#' Get a \code{mol_parameters} object for a named molecule.
#' @param name the name of the molecule.
#' @param ... arguments to pass to molecule definition function.
#' @export
get_mol_paras <- function(name, ...) {
get(paste("get_", tolower(name), "_paras", sep = ""))(...)
}
#' Return a character array of names that may be used with the
#' \code{get_mol_paras} function.
#' @return a character array of names.
#' @export
get_mol_names <- function() {
funs <- ls(getNamespace("spant"), all.names = TRUE)
funs <- funs[!funs %in% c("get_mol_paras", "get_acq_paras",
"get_1h_brain_basis_paras",
"get_1h_brain_basis_paras_v1",
"get_1h_brain_basis_paras_v2")]
sub("_paras", "", sub("get_", "", funs[grep("get_.*_paras", funs)]))
}
#' Generate a \code{mol_parameters} object for a simple spin system with one resonance.
#' @param name name of the molecule.
#' @param chem_shift chemical shift of the resonance (PPM).
#' @param nucleus nucleus (1H, 31P...).
#' @param scale_factor multiplicative scaling factor.
#' @param lw linewidth in Hz.
#' @param lg Lorentz-Gauss lineshape parameter (between 0 and 1).
#' @return mol_parameters object.
#' @export
get_uncoupled_mol <- function(name, chem_shift, nucleus, scale_factor, lw, lg) {
j_coupling_mat <- matrix(0, 1, 1)
spin_groups <- vector("list", length(chem_shift))
for (n in 1:length(chem_shift)) {
spin_group <- list(nucleus = nucleus[n], chem_shift = chem_shift[n],
j_coupling_mat = j_coupling_mat,
scale_factor = scale_factor[n], lw = lw[n], lg = lg[n])
spin_groups[[n]] <- spin_group
}
paras <- list(spin_groups = spin_groups, name = name)
class(paras) <- "mol_parameters"
paras
}
print.mol_parameters <- function(x, ...) {
cat(paste(c("Name : ", x$name, "\n")), sep = "")
cat(paste(c("Source : ", x$source, "\n")), sep = "")
cat(paste(c("Spin groups : ", length(x$spin_groups), "\n")), sep = "")
for (n in 1:length(x$spin_groups)) {
cat("\n")
cat(paste(c("Spin group ", n, "\n")), sep = "")
cat("------------\n")
cat(paste(c("Scaling factor : ", x$spin_groups[[n]]$scale_factor, "\n")), sep = "")
cat(paste(c("Linewidth (Hz) : ", x$spin_groups[[n]]$lw, "\n")), sep = "")
cat(paste(c("L/G lineshape : ", x$spin_groups[[n]]$lg, "\n\n")), sep = "")
print(data.frame(nucleus = x$spin_groups[[n]]$nucleus,
chem_shift = x$spin_groups[[n]]$chem_shift))
if (nrow(x$spin_groups[[n]]$j_coupling_mat) > 1) {
cat("\n")
cat("j-coupling matrix\n")
rownames(x$spin_groups[[n]]$j_coupling_mat) <- x$spin_groups[[n]]$chem_shift
colnames(x$spin_groups[[n]]$j_coupling_mat) <- x$spin_groups[[n]]$chem_shift
j_mat <- x$spin_groups[[n]]$j_coupling_ma
j_mat[upper.tri(j_mat, diag = TRUE)] <- NA
j_mat[j_mat == 0] <- NA
#j_mat <- t(j_mat)t
print(j_mat, na.print = "-")
}
}
}
get_m_cr_ch2_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
paras <- get_uncoupled_mol("-CrCH2", 3.913, "1H", -2, lw, lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras$source = source
paras
}
get_ala_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
nucleus <- rep("1H", 4)
chem_shift <- c(3.7746, 1.4667, 1.4667, 1.4667)
j_coupling_mat <- matrix(0, 4, 4)
j_coupling_mat[2,1] <- 7.234
j_coupling_mat[3,1] <- 7.234
j_coupling_mat[4,1] <- 7.234
j_coupling_mat[3,2] <- -14.366
j_coupling_mat[4,2] <- -14.366
j_coupling_mat[4,3] <- -14.366
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13: 129-153."
paras <- list(spin_groups = list(spin_group_a), name = "Ala", source = source)
class(paras) <- "mol_parameters"
paras
}
get_asc_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
nucleus <- rep("1H", 4)
chem_shift <- c(4.4965, 4.0072, 3.7469, 3.7194)
j_coupling_mat <- matrix(0, 4, 4)
j_coupling_mat[2,1] <- 2.055
j_coupling_mat[3,2] <- 5.78
j_coupling_mat[4,2] <- 7.373
j_coupling_mat[4,3] <- -11.585
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Detection of an antioxidant profile in the humain brain in vivo via
double editing with MEGA-PRESS. MRM. 2006; 56(6):1192-1199."
