| Title: | Read, Write, Visualize and Manipulate PDB Files |
|---|---|
| Description: | Provides tools to read, write, visualize Protein Data Bank (PDB) files and perform some structural manipulations. |
| Authors: | Leonard Mada [cre, ctb], Julien Idé [aut] |
| Maintainer: | Leonard Mada <[email protected]> |
| License: | GPL (>= 3) |
| Version: | 2.4.0 |
| Built: | 2025-02-16 05:01:32 UTC |
| Source: | https://github.com/discoleo/rpdb |
Provides tools to read, write, visualize PDB files, and perform structural manipulations.
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.
Julien Idé [email protected]
More information on the PDB format can be found here:
http://www.wwpdb.org/documentation/format33/v3.3.html
## 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())## 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 lattice vectors, Cartesian axes or PBC box to the current ‘rgl’ scene.
addABC(x, lwd = 2, labels = TRUE, cex = 2) addXYZ(lwd = 2, labels = TRUE, cex = 2) addPBCBox(x, lwd = 2)addABC(x, lwd = 2, labels = TRUE, cex = 2) addXYZ(lwd = 2, labels = TRUE, cex = 2) addPBCBox(x, lwd = 2)
x |
an object of class ‘cryst1’ containing unit cell parameters. |
lwd |
a numeric value indicating the line width used to draw the axes or the PBC box. |
labels |
a logical value indicating whether the labels of the axes have to be drawn. |
cex |
a numeric value indicating the magnification used to draw the labels of the axes. |
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.
Return (using invisible) a two-column data.frame containing the IDs and type indicators of the objects added to the scene.
visualize, rgl.open, par3d,
addLabels
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)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 current ‘rgl’ scene.
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, ...)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, ...)
x |
an R object containing atomic coordinates. |
... |
further arguments passed to or from other methods. |
at.centre |
a single element logical vector indicating if residue labels have to be added only at the position of the residue's centre-of-mass instead of at each atomic position. |
col |
the colors used to display the labels. |
eleid |
a single element logical vector indicating if the element ids have to be concatenated with the element names to prepare the labels. |
id |
vector of ID numbers of ‘rgl’ items, as returned by
|
verbose |
a logical value specifying if information have to be printed to the terminal. |
adj |
one value specifying the horizontal adjustment, or two, specifying
horizontal and vertical adjustment respectively. See
|
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"
addResLab and addEleLab return (using invisible) a
two-column data.frame containing the IDs and type indicators of the objects
added to the scene.
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)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)
Creates an object of class ‘atoms’ containing the data related to ATOM and HETATM records of a PDB file.
atoms(...) ## Default S3 method: atoms( recname, eleid, elename, alt, resname, chainid, resid, insert, x1, x2, x3, occ, temp, segid, basis = "xyz", ... ) is.atoms(x)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 passed to methods. |
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 of each element. |
x1, x2, x3
|
a numeric vector containing the first, second and third coordinate for each element. |
occ |
a numeric vector containing the occupancie 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. |
x |
an R obecjt to be tested. |
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.
atoms returns a data.frame of class ‘atoms’ with the following components:
a character vector containing the record name for each element.
a integer vector containing the element ID for each element.
a character vector containing the element name for each element.
a character vector containing the alternate location indicator for each element.
a character vector containing the residue name for each element.
a character vector containing the chain ID for each element.
a integer vector containing the residue ID for each element.
a character vector containing the codes for insertion of residue for each element.
a numeric vector containing the first, second and third coordinate for each element.
a numeric vector containing the occupencie for each element.
a numeric vector containing the temperature factor for each element.
a character vector containing the segment ID for each element.
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.
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)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)
Functions to get or set the basis of an object containing atomic coordinates.
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) <- valuebasis(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
x |
an R object containing atomic coordinates. |
value |
a single element character vector use to set the basis of
|
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.
basis:NULL or a single element
character vector. (NULL is given if the object has no basis
attribute.)
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.)
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) basis(x) x <- xyz2abc(x) basis(x)x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) basis(x) x <- xyz2abc(x) basis(x)
Compute bond lengths, angles and dihedral from atomic coordinates.
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, ...)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, ...)
... |
further arguments passed to or from other methods. |
x |
an R object containing atomic coordinates. |
sel1, sel2, sel3, sel4
|
an integer or logical vector used to select atoms defining bonds, angles or dihedrals. See details. |
id |
vector of ID numbers of ‘rgl’ items, as returned by
|
verbose |
a logical value specifying if the information have to be printed to the terminal. |
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.
A numeric vector containing atomic bond lengths (in Angstrom), angles or dihedrals (in degrees)
coords, pdb, info3d,
visualize
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)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)
Compute the Cartesian coordinates of lattice vectors, the volume or the density of a unit cell.
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, ...)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, ...)
... |
further arguments passed to or from other methods. |
abc |
a length 3 numeric vector containing the length of the a, b and c lattice vectors. |
abg |
a length 3 numeric vector containing the angles (degrees) between the a, b and c lattice vectors (alpha, beta, gamma). |
digits |
an integer used to round the lattice vectors coordinates. |
x |
an R object containing lattice parameters. |
masses |
a numeric vector containing atomic masses. |
volume |
a single element numeric vector containing the volume of the unit cell in Angstrom cube. |
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.
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.
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) cell.volume(x) cell.density(x) cell.coords(x)x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) cell.volume(x) cell.density(x) cell.coords(x)
Computes centres-of-geometry and centres-of-mass of groups of atoms.
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, ...)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, ...)
