cmf_params_tripos {conmolfields} | R Documentation |
Parameters for CMF
Description
Parameters for CMF
Usage
cmf_params_tripos(mdb)
Arguments
Examples
##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
##-- or do help(data=index) for the standard data sets.
## The function is currently defined as
# Parameters for CMF
cmf_params_tripos <- function(mdb) {
ncomp <- length(mdb)
for (imol in 1:ncomp) {
mol <- mdb[[imol]]
# count neighbouring hydrogens
natoms <- length(mol$atoms)
nchydr <- integer(natoms)
nbonds <- length(mol$bonds)
for (ibond in 1:nbonds) {
bond <- mol$bonds[[ibond]]
iat1 <- bond$at1
iat2 <- bond$at2
el1 <- mol$atoms[[iat1]]$el
el2 <- mol$atoms[[iat1]]$el
if (el1 == "H") {
nchydr[iat2] <- nchydr[iat2] + 1
}
if (el2 == "H") {
nchydr[iat1] <- nchydr[iat1] + 1
}
}
# assign parameters to atoms
for (iatom in 1:natoms) {
atom <- mol$atoms[[iatom]]
atom$hydroph <- 0.0
atom$abraham_a <- 0.0
atom$abraham_b <- 0.0
atom$abraham_e <- 0.0
atom$abraham_s <- 0.0
if (atom$syb == "C.1") {
atom$hydroph <- atom$hydroph +0.041270
atom$abraham_e <- atom$abraham_e -0.005210
atom$abraham_s <- atom$abraham_s -0.013906
if (nchydr[iatom] == 1) {
atom$hydroph <- atom$hydroph -0.093156
atom$abraham_s <- atom$abraham_s +0.045181
}
}
if (atom$syb == "C.2") {
atom$hydroph <- atom$hydroph +0.041270
atom$abraham_e <- atom$abraham_e -0.005210
atom$abraham_s <- atom$abraham_s -0.013906
atom$hydroph <- atom$hydroph +0.006410
atom$abraham_s <- atom$abraham_s +0.016508
if (nchydr[iatom] == 0) {
atom$hydroph <- atom$hydroph +0.007629
atom$abraham_b <- atom$abraham_b +0.026654
atom$abraham_e <- atom$abraham_e +0.076572
}
if (nchydr[iatom] == 1) {
atom$hydroph <- atom$hydroph +0.202552
atom$abraham_e <- atom$abraham_e +0.058299
}
if (nchydr[iatom] == 2) {
atom$hydroph <- atom$hydroph +0.422564
atom$abraham_b <- atom$abraham_b -0.041897
atom$abraham_e <- atom$abraham_e -0.019698
atom$abraham_s <- atom$abraham_s -0.098377
}
}
if (atom$syb == "C.3") {
atom$hydroph <- atom$hydroph +0.041270
atom$abraham_e <- atom$abraham_e -0.005210
atom$abraham_s <- atom$abraham_s -0.013906
atom$abraham_a <- atom$abraham_a -0.009684
if (nchydr[iatom] == 0) {
atom$hydroph <- atom$hydroph +0.089007
atom$abraham_b <- atom$abraham_b +0.096834
atom$abraham_e <- atom$abraham_e +0.153114
}
if (nchydr[iatom] == 1) {
atom$abraham_b <- atom$abraham_b +0.041221
atom$abraham_e <- atom$abraham_e +0.091218
}
if (nchydr[iatom] == 2) {
atom$hydroph <- atom$hydroph +0.208288
}
if (nchydr[iatom] == 3) {
atom$hydroph <- atom$hydroph +0.369764
atom$abraham_b <- atom$abraham_b -0.022123
atom$abraham_e <- atom$abraham_e -0.102229
atom$abraham_s <- atom$abraham_s -0.055649
}
}
if (atom$syb == "C.ar") {
atom$hydroph <- atom$hydroph +0.041270
