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Rpdb: Read, Write, Visualize and Manipulate PDB Files

  • Reanimated the Rpdb package from the CRAN archive;
  • Original author: Julien Idé;

Changes

  • [fixed] deprecated rgl functions;
  • [fixed] some Roxygen bugs in centre.R;

Usage

library(Rpdb)
# or: devtools::load_all(_path_)

x = read.pdb(file.choose())
visualize(x, type="p")

Note:

  • the default visualize is broken;
  • the protein is NOT centered in the bounding box;

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Version

Install

install.packages('Rpdb')

Version

2.3.4

License

GPL (>= 3)

Issues

Pull Requests

Stars

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Maintainer

Last Published

September 28th, 2023

Functions in Rpdb (2.3.4)

masses

Mass of Chemical Elements
elements

Periodic Table of the Elements
merge.coords

Merging Molecular Systems
inertia

Moment of Inertia of a Molecular System
mirror

Reflexion of Atomic Coordinates
mirrorHelpers

Helper Functions for reflection of Atomic Coordinates
range.coords

Range of Atomic Coordinates
addAxes

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

Rotation of Atomic Coordinates
split.pdb

Divide and Reassemble ‘pdb’ Objects
cryst1

Create ‘cryst1’ Object
distances

Inter-Atomic Distances
replicate

Replicate Atomic Coordinates
visualize

Visualize a Molecular Structure
toSymbols

Atomic Symbols Converter
reindex

Reinitialize Object Indexing
translation

Translation of Atomic Coordinates
rotationHelpers

Helper Functions for Rotation of Atomic Coordinates
viewAxis

Set the View of the ‘rgl’ Scene
universalConstants

Universal Constants
pdb

Create an Object of Class ‘pdb’
subset.atoms

Subsetting ‘atoms’ and ‘pdb’ Objects
natom

Number of Atoms in an Object Containing Atomic Coordinates
write.pdb

PDB File Writer
translationHelpers

Helper Functions for Translation of Atomic Coordinates
read.pdb

PDB File Reader
xyz2abc

From Cartesian to Fractional Coordinates and Vice Versa
wrap

Wrap Atomic Coordinates
vectorialOperations

Basic Vectorial Operations
unsplit

Reassemble Groups
basis

The Basis of an Object
atoms

Create ‘atoms’ Object
cellProperties

Properties of a Unit Cell
addLabels

Add Labels to the ‘rgl’ Scene
bond-angle-dihedral

Atomic Bond Lengths, Angles and Dihedrals
conect

Create ‘conect’ Object
centres

Centres-of-Geometry and Centres-of-Mass
coords

The Atomic Coordinates of an Object
Rpdb-package

Read, Write, Visualize and Manipulate PDB Files