read.crd.charmm: Read CRD File

In bio3d: Biological Structure Analysis

Read CRD File

Description

Read a CHARMM CARD (CRD) coordinate file.

Usage

## S3 method for class '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.

Details

See the function read.pdb for more details.

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”.

Note

Similar to the output of read.pdb, the column names of atom can be used as a convenient means of data access, namely: Atom serial number “eleno”, Atom type “elety”, Alternate location indicator “alt”, Residue name “resid”, Residue sequence number “resno”, Code for insertion of residues “insert”, Orthogonal coordinates “x”, Orthogonal coordinates “y”, Orthogonal coordinates “z”, Weighting factor “b”. See examples for further details.

Author(s)

Barry Grant

References

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

For a description of CHARMM CARD (CRD) format see:
https://academiccharmm.org/documentation/version/c49b1/io#Coordinate.

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())

## End(Not run)

bio3d documentation built on Oct. 30, 2024, 1:08 a.m.