paras <- list(spin_groups = list(spin_group_a), name = "Asc", source = source)
class(paras) <- "mol_parameters"
paras
}
get_asp_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
nucleus <- rep("1H", 3)
chem_shift <- c(3.8914, 2.8011, 2.6533)
j_coupling_mat <- matrix(0, 3, 3)
j_coupling_mat[2,1] <- 3.647
j_coupling_mat[3,1] <- 9.107
j_coupling_mat[3,2] <- -17.426
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras <- list(spin_groups = list(spin_group_a), name = "Asp", source = source)
class(paras) <- "mol_parameters"
paras
}
get_cho_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
nucleus <- c("1H", "14N")
chem_shift <- c(3.185, 0)
j_coupling_mat <- matrix(0, 2, 2)
j_coupling_mat[2,1] <- 0.57
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 9,
lw = lw, lg = lg)
nucleus <- c("1H", "1H", "1H", "1H", "14N")
chem_shift <- c(4.054, 4.054, 3.501, 3.501, 0)
j_coupling_mat <- matrix(0, 5, 5)
j_coupling_mat[2,1] <- -14.1
j_coupling_mat[3,1] <- 3.14
j_coupling_mat[4,1] <- 6.979
j_coupling_mat[5,1] <- 2.572
j_coupling_mat[3,2] <- 7.011
j_coupling_mat[4,2] <- 3.168
j_coupling_mat[5,2] <- 2.681
j_coupling_mat[4,3] <- -14.07
spin_group_b <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Corrigendum: Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras <- list(spin_groups = list(spin_group_a, spin_group_b), name = "Cho",
source = source)
class(paras) <- "mol_parameters"
paras
}
get_cr_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
paras <- get_uncoupled_mol("Cr", 3.027, "1H", 3, lw, lg)
paras_b <- get_uncoupled_mol("Cr", 3.913, "1H", 2, lw, lg)
paras$spin_groups[[2]] <- paras_b$spin_groups[[1]]
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras$source = source
paras
}
get_cr_ch2_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
paras <- get_uncoupled_mol("CrCH2", 3.913, "1H", 2, lw, lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras$source = source
paras
}
get_cr_ch3_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
paras <- get_uncoupled_mol("CrCH3", 3.027, "1H", 3, lw, lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras$source = source
paras
}
get_gaba_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
nucleus <- rep("1H", 6)
chem_shift <- c(3.0128, 3.0128, 1.889, 1.889, 2.284, 2.284)
j_coupling_mat <- matrix(0, 6, 6)
j_coupling_mat[2,1] <- -12.021
j_coupling_mat[3,1] <- 5.372
j_coupling_mat[4,1] <- 7.127
j_coupling_mat[3,2] <- 10.578
j_coupling_mat[4,2] <- 6.982
j_coupling_mat[4,3] <- -13.121
j_coupling_mat[5,3] <- 7.755
j_coupling_mat[6,3] <- 7.432
j_coupling_mat[5,4] <- 6.173
j_coupling_mat[6,4] <- 7.933
j_coupling_mat[6,5] <- -10.744
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Corrigendum: Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13: 129-153."
paras <- list(spin_groups = list(spin_group_a), name = "GABA", source = source)
class(paras) <- "mol_parameters"
paras
}
get_gaba_rt_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
nucleus <- rep("1H", 6)
#chem_shift <- c(3.0128, 3.0128, 1.889, 1.889, 2.284, 2.284)
chem_shift <- c(3.005, 3.005, 1.889, 1.889, 2.284, 2.284)
j_coupling_mat <- matrix(0, 6, 6)
j_coupling_mat[2,1] <- -12.021
j_coupling_mat[3,1] <- 5.372
j_coupling_mat[4,1] <- 7.127
j_coupling_mat[3,2] <- 10.578
j_coupling_mat[4,2] <- 6.982
j_coupling_mat[4,3] <- -13.121
j_coupling_mat[5,3] <- 7.755
j_coupling_mat[6,3] <- 7.432
j_coupling_mat[5,4] <- 6.173
j_coupling_mat[6,4] <- 7.933
j_coupling_mat[6,5] <- -10.744
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153. Modified by MW for room temperature
phantom scans."
paras <- list(spin_groups = list(spin_group_a), name = "GABA", source = source)
class(paras) <- "mol_parameters"
paras
}
get_gaba_jn_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
nucleus <- rep("1H", 6)
chem_shift <- c(2.2840, 2.2840, 1.8880, 1.8880, 3.0130, 3.0130)
j_coupling_mat <- matrix(0, 6, 6)
j_coupling_mat[2,1] <- -15.938
j_coupling_mat[3,1] <- 7.678
j_coupling_mat[4,1] <- 6.980
j_coupling_mat[3,2] <- 6.980
j_coupling_mat[4,2] <- 7.678
j_coupling_mat[4,3] <- -15.000
j_coupling_mat[5,3] <- 8.510
j_coupling_mat[6,3] <- 6.503
j_coupling_mat[5,4] <- 6.503
j_coupling_mat[6,4] <- 8.510
j_coupling_mat[6,5] <- -14.062
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "J-Difference Editing of Gamma-Aminobutyric Acid (GABA):
Simulated and Experimental Multiplet Patterns. MRM 2013;
70:1183-1191."
