Package: bio3d 2.4-4

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.

Authors:Barry Grant [aut, cre], Xin-Qiu Yao [aut], Lars Skjaerven [aut], Julien Ide [aut]

bio3d_2.4-4.tar.gz
bio3d_2.4-4.zip(r-4.5)bio3d_2.4-4.zip(r-4.4)bio3d_2.4-4.zip(r-4.3)
bio3d_2.4-4.tgz(r-4.4-x86_64)bio3d_2.4-4.tgz(r-4.4-arm64)bio3d_2.4-4.tgz(r-4.3-x86_64)bio3d_2.4-4.tgz(r-4.3-arm64)
bio3d_2.4-4.tar.gz(r-4.5-noble)bio3d_2.4-4.tar.gz(r-4.4-noble)
bio3d_2.4-4.tgz(r-4.4-emscripten)bio3d_2.4-4.tgz(r-4.3-emscripten)
bio3d.pdf |bio3d.html✨
bio3d/json (API)
NEWS

# Install 'bio3d' in R:

install.packages('bio3d', repos = c('https://bioboot.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://bitbucket.org/grantlab/bio3d

Uses libs:

zlib– Compression library
c++– GNU Standard C++ Library v3

Datasets:

aa.index - AAindex: Amino Acid Index Database
aa.table - Table of Relevant Amino Acids
atom.index - Atom Names/Types
elements - Periodic Table of the Elements
hivp - Bio3d Example Data
kinesin - Bio3d Example Data
sdENM - Index for the sdENM ff
transducin - Bio3d Example Data

On CRAN:

289 exports 5 stars 4.13 score 1 dependencies 7 dependents 27 mentions 1.0k scripts 1.5k downloads

Last updated 2 years agofrom:5b9c91f59b. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 08 2024
R-4.5-win-x86_64	NOTE	Sep 08 2024
R-4.5-linux-x86_64	NOTE	Sep 08 2024
R-4.4-win-x86_64	NOTE	Sep 08 2024
R-4.4-mac-x86_64	NOTE	Sep 08 2024
R-4.4-mac-aarch64	NOTE	Sep 08 2024
R-4.3-win-x86_64	NOTE	Sep 08 2024
R-4.3-mac-x86_64	NOTE	Sep 08 2024
R-4.3-mac-aarch64	NOTE	Sep 08 2024

Exports:aa123 aa2index aa2mass aa321 aanma aanma.pdb aanma.pdbs aln2html amsm.xyz angle.xyz as.fasta as.pdb as.pdb.default as.pdb.mol2 as.pdb.prmtop as.select as.xyz atom.select atom.select.mol2 atom.select.pdb atom.select.pdbs atom.select.prmtop atom2ele atom2ele.default atom2ele.pdb atom2mass atom2mass.default atom2mass.pdb atom2xyz basename.pdb bhattacharyya bhattacharyya.array bhattacharyya.enma bhattacharyya.matrix bhattacharyya.nma bhattacharyya.pca binding.site biounit blast.pdb bounds bounds.sse build.hessian bwr.colors cat.pdb chain.pdb check.utility clean.pdb cmap cmap.default cmap.pdb cmap.pdbs cmap.xyz cna cna.dccm cna.ensmb cnapath com com.pdb com.xyz combine.select community.aln community.tree consensus conserv convert.pdb core.cmap core.find core.find.default core.find.pdb core.find.pdbs cov.enma cov.nma covsoverlap covsoverlap.enma covsoverlap.nma dccm dccm.egnm dccm.enma dccm.gnm dccm.nma dccm.pca dccm.xyz deformation.nma diag.ind difference.vector dist.xyz dm dm.pdb dm.pdbs dm.xyz dssp dssp.pdb dssp.pdbs dssp.xyz entropy ff.aaenm ff.aaenm2 ff.anm ff.calpha ff.pfanm ff.reach ff.sdenm filter.cmap filter.dccm filter.identity filter.rmsd fit.xyz fluct.nma formula2mass gap.inspect geostas geostas.default geostas.enma geostas.nma geostas.pdb geostas.pdbs geostas.xyz get.blast get.pdb get.seq gnm gnm.pdb gnm.pdbs hclustplot hmmer identify.cna inner.prod inspect.connectivity is.gap is.mol2 is.pdb is.pdbs is.select is.xyz layout.cna lbio3d load.enmff mask mask.dccm mktrj mktrj.enma mktrj.nma mktrj.pca mono.colors motif.find mustang network.amendment nma nma.pdb nma.pdbs normalize.vector orient.pdb overlap pairwise pca pca.array pca.pdbs pca.tor pca.xyz pdb.annotate pdb.pfam pdb2aln pdb2aln.ind pdb2sse pdbaln pdbfit pdbfit.pdb pdbfit.pdbs pdbs2pdb pdbs2sse pdbseq pdbsplit pfam plot.bio3d plot.blast plot.cmap plot.cna plot.cnapath plot.core plot.dccm plot.dmat plot.ecna plot.ecnapath plot.enma plot.fasta plot.fluct plot.geostas plot.hmmer plot.matrix.loadings plot.nma plot.pca plot.pca.loadings plot.pca.score plot.pca.scree plot.rmsip plotb3 print.cna print.cnapath print.core print.enma print.fasta print.geostas print.mol2 print.nma print.pca print.pdb print.prmtop print.rle2 print.select print.sse print.xyz project.pca prune.cna pymol pymol.dccm pymol.modes pymol.nma pymol.pca pymol.pdbs read.all read.cif read.crd read.crd.amber read.crd.charmm read.dcd read.fasta read.fasta.pdb read.mol2 read.ncdf read.pdb read.pdb2 read.pdcBD read.pqr read.prmtop rgyr rle2 rmsd rmsf rmsip rmsip.default rmsip.enma rot.lsq rtb seq2aln seqaln seqaln.pair seqbind seqidentity setup.ncore sip sip.default sip.enma sip.nma sse.bridges store.atom stride struct.aln summary.cna summary.cnapath summary.pdb torsion.pdb torsion.xyz trim trim.mol2 trim.pdb trim.pdbs trim.xyz unbound uniprot var.pdbs var.xyz vec2resno vmd vmd_colors vmd.cna vmd.cnapath vmd.ecna vmd.ecnapath wrap.tor write.crd write.fasta write.mol2 write.ncdf write.pdb write.pir write.pqr xyz2atom xyz2z.pca z2xyz.pca

