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Rpdb (version 2.0)
Read, write, visualize and manipulate PDB files
Description
Provides tools to read, write, visualize PDB files and perform some structural manipulations.
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Version
Version
2.3.4
2.2
2.1
2.0
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Install
install.packages('Rpdb')
Monthly Downloads
234
Version
2.0
License
GPL
Maintainer
Julien Idé
Last Published
February 25th, 2014
Functions in Rpdb (2.0)
Search functions
toSymbols
Atomic Symbols Converter
Rpdb-package
Read, Write, Visualize and Manipulate PDB Files
subset.pdb
Subsetting
atoms
and
pdb
Objects
natom.coords
Number of Atoms in
coords
,
atoms
or
pdb
Objects
cell.coords
Unit Cell Vectors Coordinates
pdb
Create an Object of Class
pdb
elements
Periodic Table of the Elements
coords.atoms
The Atomic Coordinates of an Object of Class
atoms
merge.coords
Merge Two Objects of Class
coords
conect
Create
conect
Object
mirrorHelpers
Helper Functions for reflection of Atomic Coordinates
is.conect
Is an Object of Class
conect
?
split.pdb
Divide and Reassemble
pdb
Objects
rotationHelpers
Helper Functions for Rotation of Atomic Coordinates
wrap
Wrap Atomic Coordinates
is.cryst1
Is an Object of Class
cryst1
?
dotProd
Basic Vectorial Operations
rotation
Rotation of Atomic Coordinates
coords
The Atomic Coordinates of an Object
basis.pdb
The Basis Set of a
pdb
Object
translationHelpers
Helper Functions for Translation of Atomic Coordinates
basis
The Basis of an Object
addABC
Add Lattice Vectors to the
rgl
Scene
reindex
Reinitialize Object Indexing
is.coords
Is an Object of Class
coords
?
cell.volume
Volume of a Unit Cell
write.pdb
PDB File Writer
addPBCBox
Add a PBC Box to the
rgl
Scene
cryst1
Create
cryst1
Object
replicate
Replicate Atomic Coordinates
cell.density
Density of a Unit Cell
coords.pdb
The Coordinates of an Object of Class
pdb
mirror
Reflexion of Atomic Coordinates
unsplit
Reassemble Groups
range.coords
Range of Atomic Coordinates
merge.pdb
Merge Two Obejct of Class
pdb
visualize
Visualize a Molecular Structure
centres
Centres-of-Geometry and Centres-of-Mass
read.pdb
PDB File Reader
atoms
Create
atoms
Object
viewAxis
Set the View of the
rgl
Scene
xyz2abc
From Cartesian to Fractional Coordinates and Vis Versa
addXYZ
Add Cartesian Axes to the
rgl
Scene
natom
Number of Atoms in an Object Containing Atomic Coordinates
translation
Translation of Atomic Coordinates
is.atoms
Is an Object of Class
atoms
?
coords.data.frame
Create
coords
Object From
data.frame
or
matrix
inertia
Moment of Inertia of a Molecular System
masses
Mass of Chemical Elements
is.pdb
Is an Object of Class
pdb
?
universalConstants
universal Constants