paras <- list(spin_groups = list(spin_group_a), name = "GABA", source = source)
class(paras) <- "mol_parameters"
paras
}
get_gln_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
nucleus <- rep("1H", 5)
chem_shift <- c(3.753, 2.129, 2.109, 2.432, 2.454)
j_coupling_mat <- matrix(0, 5, 5)
j_coupling_mat[2,1] <- 5.847
j_coupling_mat[3,1] <- 6.5
j_coupling_mat[3,2] <- -14.504
j_coupling_mat[4,2] <- 9.165
j_coupling_mat[5,2] <- 6.347
j_coupling_mat[4,3] <- 6.324
j_coupling_mat[5,3] <- 9.209
j_coupling_mat[5,4] <- -15.371
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras <- list(spin_groups = list(spin_group_a), name = "Gln", source = source)
class(paras) <- "mol_parameters"
paras
}
get_gsh_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
nucleus <- c("1H")
chem_shift <- c(3.769)
j_coupling_mat <- matrix(0, 1, 1)
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 2,
lw = lw, lg = lg)
nucleus <- c("1H", "1H", "1H")
chem_shift <- c(4.5608, 2.9264, 2.9747)
j_coupling_mat <- matrix(0, 3, 3)
j_coupling_mat[2,1] <- 7.09
j_coupling_mat[3,1] <- 4.71
j_coupling_mat[3,2] <- -14.06
spin_group_b <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
nucleus <- c("1H", "1H", "1H", "1H", "1H")
chem_shift <- c(3.769, 2.159, 2.146, 2.510, 2.560)
j_coupling_mat <- matrix(0, 5, 5)
j_coupling_mat[2,1] <- 6.34
j_coupling_mat[3,1] <- 6.36
j_coupling_mat[3,2] <- -15.48
j_coupling_mat[4,2] <- 6.7
j_coupling_mat[5,2] <- 7.6
j_coupling_mat[4,3] <- 7.6
j_coupling_mat[5,3] <- 6.7
j_coupling_mat[5,4] <- -15.92
spin_group_c <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras <- list(spin_groups = list(spin_group_a, spin_group_b, spin_group_c),
name = "GSH", source = source)
class(paras) <- "mol_parameters"
paras
}
get_gly_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
paras <- get_uncoupled_mol("Gly", 3.548, "1H", 2, lw, lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras$source <- source
paras
}
get_bhb_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 0.5
nucleus <- rep("1H", 6)
chem_shift <- c(2.388, 2.294, 4.133, 1.186, 1.186, 1.186)
j_coupling_mat <- matrix(0, 6, 6)
j_coupling_mat[2,1] <- -14.5
j_coupling_mat[3,1] <- 7.3
j_coupling_mat[3,2] <- 6.3
j_coupling_mat[4,3] <- 6.3
j_coupling_mat[5,3] <- 6.3
j_coupling_mat[6,3] <- 6.3
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "In Vivo NMR Spectroscopy: Principles and Techniques,
Robin A. de Graaf"
paras <- list(spin_groups = list(spin_group_a), name = "BHB", source = source)
class(paras) <- "mol_parameters"
paras
}
get_ins_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 0.5
nucleus <- rep("1H", 6)
chem_shift <- c(3.5217, 4.0538, 3.5217, 3.6144, 3.269, 3.6144)
j_coupling_mat <- matrix(0, 6, 6)
j_coupling_mat[2,1] <- 2.889
j_coupling_mat[6,1] <- 9.998
j_coupling_mat[3,2] <- 3.006
j_coupling_mat[4,3] <- 9.997
j_coupling_mat[5,4] <- 9.485
j_coupling_mat[6,5] <- 9.482
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras <- list(spin_groups = list(spin_group_a), name = "Ins", source = source)
class(paras) <- "mol_parameters"
paras
}
get_ins_rt_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 0.5
nucleus <- rep("1H", 6)
chem_shift <- c(3.5217, 4.0538, 3.5217, 3.608, 3.265, 3.608)
j_coupling_mat <- matrix(0, 6, 6)
j_coupling_mat[2,1] <- 2.889
j_coupling_mat[6,1] <- 9.998
j_coupling_mat[3,2] <- 3.006
j_coupling_mat[4,3] <- 9.997
j_coupling_mat[5,4] <- 9.485
j_coupling_mat[6,5] <- 9.482
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153. Modified by MW for room temperature
phantom scans."