Dependencies:Rcpp

bio3d Vignettes

Rendered frombio3d_vignettes.Rmdusingknitr::rmarkdownon Sep 08 2024.

Last update: 2021-05-11
Started: 2014-10-15

Help page	Topics
Biological Structure Analysis	bio3d-package bio3d
AAindex: Amino Acid Index Database	aa.index
Table of Relevant Amino Acids	aa.table
Convert Between 1-letter and 3-letter Aminoacid Codes	aa123 aa321
Convert an Aminoacid Sequence to AAIndex Values	aa2index
Amino Acid Residues to Mass Converter	aa2mass
All Atom Normal Mode Analysis	aanma aanma.pdb rtb
Ensemble Normal Mode Analysis with All-Atom ENM	aanma.pdbs
Create a HTML Page For a Given Alignment	aln2html
Calculate the Angle Between Three Atoms	angle.xyz
Alignment to FASTA object	as.fasta
Convert to PDB format	as.pdb as.pdb.default as.pdb.mol2 as.pdb.prmtop
Convert Atomic Indices to a Select Object	as.select
Atom Names/Types	atom.index
Atom Selection from PDB and PRMTOP Structure Objects	atom.select atom.select.mol2 atom.select.pdb atom.select.pdbs atom.select.prmtop print.select
Atom Names/Types to Atomic Symbols Converter	atom2ele atom2ele.default atom2ele.pdb
Atom Names/Types to Mass Converter	atom2mass atom2mass.default atom2mass.pdb
Convert Between Atom and xyz Indices	atom2xyz xyz2atom
Manipulate PDB File Names	basename.pdb
Bhattacharyya Coefficient	bhattacharyya bhattacharyya.array bhattacharyya.enma bhattacharyya.matrix bhattacharyya.nma bhattacharyya.pca
Binding Site Residues	binding.site
Biological Units Construction	biounit
NCBI BLAST Sequence Search and Summary Plot of Hit Statistics	blast.pdb get.blast plot.blast
Bounds of a Numeric Vector	bounds
Obtain A SSE Object From An SSE Sequence Vector	bounds.sse
Color Palettes	bwr.colors mono.colors
Concatenate Multiple PDB Objects	cat.pdb
Find Possible PDB Chain Breaks	chain.pdb
Check on Missing Utility Programs	check.utility
Inspect And Clean Up A PDB Object	clean.pdb
Contact Map	cmap cmap.default cmap.pdb cmap.pdbs cmap.xyz
Protein Dynamic Correlation Network Construction and Community Analysis.	cna cna.dccm cna.ensmb
Suboptimal Path Analysis for Correlation Networks	cnapath plot.cnapath plot.ecnapath print.cnapath summary.cnapath
Center of Mass	com com.pdb com.xyz
Combine Atom Selections From PDB Structure	combine.select
Align communities from two or more networks	community.aln
Reconstruction of the Girvan-Newman Community Tree for a CNA Class Object.	community.tree
Sequence Consensus for an Alignment	consensus
Score Residue Conservation At Each Position in an Alignment	conserv
Renumber and Convert Between Various PDB formats	convert.pdb
Identification of Contact Map Core Positions	core.cmap
Identification of Invariant Core Positions	core.find core.find.default core.find.pdb core.find.pdbs
Calculate Covariance Matrix from Normal Modes	cov.enma cov.nma
Covariance Overlap	covsoverlap covsoverlap.enma covsoverlap.nma
DCCM: Dynamical Cross-Correlation Matrix	dccm
Cross-Correlation for Ensemble NMA (eNMA)	dccm.enma
Dynamic Cross-Correlation from Gaussian Network Model	dccm.egnm dccm.gnm
Dynamic Cross-Correlation from Normal Modes Analysis	dccm.nma
Dynamical Cross-Correlation Matrix from Principal Component Analysis	dccm.pca
Dynamical Cross-Correlation Matrix from Cartesian Coordinates	dccm.xyz
Deformation Analysis	deformation.nma
