Parameters for CMF
cmf_params_tripos(mdb)
mdb |
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##---- 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 }