Package: bio3d 2.4-5

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_2.4-5.tar.gz
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bio3d_2.4-5.tgz(r-4.5-x86_64)bio3d_2.4-5.tgz(r-4.5-arm64)bio3d_2.4-5.tgz(r-4.4-x86_64)bio3d_2.4-5.tgz(r-4.4-arm64)bio3d_2.4-5.tgz(r-4.3-x86_64)bio3d_2.4-5.tgz(r-4.3-arm64)
bio3d_2.4-5.tar.gz(r-4.5-noble)bio3d_2.4-5.tar.gz(r-4.4-noble)
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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

Pkgdown site:https://thegrantlab.org

Uses libs:
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

zlibcpp

8.47 score 5 stars 10 packages 1.4k scripts 2.8k downloads 27 mentions 289 exports 1 dependencies

Last updated 5 months agofrom:9ca7d28181. Checks:11 OK, 1 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 29 2025
R-4.5-win-x86_64OKMar 29 2025
R-4.5-mac-x86_64OKMar 29 2025
R-4.5-mac-aarch64OKMar 29 2025
R-4.5-linux-x86_64OKMar 29 2025
R-4.4-win-x86_64OKMar 29 2025
R-4.4-mac-x86_64OKMar 29 2025
R-4.4-mac-aarch64OKMar 29 2025
R-4.4-linux-x86_64OKMar 29 2025
R-4.3-win-x86_64NOTEMar 29 2025
R-4.3-mac-x86_64OKMar 29 2025
R-4.3-mac-aarch64OKMar 29 2025

Exports:aa123aa2indexaa2massaa321aanmaaanma.pdbaanma.pdbsaln2htmlamsm.xyzangle.xyzas.fastaas.pdbas.pdb.defaultas.pdb.mol2as.pdb.prmtopas.selectas.xyzatom.selectatom.select.mol2atom.select.pdbatom.select.pdbsatom.select.prmtopatom2eleatom2ele.defaultatom2ele.pdbatom2massatom2mass.defaultatom2mass.pdbatom2xyzbasename.pdbbhattacharyyabhattacharyya.arraybhattacharyya.enmabhattacharyya.matrixbhattacharyya.nmabhattacharyya.pcabinding.sitebiounitblast.pdbboundsbounds.ssebuild.hessianbwr.colorscat.pdbchain.pdbcheck.utilityclean.pdbcmapcmap.defaultcmap.pdbcmap.pdbscmap.xyzcnacna.dccmcna.ensmbcnapathcomcom.pdbcom.xyzcombine.selectcommunity.alncommunity.treeconsensusconservconvert.pdbcore.cmapcore.findcore.find.defaultcore.find.pdbcore.find.pdbscov.enmacov.nmacovsoverlapcovsoverlap.enmacovsoverlap.nmadccmdccm.egnmdccm.enmadccm.gnmdccm.nmadccm.pcadccm.xyzdeformation.nmadiag.inddifference.vectordist.xyzdmdm.pdbdm.pdbsdm.xyzdsspdssp.pdbdssp.pdbsdssp.xyzentropyff.aaenmff.aaenm2ff.anmff.calphaff.pfanmff.reachff.sdenmfilter.cmapfilter.dccmfilter.identityfilter.rmsdfit.xyzfluct.nmaformula2massgap.inspectgeostasgeostas.defaultgeostas.enmageostas.nmageostas.pdbgeostas.pdbsgeostas.xyzget.blastget.pdbget.seqgnmgnm.pdbgnm.pdbshclustplothmmeridentify.cnainner.prodinspect.connectivityis.gapis.mol2is.pdbis.pdbsis.selectis.xyzlayout.cnalbio3dload.enmffmaskmask.dccmmktrjmktrj.enmamktrj.nmamktrj.pcamono.colorsmotif.findmustangnetwork.amendmentnmanma.pdbnma.pdbsnormalize.vectororient.pdboverlappairwisepcapca.arraypca.pdbspca.torpca.xyzpdb.annotatepdb.pfampdb2alnpdb2aln.indpdb2ssepdbalnpdbfitpdbfit.pdbpdbfit.pdbspdbs2pdbpdbs2ssepdbseqpdbsplitpfamplot.bio3dplot.blastplot.cmapplot.cnaplot.cnapathplot.coreplot.dccmplot.dmatplot.ecnaplot.ecnapathplot.enmaplot.fastaplot.fluctplot.geostasplot.hmmerplot.matrix.loadingsplot.nmaplot.pcaplot.pca.loadingsplot.pca.scoreplot.pca.screeplot.rmsipplotb3print.cnaprint.cnapathprint.coreprint.enmaprint.fastaprint.geostasprint.mol2print.nmaprint.pcaprint.pdbprint.prmtopprint.rle2print.selectprint.sseprint.xyzproject.pcaprune.cnapymolpymol.dccmpymol.modespymol.nmapymol.pcapymol.pdbsread.allread.cifread.crdread.crd.amberread.crd.charmmread.dcdread.fastaread.fasta.pdbread.mol2read.ncdfread.pdbread.pdb2read.pdcBDread.pqrread.prmtoprgyrrle2rmsdrmsfrmsiprmsip.defaultrmsip.enmarot.lsqrtbseq2alnseqalnseqaln.pairseqbindseqidentitysetup.ncoresipsip.defaultsip.enmasip.nmasse.bridgesstore.atomstridestruct.alnsummary.cnasummary.cnapathsummary.pdbtorsion.pdbtorsion.xyztrimtrim.mol2trim.pdbtrim.pdbstrim.xyzunbounduniprotvar.pdbsvar.xyzvec2resnovmdvmd_colorsvmd.cnavmd.cnapathvmd.ecnavmd.ecnapathwrap.torwrite.crdwrite.fastawrite.mol2write.ncdfwrite.pdbwrite.pirwrite.pqrxyz2atomxyz2z.pcaz2xyz.pca

