Table Index

ChemicalAtom

The tables ChemicalAtom and ChemicalBond define the chemical bond structure of a chemical, the
charge on the constituent atoms, and encodes a two or three dimensional representation of the
structure. It is implicit that ChemicalBonds are symmetric.
Atoms that are chiral centers are have a non-zero StereoParity field. Values for this field are
defined in the Enumeration table, and are taken from MDL Molfile format defined in
http://www.mdli.com/downloads/ctfile/ctfile_subs.html . That specification is confusing because
it appears to define two redundant ways (marking atoms and marking bonds) of defining stereo
configurations. Our theory is that the redundancy exists to allow different drawings of stereo
configurations, and that for simply capturing a configuration, setting the StereoParity field
of an atom is sufficient. Also, setting the BondStereo field of a bond could simplify drawing
of chemical structures, and can allow different drawings of the same stereo configurations,
which can be desirable. But these two fields can be interpreted independently of one another.
See the appendix of the MDL specification for details on interpreting stereo configurations.
E.g. H2O could be encoded as:
ChemicalAtom (wid, 1, 'H', 0)
ChemicalAtom (wid, 2, 'O', 0)
ChemicalAtom (wid, 3, 'H', 0)
ChemicalBond (wid, 1, 2, 1)
ChemicalBond (wid, 2, 3, 1)

Columns

Column MySQL Type Oracle Type Nullable Description
ChemicalWID BIGINT NUMBER No WID of the chemical
AtomIndex SMALLINT NUMBER No Order of the atoms within the structure,
starting from 1
Atom VARCHAR VARCHAR2(2) No Element symbol of the atom
Charge SMALLINT NUMBER No Charge on the atom
X DECIMAL NUMBER Yes X display coordinates for a drawing of the chemical structure
Y DECIMAL NUMBER Yes Y display coordinates for a drawing of the chemical structure
Z DECIMAL NUMBER Yes Z display coordinates for a drawing of the chemical structure
StereoParity DECIMAL NUMBER Yes Defines parity of an atom that is a chiral center.

Enumerated Values:
0 - Not stereo.
1 - Odd parity.
2 - Even parity.
3 - Either or unmarked stereo center.

Referenced By

None.

Other Constraints

CONSTRAINT UN_ChemicalAtom UNIQUE (ChemicalWID, AtomIndex)

Indexes

Name Columns
CA_WID CHEMICALWID
CA_ATOMINDEX ATOMINDEX
CA_ATOM ATOM
CA_CHARGE CHARGE
CA_X X
CA_Y Y
CA_Z Z
CA_SPARITY STEREOPARITY