnm.pdbs.R bio3d/R/write.fasta.R bio3d/R/plot.geostas.R bio3d/R/print.cna.R bio3d/R/plotb3.R bio3d/R/mktrj.enma.R bio3d/R/dccm.xyz.R bio3d/R/stride.R bio3d/R/dccm.enma.R bio3d/R/trim.pdbs.R bio3d/R/read.pdcBD.R bio3d/R/rgyr.R bio3d/R/dccm.gnm.R bio3d/R/write.pdb.R bio3d/R/rtb.R bio3d/R/dccm.R bio3d/R/atom.select.R bio3d/R/cna.ensmb.R bio3d/R/mustang.R bio3d/R/is.mol2.R bio3d/R/get.pdb.R bio3d/R/deformation.nma.R bio3d/R/read.crd.R bio3d/R/pfam.R bio3d/R/motif.find.R bio3d/R/read.pdb2.R bio3d/R/read.prmtop.R bio3d/R/project.pca.R bio3d/R/gap.inspect.R bio3d/R/pymol.modes.R bio3d/R/load.enmff.R bio3d/R/print.sse.R bio3d/R/conserv.R bio3d/R/xyz2atom.R bio3d/R/pdbfit.R bio3d/R/torsion.xyz.R bio3d/R/plot.fasta.R bio3d/R/basename.pdb.R bio3d/R/read.dcd.R bio3d/R/read.fasta.R bio3d/R/aln2html.R bio3d/R/lbio3d.R bio3d/R/filter.rmsd.R bio3d/R/plot.cna.R bio3d/R/pca.pdbs.R bio3d/R/dist.xyz.R bio3d/R/summary.cna.R bio3d/R/read.pdb.R bio3d/R/pdbsplit.R bio3d/R/vmd_colors.R bio3d/R/com.pdb.R bio3d/R/pdb2aln.ind.R bio3d/R/formula2mass.R bio3d/R/seqbind.R bio3d/R/var.xyz.R bio3d/R/write.mol2.R bio3d/R/cov.nma.R bio3d/R/unbound.R bio3d/R/vmd.R bio3d/R/covsoverlap.R bio3d/R/atom2mass.R bio3d/R/plot.pca.loadings.R bio3d/R/dccm.nma.R bio3d/R/uniprot.R bio3d/R/com.R bio3d/R/summary.pdb.R bio3d/R/mask.dccm.R bio3d/R/filter.dccm.R bio3d/R/atom2ele.R bio3d/R/plot.hmmer.R bio3d/R/inner.prod.R bio3d/R/biounit.R bio3d/R/rle2.R bio3d/R/trim.xyz.R bio3d/R/bwr.colors.R bio3d/R/read.crd.charmm.R bio3d/R/get.seq.R bio3d/R/aanma.pdbs.R bio3d/R/plot.pca.scree.R bio3d/R/diag.ind.R bio3d/R/is.xyz.R bio3d/R/pdb2sse.R bio3d/R/network.amendment.R bio3d/R/read.cif.R bio3d/R/aanma.R bio3d/R/plot.dmat.R bio3d/R/seqaln.pair.R bio3d/R/pdbs2sse.R bio3d/R/clean.pdb.R bio3d/R/print.select.R bio3d/R/plot.enma.R bio3d/R/orient.pdb.R bio3d/R/bounds.R bio3d/R/plot.dccm.R bio3d/R/RcppExports.R bio3d/R/store.atom.R bio3d/R/blast.pdb.R bio3d/R/geostas.R bio3d/R/pdb.pfam.R bio3d/R/seqidentity.R bio3d/R/cna.R bio3d/R/sip.R bio3d/R/print.pca.R bio3d/R/dssp.pdbs.R bio3d/R/rmsf.R bio3d/R/plot.core.R bio3d/R/aa123.R bio3d/R/plot.pca.R bio3d/R/aa2mass.R bio3d/R/aa321.R bio3d/R/read.mol2.R bio3d/R/dssp.R bio3d/R/plot.matrix.loadings.R bio3d/R/layout.cna.R bio3d/R/inspect.connectivity.R bio3d/R/overlap.R bio3d/R/trim.mol2.R bio3d/R/rot.lsq.R bio3d/R/amsm.xyz.R bio3d/R/lmi.R bio3d/R/vec2resno.R bio3d/R/identify.cna.R bio3d/R/vmd.cna.R bio3d/R/bounds.sse.R bio3d/R/aanma.pdb.R bio3d/R/pymol.pdbs.R bio3d/R/atom.select.pdb.R bio3d/R/setup.ncore.R bio3d/R/fit.xyz.R bio3d/R/build.hessian.R bio3d/R/nma.pdbs.R bio3d/R/check.utility.R bio3d/R/nma_funs.R bio3d/R/cov2dccm.R bio3d/R/read.ncdf.R