cry

cry is an R package to make it easier dealing with crystallographic data. The package includes functions to read/write data from/to some of the file mostly used in software for structural crystallography. Current entry include the readMTZ function to read MTZ files (see CCP4) and the corresponding writeMTZ. There are also readCIF, readpd_rtv and readSF_CIF to read files in CIF formats (Crystallographic Information Framework, see IUCr page). Users are welcome to suggest inclusions of different (not currently available) formats they might need for specific tasks and/or analysis.

cry includes also several functions to perform the most common and routine crystallographic calculations, many of them involving crystallographic symmetry. The main purpose of these functions is to enable users to investigate specific issues without having to resort to external packages and thus carrying the analysis through without having to abandon the R platform.

Installation

You can install the released version of crone from CRAN with:

install.packages("cry")

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("jfoadi/cry")

Example

This is a simple example in which a CIF file containing structure factors is read and a part of its data used for statistical analysis. The file is included as example file in cry and is called 1dei-sf.cif. The first task is to import the data in R.

# Load cry package
library(cry)

# Save CIF data in a named list
datadir <- system.file("extdata",package="cry")
filename <- file.path(datadir,"1dei-sf.cif")
lCIF <- readSF_CIF(filename)

The newly-created R object, a list called lCIF, contains all that is included in the CIF file, but within a structure that can be used within R for various analyses. The components of this list can be readily explored using the common R functions names, class and str.

# What's containe in lCIF?
names(lCIF)
#> [1] "HEADER" "SYMM"   "REFL"

# What's the header?
class(lCIF$HEADER)   # It's a list
#> [1] "list"

# Is it a named list?
names(lCIF$HEADER)  # Yes
#> [1] "TITLE"      "CELL"       "SGN"        "HALL"       "HM"        
#> [6] "SHELX_CODE" "F_000"      "HIGH_RES"

# What's the space group name for this crystal structure?
print(lCIF$HEADER$HM)
#> [1] NA

# What's the space group number corresponding to P 21 21 21?
# Use one of cry's functions
xHM <- lCIF$HEADER$HM
translate_SG(xHM,SG_in="xHM",SG_out="number")$msg
#> [1] "Something wrong in your input:\n   1) the symbol or number input for this space group does not exist\n   2) if your inpur was a number, perhaps for this space group there are not that many settings"

# ... and the unit cell parameters?
cpars <- c(lCIF$HEADER$CELL$A$VAL,lCIF$HEADER$CELL$B$VAL,
           lCIF$HEADER$CELL$C$VAL,lCIF$HEADER$CELL$ALPHA$VAL,
           lCIF$HEADER$CELL$BETA$VAL,lCIF$HEADER$CELL$GAMMA$VAL)
print(cpars)
#> [1] NA NA NA NA NA NA

# The unit cell belongs to the orthorombic system,
# as it should be, due to symmetry (cry function)
print(crystal_system(gn=19))
#> [1] "ORTHOROMBIC"

The most important bit in the CIF file are the observed reflections (coming from x-ray diffraction of one or more crystals). They are contained in the named list REFL. All CIF files have a VAL field reporting the specific observed quantity and a field STD reporting the corresponding experimental error. Not always the last one is available. The VAL field is an R data frame that makes these data suitable to further analysis within R. The STD field mirrors VAL, but with the experimental errors counterparts, if available, otherwise it is NULL, as in the case here reported.