R: Sequence Alignment of PDB Files

pdbaln {bio3d} | R Documentation

## Sequence Alignment of PDB Files

### Description

Create multiple sequences alignments from a list of PDB files returning aligned sequence and structure records.

### Usage

    pdbaln(files, fit = FALSE, pqr = FALSE, ncore = 1,
           nseg.scale = 1, progress = NULL, ...)

### Arguments

`files` | a character vector of PDB file names. Alternatively, a list of `pdb` objects can be provided.
`fit` | logical, if TRUE coordinate superposition is performed on the input structures.
`pqr` | logical, if TRUE the input structures are assumed to be in PQR format.
`ncore` | number of CPU cores used to do the calculation. `ncore>1` requires package ‘parallel’ installed.
`nseg.scale` | split input data into specified number of segments prior to running multiple core calculation. See `fit.xyz`.
`progress` | progress bar for use with shiny web app.
`...` | extra arguments passed to `seqaln` function.

### Details

This wrapper function calls the underlying functions `read.pdb`, `pdbseq`, `seqaln` and `read.fasta.pdb` returning a list of class `"pdbs"` similar to that returned by `read.fasta.pdb`.

As these steps are often error prone it is recomended for most cases that the individual underlying functions are called in sequence with checks made on the valadity of their respective outputs to ensure sensible results.

### Value

Returns a list of class `"pdbs"` with the following five components:

`xyz` | numeric matrix of aligned C-alpha coordinates.
`resno` | character matrix of aligned residue numbers.
`b` | numeric matrix of aligned B-factor values.
`chain` | character matrix of aligned chain identifiers.
`id` | character vector of PDB sequence/structure names.
`ali` | character matrix of aligned sequences.
`call` | the matched call.

### Note

See recommendation in details section above.

### Author(s)

Barry Grant

### References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

### See Also

`read.pdb`, `pdbseq`, `seqaln`, `read.fasta`,`read.fasta.pdb`, `core.find`, `fit.xyz`, `read.all`, `pymol.pdbs`

### Examples

    ## Not run:
    ##- Align PDBs (from vector of filenames)
    #files <- get.pdb(c("4q21","5p21"), URLonly=TRUE)
    files <- get.pdb(c("4q21","5p21"), path=tempdir(), overwrite=TRUE)
    pdbaln(files)

    ##- Align PDBs (from list of existing PDB objects)
    pdblist <- list(read.pdb(files[1]), read.pdb(files[2]))
    pdbaln(pdblist)

    ## End(Not run)

[Package bio3d version 2.4-0 Index]