Read, Write, Visualize and Manipulate PDB Files
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Documentation for package ‘Rpdb’ version 2.3.4
Help Pages
A B C D E I M N P R S T U V W X
| Rpdb-package | Read, Write, Visualize and Manipulate PDB Files |
-- A --
| abc2xyz | From Cartesian to Fractional Coordinates and Vice Versa |
| abc2xyz.atoms | From Cartesian to Fractional Coordinates and Vice Versa |
| abc2xyz.coords | From Cartesian to Fractional Coordinates and Vice Versa |
| abc2xyz.distances | From Cartesian to Fractional Coordinates and Vice Versa |
| abc2xyz.pdb | From Cartesian to Fractional Coordinates and Vice Versa |
| addABC | Add Axes or PBC Box to the 'rgl' Scene |
| addAxes | Add Axes or PBC Box to the 'rgl' Scene |
| addEleLab | Add Labels to the 'rgl' Scene |
| addEleLab.atoms | Add Labels to the 'rgl' Scene |
| addEleLab.pdb | Add Labels to the 'rgl' Scene |
| addLabels | Add Labels to the 'rgl' Scene |
| addPBCBox | Add Axes or PBC Box to the 'rgl' Scene |
| addResLab | Add Labels to the 'rgl' Scene |
| addResLab.atoms | Add Labels to the 'rgl' Scene |
| addResLab.pdb | Add Labels to the 'rgl' Scene |
| addXYZ | Add Axes or PBC Box to the 'rgl' Scene |
| angle | Atomic Bond Lengths, Angles and Dihedrals |
| angle.coords | Atomic Bond Lengths, Angles and Dihedrals |
| angle.pdb | Atomic Bond Lengths, Angles and Dihedrals |
| atoms | Create 'atoms' Object |
| atoms.default | Create 'atoms' Object |
-- B --
| basis | The Basis of an Object |
| basis.default | The Basis of an Object |
| basis.pdb | The Basis of an Object |
| basis<- | The Basis of an Object |
| basis<-.default | The Basis of an Object |
| basis<-.pdb | The Basis of an Object |
| bond | Atomic Bond Lengths, Angles and Dihedrals |
| bond-angle-dihedral | Atomic Bond Lengths, Angles and Dihedrals |
| bond.coords | Atomic Bond Lengths, Angles and Dihedrals |
| bond.pdb | Atomic Bond Lengths, Angles and Dihedrals |
-- C --
| cell.coords | Properties of a Unit Cell |
| cell.coords.cryst1 | Properties of a Unit Cell |
| cell.coords.default | Properties of a Unit Cell |
| cell.coords.pdb | Properties of a Unit Cell |
| cell.density | Properties of a Unit Cell |
| cell.density.default | Properties of a Unit Cell |
| cell.density.pdb | Properties of a Unit Cell |
| cell.volume | Properties of a Unit Cell |
| cell.volume.cryst1 | Properties of a Unit Cell |
| cell.volume.pdb | Properties of a Unit Cell |
| cellProperties | Properties of a Unit Cell |
| centres | Centres-of-Geometry and Centres-of-Mass |
| centres.atoms | Centres-of-Geometry and Centres-of-Mass |
| centres.coords | Centres-of-Geometry and Centres-of-Mass |
| centres.pdb | Centres-of-Geometry and Centres-of-Mass |
| conect | Create 'conect' Object |
| conect.coords | Create 'conect' Object |
| conect.default | Create 'conect' Object |
| conect.pdb | Create 'conect' Object |
| coords | The Atomic Coordinates of an Object |
| coords.atoms | The Atomic Coordinates of an Object |
| coords.data.frame | The Atomic Coordinates of an Object |
| coords.default | The Atomic Coordinates of an Object |
| coords.matrix | The Atomic Coordinates of an Object |
| coords.pdb | The Atomic Coordinates of an Object |
| coords<- | The Atomic Coordinates of an Object |
| coords<-.atoms | The Atomic Coordinates of an Object |
| coords<-.pdb | The Atomic Coordinates of an Object |
| cryst1 | Create 'cryst1' Object |
| cryst1.default | Create 'cryst1' Object |
-- D --
| dihedral | Atomic Bond Lengths, Angles and Dihedrals |
| dihedral.coords | Atomic Bond Lengths, Angles and Dihedrals |
| dihedral.pdb | Atomic Bond Lengths, Angles and Dihedrals |
| distances | Inter-Atomic Distances |
| distances.atoms | Inter-Atomic Distances |
| distances.coords | Inter-Atomic Distances |
| distances.default | Inter-Atomic Distances |
| distances.pdb | Inter-Atomic Distances |
| dotProd | Basic Vectorial Operations |
-- E --
| elements | Periodic Table of the Elements |
-- I --
| inertia | Moment of Inertia of a Molecular System |
