Convert to PDB format

Convert Tripos Mol2 format, or Amber parameter/topology and coordinate data to PDB format.

as.pdb(...)

# S3 method for mol2
as.pdb(mol, ...)

# S3 method for prmtop
as.pdb(prmtop, crd=NULL, inds=NULL, inds.crd=inds, ncore=NULL, ...)

# S3 method for default
as.pdb(pdb=NULL, xyz=NULL, type=NULL, resno=NULL,
                   resid=NULL, eleno=NULL, elety=NULL, chain=NULL, 
                   insert=NULL, alt=NULL, o=NULL, b=NULL, segid=NULL, 
                   elesy=NULL, charge=NULL, verbose=TRUE, ...)

Arguments

...	arguments passed to and from functions.
mol	a list object of type "mol2" (obtained with read.mol2).
prmtop	a list object of type "prmtop" (obtained with read.prmtop).
crd	a list object of type "crd" (obtained with read.crd.amber).
inds	a list object of type "select" as obtained from atom.select. The indices points to which atoms in the PRMTOP object to convert.
inds.crd	same as the ‘inds’ argument, but pointing to the atoms in CRD object to convert. By default, this argument equals to ‘inds’, assuming the same number and sequence of atoms in the PRMTOP and CRD objects.
ncore	number of CPU cores used to do the calculation. ncore>1 requires package ‘parallel’ installed.
pdb	an object of class ‘pdb’ as obtained from read.pdb.
xyz	a numeric vector/matrix of Cartesian coordinates. If provided, the number of atoms in the new PDB object will be set to ncol(as.xyz(xyz))/3 (see as.xyz). If xyz is not provided the number of atoms will be based on the length of eleno, resno, or resid (in that order).
type	a character vector of record types, i.e. "ATOM" or "HETATM", with length equal to ncol(as.xyz(xyz))/3. Alternatively, a single element character vector can be provided which will be repeated to match the number of atoms.
resno	a numeric vector of residue numbers of length equal to ncol(as.xyz(xyz))/3.
resid	a character vector of residue types/ids of length equal to ncol(as.xyz(xyz))/3. Alternatively, a single element character vector can be provided which will be repeated to match the number of atoms.
eleno	a numeric vector of element/atom numbers of length equal to ncol(as.xyz(xyz))/3.
elety	a character vector of element/atom types of length equal to ncol(as.xyz(xyz))/3. Alternatively, a single element character vector can be provided which will be repeated to match the number of atoms.
chain	a character vector of chain identifiers with length equal to ncol(as.xyz(xyz))/3. Alternatively, a single element character vector can be provided which will be repeated to match the number of atoms.
insert	a character vector of insertion code with length equal to ncol(as.xyz(xyz))/3.
alt	a character vector of alternate record with length equal to ncol(as.xyz(xyz))/3.
o	a numeric vector of occupancy values of length equal to ncol(as.xyz(xyz))/3. Alternatively, a single element numeric vector can be provided which will be repeated for to match the number of atoms.
b	a numeric vector of B-factors of length equal to ncol(as.xyz(xyz))/3. Alternatively, a single element numeric vector can be provided which will be repeated to match the number of atoms.
segid	a character vector of segment id of length equal to ncol(as.xyz(xyz))/3. Alternatively, a single element character vector can be provided which will be repeated to match the number of atoms.
elesy	a character vector of element symbol of length equal to ncol(as.xyz(xyz))/3. Alternatively, a single element character vector can be provided which will be repeated to match the number of atoms.
charge	a numeric vector of atomic charge of length equal to ncol(as.xyz(xyz))/3.
verbose	logical, if TRUE details of the PDB generation process is printed to screen.

Details

This function converts Tripos Mol2 format, Amber formatted parameter/topology (PRMTOP) and coordinate objects, and vector data to a PDB object.

While as.pdb.mol2 and as.pdb.prmtop converts specific objects to a PDB object, as.pdb.default provides basic functionality to convert raw data such as vectors of e.g. residue numbers, residue identifiers, Cartesian coordinates, etc to a PDB object. When pdb is provided the returned PDB object is built from the input object with fields replaced by any input vector arguments. e.g. as.pdb(pdb, xyz=crd) will return the same PDB object, with only the Cartesian coordinates changed to crd.

Value

Returns a list of class "pdb" with the following components:

atom

a data.frame containing all atomic coordinate ATOM data, with a row per ATOM and a column per record type. See below for details of the record type naming convention (useful for accessing columns).

xyz

a numeric matrix of ATOM coordinate data of class xyz.

calpha

logical vector with length equal to nrow(atom) with TRUE values indicating a C-alpha “elety”.

call

the matched call.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696. http://ambermd.org/FileFormats.php

Author

Lars Skjaerven

See also

read.crd, read.ncdf, atom.select, read.pdb

Examples

## Vector(s) to PDB object
pdb <- as.pdb(resno=1:6, elety="CA", resid="ALA", chain="A")
#> 
#>  Summary of PDB generation:
#>  .. number of atoms in PDB determined by 'resno'
#> 
#>  .. 00000006 atom(s) from 'string' selection 
#>  .. 00000006 atom(s) in final combined selection 
#> 
#>  .. number of atoms in PDB:  6 
#>  .. number of calphas in PDB: 6 
#>  .. number of residues in PDB: 6 
#> 
pdb
#> 
#>  Call:  as.pdb.default(resno = 1:6, resid = "ALA", elety = "CA", chain = "A")
#> 
#>    Total Models#: 1
#>      Total Atoms#: 6,  XYZs#: 18  Chains#: 1  (values: A)
#> 
#>      Protein Atoms#: 6  (residues/Calpha atoms#: 6)
#>      Nucleic acid Atoms#: 0  (residues/phosphate atoms#: 0)
#> 
#>      Non-protein/nucleic Atoms#: 0  (residues: 0)
#>      Non-protein/nucleic resid values: [ none ]
#> 
#>    Protein sequence:
#>       AAAAAA
#> 
#> + attr: atom, xyz, calpha, call

if (FALSE) {
## Read a PRMTOP file
prmtop <- read.prmtop(system.file("examples/crambin.prmtop", package="bio3d"))

## Read Amber coordinates
crds <- read.crd(system.file("examples/crambin.inpcrd", package="bio3d"))

## Atom selection
ca.inds <- atom.select(prmtop, "calpha")

## Convert to PDB format
pdb <- as.pdb(prmtop, crds, inds=ca.inds)


## Read a single entry MOL2 file
## (returns a single object)
mol <- read.mol2( system.file("examples/aspirin.mol2", package="bio3d") )

## Convert to PDB
pdb <- as.pdb(mol)
}