Read, Write, Visualize and Manipulate PDB Files

Description

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

Details

This package enables users, e.g. computational chemists, to manipulate molecular structures stored in PDB files. It enables users ro read, write and visualize PDB files. Various basic structural manipulations are also supported. Conversion of Cartesian coordinates into fractional coordinates. Spliting a molecular structure into fragments. Computation of centers-of-geometry and centers-of-mass. Wrapping molecular structure using periodical boundary conditions. Translation, rotation and reflection of atomic coordinates. Calculate atomic bond lengths, angles and dihedrals.

Author(s)

Julien Idé julien.ide.fr@gmail.com

References

More information on the PDB format can be found here:
http://www.wwpdb.org/documentation/format33/v3.3.html

Examples

## Read a PDB file included in the package
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))

## Visualize the PDB file
visualize(x, mode = NULL)

## From Cartesian to fractional coordinates and vice versa
x <- xyz2abc(x)
basis(x)
natom(x, x$atoms$resid)
range(x)
centres(x)
x <- abc2xyz(x)
basis(x)
natom(x, x$atoms$resid)
range(x)
centres(x)

## Split and unsplit
F <- x$atoms$resid
x <-   split(x, F)
x <- unsplit(x, F)

## Subset and merge
x.PCB.only <- subset(x, resname == "PCB")
x.DCB.only <- subset(x, resname == "DCB")
x <- merge(x.PCB.only, x.DCB.only)

## Duplicate and wrap
x <- replicate(x, a.ind = -1:1, b.ind = -1:1, c.ind = -1:1)
x <- wrap(x)

## Write the 'pdb' object 'x' to a temporary file.
write.pdb(x, file = tempfile())

Add Axes or PBC Box to the ‘rgl’ Scene

Description

Add lattice vectors, Cartesian axes or PBC box to the current ‘rgl’ scene.

Usage

addABC(x, lwd = 2, labels = TRUE, cex = 2)

addXYZ(lwd = 2, labels = TRUE, cex = 2)

addPBCBox(x, lwd = 2)

Arguments

Details

addABC: Add the lattice vectors a, b and c to the current rgl device.
addXYZ: Add the Cartesian axes x, y and z to the current rgl device.
addPBCBox: Add a box representing the Periodic Boundary Conditions of a molecular system.

Value

Return (using invisible) a two-column data.frame containing the IDs and type indicators of the objects added to the scene.

See Also

visualize, rgl.open, par3d, addLabels

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
visualize(x, type = "l", xyz = FALSE, abc = FALSE, pbc.box = FALSE, mode = NULL)
addXYZ()
addABC(x$cryst1)
addPBCBox(x$cryst1)

Add Labels to the ‘rgl’ Scene

Description

Add Labels to the current ‘rgl’ scene.

Usage

addResLab(x, ...)

## S3 method for class 'atoms'
addResLab(x, at.centre = TRUE, col = "black", ...)

## S3 method for class 'pdb'
addResLab(x, at.centre = TRUE, col = "black", ...)

addEleLab(x, ...)

## S3 method for class 'atoms'
addEleLab(x, eleid = FALSE, col = "black", ...)

## S3 method for class 'pdb'
addEleLab(x, eleid = FALSE, col = "black", ...)

info3d(...)

## S3 method for class 'atoms'
info3d(x, id = rgl::rgl.ids(), col = "black", verbose = TRUE, adj = 0, ...)

## S3 method for class 'pdb'
info3d(x, id = rgl::rgl.ids(), col = "black", verbose = TRUE, adj = 0, ...)

Arguments

Details

addResLab add residue labels to the scene. If at.centre==TRUE only one label per residue is added at the centre of the residue. Otherwise, residue labels are added at each atomic positions. addEleLab add element labels to the scene at each atomic positions. info3d activate an interactive mode to add labels by selecting atoms by right-clicking on the current ‘rgl’ scene. To escape the interactive mode press the ESC key. The labels are as follow: "ResidResname:EleidElename"

Value

addResLab and addEleLab return (using invisible) a two-column data.frame containing the IDs and type indicators of the objects added to the scene.

See Also

pdb, visualize, measure

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
visualize(x, type = "l", mode = NULL)
addResLab(x)
x <- read.pdb(system.file("examples/Pentacene.pdb", package="Rpdb"))
visualize(x, type = "l", mode = NULL)
addEleLab(x)

Create ‘atoms’ Object

Description

Creates an object of class ‘atoms’ containing the data related to ATOM and HETATM records of a PDB file.

Usage

atoms(...)

## Default S3 method:
atoms(
  recname,
  eleid,
  elename,
  alt,
  resname,
  chainid,
  resid,
  insert,
  x1,
  x2,
  x3,
  occ,
  temp,
  segid,
  basis = "xyz",
  ...
)

is.atoms(x)

Arguments

Details

atoms is a generic function to create objects of class ‘atoms’. The purpose of this class is to store ATOM and HETATM records from PDB files. The default method creates a atoms object from its different components, i.e.: recname, eleid, elename, alt, resname, chainid, resid, insert, x1, x2, x3, occ, temp, segid and basis. All the arguments have to be specified except basis which by default is set to "xyz" (Cartesian coordinates).
is.atoms tests if an object of class ‘atoms’, i.e. if it has a “class” attribute equal to atoms.

Value

atoms returns a data.frame of class ‘atoms’ with the following components:

recname

a character vector containing the record name for each element.

eleid

a integer vector containing the element ID for each element.

elename

a character vector containing the element name for each element.

alt

a character vector containing the alternate location indicator for each element.

resname

a character vector containing the residue name for each element.

chainid

a character vector containing the chain ID for each element.

resid

a integer vector containing the residue ID for each element.

insert

a character vector containing the codes for insertion of residue for each element.

x1, x2, x3

a numeric vector containing the first, second and third coordinate for each element.

occ

a numeric vector containing the occupencie for each element.

temp

a numeric vector containing the temperature factor for each element.

segid

a character vector containing the segment ID for each element.

basis

a single element character vector indicating the type of basis vector used to express the atomic coordinates.

is.atoms returns TRUE if x is an object of class ‘atoms’ and FALSE otherwise.

See Also

basis, coords, pdb

Examples

x <- atoms(recname = c("ATOM","ATOM"), eleid = 1:2, elename = c("H","H"), alt = "",
  resname = c("H2","H2"), chainid = "", resid = c(1,1), insert = "",
  x1 = c(0,0), x2 = c(0,0), x3 = c(0,1), occ = c(0.0,0.0), temp = c(1.0,1.0),
  segid = c("H2","H2"))
print(x)
is.atoms(x)

The Basis of an Object

Description

Functions to get or set the basis of an object containing atomic coordinates.

Usage

basis(x)

## Default S3 method:
basis(x)

basis(x) <- value

## Default S3 replacement method:
basis(x) <- value

## S3 method for class 'pdb'
basis(x)

## S3 replacement method for class 'pdb'
basis(x) <- value

Arguments

Details

basis and basis<- are respectively generic accessor and replacement functions. The default methods get and set the basis attribute of an object containing atomic coordinates. This attribute indicate the type basis vector used to express atomic coordinates.
value must be equal to "xyz", for Cartesian, or "abc", for fractional coordinates.
The methods for objects of class ‘pdb’ get and set the basis attribute of its atoms component.

Value

For basis:

NULL or a single element character vector. (NULL is given if the object has no basis attribute.)

For basis<-:

the updated object. (Note that the value of basis(x) <- value is that of the assignment, value, not the return value from the left-hand side.)

See Also

coords, atoms, pdb

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
basis(x)
x <- xyz2abc(x)
basis(x)

Atomic Bond Lengths, Angles and Dihedrals

Description

Compute bond lengths, angles and dihedral from atomic coordinates.

Usage

bond(...)

## S3 method for class 'coords'
bond(x, sel1, sel2, ...)

## S3 method for class 'pdb'
bond(x, sel1, sel2, ...)

angle(...)

## S3 method for class 'coords'
angle(x, sel1, sel2, sel3, ...)

## S3 method for class 'pdb'
angle(x, sel1, sel2, sel3, ...)

dihedral(...)

