Nothing
#
# This file is part of the cry package
#
# Functions connected to reflections data.
#' Reads and output a CIF file
#'
#' @param filename A character string. The path to a valid CIF file.
#' @param message A logical variable. If TRUE (default) the function prints
#' a message highlighting what is included in the cif file.
#' @return A named list. Each name correspond to a valid field in the cif.
#'
#' @examples
#' datadir <- system.file("extdata",package="cry")
#' filename <- file.path(datadir,"AMS_DATA.cif")
#' lCIF <- readCIF(filename)
#' print(names(lCIF))
#' print(lCIF$INTRO$CELL)
#' print(lCIF$INTRO$HALL)
#' print(lCIF$INTRO$HM)
#' print(lCIF$SYMM)
#'
#' @export
readCIF <- function(filename, message=FALSE){
f <- file(filename)
lcif <- readLines(f,warn=FALSE)
l_list <- grep("loop_",lcif)
l_list1 <- append(l_list,length(lcif))
mat<-zoo::rollapply(l_list1, 2,stack)
ch <- apply(mat, 1, function(x) lcif[(x[1]+1):(x[2]-1)])
crystal_summary <- lapply(ch, ucheck, pattern="_publ_author_name")
symmetry <- lapply(ch, ucheck, pattern="_space_group_symop_operation")
reflection <- lapply(ch, ucheck, pattern="_refln_index_h")
coordinates <- lapply(ch, ucheck, pattern="_atom_site_fract_x")
anisotropy <- lapply(ch, ucheck, pattern="_atom_site_aniso_label")
symbol <- lapply(ch, ucheck, pattern="_atom_type_symbol")
geom_angle <- lapply(ch, ucheck, pattern="geom_angle_atom_site_label_1")
geom_distance <- lapply(ch, ucheck, pattern="_geom_bond_atom_site_label_1")
geom_hbond <- lapply(ch, ucheck, pattern="geom_hbond_atom_site_label_D")
geom_torsion <- lapply(ch, ucheck, pattern="geom_torsion_atom_site_label_1")
intro <- r_summ(lcif)
symm <- ansnull(symmetry)
reflections1 <- r_reflections1(lcif)
reflections2 <- if (is.na(nanona(reflection)) == FALSE) r_reflections2(nanona(reflection)) else NA
reflections <- r_reflcs(reflections1,reflections2)
coordinate <- if (is.na(nanona(coordinates)) == FALSE) clean(r_spositions(nanona(coordinates))) else NULL
#coordinate <- r_positions(ansnull(coordinates))
anisotropies <- if (is.na(nanona(anisotropy)) == FALSE) clean(r_saniso(nanona(anisotropy))) else NULL
#anisotropies <- r_aniso(ansnull(anisotropy))
symbolics <- ansnull(symbol)
angle <- if (is.na(nanona(geom_angle)) == FALSE) clean(r_angle(nanona(geom_angle))) else NULL
#angle <- r_angle(ansnull(geom_angle))
distance <- if (is.na(nanona(geom_distance)) == FALSE) clean(r_dist(nanona(geom_distance))) else NULL
#distance <- r_dist(ansnull(geom_distance))
hbond <- if (is.na(nanona(geom_hbond)) == FALSE) clean(r_hbond(nanona(geom_hbond))) else NULL
#hbond <- r_hbond(ansnull(geom_hbond))
torsion <- if (is.na(nanona(geom_torsion)) == FALSE) clean(r_torsion(nanona(geom_torsion))) else NULL
#torsion <- r_torsion(ansnull(geom_torsion))
#CIF=list(INTRO=intro,SYMM=symm,COOR=coordinate,ANISO=anisotropies)
