Package: Rpdb 2.4.0
Rpdb: Read, Write, Visualize and Manipulate PDB Files
Provides tools to read, write, visualize Protein Data Bank (PDB) files and perform some structural manipulations.
Authors:
Rpdb_2.4.0.tar.gz
Rpdb_2.4.0.zip(r-4.5)Rpdb_2.4.0.zip(r-4.4)Rpdb_2.4.0.zip(r-4.3)
Rpdb_2.4.0.tgz(r-4.4-any)Rpdb_2.4.0.tgz(r-4.3-any)
Rpdb_2.4.0.tar.gz(r-4.5-noble)Rpdb_2.4.0.tar.gz(r-4.4-noble)
Rpdb_2.4.0.tgz(r-4.4-emscripten)Rpdb_2.4.0.tgz(r-4.3-emscripten)
Rpdb.pdf |Rpdb.html✨
Rpdb/json (API)
NEWS
| # Install 'Rpdb' in R: |
| install.packages('Rpdb', repos = c('https://discoleo.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/discoleo/rpdb/issues
- elements - Periodic Table of the Elements
- universalConstants - Universal Constants
Last updated 6 months agofrom:500c0df2c9. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 18 2024 |
| R-4.5-win | NOTE | Nov 18 2024 |
| R-4.5-linux | NOTE | Nov 18 2024 |
| R-4.4-win | OK | Nov 18 2024 |
| R-4.4-mac | OK | Nov 18 2024 |
| R-4.3-win | OK | Nov 18 2024 |
| R-4.3-mac | OK | Nov 18 2024 |
Exports:abc2xyzaddABCaddEleLabaddPBCBoxaddResLabaddXYZangleatomsbasisbasis<-bondcell.coordscell.densitycell.volumecentresconectcoordscoords<-cryst1dihedraldist.pointdistancesdotProdinertiainfo3dis.atomsis.conectis.coordsis.cryst1is.crystalis.distancesis.pdbMabmassesMbcMcameasuremirrorMxyMyzMzxnatomnormpdbproj.line3dRread.pdbreindexreplicaterotVectRxRyRzTaTabcTbTctoSymbolsTxTxyzTyTzunsplitvectNormvectProdviewABviewAxisviewBCviewCAviewInertiaviewXYviewYZviewZXvisualizewrapwrite.pdbxyz2abc
Dependencies:base64encbslibcachemclidigestevaluatefastmapfontawesomefsgluehighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlifecyclemagrittrmemoisemimeR6rappdirsrglrlangrmarkdownsasstinytexxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Read, Write, Visualize and Manipulate PDB Files | Rpdb-package |
| Add Axes or PBC Box to the 'rgl' Scene | addABC addAxes addPBCBox addXYZ |
| Add Labels to the 'rgl' Scene | addEleLab addEleLab.atoms addEleLab.pdb addLabels addResLab addResLab.atoms addResLab.pdb info3d info3d.atoms info3d.pdb |
| Create 'atoms' Object | atoms atoms.default is.atoms |
| The Basis of an Object | basis basis.default basis.pdb basis<- basis<-.default basis<-.pdb |
| Atomic Bond Lengths, Angles and Dihedrals | angle angle.coords angle.pdb bond bond-angle-dihedral bond.coords bond.pdb dihedral dihedral.coords dihedral.pdb measure measure.coords measure.default measure.pdb |
| Properties of a Unit Cell | cell.coords cell.coords.cryst1 cell.coords.default cell.coords.pdb cell.density cell.density.default cell.density.pdb cell.volume cell.volume.cryst1 cell.volume.pdb cellProperties |
| Centres-of-Geometry and Centres-of-Mass | centres centres.atoms centres.coords centres.pdb |
| Create 'conect' Object | conect conect.coords conect.default conect.pdb is.conect |
| The Atomic Coordinates of an Object | coords coords.atoms coords.coords coords.data.frame coords.default coords.matrix coords.pdb coords<- coords<-.atoms coords<-.pdb is.coords |
| Create 'cryst1' Object | cryst1 cryst1.default is.cryst1 is.crystal |
| Inter-Atomic Distances | dist.point dist.point.default distances distances.atoms distances.coords distances.default distances.pdb is.distances norm norm.distances |
| Periodic Table of the Elements | elements |
| Moment of Inertia of a Molecular System | inertia inertia.atoms inertia.coords inertia.pdb |
| Mass of Chemical Elements | masses masses.default masses.pdb |
| Merging Molecular Systems | merge.atoms merge.coords merge.pdb |
| Reflexion of Atomic Coordinates | mirror mirror.coords mirror.pdb |
| Helper Functions for reflection of Atomic Coordinates | Mab Mab.coords Mab.pdb Mbc Mbc.coords Mbc.pdb Mca Mca.coords Mca.pdb mirrorHelpers Mxy Mxy.coords Mxy.pdb Myz Myz.coords Myz.pdb Mzx Mzx.coords Mzx.pdb |
| Number of Atoms in an Object Containing Atomic Coordinates | natom natom.atoms natom.coords natom.pdb |
| Create an Object of Class 'pdb' | is.pdb pdb pdb.default |
| Projections of Objects | proj.line3d proj.line3d.matrix proj.line3d.numeric |
| Range of Atomic Coordinates | range.atoms range.coords range.pdb |
| PDB File Reader | read.pdb |
| Reinitialize Object Indexing | reindex reindex.atoms reindex.pdb |
| Replicate Atomic Coordinates | replicate replicate.atoms replicate.coords replicate.pdb |
| Rotation of Atomic Coordinates | R R.coords R.pdb rotation |
| Helper Functions for Rotation of Atomic Coordinates | rotationHelpers Rx Rx.coords Rx.pdb Ry Ry.coords Ry.pdb Rz Rz.coords Rz.pdb |
| Divide and Reassemble 'pdb' Objects | split.pdb unsplit.pdb |
| Subsetting 'atoms' and 'pdb' Objects | subset.atoms subset.pdb |
| Atomic Symbols Converter | toSymbols toSymbols.character toSymbols.integer toSymbols.numeric |
| Translation of Atomic Coordinates | Tabc Tabc.coords Tabc.pdb translation Txyz Txyz.coords Txyz.pdb |
| Helper Functions for Translation of Atomic Coordinates | Ta Ta.coords Ta.pdb Tb Tb.coords Tb.pdb Tc Tc.coords Tc.pdb translationHelpers Tx Tx.coords Tx.pdb Ty Ty.coords Ty.pdb Tz Tz.coords Tz.pdb |
| Universal Constants | universalConstants |
| Reassemble Groups | unsplit unsplit.default |
| Basic Vectorial Operations | dotProd rotVect vectNorm vectorialOperations vectProd |
| Set the View of the 'rgl' Scene | viewAB viewAxis viewBC viewCA viewInertia viewXY viewYZ viewZX |
| Visualize a Molecular Structure | visualize visualize.atoms visualize.character visualize.coords visualize.data.frame visualize.matrix visualize.pdb |
| Wrap Atomic Coordinates | wrap wrap.atoms wrap.coords wrap.pdb |
| PDB File Writer | write.pdb |
| From Cartesian to Fractional Coordinates and Vice Versa | abc2xyz abc2xyz.atoms abc2xyz.coords abc2xyz.distances abc2xyz.pdb xyz2abc xyz2abc.atoms xyz2abc.coords xyz2abc.distances xyz2abc.pdb |