| inertia.atoms | Moment of Inertia of a Molecular System |
| inertia.coords | Moment of Inertia of a Molecular System |
| inertia.pdb | Moment of Inertia of a Molecular System |
| info3d | Add Labels to the 'rgl' Scene |
| info3d.atoms | Add Labels to the 'rgl' Scene |
| info3d.pdb | Add Labels to the 'rgl' Scene |
| is.atoms | Create 'atoms' Object |
| is.conect | Create 'conect' Object |
| is.coords | The Atomic Coordinates of an Object |
| is.cryst1 | Create 'cryst1' Object |
| is.distances | Inter-Atomic Distances |
| is.pdb | Create an Object of Class 'pdb' |
-- M --
| Mab | Helper Functions for reflection of Atomic Coordinates |
| Mab.coords | Helper Functions for reflection of Atomic Coordinates |
| Mab.pdb | Helper Functions for reflection of Atomic Coordinates |
| masses | Mass of Chemical Elements |
| masses.default | Mass of Chemical Elements |
| masses.pdb | Mass of Chemical Elements |
| Mbc | Helper Functions for reflection of Atomic Coordinates |
| Mbc.coords | Helper Functions for reflection of Atomic Coordinates |
| Mbc.pdb | Helper Functions for reflection of Atomic Coordinates |
| Mca | Helper Functions for reflection of Atomic Coordinates |
| Mca.coords | Helper Functions for reflection of Atomic Coordinates |
| Mca.pdb | Helper Functions for reflection of Atomic Coordinates |
| measure | Atomic Bond Lengths, Angles and Dihedrals |
| measure.coords | Atomic Bond Lengths, Angles and Dihedrals |
| measure.default | Atomic Bond Lengths, Angles and Dihedrals |
| measure.pdb | Atomic Bond Lengths, Angles and Dihedrals |
| merge.atoms | Merging Molecular Systems |
| merge.coords | Merging Molecular Systems |
| merge.pdb | Merging Molecular Systems |
| mirror | Reflexion of Atomic Coordinates |
| mirror.coords | Reflexion of Atomic Coordinates |
| mirror.pdb | Reflexion of Atomic Coordinates |
| mirrorHelpers | Helper Functions for reflection of Atomic Coordinates |
| Mxy | Helper Functions for reflection of Atomic Coordinates |
| Mxy.coords | Helper Functions for reflection of Atomic Coordinates |
| Mxy.pdb | Helper Functions for reflection of Atomic Coordinates |
| Myz | Helper Functions for reflection of Atomic Coordinates |
| Myz.coords | Helper Functions for reflection of Atomic Coordinates |
| Myz.pdb | Helper Functions for reflection of Atomic Coordinates |
| Mzx | Helper Functions for reflection of Atomic Coordinates |
| Mzx.coords | Helper Functions for reflection of Atomic Coordinates |
| Mzx.pdb | Helper Functions for reflection of Atomic Coordinates |
-- N --
| natom | Number of Atoms in an Object Containing Atomic Coordinates |
| natom.atoms | Number of Atoms in an Object Containing Atomic Coordinates |
| natom.coords | Number of Atoms in an Object Containing Atomic Coordinates |
| natom.pdb | Number of Atoms in an Object Containing Atomic Coordinates |
| norm | Inter-Atomic Distances |
| norm.distances | Inter-Atomic Distances |
-- P --
| pdb | Create an Object of Class 'pdb' |
| pdb.default | Create an Object of Class 'pdb' |
-- R --
| R | Rotation of Atomic Coordinates |
| R.coords | Rotation of Atomic Coordinates |
| R.pdb | Rotation of Atomic Coordinates |
| range.atoms | Range of Atomic Coordinates |
| range.coords | Range of Atomic Coordinates |
| range.pdb | Range of Atomic Coordinates |
| read.pdb | PDB File Reader |
| reindex | Reinitialize Object Indexing |
| reindex.atoms | Reinitialize Object Indexing |
| reindex.pdb | Reinitialize Object Indexing |
| replicate | Replicate Atomic Coordinates |
| replicate.atoms | Replicate Atomic Coordinates |
| replicate.coords | Replicate Atomic Coordinates |
| replicate.pdb | Replicate Atomic Coordinates |
| rotation | Rotation of Atomic Coordinates |
| rotationHelpers | Helper Functions for Rotation of Atomic Coordinates |
| rotVect | Basic Vectorial Operations |
| Rx | Helper Functions for Rotation of Atomic Coordinates |
| Rx.coords | Helper Functions for Rotation of Atomic Coordinates |
| Rx.pdb | Helper Functions for Rotation of Atomic Coordinates |