## S3 method for class 'coords'
dihedral(x, sel1, sel2, sel3, sel4, ...)

## S3 method for class 'pdb'
dihedral(x, sel1, sel2, sel3, sel4, ...)

measure(...)

## Default S3 method:
measure(id = rgl::rgl.ids(), verbose = TRUE, ...)

## S3 method for class 'coords'
measure(x, id = rgl::rgl.ids(), verbose = TRUE, ...)

## S3 method for class 'pdb'
measure(x, id = rgl::rgl.ids(), verbose = TRUE, ...)

Arguments

Details

The number of selected atoms with sel1, sel2, sel3 and sel4 must be the same. sel1, sel2, sel3 and sel4 respectively select the first, second, third and fouth atoms defining bonds, angles or dihedrals.

measure activate an interactive mode to compute bond lengths, angles and dihedrals by selecting atoms by right-clicing on the current ‘rgl’ scene. To escape the active mode press the ESC key.

Value

A numeric vector containing atomic bond lengths (in Angstrom), angles or dihedrals (in degrees)

See Also

coords, pdb, info3d, visualize

Examples

Pen <- read.pdb(system.file("examples/Pentacene.pdb", package="Rpdb"))
visualize(Pen, mode = NULL)
text3d(coords(Pen), texts = Pen$atoms$eleid)
bond(Pen, 3:4, 1:2)
angle(Pen, 3:4, 1:2, 5:6)
dihedral(Pen, 3:4, 1:2, 5:6, 6:5)

Properties of a Unit Cell

Description

Compute the Cartesian coordinates of lattice vectors, the volume or the density of a unit cell.

Usage

cell.coords(...)

## Default S3 method:
cell.coords(abc, abg = c(90, 90, 90), digits = 3, ...)

## S3 method for class 'cryst1'
cell.coords(x, digits = 3, ...)

## S3 method for class 'pdb'
cell.coords(x, digits = 3, ...)

cell.volume(...)

## S3 method for class 'cryst1'
cell.volume(x, ...)

## S3 method for class 'pdb'
cell.volume(x, ...)

cell.density(...)

## Default S3 method:
cell.density(masses, volume, ...)

## S3 method for class 'pdb'
cell.density(x, ...)

Arguments

Details

cell.coords is a generic function which computes a 3x3 matrix whose columns contrain the Cartesian coordinates of lattice vectors. The 'a' and 'b' vectors are assumed to be respectively along the x-axis and in the xy-plane. The default method takes directly the lattice parameters as arguments. For objects of class cryst1 the lattice parameters are first extracted from the object and then the default method is called. For objects of class pdb the lattice parameters are extracted from their cryst1 component and the default method is called.

cell.volume is a generic function to compute the volume of a unit cell. For objects of class ‘cryst1’, the unit cell parameters are directly used to compute the volume. For objects of class ‘pdb’, their cryst1 component is used.

cell.density is a generic function to compute the density of a unit cell. For objects of class ‘pdb’: First the volume of the unit cell is calculated by calling the cell.volume function on the cryst1 component of the ‘pdb’ object. Then the element names are converted into element symbols using the toSymbols function and their masses are taken from the elements data set. Finally the density is calculated using the sum of the atomic masses and the volume of the unit cell.

Value

cell.coords returns a 3x3 matrix containing the Cartesian coordinates of lattice vectors arranged by columns.
cell.volume returns a single element numeric vector containing the volume of the unit cell in Angstrom cube.
cell.density returns a single element numeric vector containing the density of the unit cell in g.cm-3.

See Also

cryst1, pdb, xyz2abc

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
cell.volume(x)
cell.density(x)
cell.coords(x)

Centres-of-Geometry and Centres-of-Mass

Description

Computes centres-of-geometry and centres-of-mass of groups of atoms.

Usage

centres(...)

## S3 method for class 'coords'
centres(x, factor = NULL, weights = NULL, unsplit = FALSE, na.rm = FALSE, ...)

## S3 method for class 'atoms'
centres(x, factor = NULL, weights = NULL, unsplit = FALSE, na.rm = FALSE, ...)

## S3 method for class 'pdb'
centres(x, factor = NULL, weights = NULL, unsplit = FALSE, na.rm = FALSE, ...)

Arguments

Details

centres is a generic function to compute centres-of-geometry and centres-of-mass from an object containing atomic coordinates. For objects of class ‘coords’, ‘atoms’ and ‘pdb’, the coordinates of x are first splitted into groups defined by factor using the split function. For each group, the weighted mean of the x1, x2 and x3 components of x are calculated using weights. By default all atoms are assumed to have the same weight (calculation of centres-of-geometry). Finally, if unplit = TRUE the coordinates of the centres are unsplitted using the unsplit function to assign to each atom the coordinates of the centre to which they are attached (used for wrapping by groups).

For objects of class ‘atoms’ and ‘pdb’ by default factor is set to x$resid and x$coordinates$resid, respectively, to compute the centre-of-geometry of the different resdiues. Notice that coordinates can be neglected for the calculation of the centres using NA values in factor.

Value

Return an object of class ‘coords’ containing the coordinates of centres.

See Also

coords, atoms, pdb, elements

and split, unsplit, factor for details about splitting data sets.

Examples

# First lets read a pdb file
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))

# Centres-of-geometry of the residues
centres(x)

# Centre-of-geometry of the whole structure
centres(x, factor = rep(1, natom(x)))
# or
centres(coords(x))

# Centres-of-geometry of the PCB and DCB residues
centres(x, factor = x$atoms$resname)

# Knowing the name of the elements forming
# the C60 of the PCBM molecules (PCB residues)
# we can compute the centres-of-geometry of
# the C60 by neglecting the other atoms of the
# PCB residues.
C60.elename <- paste0("C", sprintf("%0.3d", 1:60))

is.PCB <- x$atoms$resname == "PCB" # Produce a mask to select only the PCB residues
is.C60 <- is.PCB & x$atoms$elename %in% C60.elename # Produce a mask to keep only the C60

F <- x$atoms$resid # We use the residue IDs to split the coordinates
F[!is.C60] <- NA # We keep only the atoms of the C60

C60.centres <- centres(x, factor = F)

# Lets check the position of the C60 centres
visualize(x , mode = NULL)
spheres3d(C60.centres)
text3d(Ty(C60.centres, 2), text=paste0("PCB_", rownames(C60.centres)), cex=2)

# Centres-of-mass of the resdiues
symb <- toSymbols(x$atoms$elename) # Convert elename into elemental symbols
# Find the mass of the element in the periodic table
w <- elements[match(symb, elements[,"symb"]), "mass"] 
centres(x, weights = w)

Create ‘conect’ Object

Description

Creates an object of class ‘conect’ containing the IDs of bonded atoms defining the connectivity of a molecular system.

Usage

conect(...)

## Default S3 method:
conect(eleid.1, eleid.2, ...)

## S3 method for class 'coords'
conect(x, radii = 0.75, safety = 1.2, by.block = FALSE, ...)

## S3 method for class 'pdb'
conect(x, safety = 1.2, by.block = FALSE, ...)

is.conect(x)

Arguments

Details

conect is a generic function to create objects of class ‘conect’. The purpose of this class is to store CONECT records from PDB files, indicating the connectivity of a molecular system.
The default method creates a conect object from its different components, i.e.: eleid.1 and eleid.2. Both arguments have to be specified.
The S3 method for object of class ‘coords’ determine the connectivity from atomic coordinates. A distance matrix is computed, then, for each pair of atom the distance is compared to a bounding distance computed from atomic radii. If this distance is lower than the bounding distance then the atoms are assumed to be connected.
The S3 method for object of class ‘pdb’ first use element names to search for atomic radii in the elements data set. Then atomic coordinates and radii are passed to conect.coords.
If by.block == TRUE, a grid is defined to determined the connectivity by block. The method is slow but allow to deal with very large systems.
is.conect tests if an object of class ‘conect’, i.e. if it has a “class” attribute equal to conect.

Value

conect returns a two-column data.frame of class ‘conect’ whose rows contain the IDs of bonded atoms. The columns of this data.frame are described below:

is.conect returns TRUE if x is an object of class ‘coords’ and FALSE otherwise.