... |
further arguments passed to or from other methods. |
x |
an R object containing atomic coordinates. |
factor |
a factor used to split the atomic coordinates by groups to compute multiple centres. |
weights |
a numerical vector containing atomic weights used to compute centres-of-mass. |
unsplit |
a logical value indicating whether the coordinates of the centres have to be unsplit to repeat their coordinates for each atom used for their calculation (used for wrapping by groups). |
na.rm |
a logical value indicating whether NA values should be stripped before the computation proceeds. |
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$resid, respectively, to compute the
centre-of-geometry of the different resdiues. Notice that coordinates can be
neglected for the calculation of the centres using NA values in
factor.
Return an object of class ‘coords’ containing the coordinates of centres.
coords, atoms, pdb,
elements
and split, unsplit,
factor for details about splitting data sets.
# First lets read a pdb file x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) # Centres-of-geometry of the residues centres(x) # Centre-of-geometry of the whole structure centres(x, factor = rep(1, natom(x))) # or centres(coords(x)) # Centres-of-geometry of the PCB and DCB residues centres(x, factor = x$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$elename) # Convert elename into elemental symbols # Find the mass of the element in the periodic table w <- elements[match(symb, elements[,"symb"]), "mass"] centres(x, weights = w)# First lets read a pdb file x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) # Centres-of-geometry of the residues centres(x) # Centre-of-geometry of the whole structure centres(x, factor = rep(1, natom(x))) # or centres(coords(x)) # Centres-of-geometry of the PCB and DCB residues centres(x, factor = x$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)
Creates an object of class ‘conect’ containing the IDs of bonded atoms defining the connectivity of a molecular system.
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)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 passed to methods. |
eleid.1 |
a integer vector containing the IDs of bonded atoms. |
eleid.2 |
a integer vector containing the IDs of bonded atoms. |
x |
an R object containing atomic coordinates. |
radii |
a numeric vector containing atomic radii used to find neigbours. |
safety |
a numeric value used to extend the atomic radii. |
by.block |
a logical value indicating whether the connectivity has to be determine by block (see 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.
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:
eleid.1 |
a integer vector containing the elements IDs defining the connectivity of the system. |
eleid.2 |
a integer vector containing the elements IDs defining the connectivity of the system. |
is.conect returns TRUE if x
is an object of class ‘coords’ and FALSE otherwise.
# 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# 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
Get or set the atomic coordinates (either Cartesian or fractional coordinates) of an object.
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 'coords' coords(x, ...) ## 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)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 'coords' coords(x, ...) ## 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)
... |
further arguments passed to or from other methods. |
x |
an R object containing atomic coordinates. |
value |
an object of class ‘coords’ used for replacement |
x1, x2, x3
|
numeric vectors containing the first, second and third coordinates. |
basis |
a single element character vector indicating the type of basis vector used to express the atomic coordinates. |
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 ‘coords’, the accessor function
returns the ‘coords’ object as is.
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 sets 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 searches x, y, z or a, b, c columns in x.
If x, y, z columns are found, they are used to 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.
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
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)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 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’.
cryst1(...) ## Default S3 method: cryst1(abc, abg = c(90, 90, 90), sgroup = "P1", ...) is.cryst1(x) is.crystal(x)cryst1(...) ## Default S3 method: cryst1(abc, abg = c(90, 90, 90), sgroup = "P1", ...) is.cryst1(x) is.crystal(x)
... |
further arguments passed to or from other methods. |
abc |
a numeric vector of length 3 containing the norms of the lattice vectors a, b and c. |
abg |
a numeric vector of length 3 containing the angles between the
lattice vectors |
sgroup |
a character string giving the Hermann-Mauguin symbol of the space group. |
x |
an R object to be tested. |
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.
Function cryst1 returns a list of class ‘cryst1’ with the
following components:
abc |
a numeric vector of length 3 containing the norms of the lattice vectors a, b and c. |
abg |
a numeric vector of length 3 containing the angles between the
lattice vectors |
sgroup |
a character string giving the Hermann-Mauguin symbol of the space group. |
Function is.cryst1 returns TRUE if x is an object of class ‘cryst1’
and FALSE otherwise.
x <- cryst1(abc = c(10, 10, 10), abg = c(90,90,90), sgroup = "P1") is.cryst1(x) is.crystal(x)x <- cryst1(abc = c(10, 10, 10), abg = c(90,90,90), sgroup = "P1") is.cryst1(x) is.crystal(x)
Computes inter-atomic distance vectors.
distances(...) dist.point(...) ## 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, ...) ## Default S3 method: dist.point(data, x, y = NULL, z = NULL, subset = NULL, ...) is.distances(x) norm(...) ## S3 method for class 'distances' norm(x, type = "xyz", ...)distances(...) dist.point(...) ## 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, ...) ## Default S3 method: dist.point(data, x, y = NULL, z = NULL, subset = NULL, ...) is.distances(x) norm(...) ## S3 method for class 'distances' norm(x, type = "xyz", ...)
... |
further arguments passed to or from other methods. |
dx1, dx2, dx3
|
numeric arrays containing the first, second and third components of the distance vectors. |
basis |
a single element character vector indicating the type of basis vector used to express the coordinates. |
x, y, z
|
an R object containing atomic coordinates. |
sel1, sel2
|
integer or logical vectors defining two atomic selections between which the distance vectors are computed. |
data |
an object of type pdb, atoms or coords, containing atomic coordinates. |
subset |
enables sub-setting the coords object; |
type |
a single element character vector indicating how to project the distances vectors before computing the norms. See 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 for the ‘dist.point’ function computes the inter-atomic distances between the atoms and a specified point.
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’;
the test is limited to the class attribute.
