write.crd: Write CRD File

In bio3d: Biological Structure Analysis

Write CRD File

Description

Write a CHARMM CARD (CRD) coordinate file.

Usage

write.crd(pdb = NULL, xyz = pdb$xyz, resno = NULL, resid = NULL, 
   eleno = NULL, elety = NULL, segid = NULL, resno2 = NULL, b = NULL, 
   verbose = FALSE, file = "R.crd")

Arguments

pdb	a structure object obtained from read.pdb or read.crd.
xyz	Cartesian coordinates as a vector or 3xN matrix.
resno	vector of residue numbers of length equal to length(xyz)/3.
resid	vector of residue types/ids of length equal to length(xyz)/3.
eleno	vector of element/atom numbers of length equal to length(xyz)/3.
elety	vector of element/atom types of length equal to length(xyz)/3.
segid	vector of segment identifiers with length equal to length(xyz)/3.
resno2	vector of alternate residue numbers of length equal to length(xyz)/3.
b	vector of weighting factors of length equal to length(xyz)/3.
verbose	logical, if TRUE progress details are printed.
file	the output file name.

Details

Only the xyz argument is strictly required. Other arguments assume a default poly-ALA C-alpha structure with a blank segid and B-factors equal to 0.00.

Value

Called for its effect.

Note

Check that resno and eleno do not exceed “9999”.

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

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

Examples

## Not run: 
# Read a PDB file
pdb <- read.pdb( "1bg2" )
summary(pdb)
# Convert to CHARMM format
new <- convert.pdb(pdb, type="charmm")
summary(new)
# Write a CRD file
write.crd(new, file="4charmm.crd")

## End(Not run)

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