Rpdb: Read, write, visualize and manipulate PDB files

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

Author
Julien Idé
Date of publication
2014-04-26 14:57:10
Maintainer
Julien Idé <julien.ide.fr@gmail.com>
License
GPL
Version
2.2

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

Files in this package

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