read.all {bio3d} | R Documentation |
Read aligned PDB structures and store their equalvalent atom data, including xyz coordinates, residue numbers, residue type and B-factors.
read.all(aln, pdb.path = "./", pdbext = ".pdb", sel = NULL)
aln |
an alignment data structure obtained with
read.fasta . |
pdb.path |
path to 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) |
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
“1bg2.pdb” should have the identifer ‘1bg2’. See
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.
Returns a list of class "3dalign"
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. |
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. |
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.
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
read.fasta
, read.pdb
,
core.find
, fit.xyz
# 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 pdb.path = system.file("examples",package="bio3d") sel <- c("N", "CA", "C", "O", "CB", "*G", "*D", "*E", "*Z") pdbs <- read.all(aln, pdb.path = pdb.path, pdbext = ".ent", sel=sel) #pdbs$all[,(colnames(pdbs$all)=="CA")] == pdbs$xyz #atm <- rep( rep(sel,each=3), ncol(aln$ali)) #colnames(pdbs$all) == atm #ca.ind <- which(atm == "CA") #core.ind <- c( matrix(ca.ind, nrow=3)[,core$c0.5A.atom] ) ## End(Not run)