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Rpdb (version 2.2)

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

Install

install.packages('Rpdb')

Monthly Downloads

194

Version

2.2

License

GPL

Maintainer

Julien Idé

Last Published

April 26th, 2014

Functions in Rpdb (2.2)

masses

Mass of Chemical Elements
inertia

Moment of Inertia of a Molecular System
cellProperties

Properties of a Unit Cell
universalConstants

universal Constants
conect

Create ‘conect’ Object
split.pdb

Divide and Reassemble ‘pdb’ Objects
unsplit

Reassemble Groups
atoms

Create ‘atoms’ Object
read.pdb

PDB File Reader
write.pdb

PDB File Writer
elements

Periodic Table of the Elements
bond-angle-dihedral

Atomic Bond Lengths, Angles and Dihedrals
distances

Inter-Atomic Distances
rotation

Rotation of Atomic Coordinates
reindex

Reinitialize Object Indexing
natom

Number of Atoms in an Object Containing Atomic Coordinates
replicate

Replicate Atomic Coordinates
rotationHelpers

Helper Functions for Rotation of Atomic Coordinates
wrap

Wrap Atomic Coordinates
translationHelpers

Helper Functions for Translation of Atomic Coordinates
Rpdb-package

Read, Write, Visualize and Manipulate PDB Files
vectorialOperations

Basic Vectorial Operations
translation

Translation of Atomic Coordinates
mirrorHelpers

Helper Functions for reflection of Atomic Coordinates
basis

The Basis of an Object
addLabels

Add Labels to the ‘rgl’ Scene
addAxes

Add Axes or PBC Box to the ‘rgl’ Scene
centres

Centres-of-Geometry and Centres-of-Mass
mirror

Reflexion of Atomic Coordinates
cryst1

Create ‘cryst1’ Object
coords

The Atomic Coordinates of an Object
visualize

Visualize a Molecular Structure
merge.coords

Merging Molecular Systems
viewAxis

Set the View of the ‘rgl’ Scene
range.coords

Range of Atomic Coordinates
pdb

Create an Object of Class ‘pdb’
xyz2abc

From Cartesian to Fractional Coordinates and Vis Versa
toSymbols

Atomic Symbols Converter
subset.pdb

Subsetting ‘atoms’ and ‘pdb’ Objects