Dependencies:Rcpp

bio3d Vignettes

Rendered frombio3d_vignettes.Rmdusingknitr::rmarkdownon Mar 29 2025.

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

Readme and manuals

Help Manual

Help pageTopics
Biological Structure Analysisbio3d-package bio3d
AAindex: Amino Acid Index Databaseaa.index
Table of Relevant Amino Acidsaa.table
Convert Between 1-letter and 3-letter Aminoacid Codesaa123 aa321
Convert an Aminoacid Sequence to AAIndex Valuesaa2index
Amino Acid Residues to Mass Converteraa2mass
All Atom Normal Mode Analysisaanma aanma.pdb rtb
Ensemble Normal Mode Analysis with All-Atom ENMaanma.pdbs
Create a HTML Page For a Given Alignmentaln2html
Calculate the Angle Between Three Atomsangle.xyz
Alignment to FASTA objectas.fasta
Convert to PDB formatas.pdb as.pdb.default as.pdb.mol2 as.pdb.prmtop
Convert Atomic Indices to a Select Objectas.select
Atom Names/Typesatom.index
Atom Selection from PDB and PRMTOP Structure Objectsatom.select atom.select.mol2 atom.select.pdb atom.select.pdbs atom.select.prmtop print.select
Atom Names/Types to Atomic Symbols Converteratom2ele atom2ele.default atom2ele.pdb
Atom Names/Types to Mass Converteratom2mass atom2mass.default atom2mass.pdb
Convert Between Atom and xyz Indicesatom2xyz xyz2atom
Manipulate PDB File Namesbasename.pdb
Bhattacharyya Coefficientbhattacharyya bhattacharyya.array bhattacharyya.enma bhattacharyya.matrix bhattacharyya.nma bhattacharyya.pca
Binding Site Residuesbinding.site
Biological Units Constructionbiounit
NCBI BLAST Sequence Search and Summary Plot of Hit Statisticsblast.pdb get.blast plot.blast
Bounds of a Numeric Vectorbounds
Obtain A SSE Object From An SSE Sequence Vectorbounds.sse
Color Palettesbwr.colors mono.colors
Concatenate Multiple PDB Objectscat.pdb
Find Possible PDB Chain Breakschain.pdb
Check on Missing Utility Programscheck.utility
Inspect And Clean Up A PDB Objectclean.pdb
Contact Mapcmap 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 Networkscnapath plot.cnapath plot.ecnapath print.cnapath summary.cnapath
Center of Masscom com.pdb com.xyz
Combine Atom Selections From PDB Structurecombine.select
Align communities from two or more networkscommunity.aln
Reconstruction of the Girvan-Newman Community Tree for a CNA Class Object.community.tree
Sequence Consensus for an Alignmentconsensus
Score Residue Conservation At Each Position in an Alignmentconserv
Renumber and Convert Between Various PDB formatsconvert.pdb
Identification of Contact Map Core Positionscore.cmap
Identification of Invariant Core Positionscore.find core.find.default core.find.pdb core.find.pdbs
Calculate Covariance Matrix from Normal Modescov.enma cov.nma
Covariance Overlapcovsoverlap covsoverlap.enma covsoverlap.nma
DCCM: Dynamical Cross-Correlation Matrixdccm
Cross-Correlation for Ensemble NMA (eNMA)dccm.enma
Dynamic Cross-Correlation from Gaussian Network Modeldccm.egnm dccm.gnm
Dynamic Cross-Correlation from Normal Modes Analysisdccm.nma
Dynamical Cross-Correlation Matrix from Principal Component Analysisdccm.pca