The distances and dist.point functions 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.
coords, basis, xyz2abc, abc2xyz
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$resid == 8 d <- distances(x, is.DCB7, is.DCB8) norm(d, type = "xyz") norm(d, type = "xy") norm(d, type = "x") d <- dist.point(x, c(0,0,0), subset = is.DCB7) norm(d, type = "xyz")x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) is.DCB7 <- x$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") d <- dist.point(x, c(0,0,0), subset = is.DCB7) norm(d, type = "xyz")
This data set gives various information on chemical elements
A data frame containing for each chemical element the following information.
numatomic number
symbelemental symbol
arenegAllred and Rochow electronegativity (0.0 if unknown)
rcovcovalent radii (in Angstrom) (1.6 if unknown)
rbo"bond order" radii
rvdwvan der Waals radii (in Angstrom) (2.0 if unknown)
maxbndmaximum bond valence (6 if unknown)
massIUPAC recommended atomic masses (in amu)
elnegPauling electronegativity (0.0 if unknown)
ionizationionization potential (in eV) (0.0 if unknown)
elaffinityelectron affinity (in eV) (0.0 if unknown)
redred value for visualization
greengreen value for visualization
blueblue value for visualization
nameelement name
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
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"]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"]
Computes the inertia tensor of a molecular system from atomic coordinates and masses.
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, ...)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, ...)
... |
further arguments passed to or from other methods. |
x |
an R object containing atomic coordinates. |
m |
a numeric vector containing atomic masses. |
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.
Return the inertia tensor in a 3x3 matrix.
toSymbols, masses, viewInertia
C70 <- read.pdb(system.file("examples/C70.pdb", package="Rpdb")) inertia(C70) visualize(C70, mode = NULL) viewXY() viewInertia(C70)C70 <- read.pdb(system.file("examples/C70.pdb", package="Rpdb")) inertia(C70) visualize(C70, mode = NULL) viewXY() viewInertia(C70)
Determine the mass of chemical elements
masses(...) ## Default S3 method: masses(x, ...) ## S3 method for class 'pdb' masses(x, ...)masses(...) ## Default S3 method: masses(x, ...) ## S3 method for class 'pdb' masses(x, ...)
... |
further arguments passed to or from other methods. |
x |
either a character or an integer vector containing element symbols or atomic numbers, or an object of class ‘pdb’ from which element symbols are determined (see 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.
Return a numeric vector containing the mass of chemical elements.
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb",package="Rpdb")) masses(x) masses(c("C","Cl",NA,"AA","N"))x <- read.pdb(system.file("examples/PCBM_ODCB.pdb",package="Rpdb")) masses(x) masses(c("C","Cl",NA,"AA","N"))
Merge two objects contaning atomic coordinates
## 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, ...)## 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, ...)
x, y
|
objects of class 'coords' to be merged. |
... |
further arguments passed to or from other methods. |
reindex |
a single element logical vector indicating if residue and element IDs have to be reindexed after merging. |
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.
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.
coords, atoms, pdb,
basis, merge, merge.data.frame
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)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)
Perform a reflexion (or mirror) operation on atomic coordinates with respect to a given reflexion plane.
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, ...)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$cryst1, ...)
... |
further arguments passed to or from other methods. |
x |
an R object containing atomic coordinates. |
p1 |
a numeric vector of length 3 containing the coordinates of the
first point defining the reflexion plan. Can also be a 3x3 matrix or
data.frame containing by row |
p2 |
a numeric vector of length 3 containing the coordinates of the second point defining the reflexion plane. |
p3 |
a numeric vector of length 3 containing the coordinates of the third point defining the reflexion plane. |
mask |
a logical vector indicating the set of coordinates to which to apply the reflexion. |
cryst1 |
an object of class ‘cryst1’ use to convert fractional into Cartesian coordinates when need. |
mirror is a generic function. Method for objects of class
‘coords’ first convert the coordinates into Cartesian coordinates
using cryst1 if needed. Once reflected, the coordinates are
reconverted back to the orginal basis set using again cryst1. Method
for objects of class ‘pdb’ first extract coordinates from the object
using the function coords, perform the reflection, and update the
coordinates of the ‘pdb’ object using the function coords<-.
An object of the same class as x with reflected coordinates.
Helper functions for reflection with respect to a given Cartesian
plane or a plane defined by two lattice vectors:Mxy,
Myz, Mzx, Mab, Mbc,
Mca
Passing from Cartesian to fractional coordinates (or Vis
Versa):xyz2abc, abc2xyz
# First lets read a pdb file x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) cell <- cell.coords(x) visualize(x, mode = NULL) # Mirror operation with respect to the ab-plane visualize(mirror(x, rep(0,3), p1=cell[, "a"], p2=cell[, "b"]), mode = NULL) # Mirror operation with respect to the ab-plane for residue 1 visualize(mirror(x, rep(0,3), p1=cell[, "a"], p2=cell[, "b"], mask = x$atoms$resid == 1), mode = NULL)# First lets read a pdb file x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) cell <- cell.coords(x) visualize(x, mode = NULL) # Mirror operation with respect to the ab-plane visualize(mirror(x, rep(0,3), p1=cell[, "a"], p2=cell[, "b"]), mode = NULL) # Mirror operation with respect to the ab-plane for residue 1 visualize(mirror(x, rep(0,3), p1=cell[, "a"], p2=cell[, "b"], mask = x$atoms$resid == 1), mode = NULL)
Reflection of atomic coordinates with respect to a specific Cartesian plan or a plan defined by two lattice vectors.
Mxy(...) ## S3 method for class 'coords' Mxy(x, mask = TRUE, cryst1 = NULL, ...) ## S3 method for class 'pdb' Mxy(x, mask = TRUE, cryst1 = x$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$cryst1, mask = TRUE, ...)Mxy(...) ## S3 method for class 'coords' Mxy(x, mask = TRUE, cryst1 = NULL, ...) ## S3 method for class 'pdb' Mxy(x, mask = TRUE, cryst1 = x$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$cryst1, mask = TRUE, ...)
... |
further arguments passed to or from other methods. |
x |
an R object containing atomic coordinates. |
mask |
a logical vector indicating the set of coordinates to which to apply the reflection. |
cryst1 |
an object of class ‘cryst1’ use to convert fractional into Cartesian coordinates when need. |
These functions are helper functions to perform a reflection with respect to
a specific Cartesian plan or a plan defined by two lattice vectors. All of
them call the mirror function.
