Read a Protein Data Bank (mmCIF) coordinate file.
read.cif(file, maxlines = -1, multi = FALSE, rm.insert = FALSE, rm.alt = TRUE, verbose = TRUE)
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.
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.
logical, if TRUE multiple ATOM records are read for all models in multi-model files and their coordinates returned.
logical, if TRUE PDB insert records are ignored.
logical, if TRUE PDB alternate records are ignored.
print details of the reading process.
The current version of
read.cif reads only ATOM/HETATM records
and creates a
pdb object of the data.
read.pdb for more info.
Returns a list of class
"pdb" with the following components:
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).
a numeric matrix of class
"xyz" containing the
ATOM and HETATM coordinate data.
logical vector with length equal to
with TRUE values indicating a C-alpha “elety”.
the matched call.
Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
## Read a mmCIF file from the RCSB online database # cif <- read.cif("1hel")