See Also

pdb

Examples

# If atom 1 is connected to atom 2, 3, 4 and 5
# then we can prepare the following 'conect' object:
x <- conect(rep(1,4), 2:5)
print(x)
is.conect(x)

# Compute conectivity from coordinates
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"), CONECT = FALSE)
x$conect
x$conect <- conect(x)
x$conect

The Atomic Coordinates of an Object

Description

Get or set the atomic coordinates (either Cartesian or fractional coordinates) of an object.

Usage

coords(...)

coords(x) <- value

## Default S3 method:
coords(x1, x2, x3, basis = "xyz", ...)

## S3 method for class 'data.frame'
coords(x, basis = NULL, ...)

## S3 method for class 'matrix'
coords(x, basis = NULL, ...)

## S3 method for class 'atoms'
coords(x, ...)

## S3 replacement method for class 'atoms'
coords(x) <- value

## S3 method for class 'pdb'
coords(x, ...)

## S3 replacement method for class 'pdb'
coords(x) <- value

is.coords(x)

Arguments

Details

The purpose of the ‘coords’ class is to store the coordinates of a molecular system and facilitate their manipulation when passing from the Cartesian to fractional coordinates and vice versa.
coords and coords<- are generic accessor and replacement functions.
The default method of the coords function is actually a builder allowing to create a ‘coords’ object from its different components, i.e.: x1, x2, x3, and basis. All the arguments have to be specified except 'basis' which by default is set to "xyz" (Cartesian coordinates).

For an object of class ‘atoms’, the accessor function extracts its x1, x2 and x3 components as well as its basis attribute to create a ‘coords’ object. The replacement function set its x1, x2 and x3 components as well as its basis attribute.

For an object of class ‘pdb’, the accessor function extracts the x1, x2 and x3 components as well as the basis attribute of its atoms component to create a ‘coords’ object. The replacement function set the x1, x2 and x3 components as well as the basis attribute of its atoms component.

For ‘matrix’ and ‘data.frame’ objects, when basis==NULL this function search x, y, z or a, b, c columns in x.
If x, y, z columns are found they are used to a set the first, second and third coordinates of the returned ‘coords’ object. In that case the basis set of x is set to "xyz".
If a, b, c columns are found they are used to a set the first, second and third coordinates of the returned ‘coords’ object. In that case the basis set of x is set to "abc".
If the function doesn't found neither the x, y, z nor the a, b, c columns an error is returned.
When basis!=NULL it has to be equal to "xyz" or "abc" and x must have exactly 3 columns.

is.coords tests if x is an object of class ‘coords’, i.e. if x has a “class” attribute equal to coords.

Value

The accessor function returns a data.frame of class ‘coords’ whose columns contain the three coordinates of the atoms of a molecular system. The coordinates can either be Cartesian (basis attribute equal to "xyz") or fractional coordinates (basis attribute equal to "abc").

The replacement function returns an object of the same class as x with updated coordinates.

is.coords returns TRUE if x is an object of class ‘coords’ and FALSE otherwise

See Also

basis

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
is.coords(x)
is.coords(x$atoms)

## Replace the coordinates of x by translated coordinates
coords(x) <- coords(Tz(x, 10))
coords(x)

Create ‘cryst1’ Object

Description

Create an object of class ‘cryst1’ containing the unit cell parameters and the name of the space group to associate with an object of class ‘pdb’.

Usage

cryst1(...)

## Default S3 method:
cryst1(abc, abg = c(90, 90, 90), sgroup = "P1", ...)

is.cryst1(x)

Arguments

Details

cryst1 is a generic function to create objects of class ‘cryst1’. The purpose of this class is to store CRYST1 records from PDB files which contain the unit cell parameters and the name of the space group of a molecular system stored in a PDB file. The default method of the cryst1 function creates an object of class ‘cryst1’ from its different components, i.e.: abc, abg and sgroup. At least abc has to be specified.

is.cryst1 tests if an object is of class ‘cryst1’, i.e. if it has a “class” attribute equal to cryst1.

Value

Function cryst1 returns a list of class ‘cryst1’ with the following components:

Function is.cryst1 returns TRUE if x is an object of class ‘cryst1’ and FALSE otherwise.

See Also

cell.coords, pdb

Examples

x <- cryst1(abc = c(10, 10, 10), abg = c(90,90,90), sgroup = "P1")
is.cryst1(x)
 

Inter-Atomic Distances

Description

Computes inter-atomic distance vectors.

Usage

distances(...)

## Default S3 method:
distances(
  dx1 = numeric(0),
  dx2 = numeric(0),
  dx3 = numeric(0),
  basis = "xyz",
  ...
)

## S3 method for class 'coords'
distances(x, sel1, sel2, ...)

## S3 method for class 'atoms'
distances(x, sel1, sel2, ...)

## S3 method for class 'pdb'
distances(x, sel1, sel2, ...)

is.distances(x)

norm(...)

## S3 method for class 'distances'
norm(x, type = "xyz", ...)

Arguments

Details

The purpose of the ‘distances’ class is to store the inter-atomic distance vectors and facilitate their manipulation when passing from the Cartesian to fractional references and vice versa.
The default method of the distances function is actually a builder allowing to create a ‘distances’ object from its different components, i.e.: dx1, dx2, dx3, and basis. All the arguments have to be specified except 'basis' which by default is set to "xyz" (Cartesian reference).

For objects of class ‘coords’, ‘atoms’, ‘pdb’, two sets of atomic coordinates, defined by sel1 and sel2, are extracted and inter-atomic distance vectors are computed between these two sets.

The method of the norm function for objects of class ‘distances’ computes the norm of the distances vectors. type specify how to project the distance vectors before computing the norms. By default no projection is perform. The three dx, dy, and dz components of the distance vectors are used to compute the norm. type can take the following values:

• x: The distance vectors are projected over x.

• y: The distance vectors are projected over y.

• z: The distance vectors are projected over z.

• xy: The distance vectors are projected in the xy-plan.

• yz: The distance vectors are projected in the yz-plan.

• zx: The distance vectors are projected in the zx-plan.

• xyz: The distance vectors are not projected (The three components of the distance vectors are used to compute the norm).

is.distances tests if x is an object of class ‘distances’, i.e. if x has a “class” attribute equal to distances.

Value

The distance function return an object of class ‘distances’ containing inter-atomic distance vectors. The norm function return an array, with the same dimensions as the dx1, dx2, dx3 components of the ‘distances’ object for which the norms have to be computed, containing the norm of the distance vectors.

is.distances returns TRUE if x is an object of class ‘distances’ and FALSE otherwise

See Also

coords, basis, xyz2abc, abc2xyz

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
is.DCB7 <- x$atoms$resname == "DCB" & x$atoms$resid == 7
is.DCB8 <- x$atoms$resname == "DCB" & x$atoms$resid == 8
d <- distances(x, is.DCB7, is.DCB8)
norm(d, type = "xyz")
norm(d, type = "xy")
norm(d, type = "x")

Periodic Table of the Elements

Description

This data set gives various information on chemical elements

Format

A data frame containing for each chemical element the following information.

num

atomic number

symb

elemental symbol

areneg

Allred and Rochow electronegativity (0.0 if unknown)

rcov

covalent radii (in Angstrom) (1.6 if unknown)

rbo

"bond order" radii

rvdw

van der Waals radii (in Angstrom) (2.0 if unknown)

maxbnd

maximum bond valence (6 if unknown)

mass

IUPAC recommended atomic masses (in amu)

elneg

Pauling electronegativity (0.0 if unknown)

ionization

ionization potential (in eV) (0.0 if unknown)

elaffinity

electron affinity (in eV) (0.0 if unknown)

red

red value for visualization

green

green value for visualization

blue

blue value for visualization

name

element name

Source

Open Babel (2.3.1) file: element.txt

Created from the Blue Obelisk Cheminformatics Data Repository
Direct Source: http://www.blueobelisk.org/
http://www.blueobelisk.org/repos/blueobelisk/elements.xml includes furhter bibliographic citation information

- Allred and Rochow Electronegativity from http://www.hull.ac.uk/chemistry/electroneg.php?type=Allred-Rochow
- Covalent radii from http://dx.doi.org/10.1039/b801115j
- Van der Waals radii from http://dx.doi.org/10.1021/jp8111556

Examples

data(elements)
elements

# Get the mass of some elements
symb <- c("C","O","H")
elements[match(symb, elements[,"symb"]),"mass"]

# Get the van der Waals radii of some elements
symb <- c("C","O","H")
elements[match(symb, elements[,"symb"]),"rvdw"]

Moment of Inertia of a Molecular System

Description

Computes the inertia tensor of a molecular system from atomic coordinates and masses.