paras <- list(spin_groups = list(spin_group_a), name = "Ins", source = source)
class(paras) <- "mol_parameters"
paras
}
get_lip09_paras <- function(ft) {
paras <- get_uncoupled_mol("Lip09", 0.89, "1H", 3, 0.14 * ft / 1e6, 1)
paras$source <- "LCModel manual."
paras
}
get_lip13a_paras <- function(ft) {
paras <- get_uncoupled_mol("Lip13a", 1.28, "1H", 2, 0.15 * ft / 1e6, 1)
paras$source <- "LCModel manual."
paras
}
get_lip13b_paras <- function(ft) {
paras <- get_uncoupled_mol("Lip13b", 1.28, "1H", 2, 0.089 * ft / 1e6, 1)
paras$source <- "LCModel manual."
paras
}
get_lip20_paras <- function(ft) {
paras <- get_uncoupled_mol("Lip20", 2.04, "1H", 1.33, 0.15 * ft / 1e6, 1)
paras_b <- get_uncoupled_mol("Lip20", 2.25, "1H", 0.67, 0.15 * ft / 1e6, 1)
paras_c <- get_uncoupled_mol("Lip20", 2.8, "1H", 0.87, 0.2 * ft / 1e6, 1)
paras$spin_groups[[2]] <- paras_b$spin_groups[[1]]
paras$spin_groups[[3]] <- paras_c$spin_groups[[1]]
paras$source <- "LCModel manual."
paras
}
get_mm09_paras <- function(ft) {
paras <- get_uncoupled_mol("MM09", 0.91, "1H", 3, 0.14 * ft / 1e6, 1)
paras$source <- "LCModel manual."
paras
}
get_mm12_paras <- function(ft) {
paras <- get_uncoupled_mol("MM12", 1.21, "1H", 2, 0.15 * ft / 1e6, 1)
paras$source <- "LCModel manual."
paras
}
get_mm14_paras <- function(ft) {
paras <- get_uncoupled_mol("MM14", 1.43, "1H", 2, 0.17 * ft / 1e6, 1)
paras$source <- "LCModel manual."
paras
}
get_mm17_paras <- function(ft) {
paras <- get_uncoupled_mol("MM17", 1.67, "1H", 2, 0.15 * ft / 1e6, 1)
paras$source <- "LCModel manual."
paras
}
get_mm20_paras <- function(ft) {
paras <- get_uncoupled_mol("MM20", 2.08, "1H", 1.33, 0.15 * ft / 1e6, 1)
paras_b <- get_uncoupled_mol("MM20", 2.25, "1H", 0.33, 0.2 * ft / 1e6, 1)
paras_c <- get_uncoupled_mol("MM20", 1.95, "1H", 0.33, 0.15 * ft / 1e6, 1)
paras_d <- get_uncoupled_mol("MM20", 3.0, "1H", 0.4, 0.2 * ft / 1e6, 1)
paras$spin_groups[[2]] <- paras_b$spin_groups[[1]]
paras$spin_groups[[3]] <- paras_c$spin_groups[[1]]
paras$spin_groups[[4]] <- paras_d$spin_groups[[1]]
paras$source <- "LCModel manual."
paras
}
get_mm_3t_paras <- function(ft) {
paras <- get_uncoupled_mol("MM", 0.90, "1H", 0.72, 21.20 / 128 * ft / 1e6, 1)
paras_b <- get_uncoupled_mol("MM", 1.21, "1H", 0.28, 19.16 / 128 * ft / 1e6, 1)
paras_c <- get_uncoupled_mol("MM", 1.38, "1H", 0.38, 15.90 / 128 * ft / 1e6, 1)
paras_d <- get_uncoupled_mol("MM", 1.63, "1H", 0.05, 7.50 / 128 * ft / 1e6, 1)
paras_e <- get_uncoupled_mol("MM", 2.01, "1H", 0.45, 29.03 / 128 * ft / 1e6, 1)
paras_f <- get_uncoupled_mol("MM", 2.09, "1H", 0.36, 20.53 / 128 * ft / 1e6, 1)
paras_g <- get_uncoupled_mol("MM", 2.25, "1H", 0.36, 17.89 / 128 * ft / 1e6, 1)
paras_h <- get_uncoupled_mol("MM", 2.61, "1H", 0.04, 5.30 / 128 * ft / 1e6, 1)
paras_i <- get_uncoupled_mol("MM", 2.96, "1H", 0.20, 14.02 / 128 * ft / 1e6, 1)
paras_j <- get_uncoupled_mol("MM", 3.11, "1H", 0.11, 17.89 / 128 * ft / 1e6, 1)
paras_k <- get_uncoupled_mol("MM", 3.67, "1H", 0.64, 33.52 / 128 * ft / 1e6, 1)
paras_l <- get_uncoupled_mol("MM", 3.80, "1H", 0.07, 11.85 / 128 * ft / 1e6, 1)
paras_m <- get_uncoupled_mol("MM", 3.96, "1H", 1.00, 37.48 / 128 * ft / 1e6, 1)
paras$spin_groups[[2]] <- paras_b$spin_groups[[1]]
paras$spin_groups[[3]] <- paras_c$spin_groups[[1]]
paras$spin_groups[[4]] <- paras_d$spin_groups[[1]]
paras$spin_groups[[5]] <- paras_e$spin_groups[[1]]
paras$spin_groups[[6]] <- paras_f$spin_groups[[1]]
paras$spin_groups[[7]] <- paras_g$spin_groups[[1]]
paras$spin_groups[[8]] <- paras_h$spin_groups[[1]]
paras$spin_groups[[9]] <- paras_i$spin_groups[[1]]
paras$spin_groups[[10]] <- paras_j$spin_groups[[1]]
paras$spin_groups[[11]] <- paras_k$spin_groups[[1]]
paras$spin_groups[[12]] <- paras_l$spin_groups[[1]]
paras$spin_groups[[13]] <- paras_m$spin_groups[[1]]
paras$source <- "Birch et al Magn Reson Med. 2017 Jan; 77(1): 34-43."
