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/CONTAB


Key line: /CONTAB,m+2*NAtom,NAtom (A7,1X,I4,1X,I4)
Data line:
StrucName                     m(1X,70A1,/)
AtIx                          NAtom(1X,I3,
CTAB.AtNum,                   1X,I3,
CTAB.Weight,                  1X,I3,
CTAB.Attribute,               1X,I3,
CTAB.Charge,                  1X,I2,
CTAB.XCoord,                  1X,E12.5,
CTAB.YCoord,                  1X,E12.5,
CTAB.ZCoord,                  1X,E12.5,/,
NumNeighb,                    1X,I2,
CTAB.ConnTo[1..NumNeighb],    NumNeighb(1X,I2),
CTAB.TypConn[1..NumNeighb]    NumNeighb(1X,I1))
(two lines per atom !)
Default: StrucName = '' (empty string), NAtom = 0, CTAB.AtNum = 0, CTAB.Weight = 0, CTAB.Attribute = 0, CTAB.Charge = 0, CTAB.XCoord= 0, CTAB.YCoord = 0, CTAB.ZCoord = 0, CTAB.ConnTo[i] = 0, CTAB.TypConn[i] = 0

For historical reasons the connection table has been stored in three slightly different formats. However, for new developments only the format designated by the keyword /CONTAB should be used. The other two formats are described in this document for reference purposes only.

The keyword /CONTAB specifies the connection table and the associated graphics coordinates of the chemical structure. In addition, the name of the structure can be included. The parameter m is the number of lines used for the name and may take any value between 0 and 4. Each atom of the structure has assigned a unique identification number and is described by two text lines, the first holding the atomic parameters, the second defining the bonding partners. The following parameters are stored for each atom: the atom identification number (AtIx), the atomic number (AtNum), the atomic weight (Weight), the attributes of the atom (Attribute), the charge (Charge), the coordinates of the graphics drawing (XCoord, YCoord, ZCoord), the bonding partners (ConnTo), and the type of the bonds (TypConn).

The atoms of a connection table are numbered at will (AtIx). All references to other atoms in the bonding section of an atom entry rely on that numbering. A connection table can specify up to 999 (non-hydrogen) atoms. Hydrogen atoms normally are not entered into the connection table; they should be stored in the connection table only under special circumstances (e.g. deuterium).

The charge of an atom (CTAB.Charge) must not exceed the limits of +/- 8 elementary charges.

The attribute flag (CTAB.Attribute) of an atom serves to define some basic topological properties of that atom. It is an 8-bit code with the bits having the following meaning when set to '1':

bit 0 atom is part of a linear structure
bit 1 atom is part of a 3-, 4- or >6-membered ring
bit 2 atom is part of a 5-membered ring
bit 3 atom in 6-ring
bit 4 atom constitutes a branch (more than two bonds)
bit 5 atom in any ring
bit 6 atom is the terminating atom of a chain
bit 7 atom constitutes a fused ring bond

If the attribute is set to a value of $00, it is not defined by definition (the value $00 must not occur in any structure). Note, that the attribute value is not important for the user, and can be simply set to $00. 

The graphics coordinates (CTAB.XCoord, CTAB.YCoord, CTAB.ZCoord, which are integer values !) should be selected in a range to ensure that the resulting resolution of the drawing is not too low. Good experience has been made with a range of 0..10000 for the graphics coordinates. If any graphics coordinates are unknown (e.g. ZCoord) they should be set to zero values.

The bonding partners are defined in the second line of an atom entry. The first parameter denotes the number of bonding partners (NumNeighb). Thereafter follow the identification numbers of the neighboring atoms (CTAB.ConnTo) and the corresponding bond types (CTAB.TypConn). Any atom must not have more than 16 bonded neighbors. The type of the bonds are defined by the following values:

TypConn = 1 single bond
2 double bond
3 triple bond
4 aromatic bond

 


Last Update: 2012-Oct-20