geome = list(ANGLE=angle,DIST=distance,HBOND=hbond,TORSION=torsion)
CIF = list(HEADER=intro,SYMM=symm,REFL=reflections,COOR=coordinate,ANISO=anisotropies,SYMB=symbolics,GEOM=geome)
close(f)
if (message) {
if (!is.null(reflections)){
n <- length(reflections$F_squared_meas)
f <- as.numeric(reflections$F_squared_meas)
msg <- c("\n")
msg1 <- c(msg,sprintf("File %s read successfully.\n",filename))
msg2 <- sprintf("There are %d reflections in this file.\n",n)
msg3 <- c(msg,"Here is a summary of the observations:\n")
msg4 <- c("\n")
out <- c(msg,msg1,msg2,msg3,msg4)
cat(out)
print(summary(f))
} else {
anum <- nrow(coordinate$VAL)
msg <- c("\n")
msg <- c(msg,sprintf("File %s read successfully.\n",filename))
msg1 <- sprintf("The file does not contain reflection datablock,
please refer corresponding reflection file (fcf or hkl).\n")
msg2 <- sprintf("There are %d atoms in the molecule.\n",anum)
out <- c(msg,msg1,msg2)
cat(out)
}
}
return(CIF)
}
### accessory functions ####
stack<-function(x){
j <- c(x[1],x[2])
return(j)
}
ucheck <- function(x,pattern){
r <- unlist(x)
if (length(grep(pattern,r))>0){
piece <- r
} else
{ piece <- NA
return(piece)
}
}
ansnull <- function(x){
if (all(is.na(x)) == TRUE){
out <- NULL
} else
{ out <- x[!is.na(x)]
return(out)
}
}
nanona <- function(x){
if (all(is.na(x)) == TRUE){
out <- NA
} else
{ out <- x[!is.na(x)]
return(out)
}
}
recheck <- function(r1){
r2 <- gsub("[:):]","",gsub("[:(:]",",",r1))
r3 <- as.numeric((strsplit(r2, ",")[[1]])[1])
return(r3)
}
check <- function(pattern,word){
r <- grep(pattern, word, value = TRUE)
r1 <- if(length(r) > 0) (strsplit(r, "\\s+")[[1]])[2] else NA
r2 <- if (length(grep("[:(:]",r1,value = TRUE)>0) == TRUE) recheck(r1) else r1
return(r2)
}
check1 <- function(pattern,word){
r <- grep(pattern, word, value = TRUE)
r1 <- if(length(r) > 0) (strsplit(r, "'")[[1]])[2] else NA
return(r1)
}
clean1 <- function(x){
if (all(is.na(x)) == TRUE){
out <- NULL
} else
{ out <- nc_type(as.data.frame(x))
return(out)
}
}
clean <- function(x){
co1 <- data.frame(gsub ("[()]","",as.matrix(x),perl=T),stringsAsFactors = FALSE)
ref <- data.frame(gsub("(?<!\\))(?:\\w+|[^()])(?!\\))","",as.matrix(x),perl=T))
ref1 <- data.frame(gsub("[()]","",as.matrix(ref),perl=T),stringsAsFactors = FALSE)
ref1[ref1==""]<-NA
ref2 <- clean1(ref1)
col1 <- nc_type(co1)
return(list(VAL=col1,STD=ref2))
}
reap1 <- function(x){
if (all(is.na(x)) == TRUE){
out <- NULL
} else
{ out <- as.numeric(x)
return(out)
}
}
reap <- function(pattern,word){
r <- grep(pattern, word, value = TRUE)
r1 <- if(length(r) > 0) (strsplit(r, "\\s+")[[1]])[2] else NA
v <- as.numeric(gsub ("[()]","",as.matrix(r1),perl=T))
s <- gsub("(?<!\\))(?:\\w+|[^()])(?!\\))","",as.matrix(r1),perl=T)
s1 <- gsub("[()]","",as.matrix(s),perl=T)
s2 <- reap1(s1)
return(list(VAL=v,STD=s2))
}
nc_type <- function(data){
count <- as.numeric(ncol(data))