Usage

inertia(...)

## S3 method for class 'coords'
inertia(x, m = NULL, ...)

## S3 method for class 'atoms'
inertia(x, m = NULL, ...)

## S3 method for class 'pdb'
inertia(x, m = NULL, ...)

Arguments

Details

inertia is a generic function to compute the inertia tensor of a molecular system. For object of class ‘coords’ both atomic coordinates and masses have to be speifyed. For object of class ‘atoms’ the masses are determined from the elename component of the object (see toSymbols and masses). For object of class ‘pdb’ the atoms component is used.

Value

Return the inertia tensor in a 3x3 matrix.

See Also

toSymbols, masses, viewInertia

Examples

C70 <- read.pdb(system.file("examples/C70.pdb", package="Rpdb"))
inertia(C70)
visualize(C70, mode = NULL)
viewXY()
viewInertia(C70)

Mass of Chemical Elements

Description

Determine the mass of chemical elements

Usage

masses(...)

## Default S3 method:
masses(x, ...)

## S3 method for class 'pdb'
masses(x, ...)

Arguments

Details

masses is a generic function to determine the mass of chemical elements.

For objects of class ‘pdb’:

• First the element names are converted into element symbols using the toSymbols function.

• Then their masses are taken from the elements data set.

NA values are returned for unrecognized elements.

Value

Return a numeric vector containing the mass of chemical elements.

See Also

toSymbols

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb",package="Rpdb"))
masses(x)

masses(c("C","Cl",NA,"AA","N"))

Merging Molecular Systems

Description

Merge two objects contaning atomic coordinates

Usage

## S3 method for class 'coords'
merge(x, y, ...)

## S3 method for class 'atoms'
merge(x, y, reindex = TRUE, ...)

## S3 method for class 'pdb'
merge(x, y, reindex = TRUE, ...)

Arguments

Details

To merge x and y they must have the same basis attributes (see basis).

For objects of class ‘coords’ and ‘atoms’ the atomic coordinates are directly merged by row.

For objects of class ‘pdb’, the atoms and conect components of the two pdb objects are merged by row and the cryst1 components of x is used to build the returned object.

For objects of class ‘atoms’ and ‘pdb’ the residue and element IDs of y are shifted to avoid any confusion with those of x. If reindex == TRUE the reindex function is called to reinitialize the indexing of the returned object.

Value

Return an object of the same class as x and y merging x and y. If x and y have different basis attributes an error is returned.

See Also

coords, atoms, pdb, basis, merge, merge.data.frame

Examples

c1 <- coords( 1:3 ,  4:6 ,  7:9 , basis = "xyz")
c2 <- coords(10:12, 13:15, 16:18, basis = "xyz")
merge(c1,c2)


## Merging objects with different basis sets returns an error.
c2 <- coords(9:11, 12:14, 15:17, basis = "abc")
try(merge(c1,c2))


## Prepare a Pentacene/C70 dimer
C70 <- read.pdb(system.file("examples/C70.pdb", package="Rpdb"))
Pen <- read.pdb(system.file("examples/Pentacene.pdb", package="Rpdb"))
x <- merge(Tz(C70, 3.5, thickness=0.5), Pen)
  

Reflexion of Atomic Coordinates

Description

Perform a reflexion (or mirror) operation on atomic coordinates with respect to a given reflexion plane.

Usage

mirror(...)

## S3 method for class 'coords'
mirror(x, p1, p2 = NULL, p3 = NULL, mask = TRUE, cryst1 = NULL, ...)

## S3 method for class 'pdb'
mirror(x, p1, p2 = NULL, p3 = NULL, mask = TRUE, cryst1 = x$cryst1, ...)

Arguments

Details

mirror is a generic function. Method for objects of class ‘coords’ first convert the coordinates into Cartesian coordinates using cryst1 if needed. Once reflected, the coordinates are reconverted back to the orginal basis set using again cryst1. Method for objects of class ‘pdb’ first extract coordinates from the object using the function coords, perform the reflection, and update the coordinates of the ‘pdb’ object using the function coords<-.

Value

An object of the same class as x with reflected coordinates.

See Also

Helper functions for reflection with respect to a given Cartesian plane or a plane defined by two lattice vectors:
Mxy, Myz, Mzx, Mab, Mbc, Mca
Passing from Cartesian to fractional coordinates (or Vis Versa):
xyz2abc, abc2xyz

Examples

# First lets read a pdb file
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
cell <- cell.coords(x)
visualize(x, mode = NULL)

# Mirror operation with respect to the ab-plane
visualize(mirror(x, rep(0,3), p1=cell[, "a"], p2=cell[, "b"]), mode = NULL)
# Mirror operation with respect to the ab-plane for residue 1
visualize(mirror(x, rep(0,3), p1=cell[, "a"], p2=cell[, "b"],
   mask = x$atoms$resid == 1), mode = NULL)

Helper Functions for reflection of Atomic Coordinates

Description

Reflection of atomic coordinates with respect to a specific Cartesian plan or a plan defined by two lattice vectors.

Usage

Mxy(...)

## S3 method for class 'coords'
Mxy(x, mask = TRUE, cryst1 = NULL, ...)

## S3 method for class 'pdb'
Mxy(x, mask = TRUE, cryst1 = x$cryst1, ...)

Myz(...)

## S3 method for class 'coords'
Myz(x, mask = TRUE, cryst1 = NULL, ...)

## S3 method for class 'pdb'
Myz(x, mask = TRUE, cryst1 = x$cryst1, ...)

Mzx(...)

## S3 method for class 'coords'
Mzx(x, mask = TRUE, cryst1 = NULL, ...)

## S3 method for class 'pdb'
Mzx(x, mask = TRUE, cryst1 = x$cryst1, ...)

Mab(...)

## S3 method for class 'coords'
Mab(x, cryst1, mask = TRUE, ...)

## S3 method for class 'pdb'
Mab(x, cryst1 = x$cryst1, mask = TRUE, ...)

Mbc(...)

## S3 method for class 'coords'
Mbc(x, cryst1, mask = TRUE, ...)

## S3 method for class 'pdb'
Mbc(x, cryst1 = x$cryst1, mask = TRUE, ...)

Mca(...)

## S3 method for class 'coords'
Mca(x, cryst1, mask = TRUE, ...)

## S3 method for class 'pdb'
Mca(x, cryst1 = x$cryst1, mask = TRUE, ...)

Arguments

Details

These functions are helper functions to perform a reflection with respect to a specific Cartesian plan or a plan defined by two lattice vectors. All of them call the mirror function.

Value

An object of the same class as x with reflected coordinates.

See Also

mirror and xyz2abc, abc2xyz for passing from Cartesian to fractional coordinates (or Vis Versa).

Examples

# First lets read a pdb file
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
visualize(x, mode = NULL)

# Mirror operation with respect to the ab-plane
visualize(Mab(x), mode = NULL)
# Mirror operation with respect to the ab-plane for residue 1
visualize(Mab(x, mask = x$atoms$resid == 1), mode = NULL)

Number of Atoms in an Object Containing Atomic Coordinates

Description

Evaluates the number of atoms in an object containing atomic coordinates.

Usage

natom(x, ...)

## S3 method for class 'coords'
natom(x, factor = NULL, ...)

## S3 method for class 'atoms'
natom(x, factor = NULL, ATOM = TRUE, HETATM = TRUE, ...)

## S3 method for class 'pdb'
natom(x, factor = NULL, ATOM = TRUE, HETATM = TRUE, ...)

Arguments

Details

natom is a generic function to evalute the number of atom in an object containing atomic coordinates. The atomic coordinates of the object are first filtered to keep ATOM and/or HETATM records as indicated by the 'ATOM' and 'HETATM' arguments. Then, if factor is specify, the object is splitted to evalute the number of atoms in each group defined by factor. If factor is not specify then the total number of atoms in the object is return.

