Rpdb: Read, write, visualize and manipulate PDB files
Version 2.2

Provides tools to read, write, visualize PDB files and perform some structural manipulations.

AuthorJulien Idé
Date of publication2014-04-26 14:57:10
MaintainerJulien Idé <julien.ide.fr@gmail.com>
LicenseGPL
Version2.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("Rpdb")

Getting started

Package overview

Popular man pages

addLabels: Add Labels to the 'rgl' Scene
bond-angle-dihedral: Atomic Bond Lengths, Angles and Dihedrals
conect: Create 'conect' Object
mirror: Reflexion of Atomic Coordinates
pdb: Create an Object of Class 'pdb'
read.pdb: PDB File Reader
xyz2abc: From Cartesian to Fractional Coordinates and Vis Versa
See all...

All man pages Function index File listing

Man pages

addAxes: Add Axes or PBC Box to the 'rgl' Scene
addLabels: Add Labels to the 'rgl' Scene
atoms: Create 'atoms' Object
basis: The Basis of an Object
bond-angle-dihedral: Atomic Bond Lengths, Angles and Dihedrals
cellProperties: Properties of a Unit Cell
centres: Centres-of-Geometry and Centres-of-Mass
conect: Create 'conect' Object
coords: The Atomic Coordinates of an Object
cryst1: Create 'cryst1' Object
distances: Inter-Atomic Distances
elements: Periodic Table of the Elements
inertia: Moment of Inertia of a Molecular System
masses: Mass of Chemical Elements
merge.coords: Merging Molecular Systems
mirror: Reflexion of Atomic Coordinates
mirrorHelpers: Helper Functions for reflection of Atomic Coordinates
natom: Number of Atoms in an Object Containing Atomic Coordinates
pdb: Create an Object of Class 'pdb'
range.coords: Range of Atomic Coordinates
read.pdb: PDB File Reader
reindex: Reinitialize Object Indexing
replicate: Replicate Atomic Coordinates
rotation: Rotation of Atomic Coordinates
rotationHelpers: Helper Functions for Rotation of Atomic Coordinates
Rpdb-package: Read, Write, Visualize and Manipulate PDB Files
split.pdb: Divide and Reassemble 'pdb' Objects
subset.pdb: Subsetting 'atoms' and 'pdb' Objects
toSymbols: Atomic Symbols Converter
translation: Translation of Atomic Coordinates
translationHelpers: Helper Functions for Translation of Atomic Coordinates
universalConstants: universal Constants
unsplit: Reassemble Groups
vectorialOperations: Basic Vectorial Operations
viewAxis: Set the View of the 'rgl' Scene
visualize: Visualize a Molecular Structure
wrap: Wrap Atomic Coordinates
write.pdb: PDB File Writer
xyz2abc: From Cartesian to Fractional Coordinates and Vis Versa

