bio3d: Biological Structure Analysis

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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.

Author
Barry Grant [aut, cre], Xin-Qiu Yao [aut], Lars Skjaerven [aut], Julien Ide [aut]
Date of publication
2016-11-12 00:26:53
Maintainer
Barry Grant <bjgrant@umich.edu>
License
GPL (>= 2)
Version
2.3-1
URLs

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

Files in this package

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
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