read.all {bio3d} | R Documentation

## Read Aligned Structure Data

### Description

Read aligned PDB structures and store their equalvalent atom data, including xyz coordinates, residue numbers, residue type and B-factors.

### Usage

    read.all(aln, prefix = "", pdbext = "", sel = NULL, rm.wat=TRUE, rm.ligand=FALSE,
             compact = TRUE, ncore = NULL, ...)

### Arguments

`aln` | an alignment data structure obtained with `read.fasta`.
`prefix` | prefix to aln$id to locate PDB files.
`pdbext` | the file name extention of the PDB files.
`sel` | a selection string detailing the atom type data to store (see function store.atom)
`rm.wat` | logical, if TRUE water atoms are removed.
`rm.ligand` | logical, if TRUE ligand atoms are removed.
`compact` | logical, if TRUE the number of atoms stored for each aligned residue varies according to the amino acid type. If FALSE, the constant maximum possible number of atoms are stored for all aligned residues.
`ncore` | number of CPU cores used to do the calculation. By default (`ncore=NULL`) use all detected CPU cores.
`...` | other parameters for `read.pdb`.

### Details

The input `aln`, produced with `read.fasta`, must have identifers (i.e. sequence names) that match the PDB file names. For example the sequence corresponding to the structure file “mypdbdir/1bg2.pdb” should have the identifer ‘mypdbdir/1bg2.pdb’ or ‘1bg2’ if input ‘prefix’ and ‘pdbext’ equal ‘mypdbdir/’ and ‘pdb’. See the examples below.

Sequence miss-matches will generate errors. Thus, care should be taken to ensure that the sequences in the alignment match the sequences in their associated PDB files.

### 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.
`resid` | character matrix of aligned 3-letter residue names.
`all` | numeric matrix of aligned equalvelent atom coordinates.
`all.elety` | numeric matrix of aligned atom element types.
`all.resid` | numeric matrix of aligned three-letter residue codes.
`all.resno` | numeric matrix of aligned residue numbers.
`all.grpby` | numeric vector indicating the group of atoms belonging to the same aligned residue.
`all.hetatm` | a list of ‘pdb’ objects for non-protein atoms.

### Note

This function is still in development and is NOT part of the offical bio3d package.

The sequence character ‘X’ is useful for masking unusual or unknown residues, as it can match any other residue type.

### Author(s)

Barry Grant

### References

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

### See Also

`read.fasta`, `read.pdb`, `core.find`, `fit.xyz`

### Examples

    # still working on speeding this guy up
    ## Not run:
    ## Read sequence alignment
    file <- system.file("examples/kif1a.fa",package="bio3d")
    aln  <- read.fasta(file)

    ## Read aligned PDBs storing all data for 'sel'
    sel <- c("N", "CA", "C", "O", "CB", "*G", "*D",  "*E", "*Z")
    pdbs <- read.all(aln, sel=sel)

    atm <- colnames(pdbs$all)
    ca.ind  <- which(atm == "CA")
    core <- core.find(pdbs)
    core.ind <- c( matrix(ca.ind, nrow=3)[,core$c0.5A.atom] )

    ## Fit structures
    nxyz <- fit.xyz(pdbs$all[1,], pdbs$all,
                   fixed.inds  = core.ind,
                   mobile.inds = core.ind)

    ngap.col <- gap.inspect(nxyz)

    #npc.xray <- pca.xyz(nxyz[ ,ngap.col$f.inds])

    #a <- mktrj.pca(npc.xray, pc=1, file="pc1-all.pdb",
    #               elety=pdbs$all.elety[1,unique( ceiling(ngap.col$f.inds/3) )],
    #               resid=pdbs$all.resid[1,unique( ceiling(ngap.col$f.inds/3) )],
    #               resno=pdbs$all.resno[1,unique( ceiling(ngap.col$f.inds/3) )] )

    ## End(Not run)

[Package bio3d version 2.3-4 Index]