| Ry | Helper Functions for Rotation of Atomic Coordinates |
| Ry.coords | Helper Functions for Rotation of Atomic Coordinates |
| Ry.pdb | Helper Functions for Rotation of Atomic Coordinates |
| Rz | Helper Functions for Rotation of Atomic Coordinates |
| Rz.coords | Helper Functions for Rotation of Atomic Coordinates |
| Rz.pdb | Helper Functions for Rotation of Atomic Coordinates |
-- S --
| split.pdb | Divide and Reassemble 'pdb' Objects |
| subset.atoms | Subsetting 'atoms' and 'pdb' Objects |
| subset.pdb | Subsetting 'atoms' and 'pdb' Objects |
-- T --
| Ta | Helper Functions for Translation of Atomic Coordinates |
| Ta.coords | Helper Functions for Translation of Atomic Coordinates |
| Ta.pdb | Helper Functions for Translation of Atomic Coordinates |
| Tabc | Translation of Atomic Coordinates |
| Tabc.coords | Translation of Atomic Coordinates |
| Tabc.pdb | Translation of Atomic Coordinates |
| Tb | Helper Functions for Translation of Atomic Coordinates |
| Tb.coords | Helper Functions for Translation of Atomic Coordinates |
| Tb.pdb | Helper Functions for Translation of Atomic Coordinates |
| Tc | Helper Functions for Translation of Atomic Coordinates |
| Tc.coords | Helper Functions for Translation of Atomic Coordinates |
| Tc.pdb | Helper Functions for Translation of Atomic Coordinates |
| toSymbols | Atomic Symbols Converter |
| toSymbols.character | Atomic Symbols Converter |
| toSymbols.integer | Atomic Symbols Converter |
| toSymbols.numeric | Atomic Symbols Converter |
| translation | Translation of Atomic Coordinates |
| translationHelpers | Helper Functions for Translation of Atomic Coordinates |
| Tx | Helper Functions for Translation of Atomic Coordinates |
| Tx.coords | Helper Functions for Translation of Atomic Coordinates |
| Tx.pdb | Helper Functions for Translation of Atomic Coordinates |
| Txyz | Translation of Atomic Coordinates |
| Txyz.coords | Translation of Atomic Coordinates |
| Txyz.pdb | Translation of Atomic Coordinates |
| Ty | Helper Functions for Translation of Atomic Coordinates |
| Ty.coords | Helper Functions for Translation of Atomic Coordinates |
| Ty.pdb | Helper Functions for Translation of Atomic Coordinates |
| Tz | Helper Functions for Translation of Atomic Coordinates |
| Tz.coords | Helper Functions for Translation of Atomic Coordinates |
| Tz.pdb | Helper Functions for Translation of Atomic Coordinates |
-- U --
| universalConstants | Universal Constants |
| unsplit | Reassemble Groups |
| unsplit.default | Reassemble Groups |
| unsplit.pdb | Divide and Reassemble 'pdb' Objects |
-- V --
| vectNorm | Basic Vectorial Operations |
| vectorialOperations | Basic Vectorial Operations |
| vectProd | Basic Vectorial Operations |
| viewAB | Set the View of the 'rgl' Scene |
| viewAxis | Set the View of the 'rgl' Scene |
| viewBC | Set the View of the 'rgl' Scene |
| viewCA | Set the View of the 'rgl' Scene |
| viewInertia | Set the View of the 'rgl' Scene |
| viewXY | Set the View of the 'rgl' Scene |
| viewYZ | Set the View of the 'rgl' Scene |
| viewZX | Set the View of the 'rgl' Scene |
| visualize | Visualize a Molecular Structure |
| visualize.atoms | Visualize a Molecular Structure |
| visualize.character | Visualize a Molecular Structure |
| visualize.coords | Visualize a Molecular Structure |
| visualize.data.frame | Visualize a Molecular Structure |
| visualize.matrix | Visualize a Molecular Structure |
| visualize.pdb | Visualize a Molecular Structure |
-- W --
| wrap | Wrap Atomic Coordinates |
| wrap.atoms | Wrap Atomic Coordinates |
| wrap.coords | Wrap Atomic Coordinates |
| wrap.pdb | Wrap Atomic Coordinates |
| write.pdb | PDB File Writer |
-- X --
| xyz2abc | From Cartesian to Fractional Coordinates and Vice Versa |
| xyz2abc.atoms | From Cartesian to Fractional Coordinates and Vice Versa |
| xyz2abc.coords | From Cartesian to Fractional Coordinates and Vice Versa |
| xyz2abc.distances | From Cartesian to Fractional Coordinates and Vice Versa |
| xyz2abc.pdb | From Cartesian to Fractional Coordinates and Vice Versa |