R: Read, Write, Visualize and Manipulate PDB Files

# Read, Write, Visualize and Manipulate PDB Files

## Documentation for package ‘Rpdb’ version 2.4.5

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A B C D E F I L M N P R S T U V W X misc

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
addBBox | 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
as.coords | The Atomic Coordinates of an Object
atoms | Create 'atoms' Object
atoms.atoms | Create 'atoms' Object
atoms.default | Create 'atoms' Object
atoms.pdb | 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
bbox.pdb | Add Axes or PBC Box to the 'rgl' Scene
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.crystal | 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.crystal | 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
centres.ppRoll | Centres-of-Geometry: Rolling Window
centres.ppRoll.atoms | Centres-of-Geometry: Rolling Window
centres.ppRoll.default | Centres-of-Geometry: Rolling Window
centres.ppRoll.pdb | Centres-of-Geometry: Rolling Window
chains | Extract Chain-Codes from a PDB Molecule Extract the codes of all chains from a PDB object. 'chains' is a generic function to extract the ids of the chains from a PDB molecule.
chains.atoms | Extract Chain-Codes from a PDB Molecule Extract the codes of all chains from a PDB object. 'chains' is a generic function to extract the ids of the chains from a PDB molecule.
chains.pdb | Extract Chain-Codes from a PDB Molecule Extract the codes of all chains from a PDB object. 'chains' is a generic function to extract the ids of the chains from a PDB molecule.
conect.default | Create 'connect' Object
connect | Create 'connect' Object
connect.atoms | Create 'connect' Object
connect.character | Create 'connect' Object
connect.coords | Create 'connect' Object
connect.default | Create 'connect' Object
connect.nucleic | Connects atoms in Nucleic acids
connect.nucleic.atoms | Connects atoms in Nucleic acids
connect.nucleic.pdb | Connects atoms in Nucleic acids
connect.pdb | Create 'connect' Object
coords | The Atomic Coordinates of an Object
coords.atoms | The Atomic Coordinates of an Object
coords.coords | 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
crystal | Create 'crystal' Object
crystal.default | Create 'crystal' Object
crystal.pdb | Create 'crystal' 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
dist.point | Inter-Atomic Distances
dist.point.default | Inter-Atomic Distances
distances | Inter-Atomic Distances
distances.atoms | Inter-Atomic Distances
distances.connect | 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

## -- F --

format.pdb.title | Format "Title" Field of PDB File
format.pdb.title.character | Format "Title" Field of PDB File

## -- 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.connect | Create 'connect' Object
is.coords | The Atomic Coordinates of an Object
is.crystal | Create 'crystal' Object
is.distances | Inter-Atomic Distances
is.pdb | Create an Object of Class 'pdb'

## -- L --

lattice.range | Range of Atomic Coordinates
lattice.range.pdb | Range of Atomic Coordinates

## -- 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
merge.pdb.hetero | Merging Molecular Systems
merge.pdb.resolution | Merging Molecular Systems
merge.pdb.structure | Merging Molecular Systems
mirror | Reflection of Atomic Coordinates
mirror.coords | Reflection of Atomic Coordinates
mirror.pdb | Reflection 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.connect | Inter-Atomic Distances
norm.distances | Inter-Atomic Distances

## -- P --

pdb | Create an Object of Class 'pdb'
pdb.default | Create an Object of Class 'pdb'
print.coords | The Atomic Coordinates of an Object
proj.line3d | Projections of Objects
proj.line3d.matrix | Projections of Objects
proj.line3d.numeric | Projections of Objects

## -- 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.lattice | Range of Atomic Coordinates
range.lattice.pdb | 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 --

select | Select atoms
select.atoms | Select atoms
select.pdb | Select atoms
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
trans | Graphics Tools
translate | Graphics Tools
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 --

windowRect0 | Visualize a Molecular Structure
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

## -- misc --

[.atoms | Create 'atoms' Object