R: Read CRD File

read.crd.charmm {bio3d} | R Documentation

## 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:
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())

    ## End(Not run)

[Package bio3d version 2.4-0 Index]