bio3d/R/difference.vector.R bio3d/R/write.crd.R bio3d/R/community.tree.R bio3d/R/dm.R bio3d/R/torsion.pdb.R bio3d/R/cmap.R bio3d/R/is.pdb.R bio3d/R/dccm.pca.R bio3d/R/cat.pdb.R bio3d/R/as.pdb.mol2.R bio3d/R/fluct.nma.R bio3d/R/cmap.pdb.R bio3d/R/plot.rmsip.R bio3d/R/seq2aln.R bio3d/R/core.find.R bio3d/R/pymol.dccm.R bio3d/R/com.xyz.R bio3d/R/aa2index.R bio3d/R/plot.fluct.R bio3d/R/chain.pdb.R bio3d/R/bhattacharyya.R bio3d/R/pdb.annotate.R bio3d/R/hmmer.R bio3d/R/cna.dccm.R bio3d/R/as.pdb.prmtop.R bio3d/R/rmsip.R bio3d/R/combine.select.R bio3d/R/wrap.tor.R bio3d/R/trim.pdb.R bio3d/R/write.pqr.R bio3d/R/seqaln.R bio3d/R/print.xyz.R bio3d/R/struct.aln.R bio3d/R/atom.select.prmtop.R bio3d/R/plot.cmap.R bio3d/R/print.pdb.R bio3d/R/pdbseq.R bio3d/R/print.enma.R bio3d/R/as.fasta.R bio3d/R/nma.R bio3d/R/filter.cmap.R bio3d/R/plot.blast.R bio3d/R/convert.pdb.R bio3d/R/consensus.R bio3d/R/print.nma.R bio3d/R/pca.xyz.R
bio3d/vignettes
bio3d/vignettes/bio3d_vignettes.Rmd
bio3d/README.md
bio3d/MD5
bio3d/build
bio3d/build/vignette.rds
bio3d/DESCRIPTION
bio3d/man
bio3d/man/seqbind.Rd bio3d/man/cov.nma.Rd bio3d/man/aln2html.Rd bio3d/man/biounit.Rd bio3d/man/read.ncdf.Rd bio3d/man/orient.pdb.Rd bio3d/man/pdbsplit.Rd bio3d/man/plot.dccm.Rd bio3d/man/core.find.Rd bio3d/man/bhattacharyya.Rd bio3d/man/atom2mass.Rd bio3d/man/seqidentity.Rd bio3d/man/plot.pca.loadings.Rd bio3d/man/unbound.Rd bio3d/man/bounds.sse.Rd bio3d/man/entropy.Rd bio3d/man/community.tree.Rd bio3d/man/filter.rmsd.Rd bio3d/man/atom.index.Rd bio3d/man/clean.pdb.Rd bio3d/man/motif.find.Rd bio3d/man/pdb.annotate.Rd bio3d/man/torsion.xyz.Rd bio3d/man/write.pqr.Rd bio3d/man/aa2mass.Rd bio3d/man/conserv.Rd bio3d/man/pfam.Rd bio3d/man/read.pdcBD.Rd bio3d/man/is.select.Rd bio3d/man/dccm.nma.Rd bio3d/man/vmd.cna.Rd bio3d/man/is.xyz.Rd bio3d/man/geostas.Rd bio3d/man/dccm.gnm.Rd bio3d/man/write.crd.Rd bio3d/man/rgyr.Rd bio3d/man/atom2xyz.Rd bio3d/man/read.pqr.Rd bio3d/man/aanma.pdb.Rd bio3d/man/get.seq.Rd bio3d/man/read.crd.charmm.Rd bio3d/man/dccm.xyz.Rd bio3d/man/sip.Rd bio3d/man/read.fasta.Rd bio3d/man/example.data.Rd bio3d/man/trim.pdbs.Rd bio3d/man/vmd_colors.Rd bio3d/man/covsoverlap.Rd bio3d/man/overlap.Rd bio3d/man/sdENM.Rd bio3d/man/com.Rd bio3d/man/pdbs2pdb.Rd bio3d/man/setup.ncore.Rd bio3d/man/plot.nma.Rd bio3d/man/seqaln.Rd bio3d/man/cnapath.Rd bio3d/man/gnm.Rd bio3d/man/bounds.Rd bio3d/man/print.core.Rd bio3d/man/hmmer.Rd bio3d/man/pdbaln.Rd bio3d/man/write.pdb.Rd bio3d/man/inspect.connectivity.Rd bio3d/man/mktrj.Rd bio3d/man/trim.xyz.Rd bio3d/man/angle.xyz.Rd bio3d/man/write.mol2.Rd bio3d/man/plot.cna.Rd bio3d/man/pdb2aln.Rd bio3d/man/trim.mol2.Rd bio3d/man/bwr.colors.Rd