paras
}
get_naa_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 0.5
nucleus <- c("1H")
chem_shift <- c(2.008)
j_coupling_mat <- matrix(0, 1, 1)
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 3,
lw = lw, lg = lg)
nucleus <- c("1H", "1H", "1H")
chem_shift <- c(4.3817, 2.6727, 2.4863)
j_coupling_mat <- matrix(0, 3, 3)
j_coupling_mat[2,1] <- 3.861
j_coupling_mat[3,1] <- 9.821
j_coupling_mat[3,2] <- -15.592
spin_group_b <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras <- list(spin_groups = list(spin_group_a,spin_group_b), name = "NAA",
source = source)
class(paras) <- "mol_parameters"
paras
}
get_naa_rt_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 0.5
nucleus <- c("1H")
chem_shift <- c(2.008)
j_coupling_mat <- matrix(0, 1, 1)
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 3,
lw = lw, lg = lg)
nucleus <- c("1H", "1H", "1H")
chem_shift <- c(4.3817, 2.681, 2.4845)
j_coupling_mat <- matrix(0, 3, 3)
j_coupling_mat[2,1] <- 3.861
j_coupling_mat[3,1] <- 9.821
j_coupling_mat[3,2] <- -15.592
spin_group_b <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153. Modified by MW for room temperature
phantom scans."
paras <- list(spin_groups = list(spin_group_a,spin_group_b), name = "NAA",
source = source)
class(paras) <- "mol_parameters"
paras
}
# as above with the 7.82 resonance - that doesn't influence the upfield multiplets
get_naa2_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 0.5
nucleus <- c("1H")
chem_shift <- c(2.008)
j_coupling_mat <- matrix(0, 1, 1)
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 3,
lw = lw, lg = lg)
nucleus <- c("1H", "1H", "1H", "1H")
chem_shift <- c(4.3817, 2.6727, 2.4863, 7.8205)
j_coupling_mat <- matrix(0, 4, 4)
j_coupling_mat[2,1] <- 3.861
j_coupling_mat[3,1] <- 9.821
j_coupling_mat[3,2] <- -15.592
j_coupling_mat[4,1] <- 6.4
spin_group_b <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras <- list(spin_groups = list(spin_group_a,spin_group_b), name = "NAA",
source = source)
class(paras) <- "mol_parameters"
paras
}
get_naag_ch3_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 0.5
paras <- get_uncoupled_mol("NAAG", 2.042, "1H", 3, lw, lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153. Note, only the acetyl moiety is simualted."
paras$source <- source
paras
}
get_naag_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 0.5
nucleus <- c("1H")
chem_shift <- c(2.042)
j_coupling_mat <- matrix(0, 1, 1)
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 3,
lw = lw, lg = lg)
nucleus <- c("1H", "1H", "1H")
chem_shift <- c(4.607, 2.721, 2.519)
j_coupling_mat <- matrix(0, 3, 3)
j_coupling_mat[2,1] <- 4.412
j_coupling_mat[3,1] <- 9.515
j_coupling_mat[3,2] <- -15.910
spin_group_b <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
nucleus <- c("1H", "1H", "1H", "1H", "1H", "1H")
chem_shift <- c(4.128, 2.049, 1.881, 2.180, 2.190, 7.950)
j_coupling_mat <- matrix(0, 6, 6)
j_coupling_mat[2,1] <- 4.61
j_coupling_mat[3,1] <- 8.42
j_coupling_mat[6,1] <- 7.46
j_coupling_mat[3,2] <- -14.28
j_coupling_mat[4,2] <- 10.56
j_coupling_mat[5,2] <- 6.09
j_coupling_mat[4,3] <- 4.9
j_coupling_mat[5,3] <- 11.11
j_coupling_mat[5,4] <- -15.28
spin_group_c <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Chemical shifts are from the Govindaraju paper, J-couplings are
from : Characterisation of the 1H and 13C NMR spectra of N-
acetylaspartylglutamate and its detection in urine from patients
with Canavan disease, J Pharm Biomed Anal. 2003 Mar 10;31(3):455-63."
