Description Usage Arguments Examples
Computes coefficient at point (x,y,z) using support vectors for physico-chemical molecular fields
1 | cmf_coef_xyz_sv_ex_phch(mdb, a, ai, alpha, x, y, z, field, atomlists)
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mdb |
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a |
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ai |
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alpha |
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x |
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y |
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z |
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field |
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atomlists |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 | ##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
##-- or do help(data=index) for the standard data sets.
## The function is currently defined as
cmf_coef_xyz_sv_ex_phch <- function(mdb, a, ai, alpha, x, y, z, field, atomlists) {
coef <- 0.0
nsv <- length(ai)
for (isv in 1:nsv) {
imol <- ai[isv]
mol <- mdb[[imol]]
natoms <- length(mol$atoms)
for (iatom in atomlists[[imol]]) {
atom <- mol$atoms[[iatom]]
dist2 <- (x - atom$x)^2 + (y - atom$y)^2 + (z - atom$z)^2
if (field == "q") {
coef <- coef + a[isv] * atom$pch * exp(- alpha * dist2 / 2.0)
} else if (field == "vdw") {
dist2rel <- dist2 / (tripos_Rvdw[[atom$syb]])^2
coef <- coef + a[isv] * tripos_Evdw[[atom$syb]] * exp(- alpha * dist2rel / 2.0)
} else if (field == "logp") {
coef <- coef + a[isv] * atom$hydroph * exp(- alpha * dist2 / 2.0)
} else if (field == "abra") {
coef <- coef + a[isv] * atom$abraham_a * exp(- alpha * dist2 / 2.0)
} else if (field == "abrb") {
coef <- coef + a[isv] * atom$abraham_b * exp(- alpha * dist2 / 2.0)
} else if (field == "vdwr") {
coef <- coef + a[isv] * tripos_Rvdw[[atom$syb]] * exp(- alpha * dist2 / 2.0)
} else if (field == "abrs") {
coef <- coef + a[isv] * atom$abraham_s * exp(- alpha * dist2 / 2.0)
} else if (field == "abre") {
coef <- coef + a[isv] * atom$abraham_e * exp(- alpha * dist2 / 2.0)
}
}
}
coef
}
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