atom$abraham_e <- atom$abraham_e -0.005210
atom$abraham_s <- atom$abraham_s -0.013906
atom$hydroph <- atom$hydroph +0.194585
atom$abraham_e <- atom$abraham_e +0.117666
atom$abraham_s <- atom$abraham_s +0.070704
if (nchydr[iatom] == 0) {
atom$hydroph <- atom$hydroph +0.085378
atom$abraham_b <- atom$abraham_b +0.002903
atom$abraham_e <- atom$abraham_e +0.107527
atom$abraham_s <- atom$abraham_s +0.046501
}
if (nchydr[iatom] == 1) {
atom$abraham_e <- atom$abraham_e -0.044799
atom$abraham_s <- atom$abraham_s -0.011864
}
}
if (atom$syb == "C.cat") {
atom$abraham_e <- atom$abraham_e -0.005210
atom$abraham_s <- atom$abraham_s -0.013906
}
if (atom$syb == "N.1") {
atom$abraham_a <- atom$abraham_a +0.077667
atom$abraham_s <- atom$abraham_s +0.167948
atom$abraham_b <- atom$abraham_b +0.061824
atom$abraham_s <- atom$abraham_s +0.232745
}
if (atom$syb == "N.2") {
atom$abraham_a <- atom$abraham_a +0.077667
atom$abraham_s <- atom$abraham_s +0.167948
if (nchydr[iatom] == 1) {
atom$hydroph <- atom$hydroph -0.200643
} else {
atom$abraham_b <- atom$abraham_b -0.763354
atom$abraham_e <- atom$abraham_e +0.682859
}
}
if (atom$syb == "N.3") {
atom$abraham_a <- atom$abraham_a +0.077667
atom$abraham_s <- atom$abraham_s +0.167948
atom$hydroph <- atom$hydroph -0.091021
atom$abraham_b <- atom$abraham_b +0.367558
atom$abraham_e <- atom$abraham_e +0.099602
atom$abraham_s <- atom$abraham_s +0.084806
if (nchydr[iatom] == 0) {
atom$hydroph <- atom$hydroph -0.495588
atom$abraham_b <- atom$abraham_b +0.150946
atom$abraham_e <- atom$abraham_e +0.088502
}
if (nchydr[iatom] == 1) {
atom$hydroph <- atom$hydroph -0.452520
atom$abraham_a <- atom$abraham_a +0.163329
}
if (nchydr[iatom] == 2) {
atom$hydroph <- atom$hydroph -0.763440
atom$abraham_a <- atom$abraham_a +0.120801
atom$abraham_s <- atom$abraham_s -0.069707
}
}
if (atom$syb == "N.4") {
atom$abraham_a <- atom$abraham_a +0.077667
atom$abraham_s <- atom$abraham_s +0.167948
atom$hydroph <- atom$hydroph -4.382696
}
if (atom$syb == "N.am") {
atom$abraham_a <- atom$abraham_a +0.077667
atom$abraham_s <- atom$abraham_s +0.167948
atom$hydroph <- atom$hydroph -0.091021
if (nchydr[iatom] == 0) {
atom$hydroph <- atom$hydroph -0.495588
atom$abraham_a <- atom$abraham_a -0.096006
}
if (nchydr[iatom] == 1) {
atom$hydroph <- atom$hydroph -0.452520
}
if (nchydr[iatom] == 2) {
atom$hydroph <- atom$hydroph -0.763440
}
}
if (atom$syb == "N.ar") {
atom$abraham_a <- atom$abraham_a +0.077667
atom$abraham_s <- atom$abraham_s +0.167948
atom$abraham_a <- atom$abraham_a -0.104421
atom$abraham_b <- atom$abraham_b +0.282666
}
if (atom$syb == "N.pl3") {
atom$abraham_a <- atom$abraham_a +0.077667
atom$abraham_s <- atom$abraham_s +0.167948
