Usage
read.cif(file, maxlines = -1, multi = FALSE, rm.insert = FALSE, rm.alt = TRUE, verbose = TRUE)
Arguments
- file
- a single element character vector containing the name of
the mmCIF file to be read, or the four letter PDB identifier for
online file access.
- maxlines
- the maximum number of lines to read before giving up
with large files. By default if will read up to the end of input on
the connection.
- multi
- logical, if TRUE multiple ATOM records are read for all
models in multi-model files and their coordinates returned.
- rm.insert
- logical, if TRUE PDB insert records are ignored.
- rm.alt
- logical, if TRUE PDB alternate records are ignored.
- verbose
- print details of the reading process.
Description
Read a Protein Data Bank (mmCIF) coordinate file.
Details
The current version of read.cif reads only ATOM/HETATM records
and creates a pdb object of the data.
See read.pdb for more info.
Value
Returns a list of class "pdb" with the following components:
- atom
- a data.frame containing all atomic coordinate ATOM and
HETATM data, with a row per ATOM/HETATM and a column per record type.
See below for details of the record type naming convention (useful for
accessing columns).
- xyz
- a numeric matrix of class
"xyz" containing the
ATOM and HETATM coordinate data.
- calpha
- logical vector with length equal to
nrow(atom)
with TRUE values indicating a C-alpha “elety”.
- call
- the matched call.
References
Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
Examples
## Read a mmCIF file from the RCSB online database
# cif <- read.cif("1hel")