bio3d (version 2.4-4)

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, ...)

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”.

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.

Author

Barry Grant

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:
https://www.charmm.org/wiki//index.php/CHARMM:The_Basics.

See Also

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

Examples

if (FALSE) {
 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())
}