⚠️There's a newer version (2.3.4) of this package.Take me there.

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.

Copy Link

Version

Install

install.packages('Rpdb')

Monthly Downloads

567

Version

2.0

License

GPL

Maintainer

Julien Idé

Last Published

February 25th, 2014

Functions in Rpdb (2.0)

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

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