An object of the same class as x with reflected coordinates.
mirror and xyz2abc,
abc2xyz for passing from Cartesian to fractional coordinates
(or Vis Versa).
# First lets read a pdb file x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) visualize(x, mode = NULL) # Mirror operation with respect to the ab-plane visualize(Mab(x), mode = NULL) # Mirror operation with respect to the ab-plane for residue 1 visualize(Mab(x, mask = x$atoms$resid == 1), mode = NULL)# First lets read a pdb file x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) visualize(x, mode = NULL) # Mirror operation with respect to the ab-plane visualize(Mab(x), mode = NULL) # Mirror operation with respect to the ab-plane for residue 1 visualize(Mab(x, mask = x$atoms$resid == 1), mode = NULL)
Evaluates the number of atoms in an object containing atomic coordinates.
natom(x, ...) ## S3 method for class 'coords' natom(x, factor = NULL, ...) ## S3 method for class 'atoms' natom(x, factor = NULL, ATOM = TRUE, HETATM = TRUE, ...) ## S3 method for class 'pdb' natom(x, factor = NULL, ATOM = TRUE, HETATM = TRUE, ...)natom(x, ...) ## S3 method for class 'coords' natom(x, factor = NULL, ...) ## S3 method for class 'atoms' natom(x, factor = NULL, ATOM = TRUE, HETATM = TRUE, ...) ## S3 method for class 'pdb' natom(x, factor = NULL, ATOM = TRUE, HETATM = TRUE, ...)
x |
an R object containing atomic coordinates. |
... |
further arguments passed to or from other methods. |
factor |
a factor used to split the object and evaluate the number of atoms in each group. |
ATOM |
a single element logical vector indicating if ATOM records have to be considered or not. |
HETATM |
a single element logical vector indicating if HETATM records have to be considered or not. |
natom is a generic function to evalute the number of atom in an object
containing atomic coordinates. The atomic coordinates of the object are first
filtered to keep ATOM and/or HETATM records as indicated by the 'ATOM' and
'HETATM' arguments. Then, if factor is specify, the object is splitted
to evalute the number of atoms in each group defined by factor. If
factor is not specify then the total number of atoms in the object is
return.
Return an integer or a vector of integer of lenght equal to
nlevels(factor) (if factor is specify) indication the number
of atoms in the object or in the groups defined by factor.
coords, atoms, pdb,
factor, split
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) natom(x) natom(x, x$atoms$resid) natom(x, x$atoms$resname) natom(x, HETATM = FALSE)x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) natom(x) natom(x, x$atoms$resid) natom(x, x$atoms$resname) natom(x, HETATM = FALSE)
Creates an object of class 'pdb'.
pdb(...) ## Default S3 method: pdb( atoms, crystal = NULL, conect = NULL, remark = NULL, title = NULL, resolution = NULL, ..., cryst1 = NULL ) is.pdb(x)pdb(...) ## Default S3 method: pdb( atoms, crystal = NULL, conect = NULL, remark = NULL, title = NULL, resolution = NULL, ..., cryst1 = NULL ) is.pdb(x)
... |
further arguments passed to or from other methods. |
atoms |
a data.frame of class |
crystal |
a list of class |
conect |
a data.frame of class |
remark |
a character vector containing some REMARK records to be added to the |
title |
a character vector containing some TITLE records to be added to the |
resolution |
numeric value specifying the resolution; the unit should be specified as an attribute. |
cryst1 |
will be deprecated and replaced by argument crystal. |
x |
an R object to be tested. |
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.
pdb returns a list of class ‘pdb’ with the following components:
title |
a character vector containing the TITLE records found in a PDB file. |
remark |
a character vector containing the REMARK records found in a PDB file. |
cryst1 |
a list of class ‘cryst1’ containing the first CRYST1 record found in a PDB file. All others are ignored. |
atoms |
a data.frame of class ‘atoms’ containing the ATOM and HETATM records found in a PDB file. |
conect |
a data.frame of class ‘conect’ containing the CONECT records found in a PDB file. |
is.pdb returns TRUE if x is an object of class ‘pdb’ and FALSE otherwise.
atoms, coords, cryst1, conect and read.pdb
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)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)
Computes 3D Projections
proj.line3d(p, x, y, z, ...) ## S3 method for class 'line3d.numeric' proj(p, x, y = NULL, z = NULL, ...) ## S3 method for class 'line3d.matrix' proj(p, x, y = NULL, z = NULL, ...)proj.line3d(p, x, y, z, ...) ## S3 method for class 'line3d.numeric' proj(p, x, y = NULL, z = NULL, ...) ## S3 method for class 'line3d.matrix' proj(p, x, y = NULL, z = NULL, ...)
p |
numeric array or matrix with the x,y,z coordinates of the point or collection of points. |
x, y, z
|
an R object containing the coordinates of the end-points of the line segment; can be specified either as individual values or as a matrix. |
... |
currently not used. |
The purpose of the ‘proj’ helper functions is to compute the spatial projections of various objects on other geometrical structures. Currently, only projection of points on a line segment are implemented.
The methods for the ‘proj.line3d’ function compute the projections of 1 point or a collection of points on a line segment defined by the 2 delimiting points.
The ‘numeric’ method projects a point, while the ‘matrix’ method projects a collection of points on another geometric object.
The proj.line3d function returns an object
of class ‘proj’ containing the 3-dimensional coordinates of
the projected point, as well as a scalar value representing the fraction
of the path on the line segment.
p = c(1,2,3) line = matrix(c(0,5,2,3,1,4), nrow = 2) proj.line3d(p, line)p = c(1,2,3) line = matrix(c(0,5,2,3,1,4), nrow = 2) proj.line3d(p, line)
Determines the range of atomic coordinates.