Diagonal Indices of a Matrix	diag.ind
Difference Vector	difference.vector
Calculate the Distances Between the Rows of Two Matrices	dist.xyz
Distance Matrix Analysis	dm dm.pdb dm.pdbs dm.xyz
Secondary Structure Analysis with DSSP or STRIDE	dssp dssp.pdb dssp.pdbs dssp.xyz print.sse stride
Periodic Table of the Elements	elements
Shannon Entropy Score	entropy
Bio3d Example Data	annotation core example.data hivp kinesin pdbs transducin
Contact Map Consensus Filtering	filter.cmap
Filter for Cross-correlation Matrices (Cij)	filter.dccm
Percent Identity Filter	filter.identity
RMSD Filter	filter.rmsd
Coordinate Superposition	fit.xyz rot.lsq
NMA Fluctuations	fluct.nma
Chemical Formula to Mass Converter	formula2mass
Alignment Gap Summary	gap.inspect
GeoStaS Domain Finder	amsm.xyz geostas geostas.default geostas.enma geostas.nma geostas.pdb geostas.pdbs geostas.xyz print.geostas
Download PDB Coordinate Files	get.pdb
Download FASTA Sequence Files	get.seq
Gaussian Network Model	gnm gnm.pdb gnm.pdbs
Dendrogram with Clustering Annotation	hclustplot
HMMER Sequence Search	hmmer
Identify Points in a CNA Protein Structure Network Plot	identify.cna
Mass-weighted Inner Product	inner.prod
Check the Connectivity of Protein Structures	inspect.connectivity
Gap Characters	is.gap
Is an Object of Class 'mol2'?	is.mol2
Is an Object of Class 'pdb(s)'?	is.pdb is.pdbs
Is an Object of Class 'select'?	is.select
Is an Object of Class 'xyz'?	as.xyz is.xyz
Protein Structure Network Layout	layout.cna
List all Functions in the bio3d Package	lbio3d
ENM Force Field Loader	ff.aaenm ff.aaenm2 ff.anm ff.calpha ff.pfanm ff.reach ff.sdenm load.enmff
Mask a Subset of Atoms in a DCCM Object.	mask mask.dccm
PCA / NMA Atomic Displacement Trajectory	mktrj mktrj.enma mktrj.nma mktrj.pca
Find Sequence Motifs.	motif.find
Structure-based Sequence Alignment with MUSTANG	mustang
Amendment of a CNA Network According To A Input Community Membership Vector.	network.amendment
Normal Mode Analysis	nma
Normal Mode Analysis	build.hessian nma.pdb print.nma
Ensemble Normal Mode Analysis	nma.pdbs print.enma
Mass-Weighted Normalized Vector	normalize.vector
Orient a PDB Structure	orient.pdb
Overlap analysis	overlap
Pair Indices	pairwise
Principal Component Analysis	pca
Principal Component Analysis of an array of matrices	pca.array
Principal Component Analysis	pca.pdbs
Principal Component Analysis	pca.tor
Principal Component Analysis	pca.xyz print.pca
Get Customizable Annotations From PDB Or PFAM Databases	pdb.annotate pdb.pfam
Align a PDB structure to an existing alignment	pdb2aln
Mapping from alignment positions to PDB atomic indices	pdb2aln.ind
Obtain An SSE Sequence Vector From A PDB Object	pdb2sse
Sequence Alignment of PDB Files	pdbaln
PDB File Coordinate Superposition	pdbfit pdbfit.pdb pdbfit.pdbs
PDBs to PDB Converter	pdbs2pdb
SSE annotation for a PDBs Object	pdbs2sse
Extract The Aminoacid Sequence From A PDB Object	pdbseq
Split a PDB File Into Separate Files, One For Each Chain.	pdbsplit
Download Pfam FASTA Sequence Alignment	pfam
Plots with marginal SSE annotation	plot.bio3d plotb3
Plot Contact Matrix	plot.cmap
Protein Structure Network Plots in 2D and 3D.	plot.cna plot.ecna
Plot Core Fitting Progress	plot.core
DCCM Plot	plot.dccm