paras <- list(spin_groups = list(spin_group_a, spin_group_b, spin_group_c),
name = "NAAG", source = source)
class(paras) <- "mol_parameters"
paras
}
get_pch_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
nucleus <- c("1H")
chem_shift <- c(3.208)
j_coupling_mat <- matrix(0, 1, 1)
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 9,
lw = lw, lg = lg)
nucleus <- c("1H", "1H", "1H", "1H", "14N", "31P")
chem_shift <- c(4.2805, 4.2805, 3.641, 3.641, 0, 0)
j_coupling_mat <- matrix(0, 6, 6)
j_coupling_mat[2,1] <- -14.89
j_coupling_mat[3,1] <- 2.284
j_coupling_mat[4,1] <- 7.231
j_coupling_mat[5,1] <- 2.68
j_coupling_mat[6,1] <- 6.298
j_coupling_mat[3,2] <- 7.326
j_coupling_mat[4,2] <- 2.235
j_coupling_mat[5,2] <- 2.772
j_coupling_mat[6,2] <- 6.249
j_coupling_mat[4,3] <- -14.19
spin_group_b <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Corrigendum: Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras <- list(spin_groups = list(spin_group_a, spin_group_b), name = "PCh",
source = source)
class(paras) <- "mol_parameters"
paras
}
get_pcr_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
paras <- get_uncoupled_mol("PCr", 3.029, "1H", 3, lw, lg)
paras_b <- get_uncoupled_mol("PCr", 3.930, "1H", 2, lw, lg)
paras$spin_groups[[2]] <- paras_b$spin_groups[[1]]
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras$source <- source
paras
}
get_peth_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
nucleus <- c("1H", "1H", "1H", "1H", "31P", "14N")
chem_shift <- c(3.9765, 3.9765, 3.216, 3.216, 0, 0)
j_coupling_mat <- matrix(0, 6, 6)
j_coupling_mat[2,1] <- -14.56
j_coupling_mat[3,1] <- 3.182
j_coupling_mat[4,1] <- 6.716
j_coupling_mat[5,1] <- 7.288
j_coupling_mat[6,1] <- 0.464
j_coupling_mat[3,2] <- 7.204
j_coupling_mat[4,2] <- 2.98
j_coupling_mat[5,2] <- 7.088
j_coupling_mat[6,2] <- 0.588
j_coupling_mat[4,3] <- -14.71
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Corrigendum: Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras <- list(spin_groups = list(spin_group_a), name = "PEth", source = source)
class(paras) <- "mol_parameters"
paras
}
get_ser_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
nucleus <- rep("1H", 3)
chem_shift <- c(3.8347, 3.9379, 3.9764)
j_coupling_mat <- matrix(0, 3, 3)
j_coupling_mat[2,1] <- 5.979
j_coupling_mat[3,1] <- 3.561
j_coupling_mat[3,2] <- -12.254
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Corrigendum: Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras <- list(spin_groups = list(spin_group_a), name = "Ser", source = source)
class(paras) <- "mol_parameters"
paras
}
get_sins_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
paras <- get_uncoupled_mol("sIns", 3.34, "1H", 6, lw, lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras$source <- source
paras
}
get_suc_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
paras <- get_uncoupled_mol("Suc", 2.3920, "1H", 4, lw, lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras$source <- source
paras
}
get_tau_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
nucleus <- rep("1H", 4)
chem_shift <- c(3.4206, 3.4206, 3.2459, 3.2459)
j_coupling_mat <- matrix(0, 4, 4)
j_coupling_mat[2,1] <- -12.438
j_coupling_mat[3,1] <- 6.742
j_coupling_mat[4,1] <- 6.464
j_coupling_mat[3,2] <- 6.403
j_coupling_mat[4,2] <- 6.792
j_coupling_mat[4,3] <- -12.93
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Corrigendum: Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras <- list(spin_groups = list(spin_group_a), name = "Tau", source = source)
class(paras) <- "mol_parameters"
paras
}
get_lac_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
nucleus <- rep("1H", 4)
chem_shift <- c(4.0974, 1.3142, 1.3142, 1.3142)
j_coupling_mat <- matrix(0, 4, 4)
j_coupling_mat[2,1] <- 6.933
j_coupling_mat[3,1] <- 6.933
j_coupling_mat[4,1] <- 6.933
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras <- list(spin_groups = list(spin_group_a), name = "Lac", source = source)
class(paras) <- "mol_parameters"
paras
}
get_lac_rt_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
nucleus <- rep("1H", 4)
chem_shift <- c(4.0974, 1.3142, 1.3142, 1.3142)
j_coupling_mat <- matrix(0, 4, 4)
j_coupling_mat[2,1] <- 6.833
j_coupling_mat[3,1] <- 6.833
j_coupling_mat[4,1] <- 6.833
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153. Modified by MW for room temperature
phantom scans."