atom$hydroph <- atom$hydroph +0.483597
atom$abraham_b <- atom$abraham_b -0.296874
atom$abraham_e <- atom$abraham_e +0.060327
atom$abraham_s <- atom$abraham_s -0.351281
}
if (atom$syb == "O.2") {
atom$hydroph <- atom$hydroph -0.224286
atom$hydroph <- atom$hydroph -0.098496
atom$abraham_a <- atom$abraham_a +0.038390
atom$abraham_e <- atom$abraham_e -0.011749
atom$abraham_s <- atom$abraham_s +0.371065
}
if (atom$syb == "O.3") {
atom$hydroph <- atom$hydroph -0.224286
atom$hydroph <- atom$hydroph -0.102250
atom$abraham_s <- atom$abraham_s +0.111253
atom$abraham_b <- atom$abraham_b +0.147962
if (nchydr[iatom] == 0) {
atom$hydroph <- atom$hydroph -0.010867
atom$abraham_a <- atom$abraham_a -0.035354
atom$abraham_e <- atom$abraham_e -0.020649
} else {
atom$hydroph <- atom$hydroph -0.279404
atom$abraham_a <- atom$abraham_a +0.445333
atom$abraham_b <- atom$abraham_b +0.014953
atom$abraham_e <- atom$abraham_e +0.010690
atom$abraham_s <- atom$abraham_s +0.027754
}
}
if (atom$syb == "O.co2") {
atom$hydroph <- atom$hydroph -0.224286
}
if (atom$syb == "S.2") {
atom$hydroph <- atom$hydroph -0.077480
atom$hydroph <- atom$hydroph +0.734821
atom$abraham_e <- atom$abraham_e +0.136585
}
if (atom$syb == "S.3") {
atom$abraham_e <- atom$abraham_e +0.195277
atom$abraham_s <- atom$abraham_s +0.082278
if (nchydr[iatom] == 0) {
atom$hydroph <- atom$hydroph +0.504755
atom$abraham_b <- atom$abraham_b +0.103649
atom$abraham_e <- atom$abraham_e +0.071103
}
}
if (atom$syb == "S.o") {
atom$hydroph <- atom$hydroph -0.077480
atom$hydroph <- atom$hydroph -1.055756
}
if (atom$syb == "S.o2") {
atom$hydroph <- atom$hydroph -0.077480
atom$hydroph <- atom$hydroph +0.027576
}
if (atom$syb == "P.3") {
atom$abraham_b <- atom$abraham_b +0.686142
atom$abraham_e <- atom$abraham_e +0.103799
atom$abraham_s <- atom$abraham_s +0.215383
}
if (atom$syb == "H") {
}
if (atom$syb == "F") {
atom$hydroph <- atom$hydroph +0.269012
atom$abraham_b <- atom$abraham_b -0.077060
atom$abraham_e <- atom$abraham_e -0.220887
atom$abraham_s <- atom$abraham_s -0.077487
}
if (atom$syb == "Cl") {
atom$hydroph <- atom$hydroph +0.569605
atom$abraham_b <- atom$abraham_b -0.068040
atom$abraham_e <- atom$abraham_e -0.008902
atom$abraham_s <- atom$abraham_s +0.029923
}
if (atom$syb == "Br") {
atom$hydroph <- atom$hydroph +0.696413
atom$abraham_b <- atom$abraham_b -0.074564
atom$abraham_e <- atom$abraham_e +0.167323
atom$abraham_s <- atom$abraham_s +0.131222
}
if (atom$syb == "I") {
atom$hydroph <- atom$hydroph +0.323219
atom$abraham_e <- atom$abraham_e +0.509975
atom$abraham_s <- atom$abraham_s +0.135703
}
if (atom$syb == "Si") {
atom$hydroph <- atom$hydroph +0.617895
}
mdb[[imol]]$atoms[[iatom]] <- atom
}
}
mdb
}
[Package
conmolfields version 0.0-19
Index]