Plot Distance Matrix	plot.dmat
Plot eNMA Results	plot.enma
Plot a Multiple Sequence Alignment	plot.fasta
Plot Fluctuations	plot.fluct
Plot Geostas Results	plot.geostas
Plot a Summary of HMMER Hit Statistics.	plot.hmmer
Plot Residue-Residue Matrix Loadings	plot.matrix.loadings
Plot NMA Results	plot.nma
Plot PCA Results	plot.pca plot.pca.score plot.pca.scree
Plot Residue Loadings along PC1 to PC3	plot.pca.loadings
Plot RMSIP Results	plot.rmsip
Summarize and Print Features of a cna Network Graph	print.cna summary.cna
Printing Core Positions and Returning Indices	print.core
Printing Sequence Alignments	.print.fasta.ali print.fasta
Printing XYZ coordinates	print.xyz
Project Data onto Principal Components	project.pca xyz2z.pca z2xyz.pca
Prune A cna Network Object	prune.cna
Biomolecular Visualization with PyMOL	pymol pymol.dccm pymol.modes pymol.nma pymol.pca pymol.pdbs
Read Aligned Structure Data	read.all
Read mmCIF File	read.cif
Read Coordinate Data from Amber or Charmm	read.crd
Read AMBER Coordinate files	read.crd.amber
Read CRD File	read.crd.charmm
Read CHARMM/X-PLOR/NAMD Binary DCD files	read.dcd
Read FASTA formated Sequences	read.fasta
Read Aligned Structure Data	read.fasta.pdb
Read MOL2 File	print.mol2 read.mol2
Read AMBER Binary netCDF files	read.ncdf
Read PDB File	print.pdb read.pdb read.pdb2 summary.pdb
Read PQR output from pdcBD File	read.pdcBD
Read PQR File	read.pqr
Read AMBER Parameter/Topology files	print.prmtop read.prmtop
Radius of Gyration	rgyr
Run Length Encoding with Indices	print.rle2 rle2
Root Mean Square Deviation	rmsd
Atomic RMS Fluctuations	rmsf
Root Mean Square Inner Product	rmsip rmsip.default rmsip.enma
Index for the sdENM ff	sdENM
Add a Sequence to an Existing Alignmnet	seq2aln
Sequence Alignment with MUSCLE	seqaln
Sequence Alignment of Identical Protein Sequences	seqaln.pair
Combine Sequences by Rows Without Recycling	seqbind
Percent Identity	seqidentity
Setup for Running Bio3D Functions using Multiple CPU Cores	setup.ncore
Square Inner Product	sip sip.default sip.enma sip.nma
SSE Backbone Hydrogen Bonding	sse.bridges
Store all-atom data from a PDB object	store.atom
Structure Alignment Of Two PDB Files	struct.aln
Calculate Mainchain and Sidechain Torsion/Dihedral Angles	torsion.pdb
Calculate Torsion/Dihedral Angles	torsion.xyz
Trim a PDB Object To A Subset of Atoms.	trim trim.pdb
Trim a MOL2 Object To A Subset of Atoms.	trim.mol2
Filter or Trim a PDBs Object	trim.pdbs
Trim a XYZ Object of Cartesian Coordinates.	trim.xyz
Sequence Generation from a Bounds Vector	unbound
Fetch UniProt Entry Data.	uniprot
Pairwise Distance Variance in Cartesian Coordinates	var.pdbs var.xyz
Replicate Per-residue Vector Values	vec2resno
View CNA Protein Structure Network Community Output in VMD	vmd vmd.cna vmd.cnapath vmd.ecna vmd.ecnapath
VMD Color Palette	vmd_colors
Wrap Torsion Angle Data	wrap.tor
Write CRD File	write.crd
Write FASTA Formated Sequences	write.fasta
Write MOL2 Format Coordinate File	write.mol2
Write AMBER Binary netCDF files	write.ncdf
Write PDB Format Coordinate File	write.pdb
Write PIR Formated Sequences	write.pir
Write PQR Format Coordinate File	write.pqr

Package: bio3d 2.4-4

bio3d: Biological Structure Analysis

bio3d Vignettes

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)