paras <- list(spin_groups = list(spin_group_a), name = "Lac", source = source)
class(paras) <- "mol_parameters"
paras
}
get_glu_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
nucleus <- rep("1H", 5)
chem_shift <- c(3.7433, 2.0375, 2.1200, 2.3378, 2.352)
j_coupling_mat <- matrix(0,5,5)
j_coupling_mat[2,1] <- 7.331
j_coupling_mat[3,1] <- 4.651
j_coupling_mat[3,2] <- -14.849
j_coupling_mat[4,2] <- 6.413
j_coupling_mat[5,2] <- 8.406
j_coupling_mat[4,3] <- 8.478
j_coupling_mat[5,3] <- 6.875
j_coupling_mat[5,4] <- -15.915
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras <- list(spin_groups = list(spin_group_a), name = "Glu", source = source)
class(paras) <- "mol_parameters"
paras
}
get_glu_rt_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
nucleus <- rep("1H", 5)
chem_shift <- c(3.75, 2.0475, 2.1200, 2.3378, 2.352)
j_coupling_mat <- matrix(0,5,5)
j_coupling_mat[2,1] <- 7.331
j_coupling_mat[3,1] <- 4.651
j_coupling_mat[3,2] <- -14.849
j_coupling_mat[4,2] <- 6.413
j_coupling_mat[5,2] <- 8.406
j_coupling_mat[4,3] <- 8.478
j_coupling_mat[5,3] <- 6.875
j_coupling_mat[5,4] <- -15.915
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153. Modified by MW for room temperature
phantom scans."
paras <- list(spin_groups = list(spin_group_a), name = "Glu", source = source)
class(paras) <- "mol_parameters"
paras
}
get_a_glc_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
nucleus <- rep("1H", 7)
chem_shift <- c(5.216, 3.519, 3.698, 3.395, 3.822, 3.826, 3.749)
j_coupling_mat <- matrix(0, 7, 7)
j_coupling_mat[2,1] <- 3.8
j_coupling_mat[3,2] <- 9.6
j_coupling_mat[4,3] <- 9.4
j_coupling_mat[5,4] <- 9.9
j_coupling_mat[6,5] <- 1.5
j_coupling_mat[7,5] <- 6
j_coupling_mat[7,6] <- -12.1
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras <- list(spin_groups = list(spin_group_a), name = "aGlc", source = source)
class(paras) <- "mol_parameters"
paras
}
get_b_glc_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
nucleus <- rep("1H", 7)
chem_shift <- c(4.630, 3.230, 3.473, 3.387, 3.450, 3.882, 3.707)
j_coupling_mat <- matrix(0, 7, 7)
j_coupling_mat[2,1] <- 8.0
j_coupling_mat[3,2] <- 9.1
j_coupling_mat[4,3] <- 9.4
j_coupling_mat[5,4] <- 8.9
j_coupling_mat[6,5] <- 1.6
j_coupling_mat[7,5] <- 5.4
j_coupling_mat[7,6] <- -12.3
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras <- list(spin_groups = list(spin_group_a), name = "bGlc", source = source)
class(paras) <- "mol_parameters"
paras
}
get_glc_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
nucleus <- rep("1H", 7)
chem_shift <- c(5.216, 3.519, 3.698, 3.395, 3.822, 3.826, 3.749)
j_coupling_mat <- matrix(0, 7, 7)
j_coupling_mat[2,1] <- 3.8
j_coupling_mat[3,2] <- 9.6
j_coupling_mat[4,3] <- 9.4
j_coupling_mat[5,4] <- 9.9
j_coupling_mat[6,5] <- 1.5
j_coupling_mat[7,5] <- 6
j_coupling_mat[7,6] <- -12.1
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 0.36,
lw = lw, lg = lg)
nucleus <- rep("1H", 7)
chem_shift <- c(4.630, 3.230, 3.473, 3.387, 3.450, 3.882, 3.707)
j_coupling_mat <- matrix(0, 7, 7)
j_coupling_mat[2,1] <- 8.0
j_coupling_mat[3,2] <- 9.1
j_coupling_mat[4,3] <- 9.4
j_coupling_mat[5,4] <- 8.9
j_coupling_mat[6,5] <- 1.6
j_coupling_mat[7,5] <- 5.4
j_coupling_mat[7,6] <- -12.3
spin_group_b <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 0.64,
lw = lw, lg = lg)
source <- "Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153. This is a combination of alpha-glc (36%)
and beta-glc (64%)."