bio3d/man/read.pdb.Rd bio3d/man/print.fasta.Rd bio3d/man/get.pdb.Rd bio3d/man/layout.cna.Rd bio3d/man/pdbs2sse.Rd bio3d/man/mustang.Rd bio3d/man/as.select.Rd bio3d/man/inner.prod.Rd bio3d/man/pdbfit.Rd bio3d/man/read.fasta.pdb.Rd bio3d/man/print.xyz.Rd bio3d/man/plot.cmap.Rd bio3d/man/atom.select.Rd bio3d/man/seq2aln.Rd bio3d/man/binding.site.Rd bio3d/man/seqaln.pair.Rd bio3d/man/store.atom.Rd bio3d/man/pca.tor.Rd bio3d/man/var.xyz.Rd bio3d/man/atom2ele.Rd bio3d/man/plot.dmat.Rd bio3d/man/combine.select.Rd bio3d/man/read.crd.Rd bio3d/man/prune.cna.Rd bio3d/man/basename.pdb.Rd bio3d/man/dccm.Rd bio3d/man/plot.fasta.Rd bio3d/man/deformation.nma.Rd bio3d/man/check.utility.Rd bio3d/man/aa.table.Rd bio3d/man/write.fasta.Rd bio3d/man/lmi.Rd bio3d/man/fit.xyz.Rd bio3d/man/read.cif.Rd bio3d/man/plot.hmmer.Rd bio3d/man/torsion.pdb.Rd bio3d/man/pairwise.Rd bio3d/man/pca.xyz.Rd bio3d/man/consensus.Rd bio3d/man/pymol.Rd bio3d/man/rle2.Rd bio3d/man/write.pir.Rd bio3d/man/mask.dccm.Rd bio3d/man/fluct.nma.Rd bio3d/man/normalize.vector.Rd bio3d/man/is.gap.Rd bio3d/man/pca.array.Rd bio3d/man/as.fasta.Rd bio3d/man/pca.pdbs.Rd bio3d/man/diag.ind.Rd bio3d/man/aa123.Rd bio3d/man/filter.identity.Rd bio3d/man/vec2resno.Rd bio3d/man/hclustplot.Rd bio3d/man/read.crd.amber.Rd bio3d/man/as.pdb.Rd bio3d/man/elements.Rd bio3d/man/is.pdb.Rd bio3d/man/blast.pdb.Rd bio3d/man/dssp.Rd bio3d/man/pdbseq.Rd bio3d/man/nma.Rd bio3d/man/load.enmff.Rd bio3d/man/dccm.pca.Rd bio3d/man/pca.Rd bio3d/man/identify.cna.Rd bio3d/man/nma.pdbs.Rd bio3d/man/difference.vector.Rd bio3d/man/pdb2sse.Rd bio3d/man/dccm.enma.Rd bio3d/man/formula2mass.Rd bio3d/man/plot.enma.Rd bio3d/man/network.amendment.Rd bio3d/man/chain.pdb.Rd bio3d/man/bio3d.package.Rd bio3d/man/read.dcd.Rd bio3d/man/rmsip.Rd bio3d/man/aa2index.Rd bio3d/man/struct.aln.Rd bio3d/man/cna.Rd bio3d/man/dm.Rd bio3d/man/aa.index.Rd bio3d/man/write.ncdf.Rd bio3d/man/dist.xyz.Rd bio3d/man/filter.cmap.Rd bio3d/man/wrap.tor.Rd bio3d/man/lbio3d.Rd bio3d/man/sse.bridges.Rd bio3d/man/cmap.Rd bio3d/man/community.aln.Rd bio3d/man/rmsf.Rd bio3d/man/is.mol2.Rd bio3d/man/plot.rmsip.Rd bio3d/man/filter.dccm.Rd bio3d/man/plot.matrix.loadings.Rd bio3d/man/nma.pdb.Rd bio3d/man/read.mol2.Rd bio3d/man/aanma.pdbs.Rd bio3d/man/project.pca.Rd bio3d/man/cat.pdb.Rd bio3d/man/gap.inspect.Rd bio3d/man/convert.pdb.Rd bio3d/man/uniprot.Rd bio3d/man/plot.bio3d.Rd bio3d/man/plot.pca.Rd bio3d/man/plot.fluct.Rd bio3d/man/print.cna.Rd bio3d/man/rmsd.Rd bio3d/man/plot.core.Rd bio3d/man/pdb2aln.ind.Rd bio3d/man/trim.pdb.Rd bio3d/man/plot.geostas.Rd bio3d/man/read.prmtop.Rd bio3d/man/read.all.Rd

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