## 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, ...)## 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, ...)
x |
an R object containing atomic coordinates. |
na.rm |
logical, indicating if |
finite |
logical, indicating if all non-finite elements should be omitted. |
... |
further arguments passed to or from other methods. |
Return a data.frame whose columns contain the range of
the first, second and third coordinates of x.
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) range(x) range(range(x))x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) range(x) range(range(x))
Reads a Protein Data Bank (PDB) coordinates file.
read.pdb( file, ATOM = TRUE, HETATM = TRUE, CRYSTAL = TRUE, CONECT = TRUE, TITLE = TRUE, REMARK = TRUE, MODEL = 1, CRYST1 = NULL, resolution = TRUE, verbose = TRUE )read.pdb( file, ATOM = TRUE, HETATM = TRUE, CRYSTAL = TRUE, CONECT = TRUE, TITLE = TRUE, REMARK = TRUE, MODEL = 1, CRYST1 = NULL, resolution = TRUE, verbose = TRUE )
file |
a single element character vector containing the name of the PDB file to be read. |
ATOM |
a logical value indicating whether to read the ATOM records. |
HETATM |
a logical value indicating whether to read the HETATM records. |
CRYSTAL |
a logical value indicating whether to read the crystal cell parameters (from the CRYST1 pdb record). |
CONECT |
a logical value indicating whether to read the CONECT records. |
TITLE |
a logical value indicating whether to read the TITLE records. |
REMARK |
a logical value indicating whether to read the REMARK records. |
MODEL |
an integer vector containing the serial number of the MODEL sections to be read. Can also be equal to NULL to read all the MODEL sections or to NA to ignore MODEL records (see details). |
CRYST1 |
will be replaced by the CRYSTAL argument; existing code should be migrated to use the CRYSTAL argument. |
resolution |
logical value indicating wheter to extract the resolution (see details). |
verbose |
logical value indicating wheter to print additional information, e.g. number of models. |
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 and all ATOM and/or HETATM records are merged together to return a single object.
When multiple models are specified, each of the models is actually stored
as a separate pdb molecule in a list of pdb molecules.
If the resolution parameter is set, the function attempts to extract the resolution
from the REMARKS field. Note: The resolution is only meaningfull for X-ray crystallography.
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:
title |
a character vector containing the TITLE records found in the PDB file. |
remark |
a character vector containing the REMARK records found in the PDB file. |
cryst1 |
a list of class ‘cryst1’ containing the first CRYST1 record found in the PDB file. All others are ignored. |
atoms |
a data.frame of class ‘atoms’ containing the ATOM and HETATM records found in the PDB file. |
conect |
a data.frame of class ‘conect’ containing the CONECT records found in the PDB file. |
When multiple MODEL sections are read, a list of object of class ‘pdb’ is returned.
PDB format has been taken from: http://www.wwpdb.org/documentation/format33/v3.3.html
write.pdb, pdb, cryst1, atoms, conect
# 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")# 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 the indexing of an object.
reindex(...) ## S3 method for class 'atoms' reindex(x, eleid = TRUE, resid = TRUE, ...) ## S3 method for class 'pdb' reindex(x, eleid = TRUE, resid = TRUE, ...)reindex(...) ## S3 method for class 'atoms' reindex(x, eleid = TRUE, resid = TRUE, ...) ## S3 method for class 'pdb' reindex(x, eleid = TRUE, resid = TRUE, ...)
... |
further arguments passed to or from other methods. |
x |
an R object. |
eleid |
a single element logical vector indicating if elements IDs have to reindexed. |
resid |
a single element logical vector indicating if residues IDs have to reindexed. |
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.
Return an object of the same class as x with updated indexes.
pdb, atoms, subset.atoms, subset.pdb
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) x <- subset(x, x$atoms$eleid %in% sample(x$atoms$eleid, 10)) print(x) x <- reindex(x) print(x)x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) x <- subset(x, x$atoms$eleid %in% sample(x$atoms$eleid, 10)) print(x) x <- reindex(x) print(x)
Replicate atomic coordinates using periodic boundary conditions.
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, ...)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, ...)
x |
an R object containing atomic coordinates to be replicated. |
... |
further arguments passed to or from other methods. |
cryst1 |
an object of class ‘cryst1’ containing periodical boundary conditions used for replicating. |
a.ind |
a vector of integers indicating the positions of the replicated cells along the a-axis. |
b.ind |
a vector of integers indicating the positions of the replicated cells along the b-axis. |
c.ind |
a vector of integers indicating the positions of the replicated cells along the c-axis. |
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).
Return an object of class ‘pdb’ with replicated atomic coordinates.
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)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 around a given vector.
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, ...)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$cryst1, ...)
... |
further arguments passed to or from other methods. |
obj |
an R object containing atomic coordinates. |
angle |
the angle of the rotation in degrees. |
x |
the x-component of the rotation vector. |
y |
the y-component of the rotation vector. |
z |
the z-component of the rotation vector. |
mask |
a logical vector indicating the set of coordinates to which the rotation has to be applyed. |
cryst1 |
an object of class ‘cryst1’ use to convert fractional into Cartesian coordinates when need. |
R is generic functions. Method for objects of class ‘coords’
first convert the coordinates into Cartesian coordinates using cryst1
if needed. Once rotated, the coordinates are reconverted back to the orginal
basis set using again cryst1. Method for objects of class ‘pdb’
first extract coordinates from the object using the function coords,
perform the rotation, and update the coordinates of the ‘pdb’ object
using the function coords<-.
An object of the same class as x with rotated coordinates.