Value

Return an integer or a vector of integer of lenght equal to nlevels(factor) (if factor is specify) indication the number of atoms in the object or in the groups defined by factor.

See Also

coords, atoms, pdb, factor, split

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))

natom(x)
natom(x, x$atoms$resid)
natom(x, x$atoms$resname)
natom(x, HETATM = FALSE)
  

Create an Object of Class ‘pdb’

Description

Creates an object of class 'pdb'.

Usage

pdb(...)

## Default S3 method:
pdb(atoms, cryst1 = NULL, conect = NULL, remark = NULL, title = NULL, ...)

is.pdb(x)

Arguments

Details

This function is the generic function to create objects of class ‘pdb’. The purpose of this class is to store the data of molecular systems contained in PDB files. The default method of the pdb function creates an object of class ‘pdb’ from its different components, i.e.: title, remark, cryst1, atoms and conect. At least an object of class ‘atoms’ has to be specified.

is.pdb tests if x is an object of class ‘pdb’, i.e. if x has a “class” attribute equal to pdb.

Value

pdb returns a list of class ‘pdb’ with the following components:

is.pdb returns TRUE if x is an object of class ‘pdb’ and FALSE otherwise.

See Also

atoms, coords, cryst1, conect and read.pdb

Examples

title  <- "This is just an example"
remark <- NULL
cryst1 <- cryst1(c(10,10,10))
atoms <- atoms(recname = c("ATOM","ATOM"), eleid = 1:2, elename = c("H","H"), alt = "",
               resname = c("H2","H2"), chainid = "", resid = c(1,1), insert = "",
               x1 = c(0,0), x2 = c(0,0), x3 = c(0,1), occ = c(0.0,0.0), temp = c(1.0,1.0),
               segid = c("H2","H2"))
conect <- conect(eleid.1 = c(1), eleid.2 = c(2))
x <- pdb(atoms = atoms, cryst1 = cryst1, conect = conect, remark = remark, title = title)
is.pdb(x)

Range of Atomic Coordinates

Description

Determines the range of atomic coordinates.

Usage

## S3 method for class 'coords'
range(x, na.rm = FALSE, finite = FALSE, ...)

## S3 method for class 'atoms'
range(x, na.rm = FALSE, finite = FALSE, ...)

## S3 method for class 'pdb'
range(x, na.rm = FALSE, finite = FALSE, ...)

Arguments

Value

Return a data.frame whose columns contain the range of the first, second and third coordinates of x.

See Also

range, coords, atoms, pdb

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
range(x)
range(range(x))

PDB File Reader

Description

Reads a Protein Data Bank (PDB) coordinate file.

Usage

read.pdb(
  file,
  ATOM = TRUE,
  HETATM = TRUE,
  CRYST1 = TRUE,
  CONECT = TRUE,
  TITLE = TRUE,
  REMARK = TRUE,
  MODEL = 1
)

Arguments

Details

The read.pdb function reads the TITLE, REMARK, ATOM, HETATM, CRYST1 and CONECT records from a PDB file. Three different reading modes can be used depending on the value of MODEL:

• When MODEL is a vector of integers, MODEL sections whose serial numbers match these integers are read.

• When MODEL == NULL, all MODEL sections are read.

• When MODEL == NA, MODEL records are ignored to read all ATOM and/or HETATM records together to return a single object.

Value

When a single MODEL section is read, this function returns an object of class ‘pdb’ (a list with a class attribute equal to pdb) with the following components:

When multiple MODEL sections are read, a list of object of class ‘pdb’ is returned.

References

PDB format has been taken from: http://www.wwpdb.org/documentation/format33/v3.3.html

See Also

write.pdb, pdb, cryst1, atoms, conect

Examples

# Read a PDB file included with the package
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))

# Visualize the PDB file
visualize(x, mode = NULL)

# Write the 'pdb' object 'x' in file "Rpdb.pdb" into the current directory
write.pdb(x, file = "Rpdb.pdb")

# Cleanup
unlink("Rpdb.pdb")

Reinitialize Object Indexing

Description

Reinitialize the indexing of an object.

Usage

reindex(...)

## S3 method for class 'atoms'
reindex(x, eleid = TRUE, resid = TRUE, ...)

## S3 method for class 'pdb'
reindex(x, eleid = TRUE, resid = TRUE, ...)

Arguments

Details

reindex is a generic function to reinitialize the indexing of an object or its components. The methods for objects of class ‘atoms’ reinitialize the residue and element IDs starting from 1 and avoiding gaps in the indexes. For objects of class ‘pdb’ their atoms and conect components are reindexed consistently.

Value

Return an object of the same class as x with updated indexes.

See Also

pdb, atoms, subset.atoms, subset.pdb

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
x <- subset(x, x$atoms$eleid %in% sample(x$atoms$eleid, 10))
print(x)
x <- reindex(x)
print(x)

Replicate Atomic Coordinates

Description

Replicate atomic coordinates using periodic boundary conditions.

Usage

replicate(x, ...)

## S3 method for class 'coords'
replicate(x, cryst1 = NULL, a.ind = 0, b.ind = 0, c.ind = 0, ...)

## S3 method for class 'atoms'
replicate(x, cryst1 = NULL, a.ind = 0, b.ind = 0, c.ind = 0, ...)

## S3 method for class 'pdb'
replicate(x, a.ind = 0, b.ind = 0, c.ind = 0, cryst1 = NULL, ...)

Arguments

Details

The replicate function replicate a unit cell along the lattice vectors a, b and c as as many times as indicated by the a.ind, b.ind and c.ind arguments. Discontinuous integer vectors can be used for a.ind, b.ind and c.ind to create layered supercells (See examples).

Value

Return an object of class ‘pdb’ with replicated atomic coordinates.

See Also

coords, atoms, pdb, cryst1

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))

# Create a 3x3 supercell
y <- replicate(x, a.ind = 0:2, b.ind = 0:2, c.ind = 0:2)

# Create a 3x3 supercell which might need to be wrapped (if some molecules are outside the cell)
y <- replicate(x, a.ind = -1:1, b.ind = -1:1, c.ind = -1:1)

# Create a layered supercell with a vacuum layer in the bc-plan
y <- replicate(x, a.ind = c(0,2), b.ind = 0:2, c.ind = 0:2)

Rotation of Atomic Coordinates

Description

Rotation of atomic coordinates around a given vector.

Usage

R(...)

## S3 method for class 'coords'
R(obj, angle = 0, x = 0, y = 0, z = 1, mask = TRUE, cryst1 = NULL, ...)

## S3 method for class 'pdb'
R(obj, angle = 0, x = 0, y = 0, z = 1, mask = TRUE, cryst1 = obj$cryst1, ...)

Arguments

Details

R is generic functions. Method for objects of class ‘coords’ first convert the coordinates into Cartesian coordinates using cryst1 if needed. Once rotated, the coordinates are reconverted back to the orginal basis set using again cryst1. Method for objects of class ‘pdb’ first extract coordinates from the object using the function coords, perform the rotation, and update the coordinates of the ‘pdb’ object using the function coords<-.

Value

An object of the same class as x with rotated coordinates.

See Also

Helper functions for rotation around a given Cartesian vector:
Rx, Ry, Rz
Passing from Cartesian to fractional coordinates (or Vis Versa):
xyz2abc, abc2xyz

Examples

# First lets read a pdb file
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
cell <- cell.coords(x)
visualize(x, mode = NULL)

# Rotation of the structure around the c-axis
visualize(R(x, 90, x=cell["x","c"], y=cell["y","c"], z=cell["z","c"]),
          mode = NULL)
# Rotation of the residue 1 around the c-axis
visualize(R(x, 90, x=cell["x","c"], y=cell["y","c"], z=cell["z","c"], mask = x$atoms$resid == 1),
          mode = NULL)
          

Helper Functions for Rotation of Atomic Coordinates

Description

Rotation of atomic coordinates along a specific Cartesian vector.

Usage

Rx(...)