Functions

Mab Man page Source code
Mab.coords Man page Source code
Mab.pdb Man page Source code
Mbc Man page Source code
Mbc.coords Man page Source code
Mbc.pdb Man page Source code
Mca Man page Source code
Mca.coords Man page Source code
Mca.pdb Man page Source code
Mxy Man page Source code
Mxy.coords Man page Source code
Mxy.pdb Man page Source code
Myz Man page Source code
Myz.coords Man page Source code
Myz.pdb Man page Source code
Mzx Man page Source code
Mzx.coords Man page Source code
Mzx.pdb Man page Source code
R Man page Source code
R.coords Man page Source code
R.pdb Man page Source code
Rpdb Man page
Rpdb-package Man page
Rx Man page Source code
Rx.coords Man page Source code
Rx.pdb Man page Source code
Ry Man page Source code
Ry.coords Man page Source code
Ry.pdb Man page Source code
Rz Man page Source code
Rz.coords Man page Source code
Rz.pdb Man page Source code
Ta Man page Source code
Ta.coords Man page Source code
Ta.pdb Man page Source code
Tabc Man page Source code
Tabc.atoms Man page
Tabc.coords Man page Source code
Tabc.pdb Man page Source code
Tb Man page Source code
Tb.coords Man page Source code
Tb.pdb Man page Source code
Tc Man page Source code
Tc.coords Man page Source code
Tc.pdb Man page Source code
Tx Man page Source code
Tx.coords Man page Source code
Tx.pdb Man page Source code
Txyz Man page Source code
Txyz.atoms Man page
Txyz.coords Man page Source code
Txyz.pdb Man page Source code
Ty Man page Source code
Ty.coords Man page Source code
Ty.pdb Man page Source code
Tz Man page Source code
Tz.coords Man page Source code
Tz.pdb Man page Source code
abc2xyz Man page Source code
abc2xyz.atoms Man page Source code
abc2xyz.coords Man page Source code
abc2xyz.distances Man page Source code
abc2xyz.pdb Man page Source code
addABC Man page Source code
addEleLab Man page Source code
addEleLab.atoms Man page Source code
addEleLab.pdb Man page Source code
addLabels Man page
addPBCBox Man page Source code
addResLab Man page Source code
addResLab.atoms Man page Source code
addResLab.pdb Man page Source code
addXYZ Man page Source code
angle Man page Source code
angle.coords Man page Source code
angle.pdb Man page Source code
atoms Man page Source code
atoms.default Man page Source code
basis Man page Source code
basis.default Man page Source code
basis.pdb Man page Source code
basis<- Man page
basis<-.default Man page
basis<-.pdb Man page
bond Man page Source code
bond.coords Man page Source code
bond.pdb Man page Source code
cell.coords Man page Source code
cell.coords.cryst1 Man page Source code
cell.coords.default Man page Source code
cell.coords.pdb Man page Source code
cell.density Man page Source code
cell.density.default Man page Source code
cell.density.pdb Man page Source code
cell.volume Man page Source code
cell.volume.cryst1 Man page Source code
cell.volume.pdb Man page Source code
centres Man page Source code
centres.atoms Man page Source code
centres.coords Man page Source code
centres.pdb Man page Source code
conect Man page Source code
conect.coords Man page Source code
conect.default Man page Source code
conect.pdb Man page Source code
coords Man page Source code
coords.atoms Man page Source code
coords.data.frame Man page Source code
coords.default Man page Source code
coords.matrix Man page Source code
coords.pdb Man page Source code
coords<- Man page
coords<-.atoms Man page
coords<-.pdb Man page
cryst1 Man page Source code
cryst1.default Man page Source code
dihedral Man page Source code
dihedral.coords Man page Source code
dihedral.pdb Man page Source code
distances Man page Source code
distances.atoms Man page Source code
distances.coords Man page Source code
distances.default Man page Source code
distances.pdb Man page Source code
dotProd Man page Source code
elements Man page
inertia Man page Source code
inertia.atoms Man page Source code
inertia.coords Man page Source code
inertia.pdb Man page Source code
info3d Man page Source code
info3d.atoms Man page Source code
info3d.pdb Man page Source code
is.atoms Man page Source code
is.conect Man page Source code
is.coords Man page Source code
is.cryst1 Man page Source code
is.distances Man page Source code
is.pdb Man page Source code
masses Man page Source code
masses.default Man page Source code
masses.pdb Man page Source code
measure Man page Source code
measure.coords Man page Source code
measure.default Man page Source code
measure.pdb Man page Source code
merge.atoms Man page Source code
merge.coords Man page Source code
merge.pdb Man page Source code
mirror Man page Source code
mirror.coords Man page Source code
mirror.pdb Man page Source code
natom Man page Source code
natom.atoms Man page Source code
natom.coords Man page Source code
natom.pdb Man page Source code
norm Man page Source code
norm.distances Man page Source code
pdb Man page Source code
pdb.default Man page Source code
range.atoms Man page Source code
range.coords Man page Source code
range.pdb Man page Source code
read.pdb Man page Source code
reindex Man page Source code
reindex.atoms Man page Source code
reindex.pdb Man page Source code
replicate Man page Source code
replicate.atoms Man page Source code
replicate.coords Man page Source code
replicate.pdb Man page Source code
rotVect Man page Source code
split.pdb Man page Source code
subset.atoms Man page Source code
subset.pdb Man page Source code
toSymbols Man page Source code
toSymbols.character Man page Source code
toSymbols.integer Man page Source code
toSymbols.numeric Man page Source code
universalConstants Man page
unsplit Man page Source code
unsplit.default Man page Source code
unsplit.pdb Man page Source code
vectNorm Man page Source code
vectProd Man page Source code
viewAB Man page Source code
viewAxis Man page Source code
viewBC Man page Source code
viewCA Man page Source code
viewInertia Man page Source code
viewXY Man page Source code
viewYZ Man page Source code
viewZX Man page Source code
visualize Man page Source code
visualize.atoms Man page Source code
visualize.character Man page Source code
visualize.coords Man page Source code
visualize.data.frame Man page Source code
visualize.matrix Man page Source code
visualize.pdb Man page Source code
wrap Man page Source code
wrap.atoms Man page Source code
wrap.coords Man page Source code
wrap.pdb Man page Source code
write.pdb Man page Source code
xyz2abc Man page Source code
xyz2abc.atoms Man page Source code
xyz2abc.coords Man page Source code
xyz2abc.distances Man page Source code
xyz2abc.pdb Man page Source code