if (isTRUE(count > 2)) {
data[] <- lapply(data, function(x) numas(x))
out <- data
} else if (count == 2){
l1_data <- list(data$VAL)
l_1 <- lapply(l1_data[[1]], function(x) numas(x))
l2_data <- list(data$KEY)
l2 <- c(gsub("\\[|\\]" ,"",l2_data[[1]]))
names(l_1) <- c(l2)
out <- l_1
return(out)
}
}
numas <- function(x){
data <- x
out <- (suppressWarnings(as.numeric(data)))
if (all(is.na(out))== FALSE) {
out1 <- out
} else {
out1 <- as.character(data)
}
return(out1)
}
r_reflcs <- function(x,y){
if (all(is.na(x))== FALSE) {
out <- x
} else {
if (all(is.na(y)) == FALSE) {
out <- y
} else {
out <- NULL
}
return(out)
}
}
r_reflections1 <- function (x){
data <- unlist(x)
cu <- grep("_shelx_hkl_file", data)
l <- length(cu)
if (l > 0) {
sc <- grep(";", data)
sc1 <- sc[sc > cu]
data <- data[sc1[1]:sc1[2]]
data <- data[data !=";"]
data1 <- data[!grepl('_', data)]
lst <- lapply(split(data1, cumsum(grepl("^V", data1))),
function(x) read.table(text=x))
names(lst) <- NULL
res <- do.call(`cbind`, lst)
colnames(res) <- c("index_h","index_k","index_l","F_squared_meas","F_squared_sigma")
res <- res
} else {
res <- NA
return(res)
}
}
r_reflections2 <- function (x){
data <- unlist(x)
nskip <- length((grep("_refln",data)))
lst <- lapply(split(data, cumsum(grepl("^V", data))),
function(x) read.table(text=x,skip=nskip))
names(lst) <- NULL
res <- do.call(`cbind`, lst)
l_l <- c(grep("_refln",data,value=TRUE))
l_l <- c(gsub(" ","",l_l))
colnames(res) <- c(gsub("_refln_","",l_l))
return(res)
}
r_spositions <- function (x){
data <- unlist(x)
l_l <- c(grep("_atom",data,value=TRUE))
data1 <- data[length(l_l)+1:length(data)]
data1 <- data1[!is.na(data1)]
cu <- grep("^\\_",data1)
if ((length(cu)) >0){
data2 <- data1[1:cu[1]-1]
} else {
data2 <- data1
}
#nskip <- length((grep("_atom",data)))
lst <- lapply(split(data2, cumsum(grepl("^V", data2))),
function(x) read.table(text=x))
names(lst) <- NULL
res <- do.call(`cbind`, lst)
colnames(res) <- c(gsub("_atom_site_","",l_l))
return(res)
}
r_saniso <- function(x){
data <- unlist(x)
l_l <- c(grep("_atom",data,value=TRUE))
data1 <- data[length(l_l)+1:length(data)]
data1 <- data1[!is.na(data1)]
cu <- grep("^\\_",data1)
if ((length(cu)) >0){
data2 <- data1[1:cu[1]-1]
} else {
data2 <- data1
}
#nskip <- length((grep("_atom",data)))
lst <- lapply(split(data2, cumsum(grepl("^V", data2))),
function(x) read.table(text=x))
names(lst) <- NULL
res <- do.call(`cbind`, lst)
colnames(res) <- c(gsub("_atom_site_aniso_","",l_l))
return(res)
}
r_angle <- function(x){
data <- unlist(x)
l_l <- c(grep("_geom_angle",data,value=TRUE))
data1 <- data[length(l_l)+1:length(data)]
data1 <- data1[!is.na(data1)]
cu <- grep("^\\_",data1)
if ((length(cu)) >0){
data2 <- data1[1:cu[1]-1]
} else {
data2 <- data1
}
#nskip <- length((grep("_geom_angle",data)))
lst <- lapply(split(data2, cumsum(grepl("^V", data2))),