## S3 method for class 'coords'
Rx(x, angle = 0, mask = TRUE, cryst1 = NULL, ...)

## S3 method for class 'pdb'
Rx(x, angle = 0, mask = TRUE, cryst1 = x$cryst1, ...)

Ry(...)

## S3 method for class 'coords'
Ry(x, angle = 0, mask = TRUE, cryst1 = NULL, ...)

## S3 method for class 'pdb'
Ry(x, angle = 0, mask = TRUE, cryst1 = x$cryst1, ...)

Rz(...)

## S3 method for class 'coords'
Rz(x, angle = 0, mask = TRUE, cryst1 = NULL, ...)

## S3 method for class 'pdb'
Rz(x, angle = 0, mask = TRUE, cryst1 = x$cryst1, ...)

Arguments

Details

These functions are helper functions to perform a rotation around a specific Cartesian vector. All of them call the R function.

Value

An object of the same class as x with rotated coordinates.

See Also

R and xyz2abc, abc2xyz for passing from Cartesian to fractional coordinates (or Vis Versa).

Examples

# First lets read a pdb file
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
cell <- cell.coords(x)
visualize(x, mode = NULL)

# Rotation of the structure around the z-axis
visualize(Rz(x, 90), mode = NULL)
# Rotation of the residue 1 around the c-axis
visualize(Rz(x, 90, mask = x$atoms$resid == 1), mode = NULL)

Divide and Reassemble ‘pdb’ Objects

Description

split divides a ‘pdb’ object by groups of atoms defined by f. unsplit reverses the effect of split.

Usage

## S3 method for class 'pdb'
split(x, f, drop = FALSE, ...)

## S3 method for class 'pdb'
unsplit(value, f, drop = FALSE, ...)

Arguments

Details

split produce a list of ‘pdb’ objects with the same cryst1, title and remark components as x. Only its atoms component is splitted while its conect component is cleaned to keep only the meaningful connectivity for each ‘pdb’ object of the list returned by the function. unlist produce a ‘pdb’ object with the same cryst1, title and remark components as the first element of value. The atoms and conect components of all the elements of value are combined by row.

Value

The value returned from split is a list of ‘pdb’ objects containing the data for the groups of atoms. The components of the list are named by the levels of f (after converting to a factor, or if already a factor and drop=TRUE, dropping unused levels).
unsplit returns a ‘pdb’ object for which split(x, f) equals value.

See Also

split, unsplit, pdb

Examples

### Split a pdb file by residue IDs and write them into separate files
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))

file.names <- paste0(x$atoms$resname, "_", x$atoms$resid, ".pdb")
file.names <- unique(file.names)
pdb.resid  <- split(x, x$atoms$resid)
length(pdb.resid)
useless <- mapply(write.pdb, pdb.resid, file.names)

# Cleanup
unlink(file.names)

Subsetting ‘atoms’ and ‘pdb’ Objects

Description

Return subsets of ‘atoms’ or ‘pdb’ objects which meet conditions.

Usage

## S3 method for class 'atoms'
subset(x, subset, drop = FALSE, reindex.all = TRUE, ...)

## S3 method for class 'pdb'
subset(x, subset, drop = FALSE, reindex.all = TRUE, ...)

Arguments

Details

For an ‘atoms’ object the method is similar to the data.frame method (see subset) but allow to directly reindex the elements and residues IDs. For a ‘pdb’ object subsetting is applied on the atoms and conect components of the object in a consistent way. First the atoms component is subsetted and then the conect component is filtered to keep only the conectivity for the subset.

Value

Return a subsetted object of the same class as x.

See Also

subset, pdb, atoms, reindex

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
y <- subset(x, x$atoms$eleid %in% sample(x$atoms$eleid, 10))
is(y)
y <- subset(x$atoms, x$atoms$eleid %in% sample(x$atoms$eleid, 10))
is(y)
x <- coords(x)
y <- subset(x, x < 0)
is(y)

Atomic Symbols Converter

Description

Converts character strings or atomic numbers into atomic symbols.

Usage

toSymbols(x, ...)

## S3 method for class 'integer'
toSymbols(x, ...)

## S3 method for class 'numeric'
toSymbols(x, ...)

## S3 method for class 'character'
toSymbols(x, nletters = 3, ...)

Arguments

Details

Each elements of x are converted into atomic symbols.
When x is an integer (or numeric) vector, atomic number are search into the elements data set to find associated atomic symbols.
When x is a character vector, toSymbols first removes all leading and trailing white spaces and numbers. Then translates the first character of the character strings to uppercase and all the others to lowercase. Finally, the character strings are tested for matching with element symbols provided by the elements data set. NA are produced for no matching.

Value

a character vector containing atomic symbols

See Also

elements

Examples

x <- c(1:10)
toSymbols(x)

x <- c("C  "," o","h1","1h","UU","SI0","cR")
toSymbols(x)

# 'nletters' can be used to truncate the character strings before
# conversion, if needed:
toSymbols("SIL", nletters=3) # return NA
toSymbols("SIL", nletters=2) # return "Si"
toSymbols("SIL", nletters=1) # return "S"

Translation of Atomic Coordinates

Description

Translation of Cartesian or fractional coordinates.

Usage

Txyz(...)

## S3 method for class 'coords'
Txyz(
  obj,
  x = 0,
  y = 0,
  z = 0,
  mask = TRUE,
  thickness = NULL,
  cryst1 = NULL,
  ...
)

## S3 method for class 'pdb'
Txyz(
  obj,
  x = 0,
  y = 0,
  z = 0,
  mask = TRUE,
  thickness = NULL,
  cryst1 = obj$cryst1,
  ...
)

Tabc(...)

## S3 method for class 'coords'
Tabc(
  obj,
  a = 0,
  b = 0,
  c = 0,
  mask = TRUE,
  thickness = NULL,
  cryst1 = NULL,
  ...
)

## S3 method for class 'pdb'
Tabc(
  obj,
  a = 0,
  b = 0,
  c = 0,
  mask = TRUE,
  thickness = NULL,
  cryst1 = obj$cryst1,
  ...
)

Arguments

Details

Txyz and Tabc are generic functions. Method for objects of class ‘coords’ first convert the coordinates into Cartesian or fractional coordinates using cryst1 if needed to performed the translation. Once translated, the coordinates are reconverted back to the orginal basis set using again cryst1. Method for objects of class ‘pdb’ first extract coordinates from the object using the function coords, perform the translation, and update the coordinates of the ‘pdb’ object using the function coords<-. The thickness argument can be use to translate selected atoms by a fraction of its thickness along the translation direction. This can be use when merging two fragments centered at the origin to build a dimer to avoid atomic overlap and set the inter-fragment distance (see examples).

Value

An object of the same class as x with translated coordinates.

See Also

Helper functions for translation along given Cartesian or lattice vector:
Tx, Ty, Tz, Ta, Tb, Tc
Passing from Cartesian to fractional coordinates (or Vis Versa):
xyz2abc, abc2xyz

Examples

# First lets read a pdb file
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
visualize(x, mode = NULL)
visualize(Txyz(x, y=10), mode = NULL)
visualize(Txyz(x, y=10, mask = x$atoms$resid==1), mode = NULL)
visualize(Tabc(x, b=1 ), mode = NULL)
visualize(Tabc(x, b=1 , mask = x$atoms$resid==1), mode = NULL)

# Lets build a C70/Pentacene dimer with an inter-molecular distance equal to 3.5
C70 <- read.pdb(system.file("examples/C70.pdb", package="Rpdb"))
Pen <- read.pdb(system.file("examples/Pentacene.pdb", package="Rpdb"))
x <- merge(C70, Pen)
visualize(x, mode = NULL)
viewXY()
visualize(Txyz(x, x=0, y=0, z=3.5, mask = x$atoms$resname == "C70", thickness=0.5), mode = NULL)
viewXY()

Helper Functions for Translation of Atomic Coordinates

Description

Translation of atomic coordinates along a specific Cartesian or lattice vector.

Usage

Tx(...)

## S3 method for class 'coords'
Tx(obj, x = 0, mask = TRUE, thickness = NULL, cryst1 = NULL, ...)

## S3 method for class 'pdb'
Tx(obj, x = 0, mask = TRUE, thickness = NULL, cryst1 = obj$cryst1, ...)

Ty(...)