Files

inst
inst/examples
inst/examples/Pentacene.pdb
inst/examples/C70.pdb
inst/examples/PCBM_ODCB.pdb
NAMESPACE
data
data/elements.rda
data/universalConstants.rda
R
R/addAxes.R
R/atoms.R
R/replicate.R
R/reindex.R
R/addLabels.R
R/write.pdb.R
R/split.pdb.R
R/xyz2abc.R
R/read.pdb.R
R/natom.R
R/subset.atoms.R
R/mirrorHelpers.R
R/centres.R
R/toSymbols.R
R/coords.R
R/wrap.R
R/merge.coords.R
R/masses.R
R/cellProperties.R
R/distances.R
R/conect.R
R/mirror.R
R/translation.R
R/measure.R
R/translationHelpers.R
R/cryst1.R
R/bond-angle-dihedral.R
R/vectorialOperations.R
R/viewAxis.R
R/visualize.R
R/range.coords.R
R/rotation.R
R/unsplit.R
R/pdb.R
R/inertia.R
R/basis.R
R/rotationHelpers.R
MD5
DESCRIPTION
man
man/addAxes.Rd
man/distances.Rd
man/basis.Rd
man/toSymbols.Rd
man/centres.Rd
man/translationHelpers.Rd
man/cellProperties.Rd
man/reindex.Rd
man/Rpdb-package.Rd
man/mirrorHelpers.Rd
man/universalConstants.Rd
man/replicate.Rd
man/conect.Rd
man/bond-angle-dihedral.Rd
man/write.pdb.Rd
man/range.coords.Rd
man/read.pdb.Rd
man/coords.Rd
man/vectorialOperations.Rd
man/mirror.Rd
man/viewAxis.Rd
man/cryst1.Rd
man/split.pdb.Rd
man/pdb.Rd
man/elements.Rd
man/subset.pdb.Rd
man/merge.coords.Rd
man/wrap.Rd
man/visualize.Rd
man/translation.Rd
man/rotationHelpers.Rd
man/addLabels.Rd
man/unsplit.Rd
man/natom.Rd
man/inertia.Rd
man/masses.Rd
man/rotation.Rd
man/atoms.Rd
man/xyz2abc.Rd
Rpdb documentation built on May 19, 2017, 6:09 p.m.