Dynamical Cross-Correlation Matrix from Cartesian Coordinatesdccm.xyz
Deformation Analysisdeformation.nma
Diagonal Indices of a Matrixdiag.ind
Difference Vectordifference.vector
Calculate the Distances Between the Rows of Two Matricesdist.xyz
Distance Matrix Analysisdm dm.pdb dm.pdbs dm.xyz
Secondary Structure Analysis with DSSP or STRIDEdssp dssp.pdb dssp.pdbs dssp.xyz print.sse stride
Periodic Table of the Elementselements
Shannon Entropy Scoreentropy
Bio3d Example Dataannotation core example.data hivp kinesin pdbs transducin
Contact Map Consensus Filteringfilter.cmap
Filter for Cross-correlation Matrices (Cij)filter.dccm
Percent Identity Filterfilter.identity
RMSD Filterfilter.rmsd
Coordinate Superpositionfit.xyz rot.lsq
NMA Fluctuationsfluct.nma
Chemical Formula to Mass Converterformula2mass
Alignment Gap Summarygap.inspect
GeoStaS Domain Finderamsm.xyz geostas geostas.default geostas.enma geostas.nma geostas.pdb geostas.pdbs geostas.xyz print.geostas
Download PDB Coordinate Filesget.pdb
Download FASTA Sequence Filesget.seq
Gaussian Network Modelgnm gnm.pdb gnm.pdbs
Dendrogram with Clustering Annotationhclustplot
HMMER Sequence Searchhmmer
Identify Points in a CNA Protein Structure Network Plotidentify.cna
Mass-weighted Inner Productinner.prod
Check the Connectivity of Protein Structuresinspect.connectivity
Gap Charactersis.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 Layoutlayout.cna
List all Functions in the bio3d Packagelbio3d
ENM Force Field Loaderff.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 Trajectorymktrj mktrj.enma mktrj.nma mktrj.pca
Find Sequence Motifs.motif.find
Structure-based Sequence Alignment with MUSTANGmustang
Amendment of a CNA Network According To A Input Community Membership Vector.network.amendment
Normal Mode Analysisnma
Normal Mode Analysisbuild.hessian nma.pdb print.nma
Ensemble Normal Mode Analysisnma.pdbs print.enma
Mass-Weighted Normalized Vectornormalize.vector
Orient a PDB Structureorient.pdb
Overlap analysisoverlap
Pair Indicespairwise
Principal Component Analysispca
Principal Component Analysis of an array of matricespca.array
Principal Component Analysispca.pdbs
Principal Component Analysispca.tor
Principal Component Analysispca.xyz print.pca
Get Customizable Annotations From PDB Or PFAM Databasespdb.annotate pdb.pfam
Align a PDB structure to an existing alignmentpdb2aln
Mapping from alignment positions to PDB atomic indicespdb2aln.ind
Obtain An SSE Sequence Vector From A PDB Objectpdb2sse
Sequence Alignment of PDB Filespdbaln
PDB File Coordinate Superpositionpdbfit pdbfit.pdb pdbfit.pdbs
PDBs to PDB Converterpdbs2pdb
SSE annotation for a PDBs Objectpdbs2sse
Extract The Aminoacid Sequence From A PDB Objectpdbseq
Split a PDB File Into Separate Files, One For Each Chain.pdbsplit
Download Pfam FASTA Sequence Alignmentpfam
Plots with marginal SSE annotationplot.bio3d plotb3
Plot Contact Matrixplot.cmap
Protein Structure Network Plots in 2D and 3D.plot.cna plot.ecna
Plot Core Fitting Progressplot.core