paras <- list(spin_groups = list(spin_group_a, spin_group_b), name = "Glc", source = source)
class(paras) <- "mol_parameters"
paras
}
get_gpc_paras <- function(lw = NULL, lg = 0) {
if (is.null(lw)) lw = 2
nucleus <- c("1H")
chem_shift <- c(3.212)
j_coupling_mat <- matrix(0, 1, 1)
spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 9,
lw = lw, lg = lg)
nucleus <- c("1H", "1H", "1H", "1H", "1H", "31P")
chem_shift <- c(3.605, 3.672, 3.903, 3.871, 3.946, 0)
j_coupling_mat <- matrix(0, 6, 6)
j_coupling_mat[2,1] <- -14.78
j_coupling_mat[3,1] <- 5.77
j_coupling_mat[3,2] <- 4.53
j_coupling_mat[4,2] <- 5.77
j_coupling_mat[5,2] <- 4.53
j_coupling_mat[5,4] <- -14.78
j_coupling_mat[6,4] <- 6.03
j_coupling_mat[6,5] <- 6.03
spin_group_b <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
nucleus <- c("1H", "1H", "1H", "1H", "14N", "31P")
chem_shift <- c(4.312, 4.312, 3.659, 3.659, 0, 0)
j_coupling_mat <- matrix(0, 6, 6)
j_coupling_mat[2,1] <- -9.32
j_coupling_mat[3,1] <- 3.1
j_coupling_mat[4,1] <- 5.9
j_coupling_mat[5,1] <- 2.67
j_coupling_mat[6,1] <- 6.03
j_coupling_mat[3,2] <- 5.9
j_coupling_mat[4,2] <- 3.1
j_coupling_mat[5,2] <- 2.67
j_coupling_mat[6,2] <- 6.03
j_coupling_mat[4,3] <- -9.32
spin_group_c <- list(nucleus = nucleus, chem_shift = chem_shift,
j_coupling_mat = j_coupling_mat, scale_factor = 1,
lw = lw, lg = lg)
source <- "Corrigendum: Proton NMR chemical shifts and coupling constants for brain metabolites.
NMR Biomed. 2000; 13:129-153."
paras <- list(spin_groups = list(spin_group_a, spin_group_b, spin_group_c),
name = "GPC", source = source)
class(paras) <- "mol_parameters"
paras
}
# get_10spin_paras <- function(lw = NULL, lg = 0) {
# if (is.null(lw)) lw = 2
# nucleus <- rep("1H", 10)
# chem_shift <- c(5.216, 3.519, 3.698, 3.395, 3.822, 3.826, 3.749, 1, 2, 3)
# j_coupling_mat <- matrix(0, 10, 10)
# j_coupling_mat[2,1] <- 3.8
# j_coupling_mat[3,2] <- 9.6
# j_coupling_mat[4,3] <- 9.4
# j_coupling_mat[5,4] <- 9.9
# j_coupling_mat[6,5] <- 1.5
# j_coupling_mat[7,5] <- 6
# j_coupling_mat[7,6] <- -12.1
#
# spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
# j_coupling_mat = j_coupling_mat, scale_factor = 1,
# lw = lw, lg = lg)
#
# source <- "made up molecule"
#
# paras <- list(spin_groups = list(spin_group_a), name = "Glc", source = source)
# class(paras) <- "mol_parameters"
# paras
# }
# get_9spin_paras <- function(lw = NULL, lg = 0) {
# if (is.null(lw)) lw = 2
# nucleus <- rep("1H", 9)
# chem_shift <- c(5.216, 3.519, 3.698, 3.395, 3.822, 3.826, 3.749, 1, 2)
# j_coupling_mat <- matrix(0, 9, 9)
# j_coupling_mat[2,1] <- 3.8
# j_coupling_mat[3,2] <- 9.6
# j_coupling_mat[4,3] <- 9.4
# j_coupling_mat[5,4] <- 9.9
# j_coupling_mat[6,5] <- 1.5
# j_coupling_mat[7,5] <- 6
# j_coupling_mat[7,6] <- -12.1
#
# spin_group_a <- list(nucleus = nucleus, chem_shift = chem_shift,
# j_coupling_mat = j_coupling_mat, scale_factor = 1,
# lw = lw, lg = lg)
#
# source <- "made up molecule"
#
# paras <- list(spin_groups = list(spin_group_a), name = "Glc", source = source)
# class(paras) <- "mol_parameters"
# paras
# }
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