Helper functions for rotation around a given Cartesian vector:Rx, Ry, Rz
Passing from Cartesian to fractional coordinates (or Vis Versa):xyz2abc, abc2xyz
# First lets read a pdb file x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) cell <- cell.coords(x) visualize(x, mode = NULL) # Rotation of the structure around the c-axis visualize(R(x, 90, x=cell["x","c"], y=cell["y","c"], z=cell["z","c"]), mode = NULL) # Rotation of the residue 1 around the c-axis visualize(R(x, 90, x=cell["x","c"], y=cell["y","c"], z=cell["z","c"], mask = x$atoms$resid == 1), mode = NULL)# First lets read a pdb file x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) cell <- cell.coords(x) visualize(x, mode = NULL) # Rotation of the structure around the c-axis visualize(R(x, 90, x=cell["x","c"], y=cell["y","c"], z=cell["z","c"]), mode = NULL) # Rotation of the residue 1 around the c-axis visualize(R(x, 90, x=cell["x","c"], y=cell["y","c"], z=cell["z","c"], mask = x$atoms$resid == 1), mode = NULL)
Rotation of atomic coordinates along a specific Cartesian vector.
Rx(...) ## S3 method for class 'coords' Rx(x, angle = 0, mask = TRUE, cryst1 = NULL, ...) ## S3 method for class 'pdb' Rx(x, angle = 0, mask = TRUE, cryst1 = x$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, ...)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$cryst1, ...)
... |
further arguments passed to or from other methods. |
x |
an R object containing atomic coordinates. |
angle |
the angle of the rotation in degrees. |
mask |
a logical vector indicating the set of coordinates to which the rotation has to be applyed. |
cryst1 |
an object of class ‘cryst1’ use to convert fractional into Cartesian coordinates when need. |
These functions are helper functions to perform a rotation around a specific
Cartesian vector. All of them call the R function.
An object of the same class as x with rotated coordinates.
R and xyz2abc, abc2xyz for
passing from Cartesian to fractional coordinates (or Vis Versa).
# First lets read a pdb file x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) cell <- cell.coords(x) visualize(x, mode = NULL) # Rotation of the structure around the z-axis visualize(Rz(x, 90), mode = NULL) # Rotation of the residue 1 around the c-axis visualize(Rz(x, 90, mask = x$atoms$resid == 1), mode = NULL)# First lets read a pdb file x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) cell <- cell.coords(x) visualize(x, mode = NULL) # Rotation of the structure around the z-axis visualize(Rz(x, 90), mode = NULL) # Rotation of the residue 1 around the c-axis visualize(Rz(x, 90, mask = x$atoms$resid == 1), mode = NULL)
split divides a ‘pdb’ object by groups of atoms defined by
f. unsplit reverses the effect of split.
## S3 method for class 'pdb' split(x, f, drop = FALSE, ...) ## S3 method for class 'pdb' unsplit(value, f, drop = FALSE, ...)## S3 method for class 'pdb' split(x, f, drop = FALSE, ...) ## S3 method for class 'pdb' unsplit(value, f, drop = FALSE, ...)
x |
an object of class ‘pdb’ to be divided into groups. |
f |
a ‘factor’ in the sense that
|
drop |
logical indicating if levels that do not occur should be
dropped (if |
... |
further potential arguments passed to methods. |
value |
a list of 'pdb' objects compatible with a splitting of
|
split produce a list of ‘pdb’ objects with the same
cryst1, title and remark components as x. Only
its atoms component is splitted while its conect component is
cleaned to keep only the meaningful connectivity for each ‘pdb’ object
of the list returned by the function. unlist produce a ‘pdb’
object with the same cryst1, title and remark components
as the first element of value. The atoms and conect
components of all the elements of value are combined by row.
The value returned from split is a list of ‘pdb’
objects containing the data for the groups of atoms. The components of the
list are named by the levels of f (after converting to a factor, or if
already a factor and drop=TRUE, dropping unused levels). unsplit returns a ‘pdb’ object for which split(x, f)
equals value.
### Split a pdb file by residue IDs and write them into separate files x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) file.names <- paste0(x$atoms$resname, "_", x$atoms$resid, ".pdb") file.names <- unique(file.names) pdb.resid <- split(x, x$atoms$resid) length(pdb.resid) useless <- mapply(write.pdb, pdb.resid, file.names) # Cleanup unlink(file.names)### Split a pdb file by residue IDs and write them into separate files x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) file.names <- paste0(x$atoms$resname, "_", x$atoms$resid, ".pdb") file.names <- unique(file.names) pdb.resid <- split(x, x$atoms$resid) length(pdb.resid) useless <- mapply(write.pdb, pdb.resid, file.names) # Cleanup unlink(file.names)
Return subsets of ‘atoms’ or ‘pdb’ objects which meet conditions.
## S3 method for class 'atoms' subset(x, subset, drop = FALSE, reindex.all = TRUE, ...) ## S3 method for class 'pdb' subset(x, subset, drop = FALSE, reindex.all = TRUE, ...)## S3 method for class 'atoms' subset(x, subset, drop = FALSE, reindex.all = TRUE, ...) ## S3 method for class 'pdb' subset(x, subset, drop = FALSE, reindex.all = TRUE, ...)
x |
object to be subsetted. |
subset |
logical expression indicating elements or rows to keep: missing values are taken as false. |
drop |
passed on to [ indexing operator. |
reindex.all |
a single element logical vector indicating if residues and elements IDs have to be reindexed after subsetting. |
... |
further arguments to be passed to or from other methods. |
For an ‘atoms’ object the method is similar to the data.frame method
(see subset) but allow to directly reindex the elements and
residues IDs. For a ‘pdb’ object subsetting is applied on the
atoms and conect components of the object in a consistent way.
First the atoms component is subsetted and then the conect
component is filtered to keep only the conectivity for the subset.
Return a subsetted object of the same class as x.
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) y <- subset(x, x$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)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)
Converts character strings or atomic numbers into atomic symbols.
