SciDex
stores structure information in three categories:
- molecule (attribute to the whole molecule),
- atom
- bond
Molecule
Attributes
| ST |
Stereo
chemistry. Values are: 'rac' for racemates 'chir' for
enantiomers |
| INFO |
Information
text, which will be written in the upper left corner of
the drawing. |
| CL |
Colour
used for all atoms and bonds, which have no CL attribute
themselves. |
| CO |
Comment:
any text. |
| E |
Energy
of formation. |
| UQ |
Unique
ID. A text string to make a unique registration of a
structure, e.g. to make planar chirality or stereo
attributes, which are not found by SciDex. |
| V1
to V4 |
Numerical
values for user defined purpose. |
Atom
Attributes
| SY |
Symbol
of the chemical element.Valid symbols are: H ..Mt (the
first 109 elements) A, Q, M1, M2, X (wild cards) *
(marker for polymer repeating sides) |
| LB |
Label,
which is used in the drawing to represent the atom. No
other attributes of the atom will be written, if a label
is given to an atom. |
| CL |
Colour
used for this atom. |
| CO |
Comment:
any text. |
| UQ |
Unique
ID. A text string to make a unique description of a
atom. This can be used to reduce the symmetry of an
molecule. |
| HCO |
Hydrogen
count of the atom. |
| CHG |
Charge
of the atom. |
| RAD |
Radical
description of the atom. |
| ISO |
Isotope
mass, e.g. 13 for Carbon atoms. |
| d
NMR |
NMR
chemical shift of the atom in ppm. If the atom has a
colour, than all other atoms with the same symbol and
the same colour will get this value. The value can be
exact or an interval, e.g.:1.2 or 1.1-1.2 or <1.2 |
| ST |
Stereo
attribute yes or no.This attribute is used for the
internal R/S calculation. no forces SciDex to ignore the
stereo center, yes forces the calculation for nitrogen
atoms with three substituents. |
| V1
to V4 |
Numerical
values for user defined purpose. |
| |
Further,
X,Y and Z co-ordinates are stored for the atom. SciDex
stores Z co-ordinates, but did not use them for the
drawing. Z co-ordinates are used to calculate stereo
attributes. |
Bond
Attributes
| BO |
Bond
order. |
| CL |
Colour used
for this bond. |
| CO |
Comment:
any text. |
| J |
NMR
coupling constant in Hz. The value can be exact or an
interval, e.g.:1.2 or 1.1-1.2 or <1.2 |
| ST |
Stereo
attribute yes or no.This attribute is used for the
internal E/Z calculation of double bonds. no forces
SciDex to ignore the E/Z of a bond (e.g. fast
rotation/inversion), yes forces the calculation of E/Z
for double bond. |
| V1
až V4 |
Numerical
values for user defined purpose. |
Bond Orders
 Single
bond
Double bond E/Z isomers are defined by the angles of the
attached single bonds.
Triple bond.
Quadruple bond Attention: many other drawing programs
cannot handle this type of bonds. SciDex converts this bond
to triple bonds, if the other program cannot handle this
type of bonds.
 ,
 ,
 ,
 Stereo
bond Up stereo bond (single bond only). Down stereo
bond (single bond only).Attention: the definition of down
bonds is tricky!
 Undefined
stereo bond Single bond to a undefined stereo
center
Coordinative bond
Non bonding relation or interaction Can be used to mark
3J couplings etc.
Attention:
1. SciDex bond types are
not known to all chemical drawing programs.
2. SciDex do support all drawing types
used to define the chemical needs, but not
all types used for the graphical display used by
other drawing programs.
|