bio3d (version 2.3-4)

read.crd.charmm: Read CRD File

Description

Read a CHARMM CARD (CRD) coordinate file.

Usage

# S3 method for charmm
read.crd(file, ext = TRUE, verbose = TRUE, ...)

Arguments

file

the name of the CRD file to be read.

ext

logical, if TRUE assume expanded CRD format.

verbose

print details of the reading process.

…

arguments going nowhere.

Value

Returns a list with the following components:

atom

a character matrix containing all atomic coordinate 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 vector of coordinate data.

calpha

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

Details

See the function read.pdb for more details.

References

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

For a description of CHARMM CARD (CRD) format see: http://www.charmmtutorial.org/index.php/CHARMM:The_Basics.

See Also

write.crd, read.pdb, atom.select, write.pdb, read.dcd, read.fasta.pdb, read.fasta

Examples

# NOT RUN {
 pdb <- read.pdb("1bg2")
 crdfile <- paste(tempfile(), '.crd', sep='')
 write.crd(pdb, file=crdfile)
 crd <- read.crd(crdfile, ext=FALSE)
 ca.inds <- which(crd$calpha)
 crd$atom[ca.inds[1:20],c("x","y","z")]
# write.pdb(crd, file=tempfile())
# }