function(x) read.table(text=x))
names(lst) <- NULL
res <- do.call(`cbind`, lst)
colnames(res) <- c(gsub("_geom_angle_","",l_l))
return(res)
}
r_dist <- function(x){
data <- unlist(x)
l_l <- c(grep("_geom_bond",data,value=TRUE))
data1 <- data[length(l_l)+1:length(data)]
data1 <- data1[!is.na(data1)]
cu <- grep("^\\_",data1)
if ((length(cu)) >0){
data2 <- data1[1:cu[1]-1]
} else {
data2 <- data1
}
#nskip <- length((grep("_geom_bond",data)))
lst <- lapply(split(data2, cumsum(grepl("^V", data2))),
function(x) read.table(text=x))
names(lst) <- NULL
res <- do.call(`cbind`, lst)
colnames(res) <- c(gsub("_geom_bond_","",l_l))
return(res)
}
r_hbond <- function(x){
data <- unlist(x)
l_l <- c(grep("_geom_hbond",data,value=TRUE))
data1 <- data[length(l_l)+1:length(data)]
data1 <- data1[!is.na(data1)]
cu <- grep("^\\_",data1)
if ((length(cu)) >0){
data2 <- data1[1:cu[1]-1]
} else {
data2 <- data1
}
#nskip <- length((grep("_geom_hbond",data)))
lst <- lapply(split(data2, cumsum(grepl("^V", data2))),
function(x) read.table(text=x))
names(lst) <- NULL
res <- do.call(`cbind`, lst)
colnames(res) <- c(gsub("_geom_hbond_","",l_l))
return(res)
}
r_torsion <- function(x){
data <- unlist(x)
l_l <- c(grep("_geom_torsion",data,value=TRUE))
data1 <- data[length(l_l)+1:length(data)]
data1 <- data1[!is.na(data1)]
cu <- grep("^\\_",data1)
if ((length(cu)) >0){
data2 <- data1[1:cu[1]-1]
} else {
data2 <- data1
}
#nskip <- length((grep("_geom_torsion",data)))
lst <- lapply(split(data2, cumsum(grepl("^V", data2))),
function(x) read.table(text=x))
names(lst) <- NULL
res <- do.call(`cbind`, lst)
colnames(res) <- c(gsub("_geom_torsion_","",l_l))
return(res)
}
r_summ <- function(x){
data <- unlist(x)
formula <- check1("_chemical_formula_sum",data)
a <- reap("_cell_length_a",data)
b <- reap("_cell_length_b",data)
c <- reap("_cell_length_c",data)
al <- reap("_cell_angle_alpha",data)
be <- reap("_cell_angle_beta",data)
ga <- reap("_cell_angle_gamma",data)
v <- reap("_cell_volume",data)
den <- reap("_exptl_crystal_density_diffrn",data)
c_sy <- check("_symmetry_cell_setting",data)
sg_n <- as.numeric(check("_space_group_IT_number",data))
sg_hall<- check1("_symmetry_space_group_name_Hall",data)
sg_HM <- check1("_symmetry_space_group_name_H-M",data)
cell <- list(A=a,B=b,C=c,ALPHA=al,BETA=be,GAMMA=ga)
#sg <- list(c_sy,sg_n,sg_hall,sg_HM)
#prop <- list(v,den)
summ_c <- list(FORMULA=formula,CELL=cell,VOL=v,DEN=den,CrysSys=c_sy,SGN=sg_n,HALL=sg_hall,HM=sg_HM)
return(summ_c)
}
r_msg <- function(x){
data <- unlist(x)
a <- reap("_cell_length_a",data)
b <- reap("_cell_length_b",data)
c <- reap("_cell_length_c",data)
al <- reap("_cell_angle_alpha",data)
be <- reap("_cell_angle_beta",data)
ga <- reap("_cell_angle_gamma",data)
cell <- c(a,b,c,al,be,ga)
return(cell)
}
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