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, na = NA, ...)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, na = NA, ...)
x |
a vector to be converted into atomic symbols. |
... |
further arguments passed to or from other methods. |
nletters |
an integer used to truncate the character strings before conversion. |
na |
the default value to use for invalid or missing element symbols. |
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.
a character vector containing atomic symbols
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" toSymbols("SIL", nletters=3, na="X") # return "X"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" toSymbols("SIL", nletters=3, na="X") # return "X"
Translation of Cartesian or fractional coordinates.
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$cryst1, ... )Txyz(...) ## S3 method for class 'coords' Txyz( obj, x = 0, y = 0, z = 0, mask = TRUE, thickness = NULL, cryst1 = NULL, ... ) ## S3 method for class 'pdb' Txyz( obj, x = 0, y = 0, z = 0, mask = TRUE, thickness = NULL, cryst1 = obj$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, ... )
... |
further arguments passed to or from other methods. |
obj |
an R object containing atomic coordinates. |
x |
the x-component of the translation vector. |
y |
the y-component of the translation vector. |
z |
the z-component of the translation vector. |
mask |
a logical vector indicating the set of coordinates to which to apply the translation. |
thickness |
a numeric value indicating the fraction of the thicknees of the selected atom to be added to the translation vector (Usually 0, 0.5 or 1. See details). |
cryst1 |
an object of class ‘cryst1’ use to convert Cartesian into fraction coordinates (or Vis Versa) when need. |
a |
the a-component of the translation vector. |
b |
the b-component of the translation vector. |
c |
the c-component of the translation vector. |
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).
An object of the same class as x with translated coordinates.
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
# 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$resname == "C70", thickness=0.5), mode = NULL) viewXY()# First lets read a pdb file x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) visualize(x, mode = NULL) visualize(Txyz(x, y=10), mode = NULL) visualize(Txyz(x, y=10, mask = x$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$resname == "C70", thickness=0.5), mode = NULL) viewXY()
Translation of atomic coordinates along a specific Cartesian or lattice vector.
Tx(...) ## S3 method for class 'coords' Tx(obj, x = 0, mask = TRUE, thickness = NULL, cryst1 = NULL, ...) ## S3 method for class 'pdb' Tx(obj, x = 0, mask = TRUE, thickness = NULL, cryst1 = obj$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$cryst1, ...)Tx(...) ## S3 method for class 'coords' Tx(obj, x = 0, mask = TRUE, thickness = NULL, cryst1 = NULL, ...) ## S3 method for class 'pdb' Tx(obj, x = 0, mask = TRUE, thickness = NULL, cryst1 = obj$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$cryst1, ...)
... |
further arguments passed to or from other methods. |
obj |
an R object containing atomic coordinates. |
x |
the x-component of the translation vector. |
mask |
a logical vector indicating the set of coordinates to which to apply the translation. |
thickness |
a numeric value indicating the fraction of the thicknees of the selected atom to be added to the translation vector (Usually 0, 0.5 or 1. See details). |
cryst1 |
an object of class ‘cryst1’ use to convert Cartesian into fraction coordinates (or Vis Versa) when need. |
y |
the y-component of the translation vector. |
z |
the z-component of the translation vector. |
a |
the a-component of the translation vector. |
b |
the b-component of the translation vector. |
c |
the c-component of the translation vector. |
These functions are helper functions to perform a translation along a
specific Cartesian or lattice vector. All of them call either the Txyz
or Tabc function.
An object of the same class as x with translated coordinates.
Txyz, Tabc
Passing from Cartesian to fractional coordinates (or Vis Versa):xyz2abc, abc2xyz
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) visualize(x, mode = NULL) visualize(Ty(x, 10), mode = NULL) visualize(Ty(x, 10, mask = x$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$resname == "C70", thickness=0.5), mode = NULL) viewXY()x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) visualize(x, mode = NULL) visualize(Ty(x, 10), mode = NULL) visualize(Ty(x, 10, mask = x$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()
This data set provides various universal constants
A data frame containing for each universal constant the following information.
Quantitya character vector containing a short description of the constants.
Valuea numeric vector containing the value of the constants.
Unita character vector indicating the unit of the constants.
http://www.ebyte.it/library/educards/constants/ConstantsOfPhysicsAndMath.html
# 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"]# 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"]
unsplit reverses the effect of split.
unsplit(value, f, drop = FALSE, ...) ## Default S3 method: unsplit(value, f, drop = FALSE, ...)unsplit(value, f, drop = FALSE, ...) ## Default S3 method: unsplit(value, f, drop = FALSE, ...)
value |
a list of vectors or data frames compatible with a splitting of
|
f |
a ‘factor’ in the sense that |
drop |
logical indicating if levels that do not occur should be dropped
(if |
... |
further potential arguments passed to methods. |
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.
Returns a vector or data frame for which split(x, f) equals
value
Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) The New S Language. Wadsworth & Brooks/Cole.
cut to categorize numeric values.
strsplit to split strings.
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)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 such as scalar product and vectorial product
dotProd(U, V) vectNorm(U) rotVect(U, n = 1) vectProd(U, V)dotProd(U, V) vectNorm(U) rotVect(U, n = 1) vectProd(U, V)
U |
a numeric vector of length 3. |
V |
a numeric vector of length 3. |
n |
an integer. |
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.
Vx <- c(3,0,0) vectNorm(Vx) Vx <- Vx / vectNorm(Vx) Vy <- c(0,1,0) Vz <- vectProd(Vx, Vy) print(Vz)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 current ‘rgl’ scene aligning one vector perpendicularly to the screen and placing another one in the horizontal plane.
viewAxis(V1, V2) viewXY() viewYZ() viewZX() viewAB(cryst1) viewBC(cryst1) viewCA(cryst1) viewInertia(x, m = NULL)viewAxis(V1, V2) viewXY() viewYZ() viewZX() viewAB(cryst1) viewBC(cryst1) viewCA(cryst1) viewInertia(x, m = NULL)
V1 |
a length 3 numeric vector. |
V2 |
a length 3 numeric vector. |
cryst1 |
an object of class ‘cryst1’. |
x |
an R object containing atomic coordinates. |
m |
a numeric vector containing atomic masses. |
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.
