Read CRD File
Read a CHARMM CARD (CRD) coordinate file.
## S3 method for class 'charmm' read.crd(file, ext = TRUE, verbose = TRUE, ...)
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. |
See the function read.pdb for more details.
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 |
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.
Barry Grant
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.
## 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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.