Rpdb: Read, write, visualize and manipulate PDB files

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

View on CRAN

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

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

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.