No return value, called for side effects.
visualize, cell.coords, par3d, rgl.open
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)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)
Use the rgl library to visualize in 3D a molecular structure.
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), ... )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), ... )
... |
further arguments passed to or from other methods. |
x |
an object or the name of a PDB file containing the molecular structure to visualize. |
elename |
a character vector containing the atomic names used to chose atom colors and radii. |
cryst1 |
an object of class ‘cryst1’. See |
conect |
an object of class ‘conect’. See |
mode |
a single element character vector indicating the visualization mode (See details). |
type |
a character string indicating the visualization style (See details). |
xyz |
a logical value indicating whether the x, y and z axes have to be added to the scene. See details |
abc |
a logical value indicating whether the a, b and c axes have to be added to the scene. See details |
pbc.box |
a logical value indicating whether the pbc box has to be added to the scene. See details |
lwd |
a numeric value indication the line width used to plot the axes, the pbc box and atomic bonds when |
lwd.xyz |
a numeric value indicating the line width used to plot the x, y and z axes. |
lwd.abc |
a numeric value indicating the line width used to plot the a, b and c axes. |
lwd.pbc.box |
a numeric value indicating the line width used to plot the pbc box. |
cex.xyz |
a numeric value indicating the magnification used to plot the labels of the x, y and z axes. |
cex.abc |
a numeric value indicating the magnification used to plot the labels of the a, b and c axes. |
col |
a vector indicating the colors to use to plot each atom. |
bg |
the color of the background |
radii |
either a character string indicating the type of radii or a numeric vector specifying the radii of each atom to use to plot atoms as spheres (see details). |
add |
a logical value indicating whether the plot has be to added to a existing scene (see |
windowRect |
a vector of four integers indicating the left, top, right and bottom of the displayed window in pixels (see |
FOV |
the field of view. This controls the degree of parallax in the perspective view (see par3d). |
userMatrix |
a 4 by 4 matrix describing user actions to display the scene (see |
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.
Return (using invisible) a two-column data.frame containing the IDs and type indicators of the objects added to the scene.
addXYZ, addABC, addPBCBox, par3d, select3d, measure, info3d
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)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)
Wraps atomic coordinates using periodic boundary conditions.
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, ...)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$cryst1, factor = NULL, ...)
x |
an R object containing atomic coordinates to be wrapped. |
... |
further arguments passed to or from other methods. |
cryst1 |
an object of class ‘cryst1’ containing periodic boundary conditions used for wrapping. |
factor |
a factor used to wrap the atoms by groups. |
The wrap function translates all atoms out of the unit cell back into
the unit cell using periodic boundary conditions. To do so, the wrap
function first converts Cartesian into fractional coordinates. Then atoms
with fractional coordinates greater than 1 or lower than 0 are respectively
translated by -1 or +1. Finally, if the original atomic coordinates were
Cartesian coordinates their are reconverted into Cartesian coordinates.
Return an object of class ‘pdb’ with wrapped atomic coordinates.
coords, atoms, pdb,
cryst1, centres.pdb, xyz2abc
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) # Translation of the atoms along x-axis x$atoms$x1 <- x$atoms$x1 + 10 # Wrapping the structure y <- wrap(x)x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) # Translation of the atoms along x-axis x$atoms$x1 <- x$atoms$x1 + 10 # Wrapping the structure y <- wrap(x)
Writes a Protein Data Bank (PDB) coordinate file from an object of class ‘pdb’.
write.pdb(x, file = "Rpdb.pdb")write.pdb(x, file = "Rpdb.pdb")
x |
an object, or a list of objects, of class ‘pdb’. |
file |
a single element character vector containing the name of the PDB file to be created. |
All data stored in the ‘pdb’ object are written to a PDB file. A list of objects of class ‘pdb’ can be provided to write multiple MODEL data into a single file. In this case, each ‘pdb’ object of the list must have the same cryst1 and conect components.
To write only a subset of a ‘pdb’ object see function subset.pdb.
No return value, called for side effects.
PDB format is described at: http://www.wwpdb.org/documentation/format33/v3.3.html
read.pdb, pdb, cryst1, atoms, conect, subset.pdb
# Read a PDB file included with the package pdb <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) # Write the pdb object to file "Rpdb.pdb" in the current directory write.pdb(pdb, file = "Rpdb.pdb") # Cleanup unlink("Rpdb.pdb")# Read a PDB file included with the package pdb <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb")) # Write the pdb object to file "Rpdb.pdb" in the current directory write.pdb(pdb, file = "Rpdb.pdb") # Cleanup unlink("Rpdb.pdb")
Converts Cartesian coordinates into fractional coordinates and vice versa.
xyz2abc(...) ## S3 method for class 'coords' xyz2abc(x, cryst1, ...) ## S3 method for class 'atoms' xyz2abc(x, cryst1, ...) ## S3 method for class 'pdb' xyz2abc(x, cryst1 = x$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$cryst1, ...) ## S3 method for class 'distances' abc2xyz(x, cryst1, ...)xyz2abc(...) ## S3 method for class 'coords' xyz2abc(x, cryst1, ...) ## S3 method for class 'atoms' xyz2abc(x, cryst1, ...) ## S3 method for class 'pdb' xyz2abc(x, cryst1 = x$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 passed to methods. |
x |
an R object containing atomic coordinates. |
cryst1 |
an object of class |
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.
Return an object of the same class as x, with atomic
coordinates expressed in a different basis set.
basis, coords, atoms,
pdb, cryst1
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))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))