Module: Chem::Sybyl

Defined in:

lib/chem/db/sybyl.rb

Defined Under Namespace

Classes: SybylAtom, SybylBond, SybylMolecule

Constant Summary

SybylAtomTypes =

{
  "LP" => "lone pair",
  "Du" => "dummy atom",
  "Du.C" => "dummy carbon",
  "Hal" => "halogen",
  "Het" => "heteroatom = N, O, S, P",
  "Hev" => "heavy atom (non hydrogen)",

  "H" => "hydrogen",
  "H.spc" => "hydrogen in Single Point Charge (SPC) water model",
  "H.t3p" => "hydrogen in Transferable intermolecular Potential (TIP3P) water model",

  "C.2" => "carbon sp2",
  "C.1" => "carbon sp",
  "C.ar" => "carbon aromatic",
  "C.cat" => "carbocation (C+) used only in a guadinium group",
  "C.3" => "carbon sp3",

  "N.3" => "nitrogen sp3",
  "N.2" => "nitrogen sp2",
  "Any" => "any atom",
  "N.1" => "nitrogen sp",
  "N.ar" => "nitrogen aromatic",
  "N.am" => "nitrogen amide",
  "N.pl3" => "nitrogen trigonal planar",
  "N.4" => "nitrogen sp3 positively charged",
  "Li" => "lithium",
  "Na" => "sodium",

  "O.3" => "oxygen sp3",
  "O.2" => "oxygen sp2",
  "O.co2" => "oxygen in carboxylate and phosphate groups",
  "O.spc" => "oxygen in Single Point Charge (SPC) water model",
  "O.t3p" => "oxygen in Transferable Intermolecular Potential (TIP3P) water model",

  "Mg" => "magnesium",
  "Al" => "aluminum",
  "Si" => "silicon",
  "K" => "potassium",
  "Ca" => "calcium",

  "S.3" => "sulfur sp3",
  "S.2" => "sulfur sp2",
  "S.O" => "sulfoxide sulfur",
  "S.O2" => "sulfone sulfur",

  "Cr.th" => "chromium (tetrahedral)",
  "Cr.oh" => "chromium (octahedral)",

  "Mn" => "manganese",
  "Fe" => "iron",
  "P.3" => "phosphorous sp3",
  "Co.oh" => "cobalt (octahedral)",
  "F" => "fluorine",
  "Cu" => "copper",
  "Cl" => "chlorine",
  "Zn" => "zinc",
  "Br" => "bromine",
  "Se" => "selenium",
  "I" => "iodine",
  "Mo" => "molybdenum",
  "Sn" => "tin",
}