DCCM Plotplot.dccm
Plot Distance Matrixplot.dmat
Plot eNMA Resultsplot.enma
Plot a Multiple Sequence Alignmentplot.fasta
Plot Fluctuationsplot.fluct
Plot Geostas Resultsplot.geostas
Plot a Summary of HMMER Hit Statistics.plot.hmmer
Plot Residue-Residue Matrix Loadingsplot.matrix.loadings
Plot NMA Resultsplot.nma
Plot PCA Resultsplot.pca plot.pca.score plot.pca.scree
Plot Residue Loadings along PC1 to PC3plot.pca.loadings
Plot RMSIP Resultsplot.rmsip
Summarize and Print Features of a cna Network Graphprint.cna summary.cna
Printing Core Positions and Returning Indicesprint.core
Printing Sequence Alignments.print.fasta.ali print.fasta
Printing XYZ coordinatesprint.xyz
Project Data onto Principal Componentsproject.pca xyz2z.pca z2xyz.pca
Prune A cna Network Objectprune.cna
Biomolecular Visualization with PyMOLpymol pymol.dccm pymol.modes pymol.nma pymol.pca pymol.pdbs
Read Aligned Structure Dataread.all
Read mmCIF Fileread.cif
Read Coordinate Data from Amber or Charmmread.crd
Read AMBER Coordinate filesread.crd.amber
Read CRD Fileread.crd.charmm
Read CHARMM/X-PLOR/NAMD Binary DCD filesread.dcd
Read FASTA formated Sequencesread.fasta
Read Aligned Structure Dataread.fasta.pdb
Read MOL2 Fileprint.mol2 read.mol2
Read AMBER Binary netCDF filesread.ncdf
Read PDB Fileprint.pdb read.pdb read.pdb2 summary.pdb
Read PQR output from pdcBD Fileread.pdcBD
Read PQR Fileread.pqr
Read AMBER Parameter/Topology filesprint.prmtop read.prmtop
Radius of Gyrationrgyr
Run Length Encoding with Indicesprint.rle2 rle2
Root Mean Square Deviationrmsd
Atomic RMS Fluctuationsrmsf
Root Mean Square Inner Productrmsip rmsip.default rmsip.enma
Index for the sdENM ffsdENM
Add a Sequence to an Existing Alignmnetseq2aln
Sequence Alignment with MUSCLEseqaln
Sequence Alignment of Identical Protein Sequencesseqaln.pair
Combine Sequences by Rows Without Recyclingseqbind
Percent Identityseqidentity
Setup for Running Bio3D Functions using Multiple CPU Coressetup.ncore
Square Inner Productsip sip.default sip.enma sip.nma
SSE Backbone Hydrogen Bondingsse.bridges
Store all-atom data from a PDB objectstore.atom
Structure Alignment Of Two PDB Filesstruct.aln
Calculate Mainchain and Sidechain Torsion/Dihedral Anglestorsion.pdb
Calculate Torsion/Dihedral Anglestorsion.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 Objecttrim.pdbs
Trim a XYZ Object of Cartesian Coordinates.trim.xyz
Sequence Generation from a Bounds Vectorunbound
Fetch UniProt Entry Data.uniprot
Pairwise Distance Variance in Cartesian Coordinatesvar.pdbs var.xyz
Replicate Per-residue Vector Valuesvec2resno
View CNA Protein Structure Network Community Output in VMDvmd vmd.cna vmd.cnapath vmd.ecna vmd.ecnapath
VMD Color Palettevmd_colors
Wrap Torsion Angle Datawrap.tor
Write CRD Filewrite.crd
Write FASTA Formated Sequenceswrite.fasta
Write MOL2 Format Coordinate Filewrite.mol2
Write AMBER Binary netCDF fileswrite.ncdf
Write PDB Format Coordinate Filewrite.pdb
Write PIR Formated Sequenceswrite.pir
Write PQR Format Coordinate Filewrite.pqr