## S3 method for class 'coords'
Ty(obj, y = 0, mask = TRUE, thickness = NULL, cryst1 = NULL, ...)

## S3 method for class 'pdb'
Ty(obj, y = 0, mask = TRUE, thickness = NULL, cryst1 = obj$cryst1, ...)

Tz(...)

## S3 method for class 'coords'
Tz(obj, z = 0, mask = TRUE, thickness = NULL, cryst1 = NULL, ...)

## S3 method for class 'pdb'
Tz(obj, z = 0, mask = TRUE, thickness = NULL, cryst1 = obj$cryst1, ...)

Ta(...)

## S3 method for class 'coords'
Ta(obj, a = 0, mask = TRUE, cryst1 = NULL, ...)

## S3 method for class 'pdb'
Ta(obj, a = 0, mask = TRUE, cryst1 = obj$cryst1, ...)

Tb(...)

## S3 method for class 'coords'
Tb(obj, b = 0, mask = TRUE, cryst1 = NULL, ...)

## S3 method for class 'pdb'
Tb(obj, b = 0, mask = TRUE, cryst1 = obj$cryst1, ...)

Tc(...)

## S3 method for class 'coords'
Tc(obj, c = 0, mask = TRUE, cryst1 = NULL, ...)

## S3 method for class 'pdb'
Tc(obj, c = 0, mask = TRUE, cryst1 = obj$cryst1, ...)

Arguments

Details

These functions are helper functions to perform a translation along a specific Cartesian or lattice vector. All of them call either the Txyz or Tabc function.

Value

An object of the same class as x with translated coordinates.

See Also

Txyz, Tabc
Passing from Cartesian to fractional coordinates (or Vis Versa):
xyz2abc, abc2xyz

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
visualize(x, mode = NULL)
visualize(Ty(x, 10), mode = NULL)
visualize(Ty(x, 10, mask = x$atoms$resid==1), mode = NULL)
visualize(Tb(x, 1 ), mode = NULL)
visualize(Tb(x, 1 , mask = x$atoms$resid==1), mode = NULL)

# Lets build a C70/Pentacene dimer with an inter-molecular distance equal to 3.5
C70 <- read.pdb(system.file("examples/C70.pdb", package="Rpdb"))
Pen <- read.pdb(system.file("examples/Pentacene.pdb", package="Rpdb"))
x <- merge(C70, Pen)
visualize(x, mode = NULL)
viewXY()
visualize(Tz(x, z=3.5, mask = x$atoms$resname == "C70", thickness=0.5), mode = NULL)
viewXY()

Universal Constants

Description

This data set provides various universal constants

Format

A data frame containing for each universal constant the following information.

Quantity

a character vector containing a short description of the constants.

Value

a numeric vector containing the value of the constants.

Unit

a character vector indicating the unit of the constants.

Source

http://www.ebyte.it/library/educards/constants/ConstantsOfPhysicsAndMath.html

Examples

# Data for the speed of light
universalConstants["c",]

# Return the speed of light in m.s-1
universalConstants["c","Value"]

# Return the Planck constant in J.s
universalConstants["h","Value"]

Reassemble Groups

Description

unsplit reverses the effect of split.

Usage

unsplit(value, f, drop = FALSE, ...)

## Default S3 method:
unsplit(value, f, drop = FALSE, ...)

Arguments

Details

unsplit is a generic functions with a default method (Method dispatch takes place based on the class of the first element of value) working with lists of vectors or data frames (assumed to have compatible structure, as if created by split). It puts elements or rows back in the positions given by f. In the data frame case, row names are obtained by unsplitting the row name vectors from the elements of value.
f is recycled as necessary and if the length of x is not a multiple of the length of f a warning is printed.
Any missing values in f are dropped together with the corresponding values of x.

Value

Returns a vector or data frame for which split(x, f) equals value

References

Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) The New S Language. Wadsworth & Brooks/Cole.

See Also

cut to categorize numeric values.
strsplit to split strings.

Examples

require(stats); require(graphics)
n <- 10; nn <- 100
g <- factor(round(n * runif(n * nn)))
x <- rnorm(n * nn) + sqrt(as.numeric(g))
xg <- split(x, g)
boxplot(xg, col = "lavender", notch = TRUE, varwidth = TRUE)
sapply(xg, length)
sapply(xg, mean)

### Calculate 'z-scores' by group (standardize to mean zero, variance one)
z <- unsplit(lapply(split(x, g), scale), g)

# or

zz <- x
split(zz, g) <- lapply(split(x, g), scale)

# and check that the within-group std dev is indeed one
tapply(z, g, sd)
tapply(zz, g, sd)


### Data frame variation

# Notice that assignment form is not used since a variable is being added

g <- airquality$Month
l <- split(airquality, g)
l <- lapply(l, transform, Oz.Z = scale(Ozone))
aq2 <- unsplit(l, g)
head(aq2)
with(aq2, tapply(Oz.Z,  Month, sd, na.rm=TRUE))


### Split a matrix into a list by columns
ma <- cbind(x = 1:10, y = (-4:5)^2)
split(ma, col(ma))

split(1:10, 1:2)

Basic Vectorial Operations

Description

Basic vectorial operations such as scalar product and vectorial product

Usage

dotProd(U, V)

vectNorm(U)

rotVect(U, n = 1)

vectProd(U, V)

Arguments

Value

• dotProct return a single element numeric vector.

• vectNorm return a single element numeric vector.

• rotVect return a numeric vector of length 3.

• vectProct return a numeric vector of length 3.

See Also

matmult

Examples

Vx <- c(3,0,0)
vectNorm(Vx)
Vx <- Vx / vectNorm(Vx)
Vy <- c(0,1,0)
Vz <- vectProd(Vx, Vy)
print(Vz)

Set the View of the ‘rgl’ Scene

Description

Set the view of the current ‘rgl’ scene aligning one vector perpendicularly to the screen and placing another one in the horizontal plane.

Usage

viewAxis(V1, V2)

viewXY()

viewYZ()

viewZX()

viewAB(cryst1)

viewBC(cryst1)

viewCA(cryst1)

viewInertia(x, m = NULL)

Arguments

Details

viewAxis set the view of the current rgl scene (by setting UserMatrix; see par3d for more details) so that V1 is perpendicular to the screen and V2 is in the horizontal plane. The other functions documented here are helper functions calling viewAxis to set the view using particular Cartesian or lattice vectors. For functions viewAB, viewBC and viewCA a ‘cryst1’ object has to be specifyed to define the lattice vectors used to set the view. The function viewInertia computes the inertia tensor from the atomic coordinates and masses (see inertia) and sets the view to its eigen vectors basis set.

Value

No return value, called for side effects.

See Also

visualize, cell.coords, par3d, rgl.open

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
visualize(x, mode = NULL)
viewAB(x$cryst1)

C70 <- read.pdb(system.file("examples/C70.pdb", package="Rpdb"))
visualize(C70, mode = NULL)
viewXY()
viewInertia(C70)

Visualize a Molecular Structure

Description

Use the rgl library to visualize in 3D a molecular structure.

Usage

visualize(...)

## S3 method for class 'coords'
visualize(
  x,
  elename = NULL,
  cryst1 = NULL,
  conect = NULL,
  mode = NULL,
  type = "l",
  xyz = NULL,
  abc = NULL,
  pbc.box = NULL,
  lwd = 2,
  lwd.xyz = lwd,
  lwd.abc = lwd,
  lwd.pbc.box = lwd,
  cex.xyz = 2,
  cex.abc = 2,
  col = NULL,
  bg = "#FAFAD2",
  radii = "rvdw",
  add = FALSE,
  windowRect = c(0, 0, 800, 600),
  FOV = 0,
  userMatrix = diag(4),
  ...
)

## S3 method for class 'data.frame'
visualize(
  x,
  elename = NULL,
  cryst1 = NULL,
  conect = NULL,
  mode = NULL,
  type = "l",
  xyz = NULL,
  abc = NULL,
  pbc.box = NULL,
  lwd = 2,
  lwd.xyz = lwd,
  lwd.abc = lwd,
  lwd.pbc.box = lwd,
  cex.xyz = 2,
  cex.abc = 2,
  col = NULL,
  bg = "#FAFAD2",
  radii = "rvdw",
  add = FALSE,
  windowRect = c(0, 0, 800, 600),
  FOV = 0,
  userMatrix = diag(4),
  ...
)

## S3 method for class 'matrix'
visualize(
  x,
  elename = NULL,
  cryst1 = NULL,
  conect = NULL,
  mode = NULL,
  type = "l",
  xyz = NULL,
  abc = NULL,
  pbc.box = NULL,
  lwd = 2,
  lwd.xyz = lwd,
  lwd.abc = lwd,
  lwd.pbc.box = lwd,
  cex.xyz = 2,
  cex.abc = 2,
  col = NULL,
  bg = "#FAFAD2",
  radii = "rvdw",
  add = FALSE,
  windowRect = c(0, 0, 800, 600),
  FOV = 0,
  userMatrix = diag(4),
  ...
)

## S3 method for class 'atoms'
visualize(
  x,
  cryst1 = NULL,
  conect = NULL,
  mode = NULL,
  type = "l",
  xyz = NULL,
  abc = NULL,
  pbc.box = NULL,
  lwd = 2,
  lwd.xyz = lwd,
  lwd.abc = lwd,
  lwd.pbc.box = lwd,
  cex.xyz = 2,
  cex.abc = 2,
  col = NULL,
  bg = "#FAFAD2",
  radii = "rvdw",
  add = FALSE,
  windowRect = c(0, 0, 800, 600),
  FOV = 0,
  userMatrix = diag(4),
  ...
)

## S3 method for class 'pdb'
visualize(
  x,
  mode = NULL,
  type = "l",
  xyz = NULL,
  abc = NULL,
  pbc.box = NULL,
  lwd = 2,
  lwd.xyz = lwd,
  lwd.abc = lwd,
  lwd.pbc.box = lwd,
  cex.xyz = 2,
  cex.abc = 2,
  col = NULL,
  bg = "#FAFAD2",
  radii = "rvdw",
  add = FALSE,
  windowRect = c(0, 0, 800, 600),
  FOV = 0,
  userMatrix = diag(4),
  ...
)

## S3 method for class 'character'
visualize(
  x,
  mode = NULL,
  type = "l",
  xyz = NULL,
  abc = NULL,
  pbc.box = NULL,
  lwd = 2,
  lwd.xyz = lwd,
  lwd.abc = lwd,
  lwd.pbc.box = lwd,
  cex.xyz = 2,
  cex.abc = 2,
  col = NULL,
  bg = "#FAFAD2",
  radii = "rvdw",
  add = FALSE,
  windowRect = c(0, 0, 800, 600),
  FOV = 0,
  userMatrix = diag(4),
  ...
)

Arguments

Details

Three different visualization styles are allowed.

• When type="p": Points are drawn at each atomic positions (very light visualization mode).

• When type="l": Lines are drawn between bonded atoms. The connectivity of the system has to be specifyed.

• When type="s": Spheres are drawn at each atomic positions (heavy visualization mode).

  The radii of the spheres are given by radii.

  • When radii="rcov": Covalent radii, taken from the elements data set, are used.

  • When radii="rvdw": Van der Waals radii, taken from the elements data set, are used.

  • When radii is a numeric vector: The numeric values are used to assign to each atom a radius. If length(radii) != natom(pdb) radii is recycled.

When xyz, abc or pbc.box are NULL, the axis or pbc box are are added depending if a ‘cryst1’ object can be found.
Two different interactive visualization modes are avalable:

• When mode="measure": bond lengths, angles and dihedrals can be measured by right-clicing on the atoms.

• When mode="info": atomic labels can be added to the scene by right-clicing on the atoms. The labels are as follow: "ResidResname:EleidElename"

When mode=NULL the interactive mode is disabled. To escape the interactive mode press the ESC key.

Value

Return (using invisible) a two-column data.frame containing the IDs and type indicators of the objects added to the scene.

See Also

addXYZ, addABC, addPBCBox, par3d, select3d, measure, info3d

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
visualize(x, type = "l", mode = NULL)
visualize(x, type = "s", radii = "rcov", mode = NULL)
visualize(x, type = "s", radii = "rvdw", mode = NULL)
visualize(x, type = "p", mode = NULL)
visualize(subset(x, resid != 1), type = "l", mode = NULL)
visualize(subset(x, resid == 1), type = "s", add = TRUE, mode = NULL)

Wrap Atomic Coordinates

Description

Wraps atomic coordinates using periodic boundary conditions.

Usage

wrap(x, ...)

## S3 method for class 'coords'
wrap(x, cryst1 = NULL, factor = NULL, ...)

## S3 method for class 'atoms'
wrap(x, cryst1 = NULL, factor = NULL, ...)

## S3 method for class 'pdb'
wrap(x, cryst1 = x$cryst1, factor = NULL, ...)

Arguments

Details

The wrap function translates all atoms out of the unit cell back into the unit cell using periodic boundary conditions. To do so, the wrap function first converts Cartesian into fractional coordinates. Then atoms with fractional coordinates greater than 1 or lower than 0 are respectively translated by -1 or +1. Finally, if the original atomic coordinates were Cartesian coordinates their are reconverted into Cartesian coordinates.

Value

Return an object of class ‘pdb’ with wrapped atomic coordinates.

See Also

coords, atoms, pdb, cryst1, centres.pdb, xyz2abc

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))

# Translation of the atoms along x-axis
x$atoms$x1 <- x$atoms$x1 + 10

# Wrapping the structure
y <- wrap(x)

PDB File Writer

Description

Writes a Protein Data Bank (PDB) coordinate file from an object of class ‘pdb’.

Usage

write.pdb(x, file = "Rpdb.pdb")

Arguments

Details

All data stored in the ‘pdb’ object are written to a PDB file. A list of objects of class ‘pdb’ can be provided to write multiple MODEL data into a single file. In this case, each ‘pdb’ object of the list must have the same cryst1 and conect components.
To write only a subset of a ‘pdb’ object see function subset.pdb.

Value

No return value, called for side effects.

References

PDB format is described at: http://www.wwpdb.org/documentation/format33/v3.3.html

See Also

read.pdb, pdb, cryst1, atoms, conect, subset.pdb

Examples

# Read a PDB file included with the package
pdb <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))

# Write the pdb object to file "Rpdb.pdb" in the current directory
write.pdb(pdb, file = "Rpdb.pdb")

# Cleanup
unlink("Rpdb.pdb")

From Cartesian to Fractional Coordinates and Vice Versa

Description

Converts Cartesian coordinates into fractional coordinates and vice versa.

Usage

xyz2abc(...)

## S3 method for class 'coords'
xyz2abc(x, cryst1, ...)

## S3 method for class 'atoms'
xyz2abc(x, cryst1, ...)

## S3 method for class 'pdb'
xyz2abc(x, cryst1 = x$cryst1, ...)

## S3 method for class 'distances'
xyz2abc(x, cryst1, ...)

abc2xyz(...)

## S3 method for class 'coords'
abc2xyz(x, cryst1, ...)

## S3 method for class 'atoms'
abc2xyz(x, cryst1, ...)

## S3 method for class 'pdb'
abc2xyz(x, cryst1 = x$cryst1, ...)

## S3 method for class 'distances'
abc2xyz(x, cryst1, ...)

Arguments

Details

For atoms and pdb objects, the atomic coordinates are first extracted from x using the coords function. Then, using the periodic boundary conditions stored into cryst1, the coordinates are converted from Cartesian to fractional (for the xyz2abc functions) or from fractional to Cartesian (for the abc2xyz functions) coordinates. Finally, for atoms and pdb objects, the new atomic coordinates are reassigned to the original x object using the coords<- function and x is returned.

Value

Return an object of the same class as x, with atomic coordinates expressed in a different basis set.

See Also

basis, coords, atoms, pdb, cryst1

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
basis(x)
x <- xyz2abc(x)
basis(x)
x <- abc2xyz(x)
basis(x)


  
  # This example returns an error because the coordinates stored
  # into the PDB file are already Cartesian coordinates.
  x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
  try(x <- abc2xyz(x))